Chlorine 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 / R_free (%)*	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:

Magnesium

(Mg)

3 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 3 in 2vd9

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Chlorine Binding Sites List in 2vd9

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1392 b:16.0 occ:1.00	O	A:HOH2115	3.2	12.9	1.0
	NH2	A:ARG138	3.2	12.8	1.0
	O	A:HOH2176	3.3	8.8	1.0
	NE	A:ARG138	3.3	12.8	1.0
	ND2	A:ASN131	3.4	13.6	1.0
	O	A:HOH2169	3.4	14.1	1.0
	CZ	A:ARG138	3.7	12.6	1.0
	CB	A:HIS168	4.0	13.0	1.0
	CG1	A:ILE139	4.1	12.5	1.0
	O	A:ILE139	4.2	12.7	1.0
	CG	A:ASN131	4.4	14.3	1.0
	CG	A:MET136	4.4	11.7	1.0
	CB	A:ARG138	4.4	12.9	1.0
	OD1	A:ASN131	4.4	14.7	1.0
	N	A:ILE139	4.5	12.8	1.0
	CD	A:ARG138	4.5	12.6	1.0
	CG	A:HIS168	4.5	12.9	1.0
	C6	A:IN51394	4.6	11.4	0.5
	CG	A:ARG138	4.6	12.9	1.0
	CD2	A:HIS168	4.6	13.1	1.0
	C2A	A:EPC1395	4.8	12.2	0.5
	CB	A:MET136	4.8	11.4	1.0
	CD1	A:ILE139	4.9	12.8	1.0
	C	A:ILE139	5.0	13.2	1.0

Chlorine binding site 2 out of 3 in 2vd9

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Chlorine Binding Sites List in 2vd9

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1393 b:53.2 occ:1.00	O	A:HOH2259	2.9	59.9	1.0
	N	A:GLN216	2.9	27.2	1.0
	CA	A:PHE215	3.6	25.2	1.0
	CB	A:GLN216	3.7	28.6	1.0
	C	A:PHE215	3.7	25.9	1.0
	CA	A:GLN216	3.8	26.9	1.0
	O	A:GLN216	4.1	26.0	1.0
	CB	A:PHE215	4.1	25.2	1.0
	CD2	A:PHE215	4.4	25.3	1.0
	C	A:GLN216	4.4	26.4	1.0
	O	A:ARG214	4.5	23.9	1.0
	CG	A:PHE215	4.7	25.2	1.0
	N	A:PHE215	4.8	24.9	1.0
	O	A:PHE215	4.9	26.1	1.0

Chlorine binding site 3 out of 3 in 2vd9

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Chlorine Binding Sites List in 2vd9

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1391 b:11.5 occ:1.00	O	B:HOH2097	3.1	11.2	1.0
	O	B:HOH2175	3.1	13.6	1.0
	NH2	B:ARG138	3.3	12.2	1.0
	NE	B:ARG138	3.3	11.4	1.0
	O	B:HOH2168	3.4	11.4	1.0
	ND2	B:ASN131	3.4	14.5	1.0
	CZ	B:ARG138	3.8	11.9	1.0
	CB	B:HIS168	4.0	13.3	1.0
	CG1	B:ILE139	4.1	11.4	1.0
	O	B:ILE139	4.2	11.3	1.0
	CG	B:ASN131	4.3	14.8	1.0
	OD1	B:ASN131	4.4	15.3	1.0
	CB	B:ARG138	4.4	11.7	1.0
	CG	B:MET136	4.4	11.3	1.0
	N	B:ILE139	4.5	12.2	1.0
	CD	B:ARG138	4.5	11.8	1.0
	CG	B:HIS168	4.5	13.4	1.0
	CG	B:ARG138	4.5	11.9	1.0
	C2A	B:EPC1393	4.6	12.7	0.5
	CD2	B:HIS168	4.6	13.3	1.0
	C6	B:IN51392	4.7	13.3	0.5
	CB	B:MET136	4.9	11.1	1.0
	C	B:ILE139	4.9	12.1	1.0
	CD1	B:ILE139	4.9	11.0	1.0
	CE2	B:TYR166	5.0	12.5	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: Sat Jul 20 11:47:34 2024

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