Iodine in PDB 3nyh: Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity

Enzymatic activity of Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity

All present enzymatic activity of Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity, PDB code: 3nyh was solved by N.Pandey, A.K.Singh, M.Sinha, P.Kaur, S.Sharma, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.57 / 1.77
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.231, 79.837, 77.548, 90.00, 102.67, 90.00
R / Rfree (%) 18.8 / 23.6

Other elements in 3nyh:

The structure of Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Bromine (Br) 1 atom
Iron (Fe) 1 atom
Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity (pdb code 3nyh). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 15 binding sites of Iodine where determined in the Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity, PDB code: 3nyh:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 15 in 3nyh

Go back to Iodine Binding Sites List in 3nyh
Iodine binding site 1 out of 15 in the Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I607

b:19.6
occ:1.00
 O A:HOH915 3.3 17.6 1.0
N A:TRP46 3.4 17.2 1.0
N A:VAL342 3.4 13.8 1.0
CH2 A:TRP452 3.7 14.6 1.0
CB A:ASN341 3.8 16.9 1.0
CZ2 A:TRP452 3.8 12.5 1.0
CB A:VAL342 3.9 16.3 1.0
CA A:ARG45 3.9 17.0 1.0
O A:ALA44 3.9 18.6 1.0
CG1 A:VAL342 4.0 18.6 1.0
N A:ASN341 4.0 15.0 1.0
C A:ARG45 4.1 17.0 1.0
N A:LEU47 4.1 17.5 1.0
CE A:MET446 4.2 16.5 1.0
CD A:ARG45 4.2 17.3 1.0
CA A:VAL342 4.2 14.7 1.0
CB A:TRP46 4.2 16.8 1.0
O A:LEU47 4.3 17.8 1.0
CA A:ASN341 4.3 13.8 1.0
C A:ASN341 4.3 15.5 1.0
CA A:TRP46 4.3 16.4 1.0
CB A:SER340 4.5 15.9 1.0
NH1 A:ARG45 4.5 16.8 1.0
CB A:ARG45 4.7 16.8 1.0
C A:TRP46 4.8 17.4 1.0
C A:ALA44 4.8 17.6 1.0
N A:ARG45 4.8 16.2 1.0
CG A:TRP46 4.8 15.7 1.0
C A:SER340 4.8 14.3 1.0
SD A:MET446 4.9 19.8 1.0
CZ3 A:TRP452 4.9 14.7 1.0

Iodine binding site 2 out of 15 in 3nyh

Go back to Iodine Binding Sites List in 3nyh
Iodine binding site 2 out of 15 in the Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I608

b:31.2
occ:1.00
 O A:HOH1206 3.3 51.9 1.0
ND2 A:ASN80 3.5 22.5 1.0
O A:HOH1309 3.6 47.4 1.0
O A:HOH772 3.7 28.4 1.0
O A:HOH695 3.7 33.2 1.0
CG A:PRO145 3.8 23.3 1.0
CB A:ASN80 3.9 19.8 1.0
CG A:GLU77 4.2 22.8 1.0
CG A:ASN80 4.2 18.8 1.0
CE A:LYS81 4.3 30.0 1.0
CB A:PRO145 4.3 24.7 1.0
CG A:LYS81 4.5 23.4 1.0
CB A:ASN147 4.7 31.6 1.0
CA A:GLU77 4.7 19.1 1.0
CB A:GLU77 4.8 19.9 1.0
CD A:GLU77 4.9 29.3 1.0
CD A:LYS81 4.9 27.6 1.0
O A:GLU77 4.9 18.7 1.0
N A:ASP148 4.9 27.3 1.0

Iodine binding site 3 out of 15 in 3nyh

Go back to Iodine Binding Sites List in 3nyh
Iodine binding site 3 out of 15 in the Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I609

b:41.1
occ:0.50
 NH2 A:ARG96 3.5 19.4 1.0
NH1 A:ARG96 3.6 21.9 1.0
O A:HOH1052 3.6 36.6 1.0
O5 A:NAG596 3.7 49.4 1.0
ND2 A:ASN95 3.9 44.3 1.0
NH1 A:ARG506 4.0 23.4 1.0
CZ A:ARG96 4.0 25.6 1.0
O A:HOH818 4.0 29.4 1.0
O A:HOH664 4.1 45.4 1.0
CA A:ARG504 4.1 24.7 1.0
C6 A:NAG596 4.2 54.5 1.0
NH2 A:ARG506 4.2 26.4 1.0
C1 A:NAG596 4.3 48.6 1.0
C5 A:NAG596 4.4 53.4 1.0
C A:ARG504 4.4 21.9 1.0
C2 A:NAG596 4.4 52.3 1.0
O7 A:NAG596 4.5 56.8 1.0
CZ A:ARG506 4.5 27.4 1.0
O6 A:NAG596 4.6 56.0 1.0
O A:ARG504 4.6 23.8 1.0
CG A:ASN95 4.8 34.4 1.0
C4 A:NAG596 4.8 53.6 1.0
CB A:ARG504 4.9 25.9 1.0
CG A:ARG504 4.9 34.7 1.0
CB A:ASN95 4.9 26.9 1.0

