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Iodine in PDB 5b72: Crystal Structure of Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 A Resolution.

Enzymatic activity of Crystal Structure of Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 A Resolution.

All present enzymatic activity of Crystal Structure of Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 A Resolution.:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 A Resolution., PDB code: 5b72 was solved by 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) 72.39 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.847, 80.192, 75.086, 90.00, 105.41, 90.00
R / Rfree (%) 18.8 / 23.5

Other elements in 5b72:

The structure of Crystal Structure of Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 A Resolution. also contains other interesting chemical elements:

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

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 A Resolution. (pdb code 5b72). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 A Resolution., PDB code: 5b72:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 5b72

Go back to Iodine Binding Sites List in 5b72
Iodine binding site 1 out of 9 in the Crystal Structure of Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 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 Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I803

b:23.8
occ:0.80
 O A:HOH1056 3.3 29.4 1.0
N A:TRP46 3.4 24.8 1.0
N A:VAL342 3.5 22.3 1.0
CH2 A:TRP452 3.7 20.1 1.0
CB A:ASN341 3.9 21.2 1.0
CB A:VAL342 3.9 21.8 1.0
CA A:ARG45 3.9 22.7 1.0
CZ2 A:TRP452 4.0 19.3 1.0
O A:ALA44 4.0 20.6 1.0
N A:ASN341 4.0 20.9 1.0
C A:ARG45 4.2 24.6 1.0
N A:LEU47 4.2 27.7 1.0
CA A:VAL342 4.2 22.0 1.0
CG1 A:VAL342 4.2 20.4 1.0
C A:ASN341 4.3 22.4 1.0
CA A:ASN341 4.3 20.8 1.0
CE A:MET446 4.3 24.1 1.0
CD A:ARG45 4.3 25.0 1.0
CB A:TRP46 4.3 24.8 1.0
CA A:TRP46 4.4 25.3 1.0
O A:LEU47 4.4 26.6 1.0
CB A:SER340 4.6 19.2 1.0
NH1 A:ARG45 4.6 26.0 1.0
CB A:ARG45 4.7 25.3 1.0
SD A:MET446 4.7 24.0 1.0
C A:TRP46 4.8 25.6 1.0
C A:ALA44 4.8 23.4 1.0
N A:ARG45 4.9 22.1 1.0
C A:SER340 4.9 19.8 1.0
CG A:TRP46 4.9 22.5 1.0
CZ3 A:TRP452 5.0 20.4 1.0

Iodine binding site 2 out of 9 in 5b72

Go back to Iodine Binding Sites List in 5b72
Iodine binding site 2 out of 9 in the Crystal Structure of Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 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 Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I804

b:41.6
occ:0.65
 NH2 A:ARG453 3.4 30.0 1.0
NH1 A:ARG453 3.7 25.9 1.0
I A:IOD805 3.7 72.1 0.6
CG A:PRO509 4.0 28.0 1.0
CZ A:ARG453 4.0 29.2 1.0
CB A:PRO509 4.4 25.8 1.0
CD2 A:LEU458 4.6 29.6 1.0
CG1 A:VAL470 4.7 29.3 1.0
O A:HOH1153 4.7 54.6 1.0

Iodine binding site 3 out of 9 in 5b72

Go back to Iodine Binding Sites List in 5b72
Iodine binding site 3 out of 9 in the Crystal Structure of Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 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 Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I805

b:72.1
occ:0.60
 OG A:SER459 3.6 36.1 1.0
N A:SER459 3.6 31.4 1.0
I A:IOD804 3.7 41.6 0.7
CB A:SER459 3.9 33.8 1.0
NH2 A:ARG453 4.2 30.0 1.0
CA A:LEU458 4.3 29.9 1.0
CD2 A:LEU458 4.3 29.6 1.0
O4 A:PGE807 4.3 52.7 1.0
CA A:SER459 4.4 32.5 1.0
C A:LEU458 4.5 32.8 1.0
CB A:LEU458 4.6 27.3 1.0

