Atomistry » Chlorine » PDB 2yzr-2zgb » 2z2o
Atomistry »
  Chlorine »
    PDB 2yzr-2zgb »
      2z2o »

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 Dec 12 09:30:02 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy