Iodine in PDB 5wv3: Crystal Structure of Bovine Lactoperoxidase with A Partial GLU258-Heme Linkage at 2.07 A Resolution.

Enzymatic activity of Crystal Structure of Bovine Lactoperoxidase with A Partial GLU258-Heme Linkage at 2.07 A Resolution.

All present enzymatic activity of Crystal Structure of Bovine Lactoperoxidase with A Partial GLU258-Heme Linkage at 2.07 A Resolution.:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Bovine Lactoperoxidase with A Partial GLU258-Heme Linkage at 2.07 A Resolution., PDB code: 5wv3 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) 34.17 / 2.07
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.012, 79.809, 66.106, 90.00, 93.01, 90.00
R / Rfree (%) 16.7 / 23.6

Other elements in 5wv3:

The structure of Crystal Structure of Bovine Lactoperoxidase with A Partial GLU258-Heme Linkage at 2.07 A Resolution. also contains other interesting chemical elements:

Bromine (Br) 1 atom
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 Partial GLU258-Heme Linkage at 2.07 A Resolution. (pdb code 5wv3). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Crystal Structure of Bovine Lactoperoxidase with A Partial GLU258-Heme Linkage at 2.07 A Resolution., PDB code: 5wv3:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 5wv3

Go back to Iodine Binding Sites List in 5wv3
Iodine binding site 1 out of 3 in the Crystal Structure of Bovine Lactoperoxidase with A Partial GLU258-Heme Linkage at 2.07 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 Partial GLU258-Heme Linkage at 2.07 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I608

b:31.7
occ:1.00
 O A:HOH853 3.0 29.8 1.0
N A:TRP46 3.4 29.9 1.0
N A:VAL342 3.6 26.6 1.0
CH2 A:TRP452 3.7 30.3 1.0
CA A:ARG45 3.8 31.7 1.0
CZ2 A:TRP452 3.9 30.1 1.0
O A:ALA44 3.9 29.8 1.0
CB A:ASN341 3.9 27.6 1.0
CB A:VAL342 4.0 24.3 1.0
N A:LEU47 4.0 30.0 1.0
N A:ASN341 4.0 25.3 1.0
CG1 A:VAL342 4.1 26.5 1.0
C A:ARG45 4.1 32.3 1.0
O A:LEU47 4.2 30.6 1.0
CB A:TRP46 4.2 29.8 1.0
CA A:TRP46 4.2 30.8 1.0
CD A:ARG45 4.2 29.7 1.0
CE A:MET446 4.3 32.0 1.0
CA A:ASN341 4.3 25.7 1.0
CA A:VAL342 4.4 24.1 1.0
C A:ASN341 4.4 27.4 1.0
CB A:SER340 4.6 25.4 1.0
C A:TRP46 4.6 30.0 1.0
CB A:ARG45 4.7 32.6 1.0
C A:ALA44 4.7 29.8 1.0
N A:ARG45 4.8 31.7 1.0
NH1 A:ARG45 4.8 29.0 1.0
SD A:MET446 4.8 31.8 1.0
CG A:TRP46 4.8 32.6 1.0
C A:SER340 4.9 25.0 1.0
CG A:ARG45 4.9 33.7 1.0
CZ3 A:TRP452 5.0 30.5 1.0
CA A:LEU47 5.0 31.1 1.0

Iodine binding site 2 out of 3 in 5wv3

Go back to Iodine Binding Sites List in 5wv3
Iodine binding site 2 out of 3 in the Crystal Structure of Bovine Lactoperoxidase with A Partial GLU258-Heme Linkage at 2.07 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 Partial GLU258-Heme Linkage at 2.07 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I619

b:71.4
occ:0.50
 N A:THR425 3.7 73.1 1.0
CA A:PRO236 3.8 59.0 1.0
CB A:PRO236 4.0 57.9 1.0
N A:PRO236 4.2 61.9 1.0
CA A:THR425 4.3 81.6 1.0
CB A:PHE239 4.3 61.1 1.0
CG A:PRO236 4.4 58.7 1.0
CG A:PHE239 4.4 62.0 1.0
CD2 A:PHE239 4.5 64.7 1.0
CB A:PRO234 4.6 87.2 1.0
O A:SER235 4.7 70.0 1.0
C A:SER235 4.7 68.5 1.0
C A:PRO424 4.7 60.3 1.0
CA A:PRO424 4.8 57.1 1.0
CD A:PRO236 4.9 60.4 1.0
O A:HIS426 4.9 67.9 1.0
CG A:PRO234 4.9 86.7 1.0
N A:HIS426 4.9 78.8 1.0
O A:PRO234 5.0 75.3 1.0
CD1 A:PHE239 5.0 59.5 1.0

Iodine binding site 3 out of 3 in 5wv3

Go back to Iodine Binding Sites List in 5wv3
Iodine binding site 3 out of 3 in the Crystal Structure of Bovine Lactoperoxidase with A Partial GLU258-Heme Linkage at 2.07 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 Partial GLU258-Heme Linkage at 2.07 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I621

b:42.5
occ:0.50
 N A:OSM622 1.4 19.1 0.5
C A:OSM622 1.6 20.6 0.5
S A:OSM622 1.7 21.0 0.5
O A:OSM622 1.8 19.0 0.5
CD2 A:PHE229 3.8 63.1 1.0
N A:PHE229 3.8 59.4 1.0
OE1 A:GLU218 4.0 89.2 1.0
OD1 A:ASN216 4.0 60.1 1.0
N A:GLN217 4.1 71.9 1.0
CB A:PHE229 4.2 60.5 1.0
CG A:ASN216 4.2 58.7 1.0
ND2 A:ASN216 4.3 55.1 1.0
CB A:GLN217 4.4 80.7 1.0
CG A:PHE229 4.4 60.8 1.0
CA A:PRO228 4.5 60.5 1.0
CG A:GLN217 4.6 80.8 1.0
CA A:PHE229 4.6 58.5 1.0
N A:GLU218 4.6 77.4 1.0
CA A:ASN216 4.7 63.3 1.0
CB A:PRO228 4.7 62.2 1.0
C A:PRO228 4.7 57.9 1.0
CE2 A:PHE229 4.7 64.3 1.0
CD A:GLU218 4.8 88.0 1.0
CB A:GLU218 4.8 80.2 1.0
O A:PHE229 4.8 61.8 1.0
CA A:GLN217 4.8 78.5 1.0
C A:ASN216 5.0 68.2 1.0

Reference:

P.K.Singh, N.Iqbal, H.V.Sirohi, H.R.Bairagya, P.Kaur, S.Sharma, T.P.Singh. Structural Basis of Activation of Mammalian Heme Peroxidases Prog. Biophys. Mol. Biol. V. 133 49 2018.
ISSN: ISSN 1873-1732
PubMed: 29174286
DOI: 10.1016/J.PBIOMOLBIO.2017.11.003
Page generated: Sun Dec 13 19:41:59 2020

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