Atomistry » Copper » PDB 8prq-8s2q » 8rur
Atomistry »
  Copper »
    PDB 8prq-8s2q »
      8rur »

Copper in PDB 8rur: High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.38 Mgy]

Enzymatic activity of High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.38 Mgy]

All present enzymatic activity of High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.38 Mgy]:
1.7.2.1;

Protein crystallography data

The structure of High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.38 Mgy], PDB code: 8rur was solved by S.L.Rose, F.M.Ferroni, S.Horrell, C.D.Brondino, R.R.Eady, S.Jaho, M.A.Hough, A.L.Owen, 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) 45.00 / 1.13
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 103.92, 103.92, 64.25, 90, 90, 120
R / Rfree (%) 11.6 / 13.4

Copper Binding Sites:

The binding sites of Copper atom in the High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.38 Mgy] (pdb code 8rur). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.38 Mgy], PDB code: 8rur:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 8rur

Go back to Copper Binding Sites List in 8rur
Copper binding site 1 out of 2 in the High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.38 Mgy]


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.38 Mgy] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:11.7
occ:1.00
 ND1 A:HIS89 2.0 10.4 1.0
ND1 A:HIS140 2.0 10.0 1.0
SG A:CYS130 2.2 11.3 1.0
SD A:MET145 2.5 10.6 0.7
SD A:MET145 2.7 10.8 0.3
HB3 A:HIS140 2.9 9.5 1.0
CE1 A:HIS89 2.9 10.8 1.0
CE1 A:HIS140 3.0 11.4 1.0
HE1 A:HIS89 3.1 10.8 1.0
CG A:HIS89 3.1 10.2 1.0
CG A:HIS140 3.1 9.6 1.0
HE1 A:MET145 3.1 10.7 0.7
HE1 A:HIS140 3.1 11.2 1.0
HB3 A:HIS89 3.1 10.8 1.0
HA A:HIS89 3.2 11.0 1.0
CB A:CYS130 3.2 10.0 1.0
HB3 A:CYS130 3.2 9.9 1.0
HE2 A:MET145 3.2 10.9 0.3
CE A:MET145 3.3 10.7 0.7
HB2 A:CYS130 3.3 9.8 1.0
HG3 A:PRO132 3.4 12.4 0.3
CE A:MET145 3.4 10.9 0.3
HE1 A:MET145 3.4 10.9 0.3
CB A:HIS89 3.5 10.9 1.0
CB A:HIS140 3.5 9.7 1.0
HE2 A:MET145 3.5 10.7 0.7
HG3 A:PRO132 3.6 12.3 0.7
CA A:HIS89 3.8 10.7 1.0
H A:ASN90 3.9 11.0 1.0
HB2 A:HIS140 3.9 9.6 1.0
HG2 A:PRO132 3.9 12.4 0.7
CG A:MET145 4.0 10.8 0.7
HD3 A:PRO132 4.0 11.0 0.7
CG A:MET145 4.0 9.0 0.3
O A:PRO88 4.1 12.8 1.0
HG2 A:MET145 4.1 9.2 0.3
NE2 A:HIS140 4.1 11.9 1.0
NE2 A:HIS89 4.1 10.8 1.0
HD3 A:PRO132 4.2 11.4 0.3
CG A:PRO132 4.2 12.5 0.7
CD2 A:HIS140 4.2 11.8 1.0
HE3 A:MET145 4.2 10.8 0.7
CD2 A:HIS89 4.2 10.7 1.0
HB3 A:MET145 4.2 8.9 0.3
HG3 A:MET145 4.2 10.6 0.7
CG A:PRO132 4.3 12.4 0.3
HB3 A:MET145 4.3 10.1 0.7
HB2 A:MET145 4.3 10.0 0.7
HE3 A:MET145 4.3 10.8 0.3
HE3 A:MET56 4.4 10.9 0.5
HB2 A:MET145 4.4 8.9 0.3
HB2 A:HIS89 4.4 10.6 1.0
CB A:MET145 4.4 10.2 0.7
CB A:MET145 4.5 9.0 0.3
HG2 A:PRO132 4.5 12.4 0.3
HB3 A:MET56 4.5 10.6 0.5
SD A:MET56 4.5 13.2 0.5
CD A:PRO132 4.6 10.7 0.7
N A:ASN90 4.6 11.0 1.0
CA A:CYS130 4.6 8.7 1.0
HG2 A:MET145 4.7 10.7 0.7
HA A:HIS140 4.7 8.9 1.0
CA A:HIS140 4.7 9.0 1.0
CD A:PRO132 4.7 11.3 0.3
N A:HIS89 4.8 11.4 1.0
C A:HIS89 4.8 11.3 1.0
HB3 A:MET56 4.8 9.9 0.5
HG3 A:MET145 4.8 9.2 0.3
HE1 A:MET56 4.8 10.9 0.5
C A:PRO88 4.9 11.6 1.0
HG21 A:ILE39 4.9 12.2 1.0
HA A:CYS130 5.0 8.9 1.0
CE A:MET56 5.0 11.0 0.5

Copper binding site 2 out of 2 in 8rur

Go back to Copper Binding Sites List in 8rur
Copper binding site 2 out of 2 in the High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.38 Mgy]


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of High pH (8.0) Nitrite-Bound Msox Movie Series Dataset 2 of the Copper Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 [1.38 Mgy] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:9.1
occ:0.95
 O A:HOH795 1.9 21.2 0.5
NE2 A:HIS94 2.0 8.5 1.0
O1 A:NO2403 2.0 15.9 0.5
NE2 A:HIS129 2.0 9.0 1.0
N A:NO2403 2.1 20.0 0.5
O2 A:NO2403 2.2 18.7 0.5
CE1 A:HIS94 2.9 8.4 1.0
CD2 A:HIS129 3.0 9.2 1.0
CE1 A:HIS129 3.1 9.5 1.0
CD2 A:HIS94 3.1 8.2 1.0
HE1 A:HIS94 3.1 8.4 1.0
HD2 A:HIS129 3.1 8.9 1.0
HE1 A:HIS129 3.3 9.4 1.0
HD2 A:HIS94 3.3 8.2 1.0
OD2 A:ASP92 3.7 18.3 0.8
O A:HOH876 3.9 22.5 0.5
O A:HOH876 4.0 17.4 0.2
ND1 A:HIS94 4.1 8.1 1.0
O A:HOH844 4.1 11.9 0.2
CG A:HIS129 4.2 8.7 1.0
ND1 A:HIS129 4.2 9.0 1.0
CG A:HIS94 4.2 7.9 1.0
CG A:ASP92 4.3 14.8 0.8
OD1 A:ASP92 4.5 13.4 0.8
HG12 A:VAL127 4.7 8.6 1.0
O A:HOH766 4.9 16.2 1.0
HB3 A:ASP92 5.0 13.1 0.8

Reference:

S.L.Rose, F.M.Ferroni, S.Horrell, C.D.Brondino, R.R.Eady, S.Jaho, M.A.Hough, R.L.Owen, S.V.Antonyuk, S.S.Hasnain. Spectroscopically Validated pH-Dependent Msox Movies Provide Detailed Mechanism of Copper Nitrite Reductases. J.Mol.Biol. V. 436 68706 2024.
ISSN: ESSN 1089-8638
PubMed: 39002715
DOI: 10.1016/J.JMB.2024.168706
Page generated: Sun Aug 11 11:02:55 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy