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Chlorine in PDB 2z2o: Crystal Structure of Apo Virginiamycin B Lyase From Staphylococcus Aureus

Protein crystallography data

The structure of Crystal Structure of Apo Virginiamycin B Lyase From Staphylococcus Aureus, PDB code: 2z2o was solved by M.Korczynska, A.M.Berghuis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.543, 79.231, 188.168, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 19.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Apo Virginiamycin B Lyase From Staphylococcus Aureus (pdb code 2z2o). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Apo Virginiamycin B Lyase From Staphylococcus Aureus, PDB code: 2z2o:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 2z2o

Go back to Chlorine Binding Sites List in 2z2o
Chlorine binding site 1 out of 5 in the Crystal Structure of Apo Virginiamycin B Lyase From Staphylococcus Aureus


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 Apo Virginiamycin B Lyase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl300

b:20.4
occ:1.00
NE1 A:TRP113 3.2 16.3 1.0
N A:ASN109 3.2 23.9 1.0
N A:ASP111 3.3 19.0 1.0
CB A:ASP111 3.5 17.0 1.0
N A:PRO108 3.6 18.6 1.0
N A:GLY110 3.6 21.0 1.0
CD A:PRO108 3.6 20.4 1.0
C A:GLY107 3.7 18.6 1.0
CA A:GLY107 3.7 17.1 1.0
CB A:ASN109 3.7 26.1 1.0
C A:ASN109 3.7 23.3 1.0
CA A:ASN109 3.8 24.2 1.0
CA A:ASP111 3.9 17.3 1.0
CG A:ASP111 4.0 22.7 1.0
NH2 A:ARG124 4.1 21.2 1.0
OD2 A:ASP111 4.1 22.0 1.0
CD1 A:TRP113 4.2 16.6 1.0
CE2 A:TRP113 4.2 15.4 1.0
O A:ASP111 4.2 16.8 1.0
CG A:PRO108 4.2 21.5 1.0
O A:GLY107 4.3 18.0 1.0
C A:PRO108 4.3 21.9 1.0
C A:GLY110 4.3 20.3 1.0
O A:ASN109 4.4 23.0 1.0
N A:GLY107 4.4 17.8 1.0
C A:ASP111 4.4 16.6 1.0
CA A:PRO108 4.5 21.0 1.0
CZ2 A:TRP113 4.5 17.2 1.0
CG A:ASN109 4.5 31.2 1.0
CA A:GLY110 4.5 22.2 1.0
NE A:ARG124 4.7 18.8 1.0
CZ A:ARG124 4.7 19.7 1.0
CG A:GLU169 4.7 28.5 1.0
ND2 A:ASN109 4.7 35.2 1.0
OD1 A:ASP111 4.9 18.7 1.0

Chlorine binding site 2 out of 5 in 2z2o

Go back to Chlorine Binding Sites List in 2z2o
Chlorine binding site 2 out of 5 in the Crystal Structure of Apo Virginiamycin B Lyase From Staphylococcus Aureus


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 Apo Virginiamycin B Lyase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl300

b:21.2
occ:1.00
N B:ASN109 3.1 23.4 1.0
NE1 B:TRP113 3.2 17.6 1.0
N B:ASP111 3.3 20.2 1.0
CB B:ASN109 3.5 26.0 1.0
CA B:ASN109 3.6 24.8 1.0
N B:GLY110 3.6 23.8 1.0
CB B:ASP111 3.6 19.6 1.0
N B:PRO108 3.7 20.9 1.0
C B:GLY107 3.7 20.1 1.0
C B:ASN109 3.7 23.8 1.0
CD B:PRO108 3.7 20.1 1.0
CA B:GLY107 3.8 18.1 1.0
NH2 B:ARG124 3.8 26.4 1.0
CA B:ASP111 4.0 19.5 1.0
CG B:ASP111 4.0 23.2 1.0
OD2 B:ASP111 4.1 20.5 1.0
CD1 B:TRP113 4.2 18.0 1.0
CG B:PRO108 4.2 21.7 1.0
CE2 B:TRP113 4.2 18.1 1.0
C B:PRO108 4.2 23.1 1.0
O B:ASP111 4.2 19.1 1.0
O B:GLY107 4.2 18.9 1.0
CG B:ASN109 4.3 29.2 1.0
C B:GLY110 4.4 22.2 1.0
O B:ASN109 4.4 23.5 1.0
C B:ASP111 4.5 17.8 1.0
CA B:PRO108 4.5 22.3 1.0
CZ2 B:TRP113 4.5 18.2 1.0
N B:GLY107 4.5 17.9 1.0
CZ B:ARG124 4.5 21.7 1.0
CA B:GLY110 4.5 21.9 1.0
ND2 B:ASN109 4.6 33.8 1.0
NE B:ARG124 4.6 20.5 1.0
O B:HOH471 4.7 43.5 1.0
CG B:GLU169 4.7 26.6 1.0
OD1 B:ASP111 4.8 20.4 1.0
CB B:PRO108 4.9 22.4 1.0

