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Iodine in PDB 4njb: Crystal Structure of the Complex of Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution

Enzymatic activity of Crystal Structure of the Complex of Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution

All present enzymatic activity of Crystal Structure of the Complex of Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of the Complex of Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution, PDB code: 4njb was solved by S.Yamini, H.V.Sirohi, M.Sinha, A.Bhushan, 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) 39.02 / 2.31
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.361, 80.398, 76.284, 90.00, 103.37, 90.00
R / Rfree (%) 20.5 / 22.7

Other elements in 4njb:

The structure of Crystal Structure of the Complex of Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution also contains other interesting chemical elements:

Iron (Fe) 1 atom
Calcium (Ca) 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 Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution (pdb code 4njb). 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 Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution, PDB code: 4njb:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in 4njb

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Iodine binding site 1 out of 11 in the Crystal Structure of the Complex of Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution


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 Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I609

b:63.1
occ:1.00
 N A:THR560 3.4 55.7 1.0
NE A:ARG397 3.8 59.6 1.0
CG2 A:ILE559 3.8 57.1 1.0
CA A:ILE559 3.8 55.4 1.0
CG A:LYS561 3.9 76.4 1.0
CE A:LYS561 3.9 85.8 1.0
N A:LYS561 4.0 59.3 1.0
CD A:LYS561 4.0 79.9 1.0
O A:GLU363 4.0 63.5 1.0
NH2 A:ARG397 4.0 62.7 1.0
OG1 A:THR560 4.1 57.2 1.0
C A:ILE559 4.1 56.4 1.0
CA A:GLU363 4.2 62.0 1.0
CB A:GLU363 4.3 64.8 1.0
CB A:ILE559 4.3 57.1 1.0
CB A:LYS561 4.3 68.3 1.0
CZ A:ARG397 4.4 59.5 1.0
OE1 A:GLU363 4.4 72.0 1.0
CA A:THR560 4.5 58.4 1.0
CE2 A:TYR365 4.6 53.2 1.0
C A:GLU363 4.6 60.7 1.0
O A:HIS558 4.6 58.6 1.0
C A:THR560 4.6 59.1 1.0
NZ A:LYS561 4.7 91.7 1.0
CG A:GLU363 4.7 68.6 1.0
CG1 A:ILE559 4.7 57.6 1.0
CA A:LYS561 4.8 63.3 1.0
CD A:ARG397 4.8 57.0 1.0
CD A:GLU363 4.8 69.8 1.0
CB A:THR560 4.9 58.3 1.0
N A:ILE559 5.0 57.1 1.0

Iodine binding site 2 out of 11 in 4njb

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Iodine binding site 2 out of 11 in the Crystal Structure of the Complex of Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution


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 Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I610

b:62.4
occ:1.00
 CG A:PRO145 3.6 43.2 1.0
ND2 A:ASN80 3.7 31.9 1.0
O A:HOH702 3.7 74.6 1.0
CG A:GLU77 3.8 56.5 1.0
CB A:PRO145 4.0 44.8 1.0
CB A:ASN80 4.0 35.4 1.0
CE A:LYS81 4.1 58.2 1.0
CG A:ASN80 4.4 34.4 1.0
CG A:LYS81 4.4 51.5 1.0
CA A:GLU77 4.6 41.4 1.0
CD A:GLU77 4.7 59.2 1.0
CB A:GLU77 4.7 47.2 1.0
O A:HOH994 4.8 79.1 1.0
CD A:LYS81 4.8 56.7 1.0
O A:GLU77 4.9 42.0 1.0
C A:ASN147 4.9 59.7 1.0
O A:ASN147 5.0 60.7 1.0

Iodine binding site 3 out of 11 in 4njb

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Iodine binding site 3 out of 11 in the Crystal Structure of the Complex of Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution


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 Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I611

b:67.1
occ:1.00
 N A:THR425 3.4 54.7 1.0
CA A:PRO236 3.7 46.5 1.0
CB A:PRO236 3.8 45.0 1.0
N A:PRO236 3.9 48.7 1.0
CA A:THR425 4.0 61.4 1.0
O A:HOH1084 4.1 59.9 1.0
C A:SER235 4.2 51.8 1.0
CB A:PHE239 4.2 49.7 1.0
O A:SER235 4.3 52.5 1.0
CA A:PRO424 4.3 49.1 1.0
CD A:PRO236 4.3 46.0 1.0
C A:PRO424 4.4 52.1 1.0
CG A:PHE239 4.5 50.2 1.0
CD1 A:PHE239 4.6 51.8 1.0
CB A:PRO234 4.6 66.3 1.0
CG A:PRO236 4.7 49.3 1.0
CB A:PRO424 4.8 50.1 1.0
CZ A:PHE422 4.8 44.5 1.0
C A:THR425 4.9 61.2 1.0
C A:PRO234 4.9 62.7 1.0
O A:PRO234 4.9 63.3 1.0
N A:SER235 5.0 61.0 1.0
CG A:PRO234 5.0 68.8 1.0

