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Copper in PDB 8s63: Msox Movie Series Dataset 3 (2.85 Mgy) For As Isolated Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110) at pH 5.5.

Enzymatic activity of Msox Movie Series Dataset 3 (2.85 Mgy) For As Isolated Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110) at pH 5.5.

All present enzymatic activity of Msox Movie Series Dataset 3 (2.85 Mgy) For As Isolated Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110) at pH 5.5.:
1.7.2.1;

Protein crystallography data

The structure of Msox Movie Series Dataset 3 (2.85 Mgy) For As Isolated Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110) at pH 5.5., PDB code: 8s63 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) 52.05 / 1.17
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 103.99, 103.99, 64.57, 90, 90, 120
R / Rfree (%) 11.8 / 14.2

Copper Binding Sites:

The binding sites of Copper atom in the Msox Movie Series Dataset 3 (2.85 Mgy) For As Isolated Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110) at pH 5.5. (pdb code 8s63). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Msox Movie Series Dataset 3 (2.85 Mgy) For As Isolated Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110) at pH 5.5., PDB code: 8s63:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 8s63

Go back to Copper Binding Sites List in 8s63
Copper binding site 1 out of 2 in the Msox Movie Series Dataset 3 (2.85 Mgy) For As Isolated Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110) at pH 5.5.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Msox Movie Series Dataset 3 (2.85 Mgy) For As Isolated Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110) at pH 5.5. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:13.9
occ:1.00
 ND1 A:HIS89 2.0 12.2 1.0
ND1 A:HIS140 2.0 12.5 1.0
SG A:CYS130 2.2 12.8 1.0
SD A:MET145 2.5 14.6 1.0
HB3 A:HIS140 2.9 11.5 1.0
CE1 A:HIS89 3.0 12.7 1.0
CE1 A:HIS140 3.0 13.8 1.0
CG A:HIS89 3.1 12.0 1.0
CG A:HIS140 3.1 12.4 1.0
HE1 A:HIS89 3.1 12.6 1.0
HE1 A:MET145 3.1 15.0 1.0
HE1 A:HIS140 3.1 13.6 1.0
HA A:HIS89 3.2 12.7 1.0
HB3 A:HIS89 3.2 12.7 1.0
CB A:CYS130 3.2 11.5 1.0
HB3 A:CYS130 3.2 11.5 1.0
CE A:MET145 3.3 14.9 1.0
HB2 A:CYS130 3.3 11.4 1.0
HG3 A:PRO132 3.4 15.5 1.0
CB A:HIS140 3.5 11.5 1.0
CB A:HIS89 3.5 13.0 1.0
HE2 A:MET145 3.6 14.8 1.0
CA A:HIS89 3.8 12.4 1.0
H A:ASN90 3.9 12.4 1.0
HB2 A:HIS140 3.9 11.7 1.0
CG A:MET145 4.0 15.7 1.0
HD3 A:PRO132 4.0 13.6 1.0
NE2 A:HIS140 4.1 14.7 1.0
NE2 A:HIS89 4.1 13.0 1.0
CG A:PRO132 4.2 15.8 1.0
HE3 A:MET145 4.2 14.8 1.0
O A:PRO88 4.2 14.9 1.0
HG2 A:PRO132 4.2 15.4 1.0
CD2 A:HIS140 4.2 14.3 1.0
CD2 A:HIS89 4.2 12.2 1.0
HG3 A:MET145 4.2 14.5 1.0
HE3 A:MET56 4.3 11.8 0.5
HB3 A:MET145 4.3 11.8 1.0
HB2 A:MET145 4.4 11.8 1.0
HB2 A:HIS89 4.4 12.7 1.0
CB A:MET145 4.5 11.5 1.0
CD A:PRO132 4.6 13.3 1.0
SD A:MET56 4.6 15.7 0.5
CA A:CYS130 4.6 10.5 1.0
HB3 A:MET56 4.6 13.5 0.5
N A:ASN90 4.7 12.3 1.0
HG2 A:MET145 4.7 14.3 1.0
CA A:HIS140 4.8 11.1 1.0
HA A:HIS140 4.8 11.0 1.0
HB3 A:MET56 4.8 11.7 0.5
HE1 A:MET56 4.8 11.8 0.5
N A:HIS89 4.8 13.1 1.0
C A:HIS89 4.8 13.3 1.0
HG21 A:ILE39 4.8 13.3 1.0
HE2 A:HIS140 4.9 14.2 1.0
HE2 A:HIS89 4.9 12.7 1.0
CE A:MET56 4.9 11.9 0.5
C A:PRO88 4.9 14.4 1.0
HA A:CYS130 4.9 10.7 1.0

Copper binding site 2 out of 2 in 8s63

Go back to Copper Binding Sites List in 8s63
Copper binding site 2 out of 2 in the Msox Movie Series Dataset 3 (2.85 Mgy) For As Isolated Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110) at pH 5.5.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Msox Movie Series Dataset 3 (2.85 Mgy) For As Isolated Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110) at pH 5.5. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:11.3
occ:1.00
 NE2 A:HIS94 2.0 10.7 1.0
NE2 A:HIS129 2.0 10.6 1.0
O A:HOH512 2.0 20.4 1.0
CE1 A:HIS94 2.9 10.5 1.0
CD2 A:HIS129 2.9 11.3 1.0
CE1 A:HIS129 3.0 10.9 1.0
HE1 A:HIS94 3.0 10.3 1.0
CD2 A:HIS94 3.1 10.3 1.0
HD2 A:HIS129 3.1 10.9 1.0
HE1 A:HIS129 3.3 11.0 1.0
HD2 A:HIS94 3.3 10.1 1.0
OD2 A:ASP92 3.8 18.0 0.8
O A:HOH504 3.9 18.8 0.4
O A:HOH504 4.1 31.0 0.6
ND1 A:HIS94 4.1 10.0 1.0
CG A:HIS129 4.1 10.2 1.0
ND1 A:HIS129 4.1 10.9 1.0
O A:HOH501 4.2 13.6 0.2
CG A:HIS94 4.2 9.3 1.0
CG A:ASP92 4.3 15.4 0.8
HG12 A:VAL127 4.6 10.8 1.0
OD1 A:ASP92 4.6 14.4 0.8
HD1 A:HIS94 4.9 9.8 1.0
HD1 A:HIS129 5.0 10.6 1.0
HB3 A:ASP92 5.0 14.9 1.0
O A:HOH787 5.0 19.1 1.0

Reference:

S.L.Rose, F.Martin Ferroni, S.Horrell, C.Dante Brondino, R.R.Eady, S.Jaho, M.A.Hough, R.L.Owen, S.V.Antonyuk, S.Samar Hasnain. Spectroscopically Validated pH-Dependent Msox Movies Provide Detailed Mechanism of Copper Nitrite Reductases. J.Mol.Biol. 68706 2024.
ISSN: ESSN 1089-8638
PubMed: 39002715
DOI: 10.1016/J.JMB.2024.168706
Page generated: Wed Jul 31 10:17:14 2024

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