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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

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