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

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

All present enzymatic activity of Damage-Free Nitrite-Bound 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 Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography, PDB code: 6zau 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) 29.80 / 1.30
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 106.95, 106.95, 106.95, 90, 90, 90
R / Rfree (%) 15.6 / 20.6

Copper Binding Sites:

The binding sites of Copper atom in the Damage-Free Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography (pdb code 6zau). 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 Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography, PDB code: 6zau:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 6zau

Go back to Copper Binding Sites List in 6zau
Copper binding site 1 out of 2 in the Damage-Free Nitrite-Bound 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 Nitrite-Bound 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:18.3
occ:0.90
 ND1 A:HIS140 2.0 17.7 1.0
ND1 A:HIS89 2.0 17.8 1.0
SG A:CYS130 2.1 17.6 1.0
SD A:MET145 2.5 20.3 1.0
CE1 A:HIS140 2.9 20.7 1.0
CE1 A:HIS89 2.9 17.1 1.0
CG A:HIS140 3.0 18.3 1.0
CG A:HIS89 3.0 18.9 1.0
CB A:CYS130 3.2 15.6 1.0
CB A:HIS140 3.4 15.6 1.0
CE A:MET145 3.4 20.8 1.0
CB A:HIS89 3.4 18.0 1.0
CA A:HIS89 3.8 19.2 1.0
O A:PRO88 4.0 21.0 1.0
NE2 A:HIS140 4.0 20.4 1.0
CG A:MET145 4.1 20.7 1.0
CD2 A:HIS140 4.1 18.8 1.0
NE2 A:HIS89 4.1 18.0 1.0
CG A:PRO132 4.1 18.3 1.0
CD2 A:HIS89 4.1 18.1 1.0
CB A:MET145 4.5 19.0 1.0
N A:ASN90 4.6 18.7 1.0
CA A:CYS130 4.6 16.8 1.0
SD A:MET56 4.6 16.5 0.4
CD A:PRO132 4.6 17.1 1.0
CA A:HIS140 4.7 18.4 1.0
N A:HIS89 4.7 20.8 1.0
C A:HIS89 4.8 19.1 1.0
C A:PRO88 4.8 21.7 1.0
CE A:MET56 4.8 24.9 0.6

Copper binding site 2 out of 2 in 6zau

Go back to Copper Binding Sites List in 6zau
Copper binding site 2 out of 2 in the Damage-Free Nitrite-Bound 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 Nitrite-Bound 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:17.8
occ:0.90
 O2 A:NO2415 1.9 22.1 0.7
NE2 A:HIS94 2.0 15.9 1.0
N A:NO2415 2.0 25.3 0.7
NE2 A:HIS129 2.1 17.0 1.0
O1 A:NO2415 2.1 19.8 0.7
CE1 A:HIS94 3.0 17.3 1.0
CD2 A:HIS129 3.0 15.4 1.0
CD2 A:HIS94 3.1 15.4 1.0
CE1 A:HIS129 3.1 18.4 1.0
OD2 A:ASP92 3.5 28.4 1.0
ND1 A:HIS94 4.1 14.9 1.0
CG A:HIS94 4.2 15.3 1.0
ND1 A:HIS129 4.2 16.8 1.0
CG A:ASP92 4.2 18.5 1.0
CG A:HIS129 4.2 15.6 1.0
O A:HOH514 4.3 32.1 0.5
OD1 A:ASP92 4.6 21.0 1.0
O A:HOH678 4.7 22.1 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: Sun Jan 24 15:06:53 2021

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