Iodine binding site 4 out of 15 in 3nyh

Go back to Iodine Binding Sites List in 3nyh
Iodine binding site 4 out of 15 in the Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I610

b:42.3
occ:1.00
 O A:HOH1022 3.4 46.6 1.0
O A:HOH1392 3.5 35.8 1.0
N A:GLN217 3.7 33.2 1.0
N A:PHE229 3.7 29.8 1.0
CG A:ASN216 4.0 34.4 1.0
OD1 A:ASN216 4.0 32.1 1.0
CA A:ASN216 4.1 31.5 1.0
ND2 A:ASN216 4.1 31.5 1.0
CA A:PRO228 4.3 27.3 1.0
CD2 A:PHE229 4.3 26.7 1.0
CB A:PHE229 4.4 30.4 1.0
C A:ASN216 4.4 31.9 1.0
CB A:PRO228 4.5 26.7 1.0
C A:PRO228 4.5 28.2 1.0
CG A:GLU218 4.6 44.1 1.0
CA A:PHE229 4.6 30.6 1.0
CB A:ASN216 4.6 31.4 1.0
OD1 A:ASN231 4.7 49.4 1.0
CG A:PHE229 4.7 29.7 1.0
CD A:GLU218 4.7 51.7 1.0
CA A:GLN217 4.7 35.6 1.0
CB A:GLN217 4.7 36.5 1.0
N A:GLU218 4.8 36.1 1.0
O A:PHE229 4.8 31.3 1.0
O A:VAL215 4.9 30.3 1.0
OE2 A:GLU218 4.9 56.1 1.0

Iodine binding site 5 out of 15 in 3nyh

Go back to Iodine Binding Sites List in 3nyh
Iodine binding site 5 out of 15 in the Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I611

b:25.3
occ:1.00
 O A:HOH911 3.4 36.7 1.0
NE1 A:TRP530 3.6 22.1 1.0
O A:HOH860 3.7 27.4 1.0
O A:HOH935 3.8 26.7 1.0
CB A:PHE309 3.9 16.4 1.0
O A:HOH1298 4.0 38.2 1.0
CZ2 A:TRP530 4.0 21.8 1.0
CE2 A:TRP530 4.2 24.8 1.0
N A:ARG310 4.3 18.7 1.0
CB A:ARG310 4.4 19.8 1.0
CA A:ILE306 4.5 17.1 1.0
CZ2 A:TRP529 4.5 26.8 1.0
C A:PHE309 4.5 17.4 1.0
O A:HOH1236 4.6 40.7 1.0
CA A:ARG310 4.7 20.1 1.0
O A:ILE306 4.8 17.0 1.0
O A:GLN305 4.8 14.8 1.0
CG1 A:ILE306 4.8 20.2 1.0
CA A:PHE309 4.8 17.5 1.0
CD1 A:TRP530 4.8 25.3 1.0

Iodine binding site 6 out of 15 in 3nyh

Go back to Iodine Binding Sites List in 3nyh
Iodine binding site 6 out of 15 in the Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I612

b:32.7
occ:1.00
 O A:HOH1169 3.1 39.3 1.0
NE A:ARG397 3.5 32.8 1.0
N A:THR560 3.6 28.1 1.0
NH2 A:ARG397 3.8 31.8 1.0
O A:GLU363 3.8 32.3 1.0
CG2 A:ILE559 4.0 19.9 1.0
CG A:GLU363 4.0 33.6 1.0
N A:LYS561 4.1 27.2 1.0
CA A:ILE559 4.1 26.2 1.0
CZ A:ARG397 4.1 30.6 1.0
CB A:GLU363 4.1 33.0 1.0
CA A:GLU363 4.1 32.0 1.0
CE2 A:TYR365 4.2 22.8 1.0
C A:ILE559 4.4 26.5 1.0
OG1 A:THR560 4.4 31.7 1.0
CB A:LYS561 4.4 28.8 1.0
C A:GLU363 4.4 31.8 1.0
CB A:ILE559 4.5 25.9 1.0
CD A:LYS561 4.5 38.5 1.0
CD A:ARG397 4.5 28.6 1.0
CG1 A:ILE559 4.6 25.3 1.0
CG A:LYS561 4.6 31.2 1.0
CA A:THR560 4.7 27.2 1.0
O A:HOH1112 4.7 35.0 1.0
O A:HIS558 4.7 30.3 1.0
C A:THR560 4.8 27.6 1.0
OH A:TYR365 4.8 24.2 1.0
O A:LYS561 4.8 25.2 1.0
CA A:LYS561 4.8 26.2 1.0
OE1 A:GLU363 4.9 34.6 1.0
CD A:GLU363 4.9 37.9 1.0
CZ A:TYR365 5.0 22.5 1.0

