Magnesium in PDB 3zyy: Reductive Activator For Corrinoid,Iron-Sulfur Protein

The structure of Reductive Activator For Corrinoid,Iron-Sulfur Protein, PDB code: 3zyy was solved by S.E.Hennig, J.-H.Jeoung, S.Goetzl, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.936 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.527, 91.191, 252.887, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 25.8

The structure of Reductive Activator For Corrinoid,Iron-Sulfur Protein also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Magnesium atom in the Reductive Activator For Corrinoid,Iron-Sulfur Protein (pdb code 3zyy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Reductive Activator For Corrinoid,Iron-Sulfur Protein, PDB code: 3zyy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Reductive Activator For Corrinoid,Iron-Sulfur Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Reductive Activator For Corrinoid,Iron-Sulfur Protein within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg802 b:34.2 occ:1.00 O1 X:PO4801 1.9 36.0 1.0 O X:HOH2091 2.1 31.5 1.0 O X:HOH2182 2.1 33.7 1.0 O X:HOH2170 2.1 29.8 1.0 O X:HOH2160 2.1 33.3 1.0 O X:HOH2092 2.1 34.9 1.0 P X:PO4801 3.3 32.8 1.0 O X:HOH2169 3.7 35.1 1.0 O4 X:PO4801 3.7 40.3 1.0 OD1 X:ASP377 3.9 44.9 1.0 O2 X:PO4801 4.1 42.0 1.0 O X:HOH2094 4.2 32.7 1.0 OD2 X:ASP356 4.2 40.7 1.0 O X:HOH2251 4.2 36.5 1.0 O3 X:PO4801 4.2 38.8 1.0 O X:HOH2172 4.3 34.1 1.0 O X:HOH2093 4.3 38.9 1.0 O X:HOH2171 4.4 30.5 1.0 OD2 X:ASP377 4.4 41.6 1.0 OD2 X:ASP212 4.5 36.0 1.0 CG X:ASP377 4.5 51.0 1.0 OD1 X:ASP212 4.6 41.4 1.0 OE2 X:GLU404 4.8 56.6 1.0 O X:HOH2095 4.9 35.5 1.0 O X:HOH2130 4.9 43.0 1.0 CG X:ASP212 5.0 35.5 1.0

Magnesium binding site 2 out of 2 in the Reductive Activator For Corrinoid,Iron-Sulfur Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Reductive Activator For Corrinoid,Iron-Sulfur Protein within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg802 b:53.9 occ:1.00 O3 Y:PO4801 1.8 53.7 1.0 O Y:HOH2086 2.1 47.1 1.0 O Y:HOH2106 2.1 50.5 1.0 O Y:HOH2053 2.1 46.5 1.0 O Y:HOH2078 2.1 51.6 1.0 O Y:HOH2052 2.1 43.8 1.0 P Y:PO4801 3.2 50.4 1.0 O2 Y:PO4801 3.6 65.0 1.0 O4 Y:PO4801 3.8 53.9 1.0 O Y:HOH2087 4.1 54.6 1.0 OD1 Y:ASP377 4.1 65.5 1.0 OD2 Y:ASP356 4.1 63.7 1.0 OD2 Y:ASP212 4.3 53.1 1.0 O Y:HOH2054 4.3 40.7 1.0 O1 Y:PO4801 4.3 45.5 1.0 OD2 Y:ASP377 4.3 56.9 1.0 OD1 Y:ASP212 4.3 50.0 1.0 O Y:HOH2088 4.5 45.6 1.0 CG Y:ASP377 4.6 66.3 1.0 CG Y:ASP212 4.8 55.3 1.0 CA Y:GLY379 4.8 57.5 1.0 CA Y:GLY214 4.9 46.0 1.0 O Y:HOH2079 4.9 56.1 1.0 CB Y:ASP356 4.9 48.6 1.0 CG Y:ASP356 5.0 54.3 1.0

S.E.Hennig, J.H.Jeoung, S.Goetzl, H.Dobbek. Redox-Dependent Complex Formation By An Atp-Dependent Activator of the Corrinoid/Iron-Sulfur Protein. Proc.Natl.Acad.Sci.Usa V. 109 5235 2012.
ISSN: ISSN 0027-8424
PubMed: 22431597
DOI: 10.1073/PNAS.1117126109