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Nickel in PDB 1zvf: The Crystal Structure of 3-Hydroxyanthranilate 3,4-Dioxygenase From Saccharomyces Cerevisiae

Enzymatic activity of The Crystal Structure of 3-Hydroxyanthranilate 3,4-Dioxygenase From Saccharomyces Cerevisiae

All present enzymatic activity of The Crystal Structure of 3-Hydroxyanthranilate 3,4-Dioxygenase From Saccharomyces Cerevisiae:
1.13.11.6;

Protein crystallography data

The structure of The Crystal Structure of 3-Hydroxyanthranilate 3,4-Dioxygenase From Saccharomyces Cerevisiae, PDB code: 1zvf was solved by X.Li, M.Guo, M.Teng, L.Niu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.104, 66.195, 130.188, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 26.8

Nickel Binding Sites:

The binding sites of Nickel atom in the The Crystal Structure of 3-Hydroxyanthranilate 3,4-Dioxygenase From Saccharomyces Cerevisiae (pdb code 1zvf). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the The Crystal Structure of 3-Hydroxyanthranilate 3,4-Dioxygenase From Saccharomyces Cerevisiae, PDB code: 1zvf:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 1zvf

Go back to Nickel Binding Sites List in 1zvf
Nickel binding site 1 out of 4 in the The Crystal Structure of 3-Hydroxyanthranilate 3,4-Dioxygenase From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Crystal Structure of 3-Hydroxyanthranilate 3,4-Dioxygenase From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni201

b:36.7
occ:1.00
 NE2 A:HIS97 2.1 38.4 1.0
OE2 A:GLU55 2.1 40.0 1.0
ND1 A:HIS49 2.2 39.4 1.0
OE1 A:GLU55 2.5 33.6 1.0
CD A:GLU55 2.6 37.8 1.0
CE1 A:HIS97 2.9 37.1 1.0
O A:HOH205 3.0 23.9 1.0
CE1 A:HIS49 3.0 40.2 1.0
CD2 A:HIS97 3.2 37.1 1.0
CG A:HIS49 3.3 39.1 1.0
O A:HOH204 3.4 34.7 1.0
CB A:HIS49 3.7 39.3 1.0
ND1 A:HIS97 4.1 38.0 1.0
CG A:GLU55 4.1 38.9 1.0
NE2 A:HIS49 4.2 40.4 1.0
CG A:HIS97 4.2 37.8 1.0
CD2 A:HIS49 4.4 40.0 1.0
OE2 A:GLU111 4.4 46.2 1.0
ND2 A:ASN51 4.5 41.0 1.0
CD A:GLU111 4.9 48.8 1.0
CB A:ASN51 4.9 39.5 1.0

Nickel binding site 2 out of 4 in 1zvf

Go back to Nickel Binding Sites List in 1zvf
Nickel binding site 2 out of 4 in the The Crystal Structure of 3-Hydroxyanthranilate 3,4-Dioxygenase From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Crystal Structure of 3-Hydroxyanthranilate 3,4-Dioxygenase From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni203

b:42.4
occ:1.00
 SG A:CYS166 2.2 44.7 1.0
SG A:CYS126 2.2 42.8 1.0
SG A:CYS163 2.3 40.5 1.0
SG A:CYS129 2.3 44.0 1.0
CB A:CYS126 3.0 43.4 1.0
CB A:CYS163 3.1 42.7 1.0
CB A:CYS166 3.4 44.8 1.0
CB A:CYS129 3.4 45.5 1.0
N A:CYS129 3.8 45.9 1.0
N A:CYS166 3.8 45.8 1.0
CA A:CYS166 4.2 44.8 1.0
CA A:CYS129 4.2 45.6 1.0
CA A:CYS126 4.5 43.5 1.0
CB A:HIS128 4.5 46.0 1.0
CB A:THR168 4.5 42.7 1.0
CA A:CYS163 4.5 43.0 1.0
OG1 A:THR168 4.7 42.3 1.0
C A:HIS128 4.7 46.2 1.0
C A:CYS166 4.8 44.5 1.0
C A:CYS129 4.8 46.1 1.0
N A:ARG130 4.9 46.4 1.0
N A:HIS128 4.9 46.0 1.0
CB A:HIS165 4.9 47.9 1.0
N A:LYS167 4.9 44.3 1.0
ND1 A:HIS128 4.9 44.4 1.0
N A:THR168 4.9 43.1 1.0
CA A:HIS128 4.9 46.1 1.0
C A:HIS165 5.0 46.5 1.0
CB A:GLN131 5.0 47.5 1.0

