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Copper in PDB 6pdv: Cu-Carbonic Anhydrase II, A Nitrite Reductase

Enzymatic activity of Cu-Carbonic Anhydrase II, A Nitrite Reductase

All present enzymatic activity of Cu-Carbonic Anhydrase II, A Nitrite Reductase:
4.2.1.1;

Protein crystallography data

The structure of Cu-Carbonic Anhydrase II, A Nitrite Reductase, PDB code: 6pdv was solved by J.T.Andring, R.Mckenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.24 / 1.23
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.230, 42.400, 72.010, 90.00, 104.25, 90.00
R / Rfree (%) 15.7 / 17.5

Copper Binding Sites:

The binding sites of Copper atom in the Cu-Carbonic Anhydrase II, A Nitrite Reductase (pdb code 6pdv). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Cu-Carbonic Anhydrase II, A Nitrite Reductase, PDB code: 6pdv:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 6pdv

Go back to Copper Binding Sites List in 6pdv
Copper binding site 1 out of 2 in the Cu-Carbonic Anhydrase II, A Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cu-Carbonic Anhydrase II, A Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:11.4
occ:1.00
ND1 A:HIS119 2.0 9.5 1.0
NE2 A:HIS94 2.0 10.6 1.0
NE2 A:HIS96 2.1 10.1 1.0
O1 A:NO2304 2.1 32.9 1.0
N A:NO2304 2.8 26.1 1.0
CD2 A:HIS94 2.9 11.0 1.0
CE1 A:HIS119 2.9 9.1 1.0
HB2 A:HIS119 2.9 11.7 1.0
CG A:HIS119 3.0 8.7 1.0
HD2 A:HIS94 3.0 13.2 1.0
CD2 A:HIS96 3.1 10.4 1.0
CE1 A:HIS94 3.1 10.5 1.0
CE1 A:HIS96 3.1 10.2 1.0
HE1 A:HIS119 3.1 10.9 1.0
HD2 A:HIS96 3.2 12.4 1.0
HE1 A:HIS96 3.3 12.2 1.0
CB A:HIS119 3.4 9.7 1.0
HE1 A:HIS94 3.4 12.6 1.0
HG1 A:THR199 3.4 14.3 1.0
HB3 A:HIS119 3.6 11.7 1.0
OG1 A:THR199 3.8 11.9 1.0
O2 A:NO2304 4.0 34.4 1.0
NE2 A:HIS119 4.0 10.0 1.0
CG A:HIS94 4.0 10.4 1.0
CD2 A:HIS119 4.1 9.2 1.0
ND1 A:HIS94 4.1 10.5 1.0
O A:HOH434 4.1 29.8 1.0
OE1 A:GLU106 4.2 11.2 1.0
ND1 A:HIS96 4.2 10.5 1.0
CG A:HIS96 4.2 9.9 1.0
HH2 A:TRP209 4.3 12.8 1.0
O A:HOH584 4.3 23.1 1.0
CA A:HIS119 4.8 8.3 1.0
HE2 A:HIS119 4.8 12.0 1.0
HG23 A:THR199 4.8 14.5 1.0
HG23 A:THR200 4.9 17.8 1.0
HD1 A:HIS94 4.9 12.6 1.0
H A:HIS119 4.9 9.7 1.0
HD2 A:HIS119 4.9 11.1 1.0
HG11 A:VAL143 5.0 14.2 1.0
HD1 A:HIS96 5.0 12.6 1.0
CD A:GLU106 5.0 11.0 1.0

Copper binding site 2 out of 2 in 6pdv

Go back to Copper Binding Sites List in 6pdv
Copper binding site 2 out of 2 in the Cu-Carbonic Anhydrase II, A Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cu-Carbonic Anhydrase II, A Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:29.1
occ:0.71
N A:HIS4 2.1 27.7 0.9
ND1 A:HIS4 2.1 27.4 0.9
N A:SER2 2.1 54.1 1.0
O A:HOH403 2.2 36.5 0.9
N A:HIS3 2.4 49.7 0.9
C A:SER2 2.8 59.7 1.0
CA A:SER2 2.9 60.7 1.0
CG A:HIS4 3.0 27.0 0.9
CE1 A:HIS4 3.0 25.9 0.9
C A:HIS3 3.1 40.1 0.9
H A:TRP5 3.1 27.6 1.0
CA A:HIS4 3.1 27.8 0.9
HE1 A:HIS4 3.3 31.1 0.9
CA A:HIS3 3.3 46.5 0.5
CA A:HIS3 3.3 46.5 0.5
HB3 A:HIS4 3.3 36.6 0.9
CB A:HIS4 3.3 30.5 0.9
HB3 A:SER2 3.5 78.3 1.0
HD1 A:HIS3 3.5 42.7 0.5
HA A:SER2 3.6 72.9 1.0
ND1 A:HIS3 3.7 35.6 0.5
N A:TRP5 3.8 23.0 1.0
CB A:SER2 3.8 65.2 1.0
HA A:HIS4 3.9 33.3 0.9
C A:HIS4 3.9 22.1 0.9
O A:SER2 4.0 59.5 1.0
HA A:HIS3 4.0 55.8 0.8
CD2 A:HIS4 4.1 31.5 0.9
NE2 A:HIS4 4.1 29.8 0.9
CG A:HIS3 4.1 39.2 0.5
HB3 A:HIS3 4.2 56.0 0.5
O A:HIS3 4.3 41.2 0.9
HB2 A:HIS4 4.3 36.6 0.9
CE1 A:HIS3 4.3 35.9 0.5
CB A:HIS3 4.3 46.9 0.5
CB A:HIS3 4.3 46.7 0.5
HB2 A:SER2 4.5 78.3 1.0
HE1 A:HIS3 4.6 43.0 0.5
HD1 A:TRP5 4.6 22.0 1.0
OG A:SER2 4.7 72.5 1.0
HB2 A:HIS3 4.7 56.0 0.5
O A:TRP5 4.8 18.4 1.0
HB3 A:HIS3 4.8 56.3 0.5
CD2 A:HIS3 4.8 35.5 0.5
HE2 A:HIS4 4.9 35.8 0.9
NE2 A:HIS3 4.9 35.2 0.5
HD2 A:HIS4 4.9 37.8 0.9
CD1 A:TRP5 5.0 18.3 1.0

Reference:

J.T.Andring, R.Mckenna. Structure and Mechanism of Copper-Carbonic Anhydrase II: A Nitrite Reductase Iucrj 287 2020.
ISSN: ESSN 2052-2525
DOI: 10.1107/S2052252520000986
Page generated: Sun Dec 13 11:24:32 2020

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