Iodine binding site 4 out of 11 in 4njb

Go back to Iodine Binding Sites List in 4njb
Iodine binding site 4 out of 11 in the Crystal Structure of the Complex of Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution


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 Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I612

b:66.0
occ:1.00
 N A:PHE229 3.8 46.2 1.0
N A:GLN217 3.8 54.4 1.0
OD1 A:ASN216 3.8 56.1 1.0
CG A:ASN216 3.9 55.5 1.0
CA A:ASN216 4.0 53.5 1.0
ND2 A:ASN216 4.0 52.8 1.0
CA A:PRO228 4.1 50.9 1.0
CD2 A:PHE229 4.2 52.0 1.0
CB A:PRO228 4.3 49.3 1.0
OE2 A:GLU218 4.4 72.9 1.0
C A:ASN216 4.4 54.7 1.0
C A:PRO228 4.5 49.2 1.0
CB A:ASN216 4.5 54.7 1.0
CB A:PHE229 4.6 47.4 1.0
CG A:PHE229 4.7 49.1 1.0
N A:GLU218 4.7 63.9 1.0
O A:VAL215 4.7 59.3 1.0
CA A:PHE229 4.8 47.2 1.0
O A:HOH1113 4.8 73.2 1.0
CD A:GLU218 4.8 76.4 1.0
CA A:GLN217 4.8 59.8 1.0
CE2 A:PHE229 4.9 52.1 1.0
CB A:GLN217 5.0 58.9 1.0

Iodine binding site 5 out of 11 in 4njb

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Iodine binding site 5 out of 11 in the Crystal Structure of the Complex of Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution


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 Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I613

b:63.1
occ:1.00
 N A:LYS462 3.6 45.7 1.0
OG1 A:THR463 3.8 43.4 1.0
CA A:GLY466 4.0 41.6 1.0
N A:THR463 4.1 44.0 1.0
CA A:PRO461 4.2 47.6 1.0
C A:PRO461 4.4 47.0 1.0
CA A:LYS462 4.5 47.8 1.0
CB A:LYS462 4.5 48.2 1.0
N A:GLY466 4.6 45.9 1.0
CB A:THR463 4.7 47.6 1.0
CG2 A:THR463 4.7 45.9 1.0
C A:LYS462 4.7 45.6 1.0
CG A:LYS462 4.9 56.6 1.0
CA A:THR463 4.9 46.5 1.0
CB A:PRO461 5.0 50.3 1.0

Iodine binding site 6 out of 11 in 4njb

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Iodine binding site 6 out of 11 in the Crystal Structure of the Complex of Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution


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 Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I614

b:67.7
occ:0.50
 O A:HOH1100 2.8 57.1 1.0
O A:HOH1075 2.9 73.7 1.0
N A:PHE567 3.4 42.4 1.0
N A:ALA566 3.5 50.0 1.0
CD2 A:PHE567 3.5 45.3 1.0
C A:HIS565 3.6 51.2 1.0
CA A:HIS565 3.6 52.4 1.0
CB A:PHE567 3.8 44.6 1.0
CB A:HIS565 3.9 53.2 1.0
O A:HOH881 4.0 56.3 1.0
CG A:PHE567 4.1 47.9 1.0
O A:HOH738 4.1 48.5 1.0
CA A:PHE567 4.2 46.5 1.0
CB A:ASP311 4.3 49.7 1.0
O A:HIS565 4.3 49.6 1.0
C A:ALA566 4.3 46.1 1.0
CA A:ALA566 4.3 47.6 1.0
CG A:ASP311 4.4 52.7 1.0
O A:HOH886 4.5 59.7 1.0
O A:HOH891 4.5 66.4 1.0
CE2 A:PHE567 4.5 52.0 1.0
OD1 A:ASP311 4.5 61.4 1.0
N A:GLN568 4.8 43.9 1.0
OD2 A:ASP311 4.8 56.7 1.0
CB A:ALA566 4.9 47.2 1.0
CG A:HIS565 4.9 60.7 1.0
N A:HIS565 5.0 52.7 1.0
ND1 A:HIS565 5.0 62.8 1.0

Iodine binding site 7 out of 11 in 4njb

Go back to Iodine Binding Sites List in 4njb
Iodine binding site 7 out of 11 in the Crystal Structure of the Complex of Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution


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 Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I615

b:60.5
occ:0.70
 O A:HOH889 3.1 65.3 1.0
O A:HOH962 3.1 61.5 1.0
O A:HOH890 3.1 57.2 1.0
N A:ALA225 3.5 55.0 1.0
NH2 A:ARG278 3.7 56.7 1.0
CB A:ALA225 3.8 55.8 1.0
CG A:ARG271 3.8 43.1 1.0
CA A:LEU224 4.2 58.7 1.0
CB A:ARG271 4.2 46.6 1.0
CD A:ARG271 4.2 46.1 1.0
CD2 A:LEU224 4.3 60.4 1.0
CA A:ALA225 4.3 51.7 1.0
CB A:LEU224 4.3 59.1 1.0
C A:LEU224 4.4 55.8 1.0
CA A:ARG271 4.6 47.3 1.0
NE A:ARG271 4.7 46.5 1.0
CZ A:ARG278 4.8 59.6 1.0
CG A:LEU224 4.9 56.5 1.0

