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Magnesium in PDB 2vd8: The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252)

Enzymatic activity of The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252)

All present enzymatic activity of The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252):
5.1.1.1;

Protein crystallography data

The structure of The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252), PDB code: 2vd8 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), Structuralproteomics In Europe (Spine), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.19 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.552, 88.365, 138.968, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 19.9

Other elements in 2vd8:

The structure of The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252) 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) (pdb code 2vd8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252), PDB code: 2vd8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2vd8

Go back to Magnesium Binding Sites List in 2vd8
Magnesium binding site 1 out of 4 in the The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1390

b:23.1
occ:1.00
 O A:HOH2539 2.0 28.5 1.0
OD2 A:ASP17 2.1 17.5 1.0
O A:HOH2034 2.1 35.6 1.0
O A:HOH2035 2.2 31.4 1.0
O A:HOH2033 2.3 39.8 1.0
CG A:ASP17 3.2 12.9 1.0
CB A:ASP17 3.8 11.5 1.0
O A:HOH2039 4.1 47.3 1.0
OD1 A:ASP17 4.1 13.2 1.0
CA A:ASN376 4.2 16.1 1.0
O A:HOH2541 4.3 19.2 1.0
O A:HOH2032 4.3 24.3 1.0
ND2 A:ASN376 4.4 21.3 1.0
O A:HOH2038 4.6 23.3 1.0
N A:ASN376 4.7 15.8 1.0
O A:HOH2540 4.7 38.0 1.0
C A:ASN376 4.9 16.5 1.0
O A:HOH2013 4.9 30.4 1.0

Magnesium binding site 2 out of 4 in 2vd8

Go back to Magnesium Binding Sites List in 2vd8
Magnesium binding site 2 out of 4 in the The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:18.6
occ:1.00
 O B:HOH2221 2.1 18.8 1.0
O B:HOH2218 2.3 23.7 1.0
O B:HOH2073 3.2 33.7 1.0
OE2 B:GLU155 4.3 20.7 1.0
O B:HOH2074 4.3 13.3 1.0
O B:HOH2072 4.3 19.6 1.0
CG B:GLU155 4.6 15.2 1.0
O B:HOH2213 4.6 20.9 1.0
CD B:GLU155 4.7 17.6 1.0
O B:HOH2219 5.0 24.7 1.0

Magnesium binding site 3 out of 4 in 2vd8

Go back to Magnesium Binding Sites List in 2vd8
Magnesium binding site 3 out of 4 in the The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:18.3
occ:1.00
 O A:HOH2455 2.2 19.1 1.0
OD1 A:ASN305 4.1 23.0 1.0
O A:HOH2495 4.1 18.2 1.0
O A:HOH2488 4.3 13.5 1.0

Magnesium binding site 4 out of 4 in 2vd8

Go back to Magnesium Binding Sites List in 2vd8
Magnesium binding site 4 out of 4 in the The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of Alanine Racemase From Bacillus Anthracis (BA0252) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:27.1
occ:1.00
 O A:HOH2405 2.0 22.9 1.0
O A:HOH2404 2.0 17.4 1.0
O A:HOH2160 2.1 30.9 1.0
O A:HOH2159 2.2 31.5 1.0
O A:HOH2158 2.4 40.1 1.0
CH2 B:MLY182 3.8 26.6 1.0
O A:HOH2162 4.1 31.5 1.0
CD1 A:ILE263 4.1 23.2 1.0
O A:HOH2161 4.1 19.4 1.0
OD2 A:ASP266 4.2 18.0 1.0
O B:HOH2202 4.2 27.9 1.0
O B:HOH2201 4.2 20.5 1.0
OD1 A:ASP266 4.4 17.9 1.0
O B:HOH2254 4.7 25.5 1.0
O B:HOH2249 4.7 26.2 1.0
CG A:ASP266 4.7 17.6 1.0
O B:HOH2067 4.7 38.5 1.0
CG1 A:ILE263 4.8 19.8 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: Wed Aug 14 05:08:12 2024

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