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Iodine in PDB 5zgs: Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity

Enzymatic activity of Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity

All present enzymatic activity of Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity, PDB code: 5zgs was solved by P.K.Singh, R.P.Singh, 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) 75.26 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.924, 79.717, 77.005, 90.00, 102.22, 90.00
R / Rfree (%) 17.6 / 24.6

Other elements in 5zgs:

The structure of Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity also contains other interesting chemical elements:

Iron (Fe) 1 atom
Calcium (Ca) 1 atom
Sodium (Na) 1 atom

Iodine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity (pdb code 5zgs). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity, PDB code: 5zgs:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in 5zgs

Go back to Iodine Binding Sites List in 5zgs
Iodine binding site 1 out of 11 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in 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 the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I613

b:29.8
occ:1.00
 O A:HOH852 3.3 25.9 1.0
N A:TRP46 3.3 24.5 1.0
N A:VAL342 3.5 19.4 1.0
CH2 A:TRP452 3.7 21.7 1.0
CA A:ARG45 3.8 24.8 1.0
CB A:ASN341 3.9 23.4 1.0
CZ2 A:TRP452 3.9 21.9 1.0
CB A:VAL342 3.9 18.0 1.0
CG1 A:VAL342 3.9 19.8 1.0
O A:ALA44 3.9 24.9 1.0
N A:ASN341 4.0 20.2 1.0
N A:LEU47 4.0 23.1 1.0
C A:ARG45 4.0 24.7 1.0
CA A:TRP46 4.2 24.9 1.0
CB A:TRP46 4.2 23.2 1.0
O A:LEU47 4.3 25.7 1.0
CA A:VAL342 4.3 18.8 1.0
CA A:ASN341 4.3 20.4 1.0
C A:ASN341 4.3 21.9 1.0
CE A:MET446 4.4 26.2 1.0
CD A:ARG45 4.5 24.3 1.0
CB A:SER340 4.6 17.7 1.0
C A:TRP46 4.6 23.5 1.0
C A:ALA44 4.8 22.7 1.0
N A:ARG45 4.8 21.5 1.0
CB A:ARG45 4.8 25.7 1.0
CG A:TRP46 4.8 24.0 1.0
SD A:MET446 4.8 26.7 1.0
NH1 A:ARG45 4.8 24.3 1.0
C A:SER340 4.8 19.4 1.0
CZ3 A:TRP452 4.9 20.4 1.0

Iodine binding site 2 out of 11 in 5zgs

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Iodine binding site 2 out of 11 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in 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 the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I614

b:36.7
occ:0.80
 O A:HOH1078 3.2 52.0 1.0
O A:HOH1022 3.3 34.3 1.0
ND2 A:ASN80 3.6 27.7 1.0
CB A:ASN80 3.8 25.4 1.0
CG A:PRO145 3.9 32.2 1.0
CG A:ASN80 4.2 26.0 1.0
CE A:LYS81 4.2 31.8 1.0
CG A:GLU77 4.4 29.8 1.0
CB A:PRO145 4.4 35.0 1.0
CG A:LYS81 4.5 29.5 1.0
CA A:GLU77 4.6 25.8 1.0
CB A:GLU77 4.7 26.9 1.0
CD A:LYS81 4.9 30.1 1.0
CD A:GLU77 4.9 33.1 1.0
O A:GLU77 4.9 26.3 1.0
CB A:ASN147 5.0 46.6 1.0

Iodine binding site 3 out of 11 in 5zgs

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Iodine binding site 3 out of 11 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in 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 the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I615

b:53.2
occ:0.60
 N A:LYS462 3.5 32.7 1.0
OG1 A:THR463 3.5 33.1 1.0
S A:SCN608 3.9 60.1 1.0
CA A:GLY466 4.0 35.6 1.0
N A:THR463 4.1 34.5 1.0
CA A:PRO461 4.3 32.1 1.0
CA A:LYS462 4.3 37.3 1.0
CB A:LYS462 4.4 40.5 1.0
C A:PRO461 4.4 32.3 1.0
CG2 A:THR463 4.5 33.6 1.0
CB A:THR463 4.5 33.2 1.0
N A:GLY466 4.5 36.6 1.0
C A:LYS462 4.7 34.0 1.0
C A:SCN608 4.7 71.8 1.0
CG A:LYS462 4.7 50.3 1.0
CA A:THR463 4.9 33.9 1.0

