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Iron in PDB 3an1: Crystal Structure of Rat D428A Mutant, Urate Bound Form

Enzymatic activity of Crystal Structure of Rat D428A Mutant, Urate Bound Form

All present enzymatic activity of Crystal Structure of Rat D428A Mutant, Urate Bound Form:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Crystal Structure of Rat D428A Mutant, Urate Bound Form, PDB code: 3an1 was solved by K.Okamoto, Y.Kawaguchi, B.T.Eger, E.F.Pai, T.Nishino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.35 / 1.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.536, 138.242, 222.473, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19.8

Other elements in 3an1:

The structure of Crystal Structure of Rat D428A Mutant, Urate Bound Form also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Rat D428A Mutant, Urate Bound Form (pdb code 3an1). 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 Rat D428A Mutant, Urate Bound Form, PDB code: 3an1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3an1

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Iron binding site 1 out of 8 in the Crystal Structure of Rat D428A Mutant, Urate Bound Form


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 Rat D428A Mutant, Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:14.8
occ:1.00
 FE1 A:FES3001 0.0 14.8 1.0
S2 A:FES3001 2.2 14.4 1.0
S1 A:FES3001 2.2 15.2 1.0
SG A:CYS112 2.3 11.0 1.0
FE2 A:FES3001 2.6 14.8 1.0
SG A:CYS149 2.7 22.3 1.0
CB A:CYS112 3.2 10.2 1.0
CB A:CYS149 3.5 10.6 1.0
O A:HOH1544 3.6 12.7 1.0
N A:CYS112 3.7 10.3 1.0
CA A:CYS112 3.8 8.7 1.0
N A:GLY113 3.9 9.6 1.0
N A:CYS149 4.1 10.8 1.0
C A:CYS112 4.2 9.5 1.0
SG A:CYS147 4.4 12.1 1.0
N A:PHE114 4.4 10.0 1.0
CA A:CYS149 4.4 12.3 1.0
SG A:CYS115 4.4 15.1 1.0
N A:ARG148 4.7 9.7 1.0
C A:GLN111 4.8 10.0 1.0
N A:CYS115 4.8 10.9 1.0
CA A:GLY113 5.0 11.0 1.0

Iron binding site 2 out of 8 in 3an1

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Iron binding site 2 out of 8 in the Crystal Structure of Rat D428A Mutant, Urate Bound Form


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 Rat D428A Mutant, Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:14.8
occ:1.00
 FE2 A:FES3001 0.0 14.8 1.0
SG A:CYS115 2.2 15.1 1.0
S1 A:FES3001 2.2 15.2 1.0
S2 A:FES3001 2.2 14.4 1.0
SG A:CYS147 2.3 12.1 1.0
FE1 A:FES3001 2.6 14.8 1.0
CB A:CYS147 3.3 9.7 1.0
CB A:CYS115 3.4 9.7 1.0
CA A:CYS147 3.7 9.9 1.0
N A:ARG148 4.0 9.7 1.0
N A:CYS115 4.2 10.9 1.0
C A:CYS147 4.3 10.8 1.0
N A:CYS149 4.3 10.8 1.0
O A:HOH1757 4.4 12.9 1.0
CA A:CYS115 4.4 8.7 1.0
CB A:CYS149 4.4 10.6 1.0
SG A:CYS112 4.6 11.0 1.0
SG A:CYS149 4.7 22.3 1.0
CG2 A:THR150 4.8 10.6 1.0
N A:THR150 4.9 11.3 1.0
O A:LEU146 5.0 12.6 1.0
CA A:CYS149 5.0 12.3 1.0
N A:CYS147 5.0 9.8 1.0

Iron binding site 3 out of 8 in 3an1

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Iron binding site 3 out of 8 in the Crystal Structure of Rat D428A Mutant, Urate Bound Form


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 Rat D428A Mutant, Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:11.5
occ:1.00
 FE1 A:FES3002 0.0 11.5 1.0
S1 A:FES3002 2.2 11.8 1.0
S2 A:FES3002 2.2 12.4 1.0
SG A:CYS51 2.3 10.1 1.0
SG A:CYS73 2.3 11.4 1.0
FE2 A:FES3002 2.8 11.8 1.0
CB A:CYS73 3.2 11.0 1.0
CB A:CYS51 3.4 7.7 1.0
N A:CYS73 4.2 11.7 1.0
CB A:ASN71 4.2 12.8 1.0
CA A:CYS73 4.2 13.3 1.0
N A:GLY46 4.3 14.8 1.0
N A:CYS51 4.4 8.1 1.0
SG A:CYS43 4.4 11.4 1.0
N A:GLY44 4.4 11.0 1.0
OD1 A:ASN71 4.4 16.6 1.0
CA A:CYS51 4.5 9.3 1.0
CG A:ASN71 4.5 16.4 1.0
CA A:GLY46 4.5 16.2 1.0
SG A:CYS48 4.7 12.0 1.0
CA A:GLY44 4.7 11.9 1.0
N A:GLY49 4.9 10.0 1.0
CA A:ASN71 4.9 12.9 1.0
N A:GLU45 4.9 14.0 1.0
N A:ALA50 5.0 9.5 1.0

