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Chlorine in PDB 4ecl: Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg

Protein crystallography data

The structure of Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg, PDB code: 4ecl was solved by P.J.Stogios, Z.Wawrzak, G.Minasov, E.Evdokimova, O.Egorova, J.Cosme, R.Dileo, M.Krishnamoorthy, D.Meziane-Cherif, P.Courvalin, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.91 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.682, 82.341, 117.468, 90.00, 90.14, 90.00
R / Rfree (%) 18.1 / 23.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg (pdb code 4ecl). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg, PDB code: 4ecl:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4ecl

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Chlorine binding site 1 out of 8 in the Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:24.6
occ:0.80
 NZ A:LYS125 3.0 39.2 1.0
N A:LEU133 3.3 19.9 1.0
NE2 B:GLN316 3.5 31.8 1.0
CB A:ARG132 3.5 20.6 1.0
O A:HOH593 3.6 40.9 1.0
CE A:LYS125 3.7 37.5 1.0
CB A:LEU133 3.8 17.7 1.0
SE A:MSE130 3.9 42.3 0.7
CG A:LEU133 3.9 22.1 1.0
CA A:LEU133 4.0 22.9 1.0
O A:LEU133 4.0 20.4 1.0
CD1 A:LEU133 4.1 24.0 1.0
CG A:MSE130 4.1 32.7 1.0
OE1 B:GLN316 4.3 29.5 1.0
CD B:GLN316 4.3 33.4 1.0
C A:ARG132 4.3 22.4 1.0
CA A:ARG132 4.4 22.6 1.0
C A:LEU133 4.4 25.5 1.0
CD A:ARG132 4.4 28.6 1.0
CG A:ARG132 4.5 22.8 1.0
CD A:LYS125 4.5 34.5 1.0
O A:HOH550 4.8 34.4 1.0
O A:HOH503 4.8 22.2 1.0
N A:ARG132 4.8 18.9 1.0

Chlorine binding site 2 out of 8 in 4ecl

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Chlorine binding site 2 out of 8 in the Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:20.5
occ:0.60
 N A:SER203 3.2 15.8 1.0
O A:HOH528 3.2 23.6 1.0
N A:GLY206 3.3 25.5 1.0
O A:HOH584 3.5 30.4 1.0
CB A:ALA164 3.5 26.7 1.0
CB A:SER203 3.6 28.3 1.0
CA A:GLY206 3.6 26.5 1.0
CA A:SER203 3.8 23.9 1.0
O A:HOH518 4.0 26.9 1.0
C A:SER203 4.0 22.3 1.0
CB A:LEU161 4.0 21.6 1.0
CD1 A:LEU161 4.1 23.3 1.0
O A:SER203 4.1 21.4 1.0
OG A:SER203 4.2 41.9 1.0
C A:TYR205 4.2 26.2 1.0
C A:GLN202 4.2 19.1 1.0
CA A:GLN202 4.3 16.5 1.0
CG A:LEU161 4.4 27.8 1.0
N A:TYR205 4.5 22.3 1.0
O A:LEU161 4.6 25.9 1.0
O A:ILE201 4.6 20.9 1.0
CA A:TYR205 4.7 27.9 1.0
N A:SER204 4.7 23.4 1.0
N A:LEU161 4.8 23.6 1.0
CB A:TYR205 4.8 28.0 1.0
CA A:LEU161 4.9 23.3 1.0
CA A:ALA164 4.9 28.5 1.0

