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Copper in PDB 3x1n: Nitrite-Bound Thermostable Copper Nitrite Reductase at 320 K

Protein crystallography data

The structure of Nitrite-Bound Thermostable Copper Nitrite Reductase at 320 K, PDB code: 3x1n was solved by Y.Fukuda, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.79 / 1.55
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 116.300, 116.300, 85.652, 90.00, 90.00, 120.00
R / Rfree (%) 11.5 / 13.1

Copper Binding Sites:

The binding sites of Copper atom in the Nitrite-Bound Thermostable Copper Nitrite Reductase at 320 K (pdb code 3x1n). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Nitrite-Bound Thermostable Copper Nitrite Reductase at 320 K, PDB code: 3x1n:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 3x1n

Go back to Copper Binding Sites List in 3x1n
Copper binding site 1 out of 3 in the Nitrite-Bound Thermostable Copper Nitrite Reductase at 320 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Nitrite-Bound Thermostable Copper Nitrite Reductase at 320 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:17.7
occ:0.80
ND1 A:HIS143 2.0 19.4 1.0
ND1 A:HIS95 2.1 20.3 1.0
SD A:MET148 2.1 23.7 1.0
CE1 A:HIS95 2.9 21.2 1.0
CE1 A:HIS143 2.9 18.9 1.0
CG A:HIS143 3.1 17.1 1.0
CG A:HIS95 3.2 18.9 1.0
CE A:MET148 3.4 24.7 1.0
CG A:MET148 3.5 22.7 1.0
CB A:HIS143 3.5 16.8 1.0
CB A:HIS95 3.6 18.4 1.0
CB A:ALA135 3.6 20.8 1.0
CE3 A:TRP63 4.0 17.9 1.0
NE2 A:HIS95 4.0 20.0 1.0
NE2 A:HIS143 4.1 21.1 1.0
CB A:MET148 4.1 19.9 1.0
CD2 A:HIS95 4.2 19.9 1.0
CD2 A:HIS143 4.2 18.0 1.0
CA A:HIS95 4.2 17.9 1.0
CA A:HIS143 4.4 16.5 1.0
O A:PRO94 4.5 19.9 1.0
CZ3 A:TRP63 4.6 19.2 1.0
CB A:TRP63 4.8 17.3 1.0
CD2 A:TRP63 4.9 18.1 1.0

Copper binding site 2 out of 3 in 3x1n

Go back to Copper Binding Sites List in 3x1n
Copper binding site 2 out of 3 in the Nitrite-Bound Thermostable Copper Nitrite Reductase at 320 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Nitrite-Bound Thermostable Copper Nitrite Reductase at 320 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:16.1
occ:1.00
NE2 A:HIS134 2.0 16.8 1.0
O A:HOH679 2.0 4.4 0.3
NE2 A:HIS100 2.1 15.8 1.0
O2 A:NO2404 2.1 29.6 0.7
N A:NO2404 2.2 21.6 0.7
O1 A:NO2404 2.5 29.7 0.7
CE1 A:HIS134 3.0 16.2 1.0
CE1 A:HIS100 3.0 15.7 1.0
CD2 A:HIS134 3.0 15.5 1.0
CD2 A:HIS100 3.1 14.6 1.0
OD2 A:ASP98 4.0 20.8 1.0
ND1 A:HIS134 4.1 15.7 1.0
ND1 A:HIS100 4.1 15.8 1.0
CG A:HIS134 4.1 14.4 1.0
CG A:HIS100 4.2 14.9 1.0
O A:HOH661 4.5 34.4 1.0
CG A:ASP98 4.5 17.6 1.0
O A:HOH520 4.7 19.3 1.0
OD1 A:ASP98 4.7 18.8 1.0

Copper binding site 3 out of 3 in 3x1n

Go back to Copper Binding Sites List in 3x1n
Copper binding site 3 out of 3 in the Nitrite-Bound Thermostable Copper Nitrite Reductase at 320 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Nitrite-Bound Thermostable Copper Nitrite Reductase at 320 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:18.7
occ:0.90
NE2 A:HIS42 2.0 20.1 1.0
ND1 A:HIS83 2.0 20.9 1.0
O1 A:NO2405 2.0 24.1 0.9
N A:NO2405 2.3 28.5 0.9
O2 A:NO2405 2.4 23.9 0.9
CE1 A:HIS83 2.9 22.1 1.0
CE1 A:HIS42 2.9 22.3 1.0
CD2 A:HIS42 3.0 19.5 1.0
CG A:HIS83 3.2 20.7 1.0
CB A:HIS83 3.6 19.7 1.0
NE2 A:HIS83 4.0 23.4 1.0
ND1 A:HIS42 4.1 21.4 1.0
O A:HOH639 4.1 42.5 1.0
CG A:HIS42 4.1 18.6 1.0
CD2 A:HIS83 4.2 22.8 1.0
O A:HOH659 4.4 32.8 1.0
O A:HOH664 4.6 41.5 0.7
O A:HOH657 4.6 28.4 1.0
CG2 A:VAL36 4.7 25.7 1.0

Reference:

Y.Fukuda, T.Inoue. High-Temperature and High-Resolution Crystallography of Thermostable Copper Nitrite Reductase Chem.Commun.(Camb.) 2015.
ISSN: ESSN 1364-548X
PubMed: 25563214
DOI: 10.1039/C4CC09553G
Page generated: Sun Dec 13 11:12:53 2020

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