Iodine binding site 7 out of 15 in 3nyh

Go back to Iodine Binding Sites List in 3nyh
Iodine binding site 7 out of 15 in the Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I614

b:33.0
occ:0.50
 O A:HOH798 3.4 30.8 1.0
N A:PHE567 3.5 21.4 1.0
N A:ALA566 3.6 21.7 1.0
C A:HIS565 3.7 21.9 1.0
CB A:PHE567 3.7 21.6 1.0
CD2 A:PHE567 3.8 23.9 1.0
CA A:HIS565 3.8 23.9 1.0
CG A:PHE567 4.0 21.0 1.0
O A:HOH896 4.1 30.7 1.0
CA A:PHE567 4.1 22.0 1.0
CB A:HIS565 4.1 24.2 1.0
CB A:ASP311 4.2 20.2 1.0
O A:HOH864 4.2 26.4 1.0
O A:HIS565 4.3 22.6 1.0
O A:HOH970 4.3 42.0 1.0
CG A:ASP311 4.4 26.4 1.0
C A:ALA566 4.5 21.6 1.0
CA A:ALA566 4.5 20.5 1.0
CE2 A:PHE567 4.7 24.7 1.0
N A:GLN568 4.7 23.7 1.0
ND1 A:HIS565 4.7 29.1 1.0
OD1 A:ASP311 4.7 25.1 1.0
O A:HOH881 4.7 24.6 1.0
OD2 A:ASP311 4.8 25.1 1.0
C A:PHE567 4.9 23.2 1.0
CG A:HIS565 4.9 28.4 1.0

Iodine binding site 8 out of 15 in 3nyh

Go back to Iodine Binding Sites List in 3nyh
Iodine binding site 8 out of 15 in the Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I616

b:54.5
occ:0.50
 N A:SER356 2.9 17.1 1.0
O A:HOH888 3.0 34.8 1.0
OE1 A:GLU88 3.2 19.7 1.0
CA A:PRO355 3.4 18.4 1.0
OG A:SER356 3.5 18.4 1.0
CG1 A:VAL91 3.5 23.7 1.0
CB A:PRO355 3.5 17.6 1.0
C A:PRO355 3.6 16.8 1.0
CB A:SER356 3.8 15.6 1.0
CA A:SER356 3.9 16.6 1.0
O A:HOH1376 4.0 26.3 1.0
CD A:GLU88 4.0 23.1 1.0
CD2 A:LEU92 4.1 25.4 1.0
CB A:GLU88 4.4 23.7 1.0
CG A:GLU88 4.6 20.6 1.0
OH A:TYR85 4.6 16.4 1.0
O A:GLU88 4.7 22.6 1.0
N A:PRO355 4.7 15.0 1.0
CB A:LYS405 4.8 16.5 1.0
O A:PRO355 4.8 16.7 1.0
OE2 A:GLU88 4.9 19.5 1.0
CD A:LYS405 4.9 15.6 1.0
N A:THR357 4.9 17.4 1.0
O A:HOH785 4.9 42.3 1.0
CG A:LYS405 4.9 19.2 1.0
C A:SER356 4.9 17.1 1.0
CG A:PRO355 4.9 19.9 1.0

Iodine binding site 9 out of 15 in 3nyh

Go back to Iodine Binding Sites List in 3nyh
Iodine binding site 9 out of 15 in the Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I618

b:52.1
occ:0.50
 CZ A:PHE229 3.9 28.1 1.0
CE2 A:PHE229 3.9 30.2 1.0
CG2 A:ILE387 4.0 36.2 1.0
O A:HOH1308 4.1 50.2 1.0
O A:HOH634 4.2 52.5 1.0
CB A:ALA219 4.4 33.7 1.0
CG2 A:VAL246 4.8 27.2 1.0
O A:HOH747 4.9 40.6 1.0
CG1 A:VAL246 4.9 28.7 1.0
O A:GLU218 5.0 37.7 1.0

Iodine binding site 10 out of 15 in 3nyh

Go back to Iodine Binding Sites List in 3nyh
Iodine binding site 10 out of 15 in the Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I619

b:42.7
occ:1.00
 O A:HOH1177 3.6 36.7 1.0
NH1 A:ARG202 3.7 39.5 1.0
CA A:LEU199 4.0 27.5 1.0
N A:LEU199 4.1 31.1 1.0
CD A:ARG202 4.2 31.9 1.0
CB A:LEU199 4.2 27.2 1.0
CD1 A:LEU199 4.2 25.9 1.0
C A:SEP198 4.6 35.4 1.0
CB A:SEP198 4.6 40.5 1.0
CZ A:ARG202 4.8 40.0 1.0
CG A:LEU199 4.9 28.4 1.0
O A:SEP198 4.9 36.0 1.0
NE A:ARG202 5.0 34.0 1.0

Reference:

N.Pandey, A.K.Singh, M.Sinha, P.Kaur, S.Sharma, T.P.Singh. Crystal Structure of Lactoperoxidase Complexed Simultaneously with Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through the Substrate Diffusion Channel Reveals A Preferential Queue of the Inorganic Substrates Towards the Distal Heme Cavity To Be Published.
Page generated: Sun Dec 13 19:28:41 2020

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