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Iodine in PDB 5gls: Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety

Enzymatic activity of Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety

All present enzymatic activity of Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety:
1.11.1.7;

Protein crystallography data

The structure of Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety, PDB code: 5gls was solved by P.Tiwari, P.K.Singh, H.V.Sirohi, 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) 50.00 / 1.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.005, 79.834, 76.126, 90.00, 102.30, 90.00
R / Rfree (%) 19.2 / 24.5

Other elements in 5gls:

The structure of Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety 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 - 18;

Binding sites:

The binding sites of Iodine atom in the Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety (pdb code 5gls). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 18 binding sites of Iodine where determined in the Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety, PDB code: 5gls:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 18 in 5gls

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Iodine binding site 1 out of 18 in the Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I709

b:66.5
occ:0.40
 O A:HOH801 2.7 16.5 0.7
FE A:HEM707 2.7 21.3 1.0
OE2 A:GLU258 2.7 23.8 0.3
NE2 A:HIS109 2.8 24.0 1.0
NA A:HEM707 2.8 19.7 1.0
NE2 A:GLN105 3.1 19.6 1.0
NB A:HEM707 3.3 18.0 1.0
ND A:HEM707 3.3 20.7 1.0
C4A A:HEM707 3.4 21.3 1.0
C1A A:HEM707 3.4 20.4 1.0
CE1 A:HIS109 3.4 21.9 1.0
C4D A:HEM707 3.7 19.4 1.0
C1B A:HEM707 3.7 20.1 1.0
CHB A:HEM707 3.7 18.6 1.0
CD A:GLU258 3.8 21.7 0.3
CHA A:HEM707 3.8 19.9 1.0
NC A:HEM707 3.8 19.8 1.0
CD2 A:HIS109 4.0 21.1 1.0
CD A:GLN105 4.1 21.8 1.0
CG A:GLN105 4.1 22.9 1.0
C1D A:HEM707 4.1 19.5 1.0
O A:HOH1062 4.1 38.0 1.0
C4B A:HEM707 4.1 21.4 1.0
OE1 A:GLU258 4.2 26.1 0.7
C2A A:HEM707 4.3 21.3 1.0
C3A A:HEM707 4.3 22.0 1.0
OE1 A:GLU258 4.4 23.0 0.3
O A:HOH1068 4.5 24.5 0.3
C4C A:HEM707 4.5 17.4 1.0
C1C A:HEM707 4.6 18.9 1.0
CHD A:HEM707 4.6 17.2 1.0
NE2 A:HIS351 4.7 19.6 1.0
ND1 A:HIS109 4.7 21.5 1.0
C3D A:HEM707 4.7 20.4 1.0
CHC A:HEM707 4.7 19.3 1.0
C2B A:HEM707 4.7 17.9 1.0
CD A:GLU258 4.8 30.9 0.7
C2D A:HEM707 4.9 17.3 1.0
CD A:ARG255 4.9 25.6 1.0
CG A:GLU258 4.9 22.9 0.3
CG A:HIS109 4.9 18.9 1.0
C3B A:HEM707 5.0 21.1 1.0

Iodine binding site 2 out of 18 in 5gls

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Iodine binding site 2 out of 18 in the Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I710

b:34.3
occ:0.45
 I A:IOD711 1.3 35.9 0.6
NE1 A:TRP530 3.0 34.8 1.0
CZ2 A:TRP530 3.6 40.6 1.0
CE2 A:TRP530 3.6 37.9 1.0
CB A:PHE309 4.0 27.1 1.0
CA A:ILE306 4.1 30.1 1.0
CZ2 A:TRP529 4.2 34.8 1.0
CG1 A:ILE306 4.2 40.3 1.0
CD1 A:TRP530 4.2 37.0 1.0
OE1 A:GLU531 4.2 57.5 1.0
O A:GLN305 4.5 25.9 1.0
O A:ILE306 4.6 34.5 1.0
CB A:ILE306 4.6 33.5 1.0
N A:ARG310 4.7 32.8 1.0
CG2 A:ILE306 4.8 33.1 1.0
N A:ILE306 4.8 32.6 1.0
C A:ILE306 4.9 27.8 1.0
CH2 A:TRP530 4.9 42.2 1.0
CA A:PHE309 4.9 25.4 1.0
C A:PHE309 4.9 25.9 1.0
C A:GLN305 4.9 28.2 1.0
CD2 A:TRP530 4.9 40.0 1.0
CE2 A:TRP529 4.9 36.5 1.0
CB A:ARG310 5.0 41.9 1.0
CH2 A:TRP529 5.0 31.3 1.0

