Atomistry » Iron » PDB 3nmk-3nwv » 3nvz
Atomistry »
  Iron »
    PDB 3nmk-3nwv »
      3nvz »

Iron in PDB 3nvz: Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde

Enzymatic activity of Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde

All present enzymatic activity of Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde, PDB code: 3nvz was solved by H.Cao, R.Hille, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.20 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 133.409, 73.704, 138.922, 90.00, 97.12, 90.00
R / Rfree (%) 21.5 / 24.6

Other elements in 3nvz:

The structure of Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde (pdb code 3nvz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde, PDB code: 3nvz:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3nvz

Go back to Iron Binding Sites List in 3nvz
Iron binding site 1 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:11.8
occ:1.00
 FE1 A:FES601 0.0 11.8 1.0
S1 A:FES601 2.2 13.9 1.0
S2 A:FES601 2.3 13.2 1.0
SG A:CYS113 2.4 12.0 1.0
SG A:CYS150 2.5 14.4 1.0
FE2 A:FES601 2.7 11.4 1.0
CB A:CYS150 3.3 11.3 1.0
CB A:CYS113 3.4 11.8 1.0
O C:HOH419 3.6 12.0 1.0
N A:CYS113 3.7 12.5 1.0
CA A:CYS113 3.9 12.3 1.0
N A:GLY114 3.9 12.8 1.0
N A:CYS150 4.1 10.9 1.0
C A:CYS113 4.3 12.8 1.0
CA A:CYS150 4.4 10.4 1.0
N A:PHE115 4.4 10.3 1.0
SG A:CYS148 4.4 11.8 1.0
SG A:CYS116 4.6 13.2 1.0
N A:ARG149 4.7 11.9 1.0
C A:GLN112 4.7 12.0 1.0
CB A:GLN112 4.8 12.8 1.0
N A:CYS116 4.9 9.2 1.0
CA A:GLY114 4.9 11.8 1.0

Iron binding site 2 out of 8 in 3nvz

Go back to Iron Binding Sites List in 3nvz
Iron binding site 2 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:11.4
occ:1.00
 FE2 A:FES601 0.0 11.4 1.0
S2 A:FES601 2.2 13.2 1.0
S1 A:FES601 2.2 13.9 1.0
SG A:CYS116 2.3 13.2 1.0
SG A:CYS148 2.4 11.8 1.0
FE1 A:FES601 2.7 11.8 1.0
CB A:CYS148 3.3 10.8 1.0
CB A:CYS116 3.4 10.7 1.0
CA A:CYS148 3.6 11.0 1.0
N A:ARG149 4.0 11.9 1.0
N A:CYS116 4.2 9.2 1.0
C A:CYS148 4.2 11.7 1.0
N A:CYS150 4.3 10.9 1.0
O A:HOH177 4.4 10.8 1.0
CA A:CYS116 4.4 10.3 1.0
CB A:CYS150 4.4 11.3 1.0
SG A:CYS150 4.6 14.4 1.0
CG2 A:THR151 4.7 10.2 1.0
SG A:CYS113 4.7 12.0 1.0
O A:LEU147 4.9 11.0 1.0
N A:CYS148 4.9 11.0 1.0
CA A:CYS150 5.0 10.4 1.0

Iron binding site 3 out of 8 in 3nvz

Go back to Iron Binding Sites List in 3nvz
Iron binding site 3 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:12.9
occ:1.00
 FE1 A:FES602 0.0 12.9 1.0
S1 A:FES602 2.2 14.4 1.0
S2 A:FES602 2.2 14.4 1.0
SG A:CYS51 2.3 12.8 1.0
SG A:CYS73 2.3 14.8 1.0
FE2 A:FES602 2.8 12.5 1.0
CB A:CYS73 3.1 14.0 1.0
CB A:CYS51 3.4 12.5 1.0
N A:CYS73 4.2 14.5 1.0
CA A:CYS73 4.2 14.3 1.0
CB A:ASN71 4.3 15.6 1.0
N A:GLY46 4.4 15.2 1.0
OD1 A:ASN71 4.4 19.4 1.0
N A:CYS51 4.4 11.7 1.0
N A:GLY44 4.4 13.2 1.0
SG A:CYS43 4.4 12.8 1.0
CA A:CYS51 4.5 11.9 1.0
CG A:ASN71 4.5 17.6 1.0
CA A:GLY46 4.6 14.8 1.0
SG A:CYS48 4.7 13.2 1.0
CA A:GLY44 4.7 13.2 1.0
N A:GLY49 4.8 12.0 1.0
N A:GLU45 4.9 13.8 1.0
CA A:ASN71 4.9 14.9 1.0

