Zinc in PDB 2vmj: Type 1 Copper-Binding Loop of Nitrite Reductase Mutant: 130- Capegmvpwhvvsgm-144 to 130-Ctphpfm-136

The structure of Type 1 Copper-Binding Loop of Nitrite Reductase Mutant: 130- Capegmvpwhvvsgm-144 to 130-Ctphpfm-136, PDB code: 2vmj was solved by K.Sato, S.J.Firbank, C.Li, M.J.Banfield, C.Dennison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.53 / 2.5
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	89.813, 89.813, 143.099, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 23.2

The binding sites of Zinc atom in the Type 1 Copper-Binding Loop of Nitrite Reductase Mutant: 130- Capegmvpwhvvsgm-144 to 130-Ctphpfm-136 (pdb code 2vmj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Type 1 Copper-Binding Loop of Nitrite Reductase Mutant: 130- Capegmvpwhvvsgm-144 to 130-Ctphpfm-136, PDB code: 2vmj:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Type 1 Copper-Binding Loop of Nitrite Reductase Mutant: 130- Capegmvpwhvvsgm-144 to 130-Ctphpfm-136


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Type 1 Copper-Binding Loop of Nitrite Reductase Mutant: 130- Capegmvpwhvvsgm-144 to 130-Ctphpfm-136 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1328 b:47.1 occ:1.00 O A:HOH2088 2.0 39.6 1.0 NE2 A:HIS129 2.1 44.7 1.0 NE2 A:HIS94 2.1 40.1 1.0 CE1 A:HIS94 3.0 41.4 1.0 CD2 A:HIS129 3.1 44.6 1.0 CE1 A:HIS129 3.1 45.1 1.0 CD2 A:HIS94 3.3 42.8 1.0 OD2 A:ASP92 3.6 49.7 1.0 ND1 A:HIS94 4.2 42.9 1.0 ND1 A:HIS129 4.2 45.4 1.0 CG A:HIS129 4.2 45.7 1.0 CG A:HIS94 4.3 44.7 1.0 CG A:ASP92 4.3 50.0 1.0 OD1 A:ASP92 4.9 49.6 1.0

Zinc binding site 2 out of 3 in the Type 1 Copper-Binding Loop of Nitrite Reductase Mutant: 130- Capegmvpwhvvsgm-144 to 130-Ctphpfm-136


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Type 1 Copper-Binding Loop of Nitrite Reductase Mutant: 130- Capegmvpwhvvsgm-144 to 130-Ctphpfm-136 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1329 b:75.4 occ:1.00 NE2 A:HIS157 1.9 51.9 1.0 O A:HOH2089 2.0 49.4 1.0 OD2 A:ASP159 2.2 55.5 1.0 OD1 A:ASP159 2.6 56.4 1.0 CG A:ASP159 2.7 55.5 1.0 CD2 A:HIS157 2.8 50.4 1.0 CE1 A:HIS157 3.0 51.4 1.0 CG A:HIS157 4.0 50.5 1.0 ND1 A:HIS157 4.1 50.6 1.0 CB A:ASP159 4.2 54.8 1.0 OG1 A:THR226 4.3 53.1 1.0 CB A:THR226 4.3 54.0 1.0 N A:THR226 4.4 55.5 1.0 N A:ASP159 4.7 53.1 1.0 O A:GLY224 4.8 56.7 1.0 CA A:ASP159 4.9 55.0 1.0

Zinc binding site 3 out of 3 in the Type 1 Copper-Binding Loop of Nitrite Reductase Mutant: 130- Capegmvpwhvvsgm-144 to 130-Ctphpfm-136


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Type 1 Copper-Binding Loop of Nitrite Reductase Mutant: 130- Capegmvpwhvvsgm-144 to 130-Ctphpfm-136 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1330 b:78.9 occ:1.00 O A:HOH2090 2.0 46.8 1.0 SG A:CYS130 2.2 56.9 1.0 ND1 A:HIS133 2.4 63.2 1.0 ND1 A:HIS89 2.6 64.4 1.0 CE1 A:HIS133 3.1 64.7 1.0 CB A:CYS130 3.2 53.6 1.0 CE1 A:HIS89 3.4 65.4 1.0 SD A:MET136 3.5 55.0 1.0 CG A:HIS133 3.6 62.3 1.0 CG A:HIS89 3.6 64.8 1.0 CB A:HIS89 3.9 64.1 1.0 CA A:HIS89 4.0 64.0 1.0 CB A:HIS133 4.1 60.3 1.0 O A:PRO88 4.2 66.2 1.0 NE2 A:HIS133 4.3 62.9 1.0 CE A:MET136 4.4 54.9 1.0 CD A:PRO132 4.5 59.9 1.0 SD A:MET56 4.5 67.9 1.0 NE2 A:HIS89 4.5 65.4 1.0 CA A:CYS130 4.5 54.2 1.0 CD2 A:HIS133 4.5 62.2 1.0 CD2 A:HIS89 4.7 64.7 1.0 CG A:PRO132 4.7 59.6 1.0 N A:ASN90 4.8 61.0 1.0 C A:CYS130 4.9 55.1 1.0 C A:HIS89 5.0 62.8 1.0 N A:HIS133 5.0 60.2 1.0 CG A:MET136 5.0 53.1 1.0 N A:HIS89 5.0 65.4 1.0

K.Sato, S.J.Firbank, C.Li, M.J.Banfield, C.Dennison. The Importance of the Long Type 1 Copper-Binding Loop of Nitrite Reductase For Structure and Function. Chemistry V. 14 5820 2008.
ISSN: ISSN 0947-6539
PubMed: 18491346
DOI: 10.1002/CHEM.200701997