Iron binding site 4 out of 8 in 3an1

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Iron binding site 4 out of 8 in the Crystal Structure of Rat D428A Mutant, Urate Bound Form


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 Rat D428A Mutant, Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:11.8
occ:1.00
 FE2 A:FES3002 0.0 11.8 1.0
S1 A:FES3002 2.3 11.8 1.0
S2 A:FES3002 2.3 12.4 1.0
SG A:CYS43 2.3 11.4 1.0
SG A:CYS48 2.3 12.0 1.0
FE1 A:FES3002 2.8 11.5 1.0
N A:CYS43 3.4 10.9 1.0
CB A:CYS43 3.4 12.3 1.0
CB A:CYS48 3.5 13.6 1.0
N A:CYS48 3.6 12.6 1.0
N A:GLY44 3.9 11.0 1.0
CA A:CYS43 3.9 12.4 1.0
N A:GLY49 3.9 10.0 1.0
CA A:CYS48 3.9 10.4 1.0
C A:GLY42 4.1 11.3 1.0
C A:CYS48 4.2 9.9 1.0
C A:CYS43 4.3 12.7 1.0
N A:GLY46 4.4 14.8 1.0
N A:GLY42 4.4 11.0 1.0
N A:ALA50 4.4 9.5 1.0
CA A:GLY42 4.4 10.8 1.0
N A:GLY47 4.4 17.2 1.0
SG A:CYS73 4.5 11.4 1.0
SG A:CYS51 4.6 10.1 1.0
N A:GLU45 4.7 14.0 1.0
C A:GLY47 4.7 17.3 1.0
C A:GLY46 4.7 17.6 1.0
CA A:GLY46 4.8 16.2 1.0
CA A:GLY44 4.8 11.9 1.0
CA A:GLY49 4.9 9.7 1.0
O A:GLY42 4.9 12.1 1.0
CB A:ALA50 5.0 12.5 1.0

Iron binding site 5 out of 8 in 3an1

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Iron binding site 5 out of 8 in the Crystal Structure of Rat D428A Mutant, Urate Bound Form


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 Rat D428A Mutant, Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:14.4
occ:1.00
 FE1 B:FES4001 0.0 14.4 1.0
S2 B:FES4001 2.2 13.0 1.0
S1 B:FES4001 2.2 14.8 1.0
SG B:CYS112 2.3 11.3 1.0
FE2 B:FES4001 2.6 13.3 1.0
SG B:CYS149 2.7 20.8 1.0
CB B:CYS112 3.3 12.3 1.0
CB B:CYS149 3.5 12.7 1.0
N B:CYS112 3.6 10.3 1.0
O B:HOH1417 3.7 9.8 1.0
N B:GLY113 3.9 9.7 1.0
CA B:CYS112 3.9 11.5 1.0
N B:CYS149 4.1 11.7 1.0
C B:CYS112 4.2 10.7 1.0
SG B:CYS147 4.4 11.7 1.0
N B:PHE114 4.4 9.7 1.0
SG B:CYS115 4.4 15.2 1.0
CA B:CYS149 4.4 13.2 1.0
N B:ARG148 4.7 8.8 1.0
C B:GLN111 4.8 11.5 1.0
N B:CYS115 4.8 10.1 1.0
CA B:GLY113 4.9 11.3 1.0
CB B:GLN111 4.9 12.5 1.0

Iron binding site 6 out of 8 in 3an1

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Iron binding site 6 out of 8 in the Crystal Structure of Rat D428A Mutant, Urate Bound Form