Nickel binding site 3 out of 4 in 1zvf

Go back to Nickel Binding Sites List in 1zvf
Nickel binding site 3 out of 4 in the The Crystal Structure of 3-Hydroxyanthranilate 3,4-Dioxygenase From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The Crystal Structure of 3-Hydroxyanthranilate 3,4-Dioxygenase From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni202

b:42.8
occ:1.00
 NE2 B:HIS97 2.1 34.8 1.0
O B:HOH205 2.1 33.3 1.0
ND1 B:HIS49 2.2 38.3 1.0
OE2 B:GLU55 2.2 39.4 1.0
OE1 B:GLU55 2.5 38.0 1.0
CD B:GLU55 2.7 40.2 1.0
O B:HOH206 2.9 48.1 1.0
CE1 B:HIS97 3.0 36.0 1.0
CE1 B:HIS49 3.0 38.8 1.0
CD2 B:HIS97 3.2 34.6 1.0
CG B:HIS49 3.2 39.0 1.0
CB B:HIS49 3.6 39.7 1.0
OE2 B:GLU111 4.0 49.0 1.0
CG B:GLU55 4.2 38.8 1.0
ND1 B:HIS97 4.2 35.6 1.0
NE2 B:HIS49 4.2 38.2 1.0
CG B:HIS97 4.3 36.6 1.0
CD2 B:HIS49 4.3 39.0 1.0
ND2 B:ASN51 4.7 35.3 1.0
CB B:ASN51 4.8 37.8 1.0
CD B:GLU111 4.8 45.4 1.0

Nickel binding site 4 out of 4 in 1zvf

Go back to Nickel Binding Sites List in 1zvf
Nickel binding site 4 out of 4 in the The Crystal Structure of 3-Hydroxyanthranilate 3,4-Dioxygenase From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of The Crystal Structure of 3-Hydroxyanthranilate 3,4-Dioxygenase From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni204

b:39.1
occ:1.00
 SG B:CYS163 2.3 35.6 1.0
SG B:CYS166 2.3 37.2 1.0
SG B:CYS126 2.3 32.4 1.0
SG B:CYS129 2.4 35.4 1.0
CB B:CYS126 3.0 34.9 1.0
CB B:CYS163 3.1 37.6 1.0
CB B:CYS129 3.3 36.1 1.0
CB B:CYS166 3.5 38.6 1.0
N B:CYS129 3.7 36.1 1.0
N B:CYS166 3.7 39.0 1.0
CA B:CYS129 4.0 36.3 1.0
CA B:CYS166 4.1 38.5 1.0
CA B:CYS126 4.5 35.5 1.0
CA B:CYS163 4.6 37.9 1.0
C B:CYS129 4.7 36.9 1.0
N B:ARG130 4.7 37.6 1.0
OG1 B:THR168 4.7 39.6 1.0
CB B:THR168 4.7 39.1 1.0
C B:CYS166 4.7 38.9 1.0
CB B:HIS128 4.7 36.2 1.0
C B:HIS128 4.8 36.3 1.0
CB B:HIS165 4.8 39.6 1.0
N B:LYS167 4.8 39.1 1.0
N B:THR168 4.9 39.0 1.0
C B:HIS165 4.9 39.5 1.0
ND1 B:HIS128 4.9 35.9 1.0
CB B:GLN131 5.0 38.8 1.0
N B:GLN131 5.0 38.5 1.0

Reference:

X.Li, M.Guo, M.Teng, L.Niu. The Crystal Structure of 3-Hydroxyanthranilate 3,4-Dioxygenase From Saccharomyces Cerevisiae To Be Published.
Page generated: Wed Oct 9 16:35:22 2024

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