Iodine binding site 8 out of 11 in 4njb

Go back to Iodine Binding Sites List in 4njb
Iodine binding site 8 out of 11 in the Crystal Structure of the Complex of Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution


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 Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I616

b:44.1
occ:1.00
 N A:TRP46 3.3 40.6 1.0
N A:VAL342 3.5 29.6 1.0
O A:HOH937 3.6 40.4 1.0
CH2 A:TRP452 3.7 34.0 1.0
CB A:ASN341 3.8 36.2 1.0
CA A:ARG45 3.9 39.2 1.0
CB A:VAL342 3.9 30.8 1.0
O A:ALA44 3.9 33.8 1.0
CZ2 A:TRP452 3.9 36.7 1.0
N A:ASN341 3.9 36.1 1.0
C A:ARG45 4.0 40.5 1.0
CG1 A:VAL342 4.2 34.8 1.0
CE A:MET446 4.2 31.9 1.0
N A:LEU47 4.2 37.7 1.0
CB A:TRP46 4.2 37.6 1.0
CA A:VAL342 4.2 33.9 1.0
O A:LEU47 4.2 38.5 1.0
CA A:TRP46 4.2 40.7 1.0
CA A:ASN341 4.3 37.2 1.0
C A:ASN341 4.3 35.3 1.0
CD A:ARG45 4.4 40.1 1.0
CB A:SER340 4.5 29.4 1.0
C A:ALA44 4.7 37.6 1.0
C A:TRP46 4.8 39.9 1.0
N A:ARG45 4.8 40.0 1.0
NH1 A:ARG45 4.8 32.0 1.0
CB A:ARG45 4.8 40.6 1.0
C A:SER340 4.8 35.3 1.0
CG A:TRP46 4.9 35.5 1.0
SD A:MET446 4.9 43.6 1.0
CZ3 A:TRP452 5.0 35.4 1.0

Iodine binding site 9 out of 11 in 4njb

Go back to Iodine Binding Sites List in 4njb
Iodine binding site 9 out of 11 in the Crystal Structure of the Complex of Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution


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 Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I617

b:56.5
occ:1.00
 O A:HOH854 2.9 61.0 1.0
NE1 A:TRP530 3.6 41.9 1.0
O A:HOH1076 3.8 55.0 1.0
CZ2 A:TRP530 3.9 40.8 1.0
CB A:PHE309 4.0 38.4 1.0
CE2 A:TRP530 4.1 42.4 1.0
CB A:ARG310 4.3 50.0 1.0
N A:ARG310 4.3 44.9 1.0
CA A:ILE306 4.3 47.1 1.0
OE1 A:GLU531 4.5 61.8 1.0
CZ2 A:TRP529 4.6 41.6 1.0
CG1 A:ILE306 4.6 48.8 1.0
O A:ILE306 4.6 46.7 1.0
C A:PHE309 4.6 39.3 1.0
CA A:ARG310 4.8 47.5 1.0
O A:GLN305 4.8 43.5 1.0
CD1 A:TRP530 4.8 41.6 1.0
CA A:PHE309 4.9 40.9 1.0
CB A:ILE306 4.9 50.8 1.0
CG2 A:ILE306 5.0 51.2 1.0

Iodine binding site 10 out of 11 in 4njb

Go back to Iodine Binding Sites List in 4njb
Iodine binding site 10 out of 11 in the Crystal Structure of the Complex of Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution


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 Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I618

b:65.6
occ:1.00
 O A:HOH1105 2.9 37.7 1.0
NH1 A:ARG202 3.4 61.7 1.0
CB A:LEU199 4.1 51.1 1.0
CA A:LEU199 4.1 50.8 1.0
CD A:ARG202 4.3 56.2 1.0
N A:LEU199 4.3 51.8 1.0
CD1 A:LEU199 4.4 54.0 1.0
CZ A:ARG202 4.6 59.7 1.0
C A:SEP198 4.7 51.2 1.0
O A:SEP198 4.9 49.5 1.0
CG A:LEU199 4.9 54.0 1.0
NE A:ARG202 4.9 58.8 1.0
CB A:SEP198 4.9 46.3 1.0

Reference:

S.Yamini, H.V.Sirohi, M.Sinha, A.Bhushan, P.Kaur, S.Sharma, T.P.Singh. Crystal Structure of the Complex of Lactoperoxidase From Bovine with 3,3-Oxydipyridine at 2.31 A Resolution To Be Published.
Page generated: Sun Aug 11 18:55:26 2024

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