Iron binding site 4 out of 8 in 3nvz

Go back to Iron Binding Sites List in 3nvz
Iron binding site 4 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:12.5
occ:1.00
 FE2 A:FES602 0.0 12.5 1.0
S1 A:FES602 2.3 14.4 1.0
S2 A:FES602 2.3 14.4 1.0
SG A:CYS48 2.3 13.2 1.0
SG A:CYS43 2.4 12.8 1.0
FE1 A:FES602 2.8 12.9 1.0
N A:CYS43 3.3 13.8 1.0
CB A:CYS48 3.4 13.7 1.0
CB A:CYS43 3.5 13.8 1.0
N A:CYS48 3.5 13.9 1.0
N A:GLY49 3.8 12.0 1.0
CA A:CYS43 3.8 13.9 1.0
CA A:CYS48 3.9 13.0 1.0
N A:GLY44 3.9 13.2 1.0
C A:GLY42 4.0 14.0 1.0
C A:CYS48 4.2 12.5 1.0
C A:CYS43 4.3 14.0 1.0
N A:GLY42 4.3 13.6 1.0
CA A:GLY42 4.3 13.2 1.0
N A:GLY47 4.4 14.8 1.0
N A:GLY46 4.4 15.2 1.0
N A:ALA50 4.5 11.6 1.0
SG A:CYS73 4.5 14.8 1.0
SG A:CYS51 4.6 12.8 1.0
N A:GLU45 4.7 13.8 1.0
C A:GLY47 4.7 14.4 1.0
C A:GLY46 4.8 15.0 1.0
CA A:GLY49 4.8 12.1 1.0
CA A:GLY46 4.8 14.8 1.0
O A:GLY42 4.9 13.3 1.0
CA A:GLY44 4.9 13.2 1.0

Iron binding site 5 out of 8 in 3nvz

Go back to Iron Binding Sites List in 3nvz
Iron binding site 5 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe601

b:13.3
occ:1.00
 FE1 J:FES601 0.0 13.3 1.0
S1 J:FES601 2.2 15.3 1.0
S2 J:FES601 2.2 15.3 1.0
SG J:CYS113 2.4 13.2 1.0
SG J:CYS150 2.5 16.1 1.0
FE2 J:FES601 2.7 13.4 1.0
CB J:CYS113 3.4 13.1 1.0
CB J:CYS150 3.4 14.1 1.0
N J:CYS113 3.6 13.4 1.0
O L:HOH372 3.7 13.8 1.0
CA J:CYS113 3.9 13.0 1.0
N J:GLY114 3.9 13.4 1.0
N J:CYS150 4.2 13.2 1.0
C J:CYS113 4.3 12.9 1.0
N J:PHE115 4.4 11.4 1.0
CA J:CYS150 4.4 13.6 1.0
SG J:CYS148 4.4 14.4 1.0
SG J:CYS116 4.6 15.7 1.0
C J:GLN112 4.7 12.6 1.0
N J:ARG149 4.7 14.4 1.0
CB J:GLN112 4.9 13.4 1.0
CA J:GLY114 4.9 12.3 1.0
N J:CYS116 4.9 11.7 1.0

Iron binding site 6 out of 8 in 3nvz

Go back to Iron Binding Sites List in 3nvz
Iron binding site 6 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe601

b:13.4
occ:1.00
 FE2 J:FES601 0.0 13.4 1.0
S2 J:FES601 2.2 15.3 1.0
S1 J:FES601 2.2 15.3 1.0
SG J:CYS116 2.4 15.7 1.0
SG J:CYS148 2.4 14.4 1.0
FE1 J:FES601 2.7 13.3 1.0
CB J:CYS148 3.3 14.9 1.0
CB J:CYS116 3.5 11.8 1.0
CA J:CYS148 3.7 14.6 1.0
N J:ARG149 4.1 14.4 1.0
N J:CYS116 4.3 11.7 1.0
C J:CYS148 4.3 14.5 1.0
O J:HOH183 4.3 15.7 1.0
N J:CYS150 4.4 13.2 1.0
CB J:CYS150 4.4 14.1 1.0
CA J:CYS116 4.5 11.9 1.0
SG J:CYS150 4.5 16.1 1.0
SG J:CYS113 4.7 13.2 1.0
CG2 J:THR151 4.8 14.4 1.0
O J:LEU147 4.9 14.3 1.0
CA J:CYS150 5.0 13.6 1.0

