Zinc in PDB 8sko: X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound
Enzymatic activity of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound
All present enzymatic activity of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound:
3.5.2.6;
Protein crystallography data
The structure of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound, PDB code: 8sko
was solved by
J.B.Thoden,
H.M.Holden,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
32.98 /
1.30
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
40.136,
59.265,
84.241,
90,
98.5,
90
|
R / Rfree (%)
|
19.9 /
22.3
|
Zinc Binding Sites:
The binding sites of Zinc atom in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound
(pdb code 8sko). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound, PDB code: 8sko:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8sko
Go back to
Zinc Binding Sites List in 8sko
Zinc binding site 1 out
of 4 in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound
![](/pictures/ZN/pdb/sk/8sko-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/sk/8sko-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:8.8
occ:1.00
|
ND1
|
A:HIS122
|
2.0
|
9.0
|
1.0
|
NE2
|
A:HIS120
|
2.1
|
7.5
|
1.0
|
NE2
|
A:HIS189
|
2.1
|
8.7
|
1.0
|
S
|
A:X8Z303
|
2.3
|
15.2
|
0.8
|
CE1
|
A:HIS122
|
2.9
|
8.1
|
1.0
|
CE1
|
A:HIS120
|
3.0
|
7.4
|
1.0
|
CE1
|
A:HIS189
|
3.0
|
9.3
|
1.0
|
CG
|
A:HIS122
|
3.0
|
7.1
|
1.0
|
CD2
|
A:HIS189
|
3.1
|
8.6
|
1.0
|
CD2
|
A:HIS120
|
3.1
|
7.4
|
1.0
|
C1
|
A:X8Z303
|
3.2
|
15.7
|
0.8
|
CB
|
A:HIS122
|
3.4
|
6.9
|
1.0
|
ZN
|
A:ZN302
|
3.6
|
13.7
|
1.0
|
SG
|
A:CYS208
|
3.8
|
8.8
|
1.0
|
CB
|
A:CYS208
|
4.0
|
8.1
|
1.0
|
OD1
|
A:ASP124
|
4.1
|
9.3
|
1.0
|
NE2
|
A:HIS122
|
4.1
|
7.6
|
1.0
|
ND1
|
A:HIS120
|
4.1
|
7.0
|
1.0
|
ND1
|
A:HIS189
|
4.2
|
8.7
|
1.0
|
CG
|
A:HIS120
|
4.2
|
7.0
|
1.0
|
CD2
|
A:HIS122
|
4.2
|
7.5
|
1.0
|
CG
|
A:HIS189
|
4.2
|
8.7
|
1.0
|
CG2
|
A:THR190
|
4.4
|
10.0
|
1.0
|
OD2
|
A:ASP124
|
4.7
|
8.6
|
1.0
|
C2
|
A:X8Z303
|
4.7
|
18.2
|
0.8
|
CG
|
A:ASP124
|
4.8
|
7.6
|
1.0
|
CA
|
A:HIS122
|
4.9
|
6.1
|
1.0
|
O
|
A:HOH550
|
5.0
|
30.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8sko
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Zinc Binding Sites List in 8sko
Zinc binding site 2 out
of 4 in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound
![](/pictures/ZN/pdb/sk/8sko-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/sk/8sko-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:13.7
occ:1.00
|
OD2
|
A:ASP124
|
2.0
|
8.6
|
1.0
|
S
|
A:X8Z303
|
2.1
|
15.2
|
0.8
|
NE2
|
A:HIS250
|
2.1
|
6.4
|
1.0
|
SG
|
A:CYS208
|
2.3
|
8.8
|
1.0
|
CG
|
A:ASP124
|
2.9
|
7.6
|
1.0
|
CE1
|
A:HIS250
|
3.0
|
7.8
|
1.0
|
CD2
|
A:HIS250
|
3.1
|
7.2
|
1.0
|
C1
|
A:X8Z303
|
3.2
|
15.7
|
0.8
|
OD1
|
A:ASP124
|
3.3
|
9.3
|
1.0
|
CB
|
A:CYS208
|
3.4
|
8.1
|
1.0
|
ZN
|
A:ZN301
|
3.6
|
8.8
|
1.0
|
C2
|
A:X8Z303
|
3.8
|
18.2
|
0.8
|
ND1
|
A:HIS250
|
4.2
|
6.8
|
1.0
|
CG
|
A:HIS250
|
4.2
|
7.8
|
1.0
|
CB
|
A:ASP124
|
4.3
|
6.4
|
1.0
|
C4
|
A:X8Z303
|
4.3
|
20.8
|
0.8
|
CB
|
A:SER249
|
4.4
|
6.8
|
1.0
|
NE2
|
A:HIS189
|
4.4
|
8.7
|
1.0
|
C5
|
A:X8Z303
|
4.4
|
23.3
|
0.8
|
N