Chlorine binding site 3 out of 5 in 2z2o

Go back to Chlorine Binding Sites List in 2z2o
Chlorine binding site 3 out of 5 in the Crystal Structure of Apo Virginiamycin B Lyase From Staphylococcus Aureus


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 Apo Virginiamycin B Lyase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl300

b:23.4
occ:1.00
N C:ASN109 3.0 23.6 1.0
NE1 C:TRP113 3.3 19.7 1.0
N C:ASP111 3.4 20.4 1.0
CA C:ASN109 3.6 25.5 1.0
CB C:ASP111 3.6 21.2 1.0
N C:GLY110 3.6 23.6 1.0
C C:ASN109 3.7 25.0 1.0
C C:GLY107 3.7 20.5 1.0
CB C:ASN109 3.7 27.4 1.0
N C:PRO108 3.7 20.6 1.0
CD C:PRO108 3.7 20.4 1.0
CA C:GLY107 3.7 18.6 1.0
CA C:ASP111 4.0 20.5 1.0
NH2 C:ARG124 4.0 24.6 1.0
CG C:PRO108 4.1 21.5 1.0
CG C:ASP111 4.1 24.5 1.0
C C:PRO108 4.1 23.1 1.0
OD2 C:ASP111 4.2 24.9 1.0
CE2 C:TRP113 4.2 18.2 1.0
O C:ASP111 4.2 16.3 1.0
CD1 C:TRP113 4.2 19.5 1.0
O C:GLY107 4.2 21.1 1.0
O C:ASN109 4.4 25.1 1.0
C C:GLY110 4.4 22.2 1.0
CA C:PRO108 4.4 21.9 1.0
N C:GLY107 4.4 18.6 1.0
CZ2 C:TRP113 4.4 18.1 1.0
C C:ASP111 4.5 18.5 1.0
CG C:ASN109 4.5 29.7 1.0
OD1 C:ASN109 4.5 41.9 1.0
CA C:GLY110 4.6 23.9 1.0
CG C:GLU169 4.7 30.8 1.0
CB C:PRO108 4.8 21.6 1.0
CZ C:ARG124 4.9 22.5 1.0
OD1 C:ASP111 4.9 22.7 1.0

Chlorine binding site 4 out of 5 in 2z2o

Go back to Chlorine Binding Sites List in 2z2o
Chlorine binding site 4 out of 5 in the Crystal Structure of Apo Virginiamycin B Lyase From Staphylococcus Aureus


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 Apo Virginiamycin B Lyase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl300

