Magnesium in PDB 3vay: Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000

The structure of Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000, PDB code: 3vay was solved by Z.Hou, H.Zhang, M.Li, W.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.91 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.325, 92.274, 70.191, 90.00, 108.13, 90.00
R / Rfree (%)	19.3 / 22.4

The structure of Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 also contains other interesting chemical elements:

Iodine

(I)

15 atoms

The binding sites of Magnesium atom in the Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 (pdb code 3vay). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000, PDB code: 3vay:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:22.4 occ:1.00 O A:HOH407 2.2 20.3 1.0 O A:HOH405 2.3 20.5 1.0 O A:ASP10 2.3 19.7 1.0 O A:HOH403 2.3 16.1 1.0 OD1 A:ASP180 2.4 20.8 1.0 OD2 A:ASP8 2.5 18.2 1.0 OD1 A:ASP8 2.8 15.6 1.0 CG A:ASP8 2.9 17.8 1.0 CG A:ASP180 3.3 18.1 1.0 C A:ASP10 3.4 19.1 1.0 OD2 A:ASP180 3.6 21.1 1.0 O A:HOH446 4.0 21.6 1.0 CA A:ASP10 4.1 20.3 1.0 N A:ASP10 4.1 16.4 1.0 OD2 A:ASP185 4.1 12.7 1.0 CB A:ASP10 4.2 21.7 1.0 O A:HOH455 4.2 30.6 1.0 CG2 A:THR12 4.2 13.1 1.0 O A:HOH443 4.3 26.7 1.0 CB A:ASP8 4.3 14.1 1.0 O A:HOH408 4.4 20.9 1.0 O A:HOH508 4.4 34.0 1.0 N A:ASP11 4.4 17.4 1.0 CB A:ASP11 4.4 20.2 1.0 O A:HOH401 4.6 9.5 1.0 CB A:ASP180 4.7 15.8 1.0 CA A:ASP11 4.8 15.9 1.0 C A:LEU9 4.8 16.8 1.0 N A:ASP180 4.9 12.7 1.0 C A:ASP11 4.9 17.3 1.0 N A:THR12 4.9 15.0 1.0 CB A:HIS181 4.9 17.7 1.0 N A:HIS181 5.0 16.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:21.5 occ:1.00 O B:ASP10 2.3 19.3 1.0 O B:HOH411 2.3 22.4 1.0 O B:HOH409 2.3 18.8 1.0 OD2 B:ASP8 2.3 18.5 1.0 OD1 B:ASP180 2.4 20.1 1.0 O B:HOH403 2.5 19.0 1.0 OD1 B:ASP8 2.6 16.0 1.0 CG B:ASP8 2.7 19.0 1.0 C B:ASP10 3.4 20.9 1.0 CG B:ASP180 3.5 19.1 1.0 OD2 B:ASP180 3.9 22.7 1.0 OD2 B:ASP185 4.0 15.0 1.0 CA B:ASP10 4.1 17.9 1.0 N B:ASP10 4.1 16.7 1.0 CB B:ASP8 4.1 15.2 1.0 OG1 B:THR12 4.1 22.7 1.0 O B:HOH481 4.2 22.2 1.0 CB B:ASP10 4.3 24.6 1.0 O B:HOH512 4.3 32.1 1.0 O B:HOH428 4.4 21.6 1.0 O B:HOH477 4.4 27.2 1.0 N B:ASP11 4.4 16.8 1.0 O B:HOH401 4.5 9.7 1.0 CB B:ASP11 4.6 21.9 1.0 O B:HOH494 4.6 30.8 1.0 C B:LEU9 4.7 17.7 1.0 CB B:ASP180 4.8 18.8 1.0 N B:ASP180 4.8 15.4 1.0 CA B:ASP11 4.8 18.2 1.0 N B:THR12 4.8 14.8 1.0 C B:ASP11 4.8 17.7 1.0 N B:LEU9 4.9 18.1 1.0 N B:HIS181 4.9 17.3 1.0 CB B:HIS181 5.0 18.1 1.0

Z.Hou, H.Zhang, M.Li, W.Chang. Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 Acta Crystallogr.,Sect.D V. 69 1108 2013.
ISSN: ISSN 0907-4449
PubMed: 23695255
DOI: 10.1107/S0907444913006021