Iodine binding site 4 out of 11 in 5zgs

Go back to Iodine Binding Sites List in 5zgs
Iodine binding site 4 out of 11 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in 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 the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I616

b:55.7
occ:0.90
 O A:HOH763 3.3 43.6 1.0
N A:THR425 3.5 62.8 1.0
CA A:PRO236 3.7 41.9 1.0
N A:PRO236 3.9 45.5 1.0
CB A:PRO236 4.1 44.8 1.0
C A:SER235 4.1 46.5 1.0
CA A:THR425 4.2 65.0 1.0
O A:SER235 4.2 37.5 1.0
CB A:PHE239 4.2 39.7 1.0
CG A:PHE239 4.4 41.7 1.0
CD2 A:PHE239 4.5 45.8 1.0
CA A:PRO424 4.5 48.5 1.0
C A:PRO424 4.5 53.8 1.0
CD A:PRO236 4.6 46.9 1.0
O A:HOH1032 4.7 55.8 1.0
C A:THR425 4.7 65.3 1.0
CZ A:PHE422 4.8 40.7 1.0
CG A:PRO236 4.8 45.8 1.0
CB A:PRO424 4.9 50.4 1.0
O A:THR425 5.0 72.7 1.0
C A:PRO236 5.0 39.1 1.0

Iodine binding site 5 out of 11 in 5zgs

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Iodine binding site 5 out of 11 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in 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 the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I617

b:52.8
occ:0.90
 NE A:ARG397 3.5 33.3 1.0
CG2 A:ILE559 3.7 38.0 1.0
N A:THR560 3.7 44.6 1.0
CD A:LYS561 3.8 71.9 1.0
NH2 A:ARG397 3.9 37.9 1.0
O A:GLU363 3.9 44.0 1.0
CA A:ILE559 3.9 42.9 1.0
OG1 A:THR560 4.1 51.4 1.0
CA A:GLU363 4.1 54.6 1.0
CE1 A:TYR365 4.1 39.9 1.0
N A:LYS561 4.1 44.0 1.0
CZ A:ARG397 4.2 39.5 1.0
CB A:GLU363 4.2 60.3 1.0
CB A:ILE559 4.3 43.7 1.0
CG A:GLU363 4.3 59.9 1.0
C A:ILE559 4.3 40.9 1.0
CE A:LYS561 4.3 73.9 1.0
NZ A:LYS561 4.4 71.5 1.0
C A:GLU363 4.5 48.1 1.0
CD A:ARG397 4.5 34.5 1.0
CG A:LYS561 4.6 61.9 1.0
CB A:LYS561 4.6 53.2 1.0
CG1 A:ILE559 4.6 46.4 1.0
CA A:THR560 4.7 44.7 1.0
O A:HIS558 4.8 43.0 1.0
CD1 A:TYR365 4.8 39.0 1.0
C A:THR560 4.9 42.2 1.0
OE1 A:GLU363 4.9 59.7 1.0
O A:LYS561 4.9 45.2 1.0
CA A:LYS561 4.9 47.5 1.0
CZ A:TYR365 5.0 41.4 1.0

Iodine binding site 6 out of 11 in 5zgs

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Iodine binding site 6 out of 11 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in 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 the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I618

b:48.0
occ:0.70
 N A:PHE229 3.6 37.3 1.0
N A:GLN217 3.9 47.1 1.0
OD1 A:ASN216 3.9 54.3 1.0
CG A:ASN216 4.1 47.6 1.0
CA A:PRO228 4.1 39.7 1.0
CD2 A:PHE229 4.2 42.2 1.0
OE2 A:GLU218 4.2 77.1 1.0
CB A:PRO228 4.2 39.4 1.0
ND2 A:ASN216 4.2 47.3 1.0
CA A:ASN216 4.2 46.4 1.0
CG A:GLU218 4.3 62.8 1.0
C A:PRO228 4.4 41.6 1.0
CB A:PHE229 4.4 37.0 1.0
CA A:PHE229 4.5 37.5 1.0
CD A:GLU218 4.6 67.8 1.0
N A:GLU218 4.6 51.1 1.0
C A:ASN216 4.6 45.3 1.0
CG A:PHE229 4.7 38.5 1.0
OD1 A:ASN231 4.7 64.4 1.0
CB A:ASN216 4.8 42.9 1.0
O A:PHE229 4.8 36.8 1.0
CA A:GLN217 4.9 50.1 1.0
O A:VAL215 4.9 37.0 1.0
CB A:GLU218 5.0 53.2 1.0
CB A:GLN217 5.0 49.2 1.0

