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Magnesium in PDB 3zx5: The 3-Dimensional Structure of Mpgp From Thermus Thermophilus HB27, Covalently Bound to Vanadate and in Complex with Alpha-Mannosylglycerate and Magnesium

Enzymatic activity of The 3-Dimensional Structure of Mpgp From Thermus Thermophilus HB27, Covalently Bound to Vanadate and in Complex with Alpha-Mannosylglycerate and Magnesium

All present enzymatic activity of The 3-Dimensional Structure of Mpgp From Thermus Thermophilus HB27, Covalently Bound to Vanadate and in Complex with Alpha-Mannosylglycerate and Magnesium:
3.1.3.70;

Protein crystallography data

The structure of The 3-Dimensional Structure of Mpgp From Thermus Thermophilus HB27, Covalently Bound to Vanadate and in Complex with Alpha-Mannosylglycerate and Magnesium, PDB code: 3zx5 was solved by S.Goncalves, A.M.Esteves, H.Santos, N.Borges, P.M.Matias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.772 / 1.81
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.948, 71.263, 91.217, 90.00, 95.52, 90.00
R / Rfree (%) 16.8 / 21.26

Other elements in 3zx5:

The structure of The 3-Dimensional Structure of Mpgp From Thermus Thermophilus HB27, Covalently Bound to Vanadate and in Complex with Alpha-Mannosylglycerate and Magnesium also contains other interesting chemical elements:

Vanadium (V) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The 3-Dimensional Structure of Mpgp From Thermus Thermophilus HB27, Covalently Bound to Vanadate and in Complex with Alpha-Mannosylglycerate and Magnesium (pdb code 3zx5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The 3-Dimensional Structure of Mpgp From Thermus Thermophilus HB27, Covalently Bound to Vanadate and in Complex with Alpha-Mannosylglycerate and Magnesium, PDB code: 3zx5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3zx5

Go back to Magnesium Binding Sites List in 3zx5
Magnesium binding site 1 out of 2 in the The 3-Dimensional Structure of Mpgp From Thermus Thermophilus HB27, Covalently Bound to Vanadate and in Complex with Alpha-Mannosylglycerate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The 3-Dimensional Structure of Mpgp From Thermus Thermophilus HB27, Covalently Bound to Vanadate and in Complex with Alpha-Mannosylglycerate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg260

b:30.7
occ:1.00
OD2 A:ASP6 2.1 34.9 1.0
O3 A:VN4261 2.1 27.1 1.0
OD1 A:ASP202 2.2 33.4 1.0
O A:ASP8 2.2 38.0 1.0
O A:HOH2006 2.2 28.2 1.0
O A:HOH2005 2.3 27.9 1.0
CG A:ASP6 3.0 32.2 1.0
CG A:ASP202 3.1 42.5 1.0
OD1 A:ASP6 3.3 26.5 1.0
OD2 A:ASP202 3.4 37.8 1.0
C A:ASP8 3.4 36.8 1.0
V A:VN4261 3.5 28.6 1.0
OD2 A:ASP206 3.9 31.2 1.0
OG1 A:THR10 4.0 31.3 1.0
O13 A:2M8262 4.1 34.1 1.0
CB A:ASP8 4.1 46.0 1.0
CA A:ASP8 4.1 36.1 1.0
OG A:SER203 4.2 58.1 1.0
N A:ASP8 4.3 28.3 1.0
N A:GLY9 4.3 38.7 1.0
CB A:ASP6 4.4 26.7 1.0
CA A:GLY9 4.5 40.1 1.0
CB A:ASP202 4.5 37.0 1.0
N A:ASP202 4.6 29.1 1.0
O A:HOH2004 4.6 43.3 1.0
C A:GLY9 4.6 39.5 1.0
N A:THR10 4.7 34.2 1.0
CB A:SER203 4.7 45.9 1.0
O2 A:VN4261 4.7 27.5 1.0
O1 A:VN4261 4.7 26.8 1.0
C A:LEU7 4.8 35.2 1.0
N A:SER203 4.8 31.9 1.0
CG A:ASP206 4.9 28.6 1.0
OD1 A:ASN205 4.9 34.8 1.0
CA A:ASP202 4.9 29.6 1.0
CB A:THR10 5.0 33.0 1.0
OD1 A:ASP206 5.0 32.1 1.0
N A:GLY166 5.0 30.1 1.0

Magnesium binding site 2 out of 2 in 3zx5

Go back to Magnesium Binding Sites List in 3zx5
Magnesium binding site 2 out of 2 in the The 3-Dimensional Structure of Mpgp From Thermus Thermophilus HB27, Covalently Bound to Vanadate and in Complex with Alpha-Mannosylglycerate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The 3-Dimensional Structure of Mpgp From Thermus Thermophilus HB27, Covalently Bound to Vanadate and in Complex with Alpha-Mannosylglycerate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg260

b:23.2
occ:1.00
O2 B:VN4261 2.1 18.6 1.0
OD2 B:ASP6 2.1 20.7 1.0
OD1 B:ASP202 2.1 21.9 1.0
O B:ASP8 2.2 22.3 1.0
O B:HOH2010 2.2 22.1 1.0
O B:HOH2006 2.2 20.2 1.0
CG B:ASP6 3.1 19.1 1.0
CG B:ASP202 3.1 26.8 1.0
C B:ASP8 3.3 19.8 1.0
OD2 B:ASP202 3.4 28.4 1.0
V B:VN4261 3.5 23.5 1.0
OD1 B:ASP6 3.5 20.0 1.0
OD2 B:ASP206 4.1 21.5 1.0
OG1 B:THR10 4.1 22.0 1.0
CA B:ASP8 4.1 21.5 1.0
CB B:ASP8 4.2 21.2 1.0
OG B:SER203 4.2 26.1 0.6
N B:GLY9 4.3 19.9 1.0
N B:ASP8 4.3 22.0 1.0
O B:HOH2003 4.3 34.0 1.0
CA B:GLY9 4.4 22.9 1.0
CB B:ASP6 4.4 18.8 1.0
CB B:ASP202 4.5 21.6 1.0
CB B:SER203 4.5 19.4 0.6
C B:GLY9 4.5 24.8 1.0
N B:THR10 4.6 22.5 1.0
CB B:SER203 4.6 20.9 0.4
N B:ASP202 4.6 24.4 1.0
O1 B:VN4261 4.7 21.3 1.0
O3 B:VN4261 4.8 21.4 1.0
N B:SER203 4.8 21.4 1.0
C23 B:2M8262 4.8 24.4 1.0
C B:LEU7 4.8 19.1 1.0
O13 B:2M8262 4.8 29.6 1.0
N B:GLY166 4.8 24.3 1.0
CB B:THR10 4.9 20.6 1.0
OD1 B:ASN205 4.9 21.3 1.0
CA B:ASP202 4.9 23.4 1.0
C B:ASP202 5.0 22.9 1.0

Reference:

S.Goncalves, A.M.Esteves, H.Santos, N.Borges, P.M.Matias. The Three-Dimensional Structure of Mannosyl-3- Phosphoglycerate Phosphatase From Thermus Thermophilus HB27: A New Member of the Haloalkanoic Acid Dehalogenase Superfamily. Biochemistry V. 50 9551 2011.
ISSN: ISSN 0006-2960
PubMed: 21961705
DOI: 10.1021/BI201171H
Page generated: Mon Dec 14 09:04:50 2020

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