Chlorine binding site 3 out of 8 in 4ecl

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Chlorine binding site 3 out of 8 in the Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:33.2
occ:0.79
 NZ B:LYS125 3.0 27.9 0.5
NE2 A:GLN316 3.1 39.2 1.0
N B:LEU133 3.3 27.5 1.0
CE B:MSE130 3.4 21.8 1.0
CE B:LYS125 3.5 33.7 0.5
CB B:ARG132 3.5 39.6 1.0
CB B:LEU133 3.6 26.0 1.0
CE B:LYS125 3.7 32.1 0.5
CG B:LEU133 3.7 27.0 1.0
NZ B:LYS125 3.8 33.7 0.5
CA B:LEU133 3.9 30.7 1.0
CD1 B:LEU133 4.0 29.1 1.0
CD A:GLN316 4.0 35.7 1.0
OE1 A:GLN316 4.1 31.6 1.0
O B:LEU133 4.1 32.2 1.0
CD B:LYS125 4.1 32.5 0.5
C B:ARG132 4.3 29.8 1.0
CD B:LYS125 4.3 32.9 0.5
CD B:ARG132 4.4 42.5 1.0
C B:LEU133 4.4 31.4 1.0
CA B:ARG132 4.5 36.2 1.0
O B:HOH570 4.5 29.3 1.0
CG B:ARG132 4.5 45.5 1.0

Chlorine binding site 4 out of 8 in 4ecl

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Chlorine binding site 4 out of 8 in the Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:13.9
occ:0.45
 O B:HOH538 3.0 27.5 1.0
N B:SER203 3.1 26.7 1.0
N B:GLY206 3.2 27.6 1.0
CA B:GLY206 3.5 26.9 1.0
CB B:ALA164 3.5 33.9 1.0
CB B:SER203 3.5 25.1 1.0
CA B:SER203 3.7 29.9 1.0
CB B:LEU161 3.7 26.4 1.0
CD1 B:LEU161 4.0 30.8 1.0
C B:SER203 4.0 22.3 1.0
O B:HOH615 4.1 28.3 1.0
O B:SER203 4.1 25.1 1.0
C B:GLN202 4.1 24.3 1.0
C B:TYR205 4.2 35.2 1.0
CG B:LEU161 4.2 29.3 1.0
CA B:GLN202 4.2 28.5 1.0
OG B:SER203 4.3 43.1 1.0
N B:TYR205 4.5 27.1 1.0
O B:ILE201 4.6 26.3 1.0
O B:LEU161 4.6 37.7 1.0
CA B:LEU161 4.7 32.2 1.0
CA B:TYR205 4.7 31.1 1.0
N B:LEU161 4.7 27.9 1.0
N B:SER204 4.8 23.6 1.0
CB B:TYR205 4.9 36.4 1.0
CA B:ALA164 4.9 36.9 1.0
O B:TYR205 5.0 33.0 1.0
C B:GLY206 5.0 25.6 1.0

Chlorine binding site 5 out of 8 in 4ecl

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Chlorine binding site 5 out of 8 in the Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:33.8
occ:0.86
 O C:HOH534 2.9 32.5 1.0
N C:SER203 3.1 23.8 1.0
N C:GLY206 3.2 27.7 1.0
CB C:SER203 3.4 27.8 1.0
CA C:GLY206 3.5 26.0 1.0
CB C:ALA164 3.6 34.6 1.0
CA C:SER203 3.6 25.9 1.0
C C:SER203 3.9 24.1 1.0
CD1 C:LEU161 4.0 32.1 1.0
OG C:SER203 4.0 35.7 1.0
O C:SER203 4.0 30.2 1.0
O C:HOH596 4.1 27.8 1.0
CB C:LEU161 4.1 26.9 1.0
C C:GLN202 4.2 24.0 1.0
C C:TYR205 4.2 31.6 1.0
CA C:GLN202 4.3 27.1 1.0
CG C:LEU161 4.4 29.8 1.0
O C:HOH644 4.4 54.1 1.0
N C:TYR205 4.4 19.5 1.0
CA C:TYR205 4.7 26.7 1.0
O C:ILE201 4.7 31.8 1.0
N C:SER204 4.7 20.5 1.0
CB C:TYR205 4.8 24.3 1.0
O C:LEU161 4.8 36.1 1.0
N C:LEU161 4.9 26.2 1.0
C C:GLY206 5.0 29.3 1.0
CA C:ALA164 5.0 39.3 1.0