b:25.7
occ:1.00
N D:ASN109 3.1 23.9 1.0
NE1 D:TRP113 3.1 15.3 1.0
N D:ASP111 3.4 23.4 1.0
CB D:ASP111 3.5 21.6 1.0
CB D:ASN109 3.5 26.5 1.0
CA D:ASN109 3.5 25.9 1.0
C D:ASN109 3.6 25.6 1.0
CD D:PRO108 3.7 19.2 1.0
N D:GLY110 3.7 26.8 1.0
N D:PRO108 3.8 20.3 1.0
C D:GLY107 3.8 18.8 1.0
CA D:GLY107 3.8 17.7 1.0
NH2 D:ARG124 3.9 22.4 1.0
CA D:ASP111 3.9 22.0 1.0
CD1 D:TRP113 4.0 20.0 1.0
CE2 D:TRP113 4.1 14.5 1.0
CG D:ASP111 4.1 27.6 1.0
O D:ASN109 4.1 25.3 1.0
O D:ASP111 4.2 21.6 1.0
C D:PRO108 4.2 23.9 1.0
OD2 D:ASP111 4.3 33.1 1.0
CG D:PRO108 4.3 20.0 1.0
CG D:ASN109 4.3 30.2 1.0
O D:GLY107 4.3 18.5 1.0
C D:ASP111 4.4 21.3 1.0
CZ2 D:TRP113 4.4 14.5 1.0
C D:GLY110 4.4 24.7 1.0
N D:GLY107 4.5 18.5 1.0
CA D:PRO108 4.6 21.4 1.0
CA D:GLY110 4.6 26.2 1.0
CZ D:ARG124 4.6 22.2 1.0
NE D:ARG124 4.6 24.1 1.0
CG D:GLU169 4.6 27.1 1.0
OD1 D:ASN109 4.8 39.2 1.0
OD1 D:ASP111 4.9 25.2 1.0

Chlorine binding site 5 out of 5 in 2z2o

Go back to Chlorine Binding Sites List in 2z2o
Chlorine binding site 5 out of 5 in the Crystal Structure of Apo Virginiamycin B Lyase From Staphylococcus Aureus


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 Apo Virginiamycin B Lyase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:38.7
occ:1.00
OE2 D:GLU133 2.7 18.6 1.0
OG D:SER99 2.9 21.0 1.0
N D:ASN96 2.9 20.7 1.0
ND2 D:ASN96 2.9 23.5 1.0
CB D:ASN96 3.2 23.5 1.0
OE1 D:GLU116 3.4 20.3 1.0
OE1 D:GLU133 3.4 19.8 1.0
NH1 D:ARG121 3.4 20.4 1.0
CD D:GLU133 3.4 19.9 1.0
O D:ASN96 3.4 23.2 1.0
CA D:ASN96 3.5 23.0 1.0
CG D:ASN96 3.6 24.9 1.0
CD D:PRO95 3.6 21.1 1.0
CB D:LEU94 3.6 18.7 1.0
N D:PRO95 3.7 19.9 1.0
CG D:PRO95 3.7 22.0 1.0
C D:ASN96 3.9 23.3 1.0
C D:PRO95 3.9 21.9 1.0
CB D:SER99 4.0 20.1 1.0
OE2 D:GLU116 4.0 22.1 1.0
CD D:GLU116 4.0 16.6 1.0
C D:LEU94 4.1 18.8 1.0
CZ D:ARG121 4.2 24.0 1.0
CA D:PRO95 4.2 21.6 1.0
CA D:LEU94 4.4 19.7 1.0
CB D:PRO95 4.6 21.3 1.0
NE D:ARG121 4.6 26.1 1.0
CG D:LEU94 4.6 18.7 1.0
CD D:ARG121 4.6 20.3 1.0
OD1 D:ASN96 4.8 28.5 1.0
CD1 D:LEU94 4.8 17.8 1.0
O D:HOH334 4.8 27.6 1.0
O D:LEU94 4.8 20.2 1.0
CD2 D:LEU94 4.9 21.7 1.0
CG D:GLU133 4.9 19.9 1.0
NH2 D:ARG121 4.9 26.0 1.0

Reference:

M.Korczynska, T.A.Mukhtar, G.D.Wright, A.M.Berghuis. Structural Basis For Streptogramin B Resistance in Staphylococcus Aureus By Virginiamycin B Lyase Proc.Natl.Acad.Sci.Usa V. 104 10388 2007.
ISSN: ISSN 0027-8424
PubMed: 17563376
DOI: 10.1073/PNAS.0701809104
Page generated: Sat Jul 20 15:24:16 2024

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