Magnesium in PDB 5err: Gephe in Complex with Mg(2+) - Adp

All present enzymatic activity of Gephe in Complex with Mg(2+) - Adp:
2.10.1.1; 2.7.7.75;

The structure of Gephe in Complex with Mg(2+) - Adp, PDB code: 5err was solved by V.B.Kasaragod, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.84 / 1.65
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	87.681, 99.534, 113.029, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 18.3

The binding sites of Magnesium atom in the Gephe in Complex with Mg(2+) - Adp (pdb code 5err). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Gephe in Complex with Mg(2+) - Adp, PDB code: 5err:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Gephe in Complex with Mg(2+) - Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gephe in Complex with Mg(2+) - Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:18.6 occ:1.00 O2A A:ADP801 2.0 17.9 1.0 O A:HOH990 2.0 14.0 1.0 O A:HOH1141 2.0 18.5 1.0 O A:HOH1202 2.1 20.6 1.0 O A:HOH981 2.1 21.2 1.0 O A:HOH1060 2.1 19.9 1.0 PA A:ADP801 3.2 20.1 1.0 H A:GLY573 3.4 19.2 1.0 O1A A:ADP801 3.7 22.6 1.0 O5' A:ADP801 3.8 18.1 1.0 OE2 A:GLU509 3.8 21.8 1.0 H8 A:ADP801 3.8 17.1 1.0 HA2 A:GLY507 3.8 19.1 1.0 H2' A:ADP801 3.9 21.5 1.0 HA3 A:GLY507 3.9 19.1 1.0 N A:GLY573 4.0 16.0 1.0 O A:THR506 4.1 16.9 1.0 HA3 A:GLY572 4.1 18.0 1.0 OD1 A:ASP549 4.1 30.5 1.0 OE1 A:GLU509 4.2 19.9 1.0 HA2 A:GLY573 4.3 22.0 1.0 CA A:GLY507 4.3 15.9 1.0 OD1 A:ASP580 4.4 32.4 1.0 CD A:GLU509 4.4 19.4 1.0 OD2 A:ASP549 4.5 28.3 1.0 O3A A:ADP801 4.5 20.2 1.0 HA2 A:GLY572 4.6 18.0 1.0 CA A:GLY573 4.7 18.3 1.0 CG A:ASP549 4.7 28.6 1.0 CA A:GLY572 4.7 15.0 1.0 OG1 A:THR506 4.7 18.2 1.0 C8 A:ADP801 4.7 14.2 1.0 C A:THR506 4.7 16.6 1.0 C A:GLY572 4.8 15.7 1.0 HA3 A:GLY573 4.9 22.0 1.0 MG A:MG803 4.9 25.1 1.0 N A:GLY507 4.9 15.5 1.0 HG1 A:THR506 5.0 21.9 1.0 C2' A:ADP801 5.0 17.9 1.0

Magnesium binding site 2 out of 2 in the Gephe in Complex with Mg(2+) - Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gephe in Complex with Mg(2+) - Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:25.1 occ:1.00 O1A A:ADP801 2.0 22.6 1.0 O1B A:ADP801 2.1 24.5 1.0 OD2 A:ASP580 2.3 35.7 1.0 OD1 A:ASP580 2.4 32.4 1.0 HB2 A:SER575 2.7 34.7 1.0 CG A:ASP580 2.7 36.4 1.0 PA A:ADP801 3.2 20.1 1.0 PB A:ADP801 3.2 26.4 1.0 H A:SER575 3.6 23.6 1.0 O3A A:ADP801 3.6 20.2 1.0 CB A:SER575 3.6 28.9 1.0 O3B A:ADP801 3.6 31.8 1.0 O A:HOH1060 3.9 19.9 1.0 O2A A:ADP801 3.9 17.9 1.0 H A:GLY577 4.0 49.7 1.0 O A:HOH927 4.0 38.4 1.0 HG A:SER575 4.0 37.0 1.0 HA3 A:GLY577 4.0 49.3 1.0 HB3 A:SER575 4.1 34.7 1.0 H A:GLY573 4.1 19.2 1.0 OG A:SER575 4.1 30.8 1.0 CB A:ASP580 4.2 33.1 1.0 HA2 A:GLY573 4.3 22.0 1.0 H5'1 A:ADP801 4.3 21.3 1.0 N A:SER575 4.3 19.7 1.0 O5' A:ADP801 4.5 18.1 1.0 CA A:SER575 4.5 24.4 1.0 O2B A:ADP801 4.5 29.4 1.0 O A:HOH1124 4.5 36.5 1.0 HB3 A:ASP580 4.5 39.7 1.0 H A:VAL574 4.6 21.8 1.0 HB2 A:ASP580 4.6 39.7 1.0 N A:GLY577 4.7 41.4 1.0 N A:GLY573 4.8 16.0 1.0 CA A:GLY577 4.8 41.1 1.0 C5' A:ADP801 4.9 17.7 1.0 CA A:GLY573 4.9 18.3 1.0 C A:SER575 4.9 27.5 1.0 O A:HOH1202 4.9 20.6 1.0 MG A:MG802 4.9 18.6 1.0 N A:VAL574 5.0 18.1 1.0

V.B.Kasaragod, H.Schindelin. Structural Framework For Metal Incorporation During Molybdenum Cofactor Biosynthesis. Structure V. 24 782 2016.
ISSN: ISSN 0969-2126
PubMed: 27112598
DOI: 10.1016/J.STR.2016.02.023