Chlorine binding site 6 out of 8 in 4ecl

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Chlorine binding site 6 out of 8 in the Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:53.9
occ:1.00
 N D:ILE332 3.2 24.9 1.0
O D:HOH516 3.5 24.5 1.0
CA D:SER331 3.7 28.3 1.0
C D:SER331 4.0 31.7 1.0
CB D:ILE332 4.2 29.8 1.0
CB D:SER331 4.2 30.6 1.0
CA D:ILE332 4.3 27.0 1.0
CG1 D:ILE332 4.4 35.9 1.0
OG D:SER331 4.5 34.9 1.0
CD1 D:ILE332 4.6 35.8 1.0
O D:ILE332 4.7 32.0 1.0
O D:GLY330 4.8 32.4 1.0
N D:SER331 4.8 29.7 1.0
C D:ILE332 5.0 28.9 1.0

Chlorine binding site 7 out of 8 in 4ecl

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Chlorine binding site 7 out of 8 in the Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:36.4
occ:0.98
 N D:SER203 3.1 14.0 1.0
N D:GLY206 3.1 22.7 1.0
O D:HOH521 3.1 31.2 1.0
O D:HOH607 3.4 31.1 1.0
CB D:SER203 3.4 20.0 1.0
CA D:GLY206 3.5 25.2 1.0
CB D:ALA164 3.6 28.9 1.0
CA D:SER203 3.6 19.4 1.0
O D:HOH559 3.7 24.6 1.0
C D:SER203 3.8 25.5 1.0
O D:SER203 3.9 24.2 1.0
C D:TYR205 4.1 26.5 1.0
CB D:LEU161 4.1 15.0 1.0
OG D:SER203 4.1 28.9 1.0
C D:GLN202 4.1 17.1 1.0
CD1 D:LEU161 4.2 21.7 1.0
CA D:GLN202 4.3 21.5 1.0
N D:TYR205 4.3 13.6 1.0
CA D:TYR205 4.5 22.1 1.0
N D:SER204 4.6 23.8 1.0
CG D:LEU161 4.6 19.4 1.0
CB D:TYR205 4.7 23.3 1.0
O D:LEU161 4.7 20.6 1.0
O D:ILE201 4.8 23.9 1.0
C D:GLY206 4.9 28.4 1.0
CB D:GLN202 4.9 28.1 1.0
CA D:ALA164 5.0 30.4 1.0
O D:TYR205 5.0 24.2 1.0

Chlorine binding site 8 out of 8 in 4ecl

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Chlorine binding site 8 out of 8 in the Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of the Cytoplasmic Domain of Vancomycin Resistance Serine Racemase Vantg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl403

b:39.5
occ:1.00
 NZ D:LYS125 3.0 37.7 1.0
O D:HOH584 3.3 29.6 1.0
N D:LEU133 3.4 22.0 1.0
NE2 C:GLN316 3.4 23.6 1.0
CB D:ARG132 3.5 15.0 1.0
CE D:LYS125 3.7 37.9 1.0
SE D:MSE130 3.8 49.8 0.8
CB D:LEU133 3.9 26.6 1.0
CG D:MSE130 3.9 36.8 1.0
CA D:LEU133 4.1 26.4 1.0
O D:LEU133 4.1 21.7 1.0
CG D:LEU133 4.2 23.9 1.0
CD1 D:LEU133 4.4 24.3 1.0
CD D:ARG132 4.4 25.2 1.0
CD C:GLN316 4.4 30.9 1.0
C D:ARG132 4.4 23.0 1.0
CA D:ARG132 4.4 20.4 1.0
OE1 C:GLN316 4.5 24.1 1.0
CG D:ARG132 4.5 19.6 1.0
C D:LEU133 4.6 28.1 1.0
CD D:LYS125 4.6 36.4 1.0
CB D:MSE130 4.8 27.6 1.0
N D:ARG132 4.8 21.1 1.0
CB D:HIS160 4.9 32.7 1.0
O D:HOH547 4.9 27.0 1.0
ND1 D:HIS160 5.0 44.9 1.0

Reference:

D.Meziane-Cherif, P.J.Stogios, E.Evdokimova, O.Egorova, A.Savchenko, P.Courvalin. Structural and Functional Adaptation of Vancomycin Resistance Vant Serine Racemases. Mbio V. 6 00806 2015.
ISSN: ESSN 2150-7511
PubMed: 26265719
DOI: 10.1128/MBIO.00806-15
Page generated: Sun Jul 21 12:45:51 2024

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