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Copper in PDB 8ryr: Msox Movie Series Dataset 4 (4.6 Mgy) For Nitrite Bound Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 at pH 8.

Enzymatic activity of Msox Movie Series Dataset 4 (4.6 Mgy) For Nitrite Bound Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 at pH 8.

All present enzymatic activity of Msox Movie Series Dataset 4 (4.6 Mgy) For Nitrite Bound Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 at pH 8.:
1.7.2.1;

Protein crystallography data

The structure of Msox Movie Series Dataset 4 (4.6 Mgy) For Nitrite Bound Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 at pH 8., PDB code: 8ryr 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) 45.13 / 1.25
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 104.12, 104.12, 64.36, 90, 90, 120
R / Rfree (%) 10.7 / 13.1

Copper Binding Sites:

The binding sites of Copper atom in the Msox Movie Series Dataset 4 (4.6 Mgy) For Nitrite Bound Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 at pH 8. (pdb code 8ryr). 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 4 (4.6 Mgy) For Nitrite Bound Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 at pH 8., PDB code: 8ryr:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 8ryr

Go back to Copper Binding Sites List in 8ryr
Copper binding site 1 out of 2 in the Msox Movie Series Dataset 4 (4.6 Mgy) For Nitrite Bound Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 at pH 8.


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 4 (4.6 Mgy) For Nitrite Bound Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 at pH 8. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:13.8
occ:1.00
 ND1 A:HIS89 2.0 11.3 1.0
ND1 A:HIS140 2.0 11.8 1.0
SG A:CYS130 2.2 13.0 1.0
SD A:MET145 2.5 13.1 0.8
SD A:MET145 2.7 13.2 0.2
HB3 A:HIS140 2.9 11.0 1.0
CE1 A:HIS89 3.0 12.1 1.0
CE1 A:HIS140 3.0 13.0 1.0
HE1 A:HIS89 3.1 12.1 1.0
HE1 A:HIS140 3.1 13.0 1.0
CG A:HIS89 3.1 11.7 1.0
CG A:HIS140 3.1 11.4 1.0
HB3 A:HIS89 3.1 11.9 1.0
HE1 A:MET145 3.2 12.7 0.8
HA A:HIS89 3.2 12.2 1.0
CB A:CYS130 3.2 11.6 1.0
HB3 A:CYS130 3.2 11.4 1.0
HE2 A:MET145 3.3 13.3 0.2
CE A:MET145 3.3 12.6 0.8
HB2 A:CYS130 3.3 11.5 1.0
CE A:MET145 3.4 13.3 0.2
CB A:HIS140 3.5 11.1 1.0
CB A:HIS89 3.5 11.9 1.0
HE1 A:MET145 3.5 13.3 0.2
HE2 A:MET145 3.5 12.7 0.8
HG3 A:PRO132 3.6 13.7 0.3
HG3 A:PRO132 3.7 14.3 0.7
CA A:HIS89 3.8 11.9 1.0
HG2 A:PRO132 3.9 14.3 0.7
H A:ASN90 3.9 12.0 1.0
HB2 A:HIS140 3.9 11.1 1.0
CG A:MET145 4.0 12.3 0.8
CG A:MET145 4.0 11.5 0.2
HD3 A:PRO132 4.0 13.2 0.7
HG2 A:MET145 4.1 11.5 0.2
HD3 A:PRO132 4.1 13.3 0.3
NE2 A:HIS140 4.1 13.6 1.0
CG A:PRO132 4.1 14.6 0.7
NE2 A:HIS89 4.1 12.4 1.0
CD2 A:HIS140 4.2 13.4 1.0
O A:PRO88 4.2 14.5 1.0
HE3 A:MET145 4.2 12.7 0.8
CD2 A:HIS89 4.2 12.2 1.0
HG3 A:MET145 4.2 12.2 0.8
HB3 A:MET145 4.3 10.7 0.2
HB3 A:MET145 4.3 10.8 0.8
HB2 A:MET145 4.3 10.7 0.2
HB2 A:MET145 4.3 10.9 0.8
HE3 A:MET145 4.3 13.3 0.2
HE3 A:MET56 4.3 11.4 0.5
HB2 A:HIS89 4.4 11.8 1.0
CB A:MET145 4.4 10.7 0.2
CG A:PRO132 4.4 13.8 0.3
CB A:MET145 4.5 10.9 0.8
SD A:MET56 4.6 16.6 0.5
CD A:PRO132 4.6 13.2 0.7
HB3 A:PRO132 4.6 13.9 0.3
HB3 A:MET56 4.6 13.6 0.5
CA A:CYS130 4.6 10.2 1.0
N A:ASN90 4.6 12.0 1.0
HG2 A:MET145 4.7 12.1 0.8
CD A:PRO132 4.7 13.4 0.3
CA A:HIS140 4.7 10.5 1.0
HA A:HIS140 4.8 10.4 1.0
HE1 A:MET56 4.8 11.4 0.5
HB3 A:MET56 4.8 11.0 0.5
N A:HIS89 4.8 12.5 1.0
HG3 A:MET145 4.8 11.5 0.2
C A:HIS89 4.8 12.3 1.0
HE2 A:HIS140 4.9 13.3 0.0
C A:PRO88 4.9 13.0 1.0
HG21 A:ILE39 4.9 13.8 1.0
HE2 A:HIS89 4.9 11.9 0.0
HA A:CYS130 4.9 10.4 1.0
CE A:MET56 4.9 11.6 0.5

Copper binding site 2 out of 2 in 8ryr

Go back to Copper Binding Sites List in 8ryr
Copper binding site 2 out of 2 in the Msox Movie Series Dataset 4 (4.6 Mgy) For Nitrite Bound Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 at pH 8.


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 4 (4.6 Mgy) For Nitrite Bound Brjnir (Cu Containing Nitrite Reductase (Nirk) From Bradyrhizobium Japonicum USDA110 at pH 8. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:11.1
occ:1.00
 O A:HOH789 1.9 20.6 0.5
NE2 A:HIS94 2.0 9.6 1.0
NE2 A:HIS129 2.0 10.1 1.0
O1 A:NO2403 2.0 23.2 0.5
N A:NO2403 2.2 25.1 0.5
O2 A:NO2403 2.3 22.6 0.2
CE1 A:HIS94 2.9 10.0 1.0
CD2 A:HIS129 3.0 10.5 1.0
CE1 A:HIS129 3.1 10.4 1.0
CD2 A:HIS94 3.1 9.6 1.0
HE1 A:HIS94 3.1 9.7 1.0
HD2 A:HIS129 3.1 10.3 1.0
HE1 A:HIS129 3.3 10.3 1.0
HD2 A:HIS94 3.3 9.4 1.0
OD2 A:ASP92 3.7 19.7 0.5
O A:HOH872 4.0 24.2 0.5
O A:HOH872 4.0 14.9 0.2
ND1 A:HIS94 4.1 9.3 1.0
O A:HOH828 4.2 16.2 0.5
ND1 A:HIS129 4.2 10.2 1.0
CG A:HIS129 4.2 10.2 1.0
CG A:HIS94 4.2 8.7 1.0
CG A:ASP92 4.4 18.0 0.5
OD1 A:ASP92 4.6 15.8 0.5
HG12 A:VAL127 4.7 10.0 1.0
HD1 A:HIS94 4.9 9.4 0.0
HD1 A:HIS129 5.0 9.5 0.0

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 10:13:51 2024

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