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 Rat D428A Mutant, Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:13.3
occ:1.00
 FE2 B:FES4001 0.0 13.3 1.0
S1 B:FES4001 2.2 14.8 1.0
SG B:CYS115 2.2 15.2 1.0
S2 B:FES4001 2.3 13.0 1.0
SG B:CYS147 2.3 11.7 1.0
FE1 B:FES4001 2.6 14.4 1.0
CB B:CYS115 3.3 11.7 1.0
CB B:CYS147 3.3 10.4 1.0
CA B:CYS147 3.7 8.9 1.0
N B:ARG148 4.1 8.8 1.0
N B:CYS149 4.3 11.7 1.0
N B:CYS115 4.3 10.1 1.0
C B:CYS147 4.3 10.2 1.0
O B:HOH1522 4.3 12.0 1.0
CA B:CYS115 4.4 8.1 1.0
CB B:CYS149 4.5 12.7 1.0
SG B:CYS112 4.6 11.3 1.0
SG B:CYS149 4.6 20.8 1.0
CG2 B:THR150 4.7 11.4 1.0
N B:THR150 5.0 11.5 1.0
N B:GLY113 5.0 9.7 1.0
CA B:CYS149 5.0 13.2 1.0

Iron binding site 7 out of 8 in 3an1

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Iron binding site 7 out of 8 in the Crystal Structure of Rat D428A Mutant, Urate Bound Form


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 Rat D428A Mutant, Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:9.0
occ:1.00
 FE1 B:FES4002 0.0 9.0 1.0
S1 B:FES4002 2.2 9.1 1.0
S2 B:FES4002 2.2 8.7 1.0
SG B:CYS51 2.3 8.8 1.0
SG B:CYS73 2.3 10.6 1.0
FE2 B:FES4002 2.8 9.7 1.0
CB B:CYS73 3.1 9.8 1.0
CB B:CYS51 3.5 7.1 1.0
N B:CYS73 4.2 9.1 1.0
CB B:ASN71 4.2 7.2 1.0
CA B:CYS73 4.2 9.8 1.0
N B:CYS51 4.3 7.7 1.0
N B:GLY46 4.4 10.6 1.0
SG B:CYS43 4.4 9.8 1.0
N B:GLY44 4.4 7.8 1.0
OD1 B:ASN71 4.5 14.0 1.0
CA B:CYS51 4.5 8.3 1.0
CG B:ASN71 4.5 10.4 1.0
CA B:GLY46 4.6 12.3 1.0
SG B:CYS48 4.6 10.4 1.0
CA B:GLY44 4.7 9.1 1.0
N B:GLY49 4.8 8.9 1.0
CA B:ASN71 4.9 7.6 1.0
N B:GLU45 4.9 9.8 1.0
N B:ALA50 5.0 7.9 1.0

Iron binding site 8 out of 8 in 3an1

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Iron binding site 8 out of 8 in the Crystal Structure of Rat D428A Mutant, Urate Bound Form


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 Rat D428A Mutant, Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:9.7
occ:1.00
 FE2 B:FES4002 0.0 9.7 1.0
S1 B:FES4002 2.3 9.1 1.0
S2 B:FES4002 2.3 8.7 1.0
SG B:CYS48 2.3 10.4 1.0
SG B:CYS43 2.3 9.8 1.0
FE1 B:FES4002 2.8 9.0 1.0
CB B:CYS48 3.4 12.3 1.0
N B:CYS43 3.4 9.0 1.0
CB B:CYS43 3.5 9.9 1.0
N B:CYS48 3.6 10.6 1.0
N B:GLY44 3.8 7.8 1.0
N B:GLY49 3.9 8.9 1.0
CA B:CYS43 3.9 9.2 1.0
CA B:CYS48 3.9 9.4 1.0
C B:GLY42 4.1 8.3 1.0
C B:CYS48 4.2 9.9 1.0
C B:CYS43 4.3 10.4 1.0
N B:GLY42 4.3 8.6 1.0
N B:ALA50 4.4 7.9 1.0
N B:GLY46 4.4 10.6 1.0
N B:GLY47 4.4 14.1 1.0
CA B:GLY42 4.4 8.4 1.0
SG B:CYS73 4.5 10.6 1.0
N B:GLU45 4.6 9.8 1.0
SG B:CYS51 4.6 8.8 1.0
C B:GLY46 4.8 15.5 1.0
C B:GLY47 4.8 17.5 1.0
CA B:GLY49 4.8 8.6 1.0
CA B:GLY46 4.8 12.3 1.0
CA B:GLY44 4.8 9.1 1.0
O B:GLY42 4.9 10.2 1.0

Reference:

K.Okamoto, Y.Kawaguchi, B.T.Eger, E.F.Pai, T.Nishino. Crystal Structures of Urate Bound Form of Xanthine Oxidoreductase: Substrate Orientation and Structure of the Key Reaction Intermediate J.Am.Chem.Soc. V. 132 17080 2010.
ISSN: ISSN 0002-7863
PubMed: 21077683
DOI: 10.1021/JA1077574
Page generated: Sun Dec 13 15:00:59 2020

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