Iodine binding site 7 out of 11 in 5zgs

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Iodine binding site 7 out of 11 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in 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 the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I619

b:54.0
occ:0.50
 O A:HOH794 2.7 44.8 1.0
O A:HOH808 3.0 49.6 1.0
N A:PHE567 3.5 27.4 1.0
CA A:HIS565 3.6 38.5 1.0
C A:HIS565 3.6 32.9 1.0
N A:ALA566 3.6 31.8 1.0
CD2 A:PHE567 3.7 35.9 1.0
CB A:PHE567 3.8 27.8 1.0
CB A:HIS565 3.8 43.0 1.0
O A:HOH886 4.0 36.4 1.0
O A:HOH714 4.0 33.4 1.0
CG A:PHE567 4.1 31.8 1.0
CA A:PHE567 4.1 29.6 1.0
CB A:ASP311 4.2 31.0 1.0
O A:HIS565 4.3 30.2 1.0
CG A:ASP311 4.4 31.9 1.0
C A:ALA566 4.5 29.3 1.0
O A:HOH947 4.6 33.9 1.0
CA A:ALA566 4.6 28.9 1.0
N A:GLN568 4.6 31.3 1.0
OD1 A:ASP311 4.7 32.6 1.0
ND1 A:HIS565 4.7 57.5 1.0
CE2 A:PHE567 4.7 34.9 1.0
CG A:HIS565 4.8 49.4 1.0
OD2 A:ASP311 4.8 33.1 1.0
C A:PHE567 4.8 30.5 1.0
O A:HOH984 4.8 40.3 1.0
N A:HIS565 5.0 39.1 1.0

Iodine binding site 8 out of 11 in 5zgs

Go back to Iodine Binding Sites List in 5zgs
Iodine binding site 8 out of 11 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in 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 the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I620

b:58.1
occ:0.50
 O A:HOH1094 3.4 54.8 1.0
N A:ALA225 3.4 40.0 1.0
O A:HOH998 3.7 49.1 1.0
O A:HOH835 3.7 44.5 1.0
CB A:ALA225 3.8 37.5 1.0
CG A:ARG271 4.0 34.3 1.0
CA A:LEU224 4.1 41.4 1.0
CD A:ARG271 4.2 34.3 1.0
CA A:ALA225 4.3 36.1 1.0
C A:LEU224 4.3 39.7 1.0
CB A:LEU224 4.3 40.6 1.0
CD2 A:LEU224 4.3 45.8 1.0
NH2 A:ARG278 4.4 51.2 1.0
CB A:ARG271 4.5 36.7 1.0
NE A:ARG271 4.6 31.4 1.0
CG A:LEU224 4.8 42.5 1.0
CA A:ARG271 4.9 40.1 1.0

Iodine binding site 9 out of 11 in 5zgs

Go back to Iodine Binding Sites List in 5zgs
Iodine binding site 9 out of 11 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in 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 the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I621

b:61.0
occ:0.50
 O A:HOH869 2.9 37.1 1.0
O A:HOH1112 3.3 52.2 1.0
CD A:ARG31 3.9 51.5 1.0
CE2 A:TYR331 3.9 36.2 1.0
ND2 A:ASN333 3.9 40.4 1.0
NH1 A:ARG31 4.1 51.7 1.0
CD A:ARG527 4.6 31.8 1.0
CD2 A:TYR331 4.6 32.8 1.0
CB A:ASN333 4.7 36.3 1.0
CG A:ARG31 4.7 49.8 1.0
CB A:ARG31 4.8 44.4 1.0
CG A:ASN333 4.8 36.8 1.0
O A:HOH1156 4.8 40.2 1.0
OH A:TYR331 4.8 33.9 1.0
CZ A:TYR331 4.8 31.9 1.0
NE A:ARG31 4.9 53.0 1.0
CZ A:ARG31 4.9 56.3 1.0

Iodine binding site 10 out of 11 in 5zgs

Go back to Iodine Binding Sites List in 5zgs
Iodine binding site 10 out of 11 in the Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in 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 the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I622

b:37.7
occ:1.00
 O A:HOH1033 3.1 35.0 1.0
O A:HOH761 3.7 39.9 1.0
NE1 A:TRP530 3.8 36.7 1.0
CB A:PHE309 3.8 26.0 1.0
O A:HOH931 3.9 37.3 1.0
CZ2 A:TRP530 4.1 37.8 1.0
N A:ARG310 4.2 28.7 1.0
CE2 A:TRP530 4.3 36.9 1.0
CA A:ILE306 4.5 26.4 1.0
CZ2 A:TRP529 4.5 33.6 1.0
C A:PHE309 4.5 26.8 1.0
CB A:ARG310 4.5 31.6 1.0
CA A:PHE309 4.7 25.2 1.0
CA A:ARG310 4.7 28.8 1.0
O A:ILE306 4.8 26.7 1.0
CG1 A:ILE306 4.8 34.3 1.0
O A:GLN305 4.8 25.8 1.0
CD1 A:TRP530 5.0 35.9 1.0
CG2 A:ILE306 5.0 28.6 1.0
CG A:PHE309 5.0 24.4 1.0
CB A:ILE306 5.0 30.0 1.0

Reference:

P.K.Singh, R.P.Singh, P.Kaur, S.Sharma, T.P.Singh. Crystal Structure of the Complex of Bovine Lactoperoxidase with Multiple Scn and Oscn Ions in the Distal Heme Cavity To Be Published.
Page generated: Sun Aug 11 22:24:17 2024

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