Iodine binding site 4 out of 9 in 5b72

Go back to Iodine Binding Sites List in 5b72
Iodine binding site 4 out of 9 in the Crystal Structure of Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 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 Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I814

b:47.4
occ:0.70
 O A:HOH947 3.1 59.2 1.0
ND2 A:ASN80 3.6 30.4 1.0
CG A:PRO145 3.8 27.1 1.0
CB A:ASN80 4.0 26.4 1.0
CE A:LYS81 4.0 42.4 1.0
O A:LYS146 4.1 62.9 1.0
CB A:PRO145 4.3 29.1 1.0
CG A:ASN80 4.3 29.2 1.0
CG A:GLU77 4.4 30.5 1.0
NZ A:LYS81 4.5 47.5 1.0
CD A:LYS81 4.7 42.5 1.0
CG A:LYS81 4.7 36.1 1.0
CA A:GLU77 4.8 24.0 1.0
CD A:GLU77 4.8 37.4 1.0
OE2 A:GLU77 4.8 44.8 1.0
CB A:GLU77 4.9 27.3 1.0
O A:ASN147 4.9 45.2 1.0

Iodine binding site 5 out of 9 in 5b72

Go back to Iodine Binding Sites List in 5b72
Iodine binding site 5 out of 9 in the Crystal Structure of Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 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 Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I815

b:34.2
occ:0.90
 N A:PHE229 3.7 33.7 1.0
N A:GLN217 3.8 33.2 1.0
CA A:ASN216 4.1 31.8 1.0
CG A:ASN216 4.1 29.8 1.0
OD1 A:ASN216 4.1 26.9 1.0
CD2 A:PHE229 4.2 31.0 1.0
ND2 A:ASN216 4.3 34.0 1.0
CA A:PRO228 4.3 27.3 1.0
CB A:PHE229 4.4 30.8 1.0
CB A:PRO228 4.4 27.5 1.0
C A:ASN216 4.5 31.1 1.0
OE1 A:GLU218 4.5 61.1 1.0
CB A:GLN217 4.5 35.5 1.0
O A:PHE229 4.5 39.3 1.0
C A:PRO228 4.5 30.6 1.0
CA A:PHE229 4.6 33.5 1.0
ND2 A:ASN231 4.6 67.2 1.0
CG A:PHE229 4.6 30.7 1.0
N A:GLU218 4.6 38.7 1.0
CA A:GLN217 4.7 35.0 1.0
CG A:GLU218 4.7 44.9 1.0
CB A:ASN216 4.7 30.3 1.0
O A:VAL215 4.8 35.0 1.0
CG A:GLN217 4.9 41.4 1.0

Iodine binding site 6 out of 9 in 5b72

Go back to Iodine Binding Sites List in 5b72
Iodine binding site 6 out of 9 in the Crystal Structure of Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 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 Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I816

b:31.0
occ:1.00
 NE A:ARG397 3.6 30.4 1.0
NH2 A:ARG397 3.6 28.5 1.0
N A:THR560 3.8 24.4 1.0
CG A:GLU363 3.9 39.6 1.0
N A:LYS561 3.9 27.8 1.0
CE A:LYS561 3.9 43.2 1.0
CG A:LYS561 4.0 36.4 1.0
CZ A:ARG397 4.1 32.1 1.0
CA A:ILE559 4.1 26.3 1.0
O A:GLU363 4.1 35.3 1.0
OG1 A:THR560 4.2 29.0 1.0
CA A:GLU363 4.2 34.3 1.0
CG2 A:ILE559 4.2 28.6 1.0
CB A:LYS561 4.2 32.1 1.0
CB A:GLU363 4.3 37.4 1.0
C A:ILE559 4.5 26.1 1.0
CE1 A:TYR365 4.5 28.8 1.0
CB A:ILE559 4.6 28.9 1.0
NZ A:LYS561 4.6 40.3 1.0
CD A:LYS561 4.6 39.1 1.0
CD A:ARG397 4.7 28.6 1.0
C A:GLU363 4.7 33.7 1.0
CA A:LYS561 4.7 28.4 1.0
CA A:THR560 4.7 26.6 1.0
C A:THR560 4.8 25.8 1.0
O A:HIS558 4.8 33.2 1.0
CG1 A:ILE559 4.8 28.8 1.0
O A:LYS561 4.9 27.6 1.0

