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Copper in PDB 5ocb: Crystal Structure of Nitric Oxide Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii

Protein crystallography data

The structure of Crystal Structure of Nitric Oxide Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii, PDB code: 5ocb was solved by J.Dong, D.Sasaki, R.Eady, S.V.Antonyuk, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.61 / 1.78
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 180.460, 180.460, 180.460, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 16.2

Other elements in 5ocb:

The structure of Crystal Structure of Nitric Oxide Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii also contains other interesting chemical elements:

Iron (Fe) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Nitric Oxide Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii (pdb code 5ocb). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure of Nitric Oxide Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii, PDB code: 5ocb:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 5ocb

Go back to Copper Binding Sites List in 5ocb
Copper binding site 1 out of 2 in the Crystal Structure of Nitric Oxide Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Nitric Oxide Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:18.7
occ:1.00
ND1 A:HIS143 2.1 18.1 1.0
ND1 A:HIS94 2.1 19.6 1.0
SG A:CYS135 2.2 18.5 1.0
SD A:MET148 2.6 19.3 1.0
CE1 A:HIS143 3.0 18.3 1.0
CE1 A:HIS94 3.0 19.4 1.0
CG A:HIS143 3.1 17.2 1.0
CG A:HIS94 3.1 19.2 1.0
CB A:CYS135 3.2 17.0 1.0
CE A:MET148 3.4 19.2 1.0
CB A:HIS94 3.5 19.8 1.0
CB A:HIS143 3.5 18.0 1.0
CA A:HIS94 3.8 18.9 1.0
O A:PRO93 4.0 18.3 1.0
NE2 A:HIS143 4.1 18.1 1.0
CD2 A:HIS143 4.1 17.8 1.0
CG A:MET148 4.2 17.3 1.0
NE2 A:HIS94 4.2 19.6 1.0
CD2 A:HIS94 4.2 19.1 1.0
OG1 A:THR137 4.3 19.1 1.0
CB A:THR137 4.3 18.6 1.0
N A:ASN95 4.6 17.5 1.0
CE3 A:TRP61 4.6 17.4 1.0
CA A:CYS135 4.6 15.9 1.0
CA A:HIS143 4.6 16.7 1.0
CB A:MET148 4.7 16.4 1.0
N A:HIS94 4.7 18.8 1.0
C A:HIS94 4.7 19.6 1.0
C A:PRO93 4.8 18.2 1.0

Copper binding site 2 out of 2 in 5ocb

Go back to Copper Binding Sites List in 5ocb
Copper binding site 2 out of 2 in the Crystal Structure of Nitric Oxide Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Nitric Oxide Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:18.2
occ:0.70
NE2 A:HIS134 2.0 18.9 1.0
N A:NO504 2.0 17.2 0.7
NE2 A:HIS99 2.1 16.3 1.0
O A:HOH681 2.1 16.7 0.3
O A:HOH663 2.1 43.3 0.3
O A:NO504 2.8 17.3 0.7
CD2 A:HIS134 2.9 18.5 1.0
CE1 A:HIS99 3.0 16.2 1.0
CE1 A:HIS134 3.0 18.2 1.0
CD2 A:HIS99 3.1 15.3 1.0
ND2 A:ASN97 3.8 19.2 1.0
CG A:HIS134 4.1 17.0 1.0
ND1 A:HIS134 4.1 18.6 1.0
ND1 A:HIS99 4.1 16.4 1.0
CG A:HIS99 4.2 15.2 1.0
CG A:ASN97 4.4 17.2 1.0
O A:HOH912 4.4 16.7 0.7
OD1 A:ASN97 4.7 18.2 1.0
O A:HOH864 4.8 22.2 0.7

Reference:

J.Dong, D.Sasaki, R.Eady, S.V.Antonyuk, S.S.Hasnain. Activation of Redox Tyrosine Switch Is Required For Ligand Binding at the Catalytic Site in Heme-Cu Nitrite Reductases To Be Published.
Page generated: Sun Dec 13 11:19:18 2020

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