Iron binding site 7 out of 8 in 3nvz

Go back to Iron Binding Sites List in 3nvz
Iron binding site 7 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe602

b:13.9
occ:1.00
 FE1 J:FES602 0.0 13.9 1.0
S2 J:FES602 2.2 14.8 1.0
S1 J:FES602 2.2 15.4 1.0
SG J:CYS51 2.3 14.3 1.0
SG J:CYS73 2.4 15.0 1.0
FE2 J:FES602 2.7 14.2 1.0
CB J:CYS73 3.1 14.5 1.0
CB J:CYS51 3.4 14.0 1.0
N J:CYS73 4.2 13.9 1.0
CA J:CYS73 4.3 14.5 1.0
CB J:ASN71 4.3 14.9 1.0
N J:CYS51 4.3 12.6 1.0
N J:GLY46 4.4 15.9 1.0
N J:GLY44 4.4 14.6 1.0
OD1 J:ASN71 4.4 17.8 1.0
SG J:CYS43 4.4 15.3 1.0
CG J:ASN71 4.5 15.0 1.0
CA J:CYS51 4.5 13.5 1.0
CA J:GLY46 4.6 16.2 1.0
SG J:CYS48 4.6 15.6 1.0
CA J:GLY44 4.7 14.1 1.0
N J:GLY49 4.7 13.1 1.0
N J:GLU45 4.9 15.0 1.0
CA J:ASN71 5.0 14.8 1.0

Iron binding site 8 out of 8 in 3nvz

Go back to Iron Binding Sites List in 3nvz
Iron binding site 8 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe602

b:14.2
occ:1.00
 FE2 J:FES602 0.0 14.2 1.0
S2 J:FES602 2.2 14.8 1.0
S1 J:FES602 2.3 15.4 1.0
SG J:CYS48 2.3 15.6 1.0
SG J:CYS43 2.4 15.3 1.0
FE1 J:FES602 2.7 13.9 1.0
CB J:CYS48 3.4 16.1 1.0
N J:CYS43 3.4 14.8 1.0
CB J:CYS43 3.5 14.4 1.0
N J:CYS48 3.5 17.5 1.0
N J:GLY49 3.8 13.1 1.0
CA J:CYS48 3.8 15.2 1.0
CA J:CYS43 3.9 14.6 1.0
N J:GLY44 3.9 14.6 1.0
C J:GLY42 4.1 14.2 1.0
C J:CYS48 4.2 14.2 1.0
C J:CYS43 4.3 15.2 1.0
N J:GLY42 4.3 13.2 1.0
N J:GLY47 4.3 17.2 1.0
CA J:GLY42 4.4 13.7 1.0
N J:ALA50 4.5 13.4 1.0
N J:GLY46 4.5 15.9 1.0
SG J:CYS73 4.5 15.0 1.0
SG J:CYS51 4.6 14.3 1.0
N J:GLU45 4.7 15.0 1.0
C J:GLY47 4.7 17.7 1.0
C J:GLY46 4.8 17.2 1.0
CA J:GLY49 4.8 13.0 1.0
O J:GLY42 4.9 13.2 1.0
CA J:GLY46 4.9 16.2 1.0
CA J:GLY44 4.9 14.1 1.0
CB J:ALA50 5.0 12.8 1.0

Reference:

H.Cao, J.Hall, R.Hille. Substrate Orientation and Specificity in Xanthine Oxidase: Crystal Structures of the Enzyme in Complex with Indole-3-Acetaldehyde and Guanine. Biochemistry V. 53 533 2014.
ISSN: ISSN 0006-2960
PubMed: 24397336
DOI: 10.1021/BI401465U
Page generated: Sun Aug 4 16:46:32 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy