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Magnesium in PDB 2vd9: The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252) with Bound L-Ala-P

Enzymatic activity of The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252) with Bound L-Ala-P

All present enzymatic activity of The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252) with Bound L-Ala-P:
5.1.1.1;

Protein crystallography data

The structure of The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252) with Bound L-Ala-P, PDB code: 2vd9 was solved by K.Au, J.Ren, T.S.Walter, K.Harlos, J.E.Nettleship, R.J.Owens, D.I.Stuart, R.M.Esnouf, Oxford Protein Production Facility (Oppf), Structural Proteomics In Europe (Spine), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.64 / 2.1
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.692, 96.504, 140.660, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 23.9

Other elements in 2vd9:

The structure of The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252) with Bound L-Ala-P also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252) with Bound L-Ala-P (pdb code 2vd9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252) with Bound L-Ala-P, PDB code: 2vd9:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 2vd9

Go back to Magnesium Binding Sites List in 2vd9
Magnesium binding site 1 out of 3 in the The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252) with Bound L-Ala-P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252) with Bound L-Ala-P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1390

b:24.2
occ:1.00
 O A:HOH2336 2.9 22.0 1.0
N A:MLY333 3.0 17.0 1.0
O A:HOH2167 3.1 34.1 1.0
O A:HOH2364 3.2 40.8 1.0
CB A:MLY333 3.5 18.3 1.0
O A:HOH2157 3.7 39.0 1.0
CA A:THR332 3.7 16.8 1.0
C A:THR332 3.9 16.9 1.0
CA A:MLY333 3.9 16.9 1.0
O A:HOH2337 4.0 11.2 1.0
CG2 A:THR332 4.1 16.2 1.0
O A:HOH2369 4.3 27.8 1.0
O A:GLY331 4.4 16.8 1.0
CB A:THR332 4.4 16.6 1.0
OD1 A:ASN305 4.5 16.5 1.0
O A:HOH2365 4.7 22.8 1.0
N A:THR332 4.8 16.6 1.0
O A:MLY333 4.8 16.0 1.0
O A:HOH2162 4.9 38.5 1.0
C A:MLY333 4.9 16.5 1.0
OG1 A:THR332 4.9 16.5 1.0
CG A:MLY333 4.9 19.3 1.0

Magnesium binding site 2 out of 3 in 2vd9

Go back to Magnesium Binding Sites List in 2vd9
Magnesium binding site 2 out of 3 in the The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252) with Bound L-Ala-P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252) with Bound L-Ala-P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1391

b:73.8
occ:1.00
 CD1 A:ILE263 3.4 22.1 1.0
OD2 A:ASP266 3.7 18.3 1.0
OD1 A:ASP266 3.8 19.0 1.0
CH1 B:MLY182 3.9 28.1 1.0
CG A:ASP266 4.2 19.0 1.0
CG1 A:ILE263 4.3 22.1 1.0
O A:HOH2305 4.7 30.6 1.0

Magnesium binding site 3 out of 3 in 2vd9

Go back to Magnesium Binding Sites List in 2vd9
Magnesium binding site 3 out of 3 in the The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252) with Bound L-Ala-P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252) with Bound L-Ala-P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1390

b:82.0
occ:1.00
 OE2 B:GLU155 3.1 26.4 1.0
OE1 B:GLU155 3.5 26.7 1.0
CD B:GLU155 3.6 26.0 1.0
O B:HOH2203 4.3 60.5 1.0
O B:HOH2197 4.9 61.9 1.0
CG B:GLU155 5.0 25.5 1.0

Reference:

K.Au, J.Ren, T.S.Walter, K.Harlos, J.E.Nettleship, R.J.Owens, D.I.Stuart, R.M.Esnouf. Structures of An Alanine Racemase From Bacillus Anthracis (BA0252) in the Presence and Absence of (R)-1-Aminoethylphosphonic Acid (L-Ala-P). Acta Crystallogr.,Sect.F V. 64 327 2008.
ISSN: ISSN 1744-3091
PubMed: 18453697
DOI: 10.1107/S1744309108007252
Page generated: Mon Dec 14 07:41:36 2020

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