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

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

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

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 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 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

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