|
A:X8Z303
|
4.5
|
23.0
|
0.8
|
O
|
A:HOH543
|
4.5
|
25.6
|
1.0
|
NE2
|
A:HIS120
|
4.6
|
7.5
|
1.0
|
OG
|
A:SER249
|
4.6
|
6.7
|
1.0
|
CE1
|
A:HIS189
|
4.7
|
9.3
|
1.0
|
CA
|
A:CYS208
|
4.7
|
9.0
|
1.0
|
CE1
|
A:HIS120
|
4.7
|
7.4
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8sko
Go back to
Zinc Binding Sites List in 8sko
Zinc binding site 3 out
of 4 in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound
![](/pictures/ZN/pdb/sk/8sko-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/sk/8sko-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:8.9
occ:1.00
|
ND1
|
B:HIS122
|
2.0
|
7.6
|
1.0
|
NE2
|
B:HIS189
|
2.1
|
9.6
|
1.0
|
NE2
|
B:HIS120
|
2.1
|
6.9
|
1.0
|
S
|
B:X8Z303
|
2.3
|
14.3
|
0.8
|
CE1
|
B:HIS120
|
3.0
|
6.4
|
1.0
|
CE1
|
B:HIS122
|
3.0
|
7.5
|
1.0
|
CE1
|
B:HIS189
|
3.0
|
10.5
|
1.0
|
CG
|
B:HIS122
|
3.0
|
7.4
|
1.0
|
CD2
|
B:HIS189
|
3.1
|
9.0
|
1.0
|
CD2
|
B:HIS120
|
3.1
|
6.7
|
1.0
|
C1
|
B:X8Z303
|
3.2
|
16.8
|
0.8
|
CB
|
B:HIS122
|
3.4
|
6.7
|
1.0
|
ZN
|
B:ZN302
|
3.6
|
12.8
|
1.0
|
SG
|
B:CYS208
|
3.9
|
10.5
|
1.0
|
OD1
|
B:ASP124
|
4.0
|
8.1
|
1.0
|
CB
|
B:CYS208
|
4.0
|
9.6
|
1.0
|
NE2
|
B:HIS122
|
4.1
|
8.0
|
1.0
|
ND1
|
B:HIS120
|
4.1
|
6.4
|
1.0
|
CD2
|
B:HIS122
|
4.1
|
7.8
|
1.0
|
ND1
|
B:HIS189
|
4.1
|
10.4
|
1.0
|
CG
|
B:HIS120
|
4.2
|
6.8
|
1.0
|
CG
|
B:HIS189
|
4.2
|
9.3
|
1.0
|
CG2
|
B:THR190
|
4.4
|
9.6
|
1.0
|
C2
|
B:X8Z303
|
4.6
|
18.7
|
0.8
|
OD2
|
B:ASP124
|
4.7
|
9.4
|
1.0
|
CG
|
B:ASP124
|
4.8
|
7.8
|
1.0
|
CA
|
B:HIS122
|
4.9
|
6.1
|
1.0
|
O1
|
B:X8Z303
|
5.0
|
18.9
|
0.8
|
|
Zinc binding site 4 out
of 4 in 8sko
Go back to
Zinc Binding Sites List in 8sko
Zinc binding site 4 out
of 4 in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound
![](/pictures/ZN/pdb/sk/8sko-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/sk/8sko-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:12.8
occ:1.00
|
OD2
|
B:ASP124
|
2.0
|
9.4
|
1.0
|
NE2
|
B:HIS250
|
2.1
|
8.3
|
1.0
|
S
|
B:X8Z303
|
2.1
|
14.3
|
0.8
|
SG
|
B:CYS208
|
2.4
|
10.5
|
1.0
|
CG
|
B:ASP124
|
2.9
|
7.8
|
1.0
|
CE1
|
B:HIS250
|
3.0
|
9.8
|
1.0
|
CD2
|
B:HIS250
|
3.1
|
9.2
|
1.0
|
OD1
|
B:ASP124
|
3.2
|
8.1
|
1.0
|
C1
|
B:X8Z303
|
3.3
|
16.8
|
0.8
|
CB
|
B:CYS208
|
3.4
|
9.6
|
1.0
|
ZN
|
B:ZN301
|
3.6
|
8.9
|
1.0
|
C2
|
B:X8Z303
|
3.8
|
18.7
|
0.8
|
ND1
|
B:HIS250
|
4.2
|
9.8
|
1.0
|
C5
|
B:X8Z303
|
4.2
|
23.5
|
0.8
|
CG
|
B:HIS250
|
4.2
|
10.2
|
1.0
|
CB
|
B:ASP124
|
4.3
|
6.8
|
1.0
|
C4
|
B:X8Z303
|
4.3
|
21.1
|
0.8
|
CB
|
B:SER249
|
4.3
|
7.0
|
1.0
|
N
|
B:X8Z303
|
4.4
|
22.9
|
0.8
|
NE2
|
B:HIS189
|
4.4
|
9.6
|
1.0
|
O
|
B:HOH548
|
4.6
|
28.1
|
1.0
|
OG
|
B:SER249
|
4.6
|
7.6
|
1.0
|
NE2
|
B:HIS120
|
4.6
|
6.9
|
1.0
|
CE1
|
B:HIS189
|
4.6
|
10.5
|
1.0
|
CE1
|
B:HIS120
|
4.7
|
6.4
|
1.0
|
CA
|
B:CYS208
|
4.7
|
9.3
|
1.0
|
|
Reference:
J.B.Thoden,
B.M.Benin,
A.Priebe,
W.S.Shin,
R.Muthyala,
Y.Y.Sham,
H.M.Holden.
Characterization of A Novel Inhibitor For the New Delhi Metallo-Beta-Lactamase-4: Implications For Drug Design and Combating Bacterial Drug Resistance. J.Biol.Chem. 05135 2023.
ISSN: ESSN 1083-351X
PubMed: 37549809
DOI: 10.1016/J.JBC.2023.105135
Page generated: Thu Dec 28 13:38:22 2023
|