Iodine binding site 3 out of 18 in 5gls

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Iodine binding site 3 out of 18 in the Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I711

b:35.9
occ:0.55
 I A:IOD710 1.3 34.3 0.5
CB A:PHE309 3.8 27.1 1.0
N A:ARG310 4.1 32.8 1.0
NE1 A:TRP530 4.3 34.8 1.0
C A:PHE309 4.3 25.9 1.0
CZ2 A:TRP530 4.4 40.6 1.0
CB A:ARG310 4.4 41.9 1.0
OE1 A:GLU531 4.4 57.5 1.0
CA A:ARG310 4.6 34.0 1.0
CA A:PHE309 4.6 25.4 1.0
CE2 A:TRP530 4.7 37.9 1.0
O A:PHE309 4.7 25.6 1.0
O A:ILE306 4.8 34.5 1.0
O A:HOH995 4.9 50.4 1.0
CZ2 A:TRP529 4.9 34.8 1.0
CA A:ILE306 4.9 30.1 1.0
CG A:PHE309 5.0 27.0 1.0

Iodine binding site 4 out of 18 in 5gls

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Iodine binding site 4 out of 18 in the Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I712

b:20.3
occ:0.50
 I A:IOD715 0.5 18.2 0.5
N A:TRP46 3.2 19.4 1.0
N A:VAL342 3.4 13.3 1.0
O A:HOH910 3.6 21.0 1.0
CA A:ARG45 3.8 20.3 1.0
CH2 A:TRP452 3.8 19.1 1.0
O A:ALA44 3.8 20.8 1.0
N A:ASN341 3.9 14.6 1.0
CB A:VAL342 3.9 14.5 1.0
CB A:ASN341 3.9 17.9 1.0
CB A:TRP46 4.0 19.3 1.0
C A:ARG45 4.0 22.4 1.0
CG1 A:VAL342 4.0 15.8 1.0
N A:LEU47 4.0 16.8 1.0
CA A:TRP46 4.1 18.9 1.0
CZ2 A:TRP452 4.1 20.1 1.0
CA A:VAL342 4.2 14.1 1.0
CA A:ASN341 4.3 14.7 1.0
C A:ASN341 4.3 15.2 1.0
CB A:SER340 4.3 15.5 1.0
CE A:MET446 4.4 18.7 1.0
O A:LEU47 4.4 18.1 1.0
CD A:ARG45 4.5 20.3 1.0
C A:TRP46 4.6 20.1 1.0
CG A:TRP46 4.6 19.9 1.0
C A:ALA44 4.6 20.3 1.0
N A:ARG45 4.7 18.3 1.0
C A:SER340 4.7 14.7 1.0
CB A:ARG45 4.7 20.3 1.0
OG A:SER340 4.8 15.0 1.0
CZ3 A:TRP452 4.9 18.4 1.0
CA A:SER340 4.9 15.7 1.0

Iodine binding site 5 out of 18 in 5gls

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Iodine binding site 5 out of 18 in the Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I713

b:30.4
occ:0.40
 I A:IOD714 0.9 28.1 0.4
O A:HOH1138 2.6 51.5 1.0
O A:HOH860 3.1 39.3 1.0
CE A:LYS81 3.8 33.3 1.0
ND2 A:ASN80 3.9 29.4 1.0
CB A:ASN80 3.9 23.7 1.0
CG A:GLU77 3.9 30.2 1.0
CG A:PRO145 4.0 28.8 1.0
CG A:LYS81 4.1 30.2 1.0
CB A:PRO145 4.4 30.0 1.0
CG A:ASN80 4.4 26.0 1.0
CD A:LYS81 4.6 31.7 1.0
CA A:GLU77 4.6 24.4 1.0
CD A:GLU77 4.6 35.9 1.0
O A:GLU77 4.7 25.1 1.0
O A:LYS146 4.7 57.6 1.0
CB A:GLU77 4.7 28.0 1.0
NZ A:LYS81 4.8 31.3 1.0
OE2 A:GLU77 4.9 34.9 1.0
CB A:ASN147 5.0 50.5 1.0

Iodine binding site 6 out of 18 in 5gls

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Iodine binding site 6 out of 18 in the Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I714

b:28.1
occ:0.40
 I A:IOD713 0.9 30.4 0.4
O A:HOH860 3.1 39.3 1.0
O A:HOH1138 3.2 51.5 1.0
ND2 A:ASN80 3.3 29.4 1.0
CG A:PRO145 3.5 28.8 1.0
CB A:ASN80 3.9 23.7 1.0
CB A:PRO145 4.1 30.0 1.0
CG A:ASN80 4.1 26.0 1.0
O A:LYS146 4.2 57.6 1.0
CG A:GLU77 4.4 30.2 1.0
CB A:ASN147 4.5 50.5 1.0
N A:ASP148 4.6 34.9 1.0
C A:ASN147 4.7 40.6 1.0
CE A:LYS81 4.7 33.3 1.0
CD A:PRO145 4.8 30.5 1.0
CA A:ASP148 4.8 31.1 1.0
CA A:GLU77 4.8 24.4 1.0
O A:ASN147 4.9 38.9 1.0

