Magnesium in PDB 1zv2: Cu-Containing Nitrite Reductase

All present enzymatic activity of Cu-Containing Nitrite Reductase:
1.7.2.1;

The structure of Cu-Containing Nitrite Reductase, PDB code: 1zv2 was solved by F.Jacobson, H.Guo, K.Olesen, M.Okvist, R.Neutze, L.Sjolin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.70 / 1.74
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	72.381, 72.381, 147.509, 90.00, 90.00, 120.00
R / Rfree (%)	15.5 / 19.4

The structure of Cu-Containing Nitrite Reductase also contains other interesting chemical elements:

Copper

(Cu)

2 atoms

The binding sites of Magnesium atom in the Cu-Containing Nitrite Reductase (pdb code 1zv2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cu-Containing Nitrite Reductase, PDB code: 1zv2:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cu-Containing Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cu-Containing Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:21.0 occ:1.00 O A:HOH535 2.0 20.5 1.0 O A:HOH779 2.1 17.1 1.0 O A:HOH625 2.1 20.5 1.0 O A:HOH697 2.1 27.4 1.0 O A:HOH769 2.1 18.8 1.0 O A:HOH586 4.1 19.3 1.0 O A:HOH681 4.2 20.3 1.0 O A:HOH605 4.3 22.9 1.0 O A:HOH777 4.3 37.0 1.0 O A:HOH655 4.3 26.3 1.0 OD2 A:ASP294 4.5 10.3 1.0 O A:HOH674 4.6 29.3 1.0 CG A:ASP294 4.6 10.3 1.0 CB A:ASP294 4.8 8.6 1.0 O A:HOH507 4.9 10.5 1.0 O A:HOH570 5.0 20.8 1.0

Magnesium binding site 2 out of 3 in the Cu-Containing Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cu-Containing Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:13.2 occ:1.00 OD1 A:ASP220 2.0 13.1 1.0 O A:HOH733 2.0 13.6 1.0 O A:HOH778 2.0 14.1 1.0 O A:HOH537 2.1 16.3 1.0 O A:HOH783 2.2 18.0 1.0 OG1 A:THR224 2.2 12.8 1.0 CG A:ASP220 3.2 15.4 1.0 CB A:THR224 3.3 15.4 1.0 CB A:ASP220 3.7 16.0 1.0 OD1 A:ASP222 4.0 15.7 1.0 OD2 A:ASP220 4.2 13.9 1.0 CG2 A:THR224 4.2 13.5 1.0 OD2 A:ASP222 4.3 18.4 1.0 C A:THR224 4.4 14.8 1.0 CA A:THR224 4.4 14.3 1.0 O A:THR224 4.4 14.3 1.0 O A:TYR225 4.5 15.2 1.0 CG A:ASP222 4.6 18.4 1.0 N A:TYR225 4.8 14.0 1.0

Magnesium binding site 3 out of 3 in the Cu-Containing Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cu-Containing Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:28.0 occ:1.00 O A:HOH663 1.9 24.0 1.0 O A:HOH781 2.0 29.8 1.0 O A:HOH715 2.1 27.8 1.0 O A:HOH648 2.1 23.3 1.0 O A:HOH528 2.2 11.3 1.0 O A:HOH785 2.3 19.7 1.0 O A:HOH607 3.7 16.6 1.0 O A:HOH618 3.9 17.4 1.0 OD2 A:ASP96 4.1 14.7 1.0 OD1 A:ASP96 4.2 15.4 1.0 O A:GLU74 4.4 11.8 1.0 CG A:ASP96 4.5 14.3 1.0 O A:HOH748 4.6 38.3 1.0 O A:HOH608 4.6 24.8 1.0 OE1 A:GLU74 4.8 19.2 1.0

F.Jacobson, H.Guo, K.Olesen, M.Okvist, R.Neutze, L.Sjolin. Structures of the Oxidized and Reduced Forms of Nitrite Reductase From Rhodobacter Sphaeroides 2.4.3 at High pH: Changes in the Interactions of the Type 2 Copper. Acta Crystallogr.,Sect.D V. 61 1190 2005.
ISSN: ISSN 0907-4449
PubMed: 16131751
DOI: 10.1107/S0907444905017488