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Copper in PDB 6zas: Damage-Free As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography

Enzymatic activity of Damage-Free As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography

All present enzymatic activity of Damage-Free As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography:
1.7.2.1;

Protein crystallography data

The structure of Damage-Free As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography, PDB code: 6zas was solved by S.L.Rose, S.V.Antonyuk, D.Sasaki, K.Yamashita, K.Hirata, G.Ueno, H.Ago, R.R.Eady, T.Tosha, M.Yamamoto, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.91 / 1.30
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 107.01, 107.01, 107.01, 90, 90, 90
R / Rfree (%) 15.1 / 20.6

Copper Binding Sites:

The binding sites of Copper atom in the Damage-Free As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography (pdb code 6zas). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Damage-Free As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography, PDB code: 6zas:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 6zas

Go back to Copper Binding Sites List in 6zas
Copper binding site 1 out of 2 in the Damage-Free As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Damage-Free As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:19.2
occ:0.95
ND1 A:HIS89 2.0 17.4 1.0
ND1 A:HIS140 2.0 17.4 1.0
SG A:CYS130 2.1 18.9 1.0
SD A:MET145 2.6 20.1 1.0
CE1 A:HIS140 2.9 18.2 1.0
CE1 A:HIS89 2.9 19.5 1.0
CG A:HIS89 3.0 18.1 1.0
CG A:HIS140 3.0 17.4 1.0
CB A:CYS130 3.2 15.9 1.0
CE A:MET145 3.4 20.0 1.0
CB A:HIS89 3.4 18.7 1.0
CB A:HIS140 3.4 16.9 1.0
CA A:HIS89 3.7 20.3 1.0
CG A:MET145 4.0 21.0 1.0
O A:PRO88 4.0 20.1 1.0
NE2 A:HIS140 4.0 20.2 1.0
NE2 A:HIS89 4.0 20.0 1.0
CD2 A:HIS140 4.1 19.0 1.0
CD2 A:HIS89 4.1 18.4 1.0
CG A:PRO132 4.2 21.0 1.0
CB A:MET145 4.5 19.3 1.0
N A:ASN90 4.6 19.2 1.0
CA A:CYS130 4.6 17.3 1.0
SD A:MET56 4.6 19.4 0.5
CD A:PRO132 4.7 20.0 1.0
CA A:HIS140 4.7 14.9 1.0
N A:HIS89 4.7 22.4 1.0
C A:HIS89 4.7 19.6 1.0
C A:PRO88 4.8 19.5 1.0

Copper binding site 2 out of 2 in 6zas

Go back to Copper Binding Sites List in 6zas
Copper binding site 2 out of 2 in the Damage-Free As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Damage-Free As-Isolated Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu407

b:17.7
occ:0.90
O A:HOH504 1.9 24.2 0.8
NE2 A:HIS94 2.0 16.0 1.0
O A:HOH771 2.1 22.0 1.0
NE2 A:HIS129 2.1 17.0 1.0
CE1 A:HIS94 2.9 14.8 1.0
CD2 A:HIS94 3.1 17.2 1.0
CD2 A:HIS129 3.1 15.4 1.0
CE1 A:HIS129 3.2 17.5 1.0
OD2 A:ASP92 3.8 27.8 1.0
O A:HOH689 4.0 38.6 1.0
ND1 A:HIS94 4.1 15.7 1.0
CG A:HIS94 4.2 15.6 1.0
CG A:ASP92 4.2 21.3 1.0
ND1 A:HIS129 4.3 17.2 1.0
CG A:HIS129 4.3 17.7 1.0
OD1 A:ASP92 4.4 19.9 1.0
O A:HOH644 4.7 22.2 1.0

Reference:

S.L.Rose, S.V.Antonyuk, D.Sasaki, K.Yamashita, K.Hirata, G.Ueno, H.Ago, R.R.Eady, T.Tosha, M.Yamamoto, S.S.Hasnain. An Unprecedented Insight Into the Catalytic Mechanism of Copper Nitrite Reductase From Atomic-Resolution and Damage-Free Structures Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ABD8523
Page generated: Mon Jul 14 07:35:13 2025

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