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Copper in PDB 6zav: No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.19 A Resolution (Unrestrained, Full Matrix Refinement By Shelx)

Enzymatic activity of No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.19 A Resolution (Unrestrained, Full Matrix Refinement By Shelx)

All present enzymatic activity of No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.19 A Resolution (Unrestrained, Full Matrix Refinement By Shelx):
1.7.2.1;

Protein crystallography data

The structure of No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.19 A Resolution (Unrestrained, Full Matrix Refinement By Shelx), PDB code: 6zav 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) 30.00 / 1.19
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 107.467, 107.467, 107.467, 90, 90, 90
R / Rfree (%) n/a / n/a

Copper Binding Sites:

The binding sites of Copper atom in the No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.19 A Resolution (Unrestrained, Full Matrix Refinement By Shelx) (pdb code 6zav). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.19 A Resolution (Unrestrained, Full Matrix Refinement By Shelx), PDB code: 6zav:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 6zav

Go back to Copper Binding Sites List in 6zav
Copper binding site 1 out of 2 in the No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.19 A Resolution (Unrestrained, Full Matrix Refinement By Shelx)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.19 A Resolution (Unrestrained, Full Matrix Refinement By Shelx) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:14.0
occ:1.00
 ND1 A:HIS89 2.1 11.9 1.0
ND1 A:HIS140 2.1 12.5 1.0
SG A:CYS130 2.2 12.6 1.0
SD A:MET145 2.5 13.1 1.0
CE1 A:HIS140 3.0 12.6 1.0
CE1 A:HIS89 3.0 12.2 1.0
CG A:HIS89 3.1 11.9 1.0
CG A:HIS140 3.2 12.5 1.0
CB A:CYS130 3.2 12.7 1.0
CE A:MET145 3.3 14.2 1.0
CB A:HIS89 3.5 11.6 1.0
CB A:HIS140 3.5 11.8 1.0
CA A:HIS89 3.8 12.0 1.0
CG A:MET145 3.9 13.7 1.0
NE2 A:HIS140 4.2 13.4 1.0
NE2 A:HIS89 4.2 11.6 1.0
O A:PRO88 4.2 13.6 1.0
CD2 A:HIS140 4.2 13.7 1.0
CG A:PRO132 4.2 14.2 0.6
CD2 A:HIS89 4.2 12.2 1.0
CG A:PRO132 4.3 15.8 0.4
CB A:MET145 4.5 11.9 1.0
SD A:MET56 4.6 14.2 0.3
CD A:PRO132 4.6 11.9 0.6
CA A:CYS130 4.7 11.2 1.0
N A:ASN90 4.7 12.0 1.0
CA A:HIS140 4.7 11.3 1.0
C A:HIS89 4.8 12.2 1.0
N A:HIS89 4.9 12.5 1.0
CD A:PRO132 4.9 13.5 0.4
C A:PRO88 4.9 12.6 1.0
CE A:MET56 5.0 13.4 0.7

Copper binding site 2 out of 2 in 6zav

Go back to Copper Binding Sites List in 6zav
Copper binding site 2 out of 2 in the No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.19 A Resolution (Unrestrained, Full Matrix Refinement By Shelx)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.19 A Resolution (Unrestrained, Full Matrix Refinement By Shelx) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:13.9
occ:1.00
 NE2 A:HIS129 2.0 12.0 1.0
NE2 A:HIS94 2.0 10.7 1.0
O A:NO503 2.1 23.8 0.7
N A:NO503 2.2 29.0 0.7
CD2 A:HIS129 2.9 12.1 1.0
CE1 A:HIS94 2.9 10.6 1.0
CE1 A:HIS129 3.0 12.3 1.0
CD2 A:HIS94 3.1 10.7 1.0
OD2 A:ASP92 3.7 20.6 0.8
ND1 A:HIS94 4.1 10.2 1.0
CG A:HIS129 4.1 10.7 1.0
ND1 A:HIS129 4.1 11.6 1.0
CG A:HIS94 4.2 9.7 1.0
O A:HOH629 4.2 32.6 0.5
CG A:ASP92 4.4 15.2 0.8
OD1 A:ASP92 4.6 15.6 0.8

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: Wed Jul 31 07:58:33 2024

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