Iodine binding site 7 out of 18 in 5gls

Go back to Iodine Binding Sites List in 5gls
Iodine binding site 7 out of 18 in the Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I715

b:18.2
occ:0.50
 I A:IOD712 0.5 20.3 0.5
O A:HOH910 3.1 21.0 1.0
N A:VAL342 3.5 13.3 1.0
N A:TRP46 3.5 19.4 1.0
CB A:ASN341 3.8 17.9 1.0
CH2 A:TRP452 3.8 19.1 1.0
CZ2 A:TRP452 3.9 20.1 1.0
CA A:ARG45 3.9 20.3 1.0
CE A:MET446 3.9 18.7 1.0
CB A:VAL342 3.9 14.5 1.0
N A:ASN341 4.1 14.6 1.0
O A:ALA44 4.1 20.8 1.0
N A:LEU47 4.1 16.8 1.0
O A:LEU47 4.1 18.1 1.0
C A:ARG45 4.2 22.4 1.0
CG1 A:VAL342 4.3 15.8 1.0
C A:ASN341 4.3 15.2 1.0
CD A:ARG45 4.3 20.3 1.0
CA A:VAL342 4.3 14.1 1.0
CA A:ASN341 4.3 14.7 1.0
CB A:TRP46 4.4 19.3 1.0
CA A:TRP46 4.4 18.9 1.0
NH1 A:ARG45 4.6 19.7 1.0
CB A:ARG45 4.7 20.3 1.0
SD A:MET446 4.8 18.9 1.0
CB A:SER340 4.8 15.5 1.0
C A:TRP46 4.8 20.1 1.0
C A:ALA44 4.9 20.3 1.0
N A:ARG45 4.9 18.3 1.0
CG A:ARG45 4.9 21.1 1.0

Iodine binding site 8 out of 18 in 5gls

Go back to Iodine Binding Sites List in 5gls
Iodine binding site 8 out of 18 in the Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I716

b:62.3
occ:0.35
 I A:IOD720 1.6 64.8 0.3
O A:HOH926 2.9 41.6 1.0
CD A:ARG31 3.3 46.0 1.0
NE A:ARG31 3.5 43.0 1.0
CG A:ARG31 3.6 39.7 1.0
ND2 A:ASN333 3.9 46.8 1.0
CB A:ARG31 4.1 38.8 1.0
O A:HOH1120 4.1 44.9 1.0
CE2 A:TYR331 4.1 37.5 1.0
CD A:ARG527 4.4 30.8 1.0
CB A:ASN333 4.7 34.6 1.0
OH A:TYR331 4.8 32.3 1.0
CZ A:ARG31 4.8 42.2 1.0
CG A:ASN333 4.8 41.4 1.0
CZ A:TYR331 5.0 34.0 1.0
CD2 A:TYR331 5.0 35.8 1.0

Iodine binding site 9 out of 18 in 5gls

Go back to Iodine Binding Sites List in 5gls
Iodine binding site 9 out of 18 in the Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I717

b:54.7
occ:0.40
 O A:HOH1124 3.2 44.3 1.0
OG1 A:THR66 3.6 25.6 1.0
N A:THR66 3.7 27.7 1.0
CA A:LYS65 4.2 40.1 1.0
O A:ARG64 4.2 57.4 1.0
O A:HOH931 4.3 44.8 1.0
CB A:THR66 4.4 27.1 1.0
CG2 A:THR66 4.4 31.3 1.0
CG A:LYS65 4.4 55.8 1.0
C A:LYS65 4.4 34.1 1.0
O A:THR66 4.5 26.3 1.0
CA A:THR66 4.5 28.5 1.0
O A:HOH802 4.6 37.6 1.0
NZ A:LYS65 4.6 71.4 1.0
C A:THR66 4.9 31.0 1.0
CB A:LYS65 4.9 42.6 1.0
CE A:LYS65 4.9 65.7 1.0

Iodine binding site 10 out of 18 in 5gls

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Iodine binding site 10 out of 18 in the Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of Bovine Lactoperoxidase with A Partially Modified Covalent Bond with Heme Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I718

b:63.9
occ:0.40
 O A:HOH951 3.3 45.4 1.0
CG A:PRO197 3.6 41.5 1.0
CB A:PRO197 3.6 41.5 1.0
CA A:PRO197 3.7 39.3 1.0
CB A:ILE24 4.2 38.4 1.0
CG1 A:ILE24 4.3 37.8 1.0
CD A:PRO197 4.6 36.5 1.0
N A:PRO197 4.6 38.9 1.0
O A:PRO197 4.6 40.5 1.0
C A:PRO197 4.6 32.0 1.0
CG2 A:ILE24 4.7 39.7 1.0

Reference:

P.K.Singh, H.V.Sirohi, N.Iqbal, P.Tiwari, P.Kaur, S.Sharma, T.P.Singh. Structure of Bovine Lactoperoxidase with A Partially Linked Heme Moiety at 1.98 Angstrom Resolution Biochim. Biophys. Acta V.1865 329 2016.
ISSN: ISSN 0006-3002
PubMed: 27986533
DOI: 10.1016/J.BBAPAP.2016.12.006
Page generated: Sun Aug 11 21:00:15 2024

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