Iodine binding site 7 out of 9 in 5b72

Go back to Iodine Binding Sites List in 5b72
Iodine binding site 7 out of 9 in the Crystal Structure of Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 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 Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I817

b:33.5
occ:0.80
 OG1 A:THR463 3.6 31.9 1.0
N A:LYS462 3.7 33.8 1.0
C4 A:PGE807 3.9 48.8 1.0
CA A:GLY466 4.0 27.8 1.0
N A:THR463 4.0 30.8 1.0
C3 A:PGE807 4.1 49.2 1.0
CG2 A:THR463 4.2 29.7 1.0
CA A:PRO461 4.3 28.0 1.0
CB A:THR463 4.4 28.5 1.0
N A:GLY466 4.4 27.0 1.0
C A:PRO461 4.5 31.5 1.0
CA A:LYS462 4.5 35.0 1.0
CB A:LYS462 4.6 36.8 1.0
C A:LYS462 4.7 33.9 1.0
CA A:THR463 4.8 27.9 1.0
O3 A:PGE807 4.9 49.5 1.0
O A:GLN460 5.0 30.4 1.0
CB A:PRO461 5.0 31.2 1.0
CG A:LYS462 5.0 38.0 1.0

Iodine binding site 8 out of 9 in 5b72

Go back to Iodine Binding Sites List in 5b72
Iodine binding site 8 out of 9 in the Crystal Structure of Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 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 Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I818

b:73.5
occ:0.60
 OG A:SER359 3.0 28.5 1.0
CB A:SER359 3.6 27.1 1.0
CG A:PRO367 3.8 38.2 1.0
CD2 A:LEU361 4.0 29.1 1.0
CB A:PRO367 4.0 38.3 1.0
CE A:LYS402 4.1 44.5 1.0
NZ A:LYS402 4.2 47.7 1.0
CB A:GLU373 4.2 36.2 1.0
CA A:PRO367 4.3 37.4 1.0
CG A:GLU373 4.6 47.1 1.0
OE2 A:GLU373 4.6 61.1 1.0
CB A:ALA372 4.6 30.9 1.0
CA A:SER359 4.8 24.5 1.0
CD A:PRO367 4.8 37.0 1.0
N A:PRO367 4.9 39.8 1.0
CA A:GLU373 4.9 33.3 1.0
N A:GLU373 4.9 27.9 1.0
CD A:GLU373 4.9 53.7 1.0
C A:ALA372 5.0 32.1 1.0

Iodine binding site 9 out of 9 in 5b72

Go back to Iodine Binding Sites List in 5b72
Iodine binding site 9 out of 9 in the Crystal Structure of Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 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 Bovine Lactoperoxidase with A Broken Covalent Bond Between GLU258 and Heme Moiety at 1.98 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I819

b:74.9
occ:0.60
 OE1 A:GLN468 3.7 52.8 1.0
OG1 A:THR469 3.7 34.8 1.0
CB A:GLN468 3.9 38.2 1.0
N A:THR469 3.9 26.7 1.0
CA A:THR469 4.0 29.8 1.0
C A:GLN468 4.0 29.6 1.0
O A:GLN468 4.2 30.6 1.0
CB A:THR469 4.4 29.8 1.0
CD A:GLN468 4.7 46.3 1.0
CA A:GLN468 4.7 31.7 1.0
O A:LYS465 4.8 34.9 1.0
CG A:GLN468 4.9 43.1 1.0
CG2 A:THR469 5.0 32.0 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 20:35:57 2024

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