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
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