Zinc in PDB 7uox: NDM1-Inhibitor Co-Structure
Protein crystallography data
The structure of NDM1-Inhibitor Co-Structure, PDB code: 7uox
was solved by
G.Scapin,
T.O.Fischmann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
14.49 /
0.99
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
39.03,
78.81,
134.81,
90,
90,
90
|
R / Rfree (%)
|
13.7 /
14.8
|
Other elements in 7uox:
The structure of NDM1-Inhibitor Co-Structure also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the NDM1-Inhibitor Co-Structure
(pdb code 7uox). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
NDM1-Inhibitor Co-Structure, PDB code: 7uox:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 7uox
Go back to
Zinc Binding Sites List in 7uox
Zinc binding site 1 out
of 4 in the NDM1-Inhibitor Co-Structure
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn303
b:6.1
occ:1.00
|
O
|
A:HOH409
|
1.9
|
6.4
|
1.0
|
NE2
|
A:HIS120
|
2.0
|
5.8
|
1.0
|
NE2
|
A:HIS189
|
2.0
|
5.3
|
1.0
|
ND1
|
A:HIS122
|
2.0
|
5.4
|
1.0
|
CD2
|
A:HIS189
|
3.0
|
5.1
|
1.0
|
CE1
|
A:HIS122
|
3.0
|
5.8
|
1.0
|
CE1
|
A:HIS120
|
3.0
|
6.2
|
1.0
|
CD2
|
A:HIS120
|
3.0
|
5.2
|
1.0
|
CG
|
A:HIS122
|
3.0
|
5.2
|
1.0
|
CE1
|
A:HIS189
|
3.1
|
5.4
|
1.0
|
CB
|
A:HIS122
|
3.3
|
5.2
|
1.0
|
O
|
A:O0L306
|
3.5
|
9.3
|
1.0
|
OD1
|
A:ASP124
|
3.9
|
4.7
|
0.5
|
ZN
|
A:ZN304
|
4.0
|
4.7
|
1.0
|
OD1
|
A:ASP124
|
4.0
|
6.8
|
0.5
|
SG
|
A:CYS208
|
4.1
|
6.2
|
1.0
|
NE2
|
A:HIS122
|
4.1
|
6.0
|
1.0
|
CG
|
A:HIS189
|
4.1
|
4.7
|
1.0
|
CG
|
A:HIS120
|
4.1
|
5.2
|
1.0
|
ND1
|
A:HIS120
|
4.1
|
6.0
|
1.0
|
CD2
|
A:HIS122
|
4.1
|
5.8
|
1.0
|
ND1
|
A:HIS189
|
4.2
|
5.2
|
1.0
|
N3
|
A:O0L306
|
4.3
|
6.8
|
1.0
|
CB
|
A:CYS208
|
4.3
|
5.6
|
1.0
|
CG2
|
A:THR190
|
4.4
|
5.6
|
1.0
|
OXT
|
A:ACT301
|
4.4
|
9.8
|
1.0
|
N2
|
A:O0L306
|
4.7
|
6.6
|
1.0
|
O
|
A:ACT301
|
4.8
|
10.9
|
1.0
|
C
|
A:O0L306
|
4.8
|
9.1
|
1.0
|
CA
|
A:HIS122
|
4.8
|
4.8
|
1.0
|
CG
|
A:ASP124
|
4.8
|
6.2
|
0.5
|
OD2
|
A:ASP124
|
4.8
|
4.6
|
0.5
|
OD2
|
A:ASP124
|
4.8
|
10.4
|
0.5
|
C
|
A:ACT301
|
4.8
|
8.7
|
1.0
|
CG
|
A:ASP124
|
4.8
|
6.2
|
0.5
|
O
|
A:HOH412
|
4.9
|
14.7
|
1.0
|
C13
|
A:O0L306
|
4.9
|
7.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 7uox
Go back to
Zinc Binding Sites List in 7uox
Zinc binding site 2 out
of 4 in the NDM1-Inhibitor Co-Structure
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn304
b:4.7
occ:1.00
|
OD2
|
A:ASP124
|
2.1
|
4.6
|
0.5
|
NE2
|
A:HIS250
|
2.2
|
5.9
|
1.0
|
N3
|
A:O0L306
|
2.2
|
6.8
|
1.0
|
OD2
|
A:ASP124
|
2.2
|
10.4
|
0.5
|
SG
|
A:CYS208
|
2.4
|
6.2
|
1.0
|
O
|
A:HOH409
|
2.6
|
6.4
|
1.0
|
N2
|
A:O0L306
|
3.0
|
6.6
|
1.0
|
CG
|
A:ASP124
|
3.1
|
6.2
|
0.5
|
CE1
|
A:HIS250
|
3.2
|
6.0
|
1.0
|
CD2
|
A:HIS250
|
3.2
|
6.4
|
1.0
|
CG
|
A:ASP124
|
3.2
|
6.2
|
0.5
|
C13
|
A:O0L306
|
3.3
|
7.0
|
1.0
|
OD1
|
A:ASP124
|
3.4
|
4.7
|
0.5
|
CB
|
A:CYS208
|
3.5
|
5.6
|
1.0
|
OD1
|
A:ASP124
|
3.6
|
6.8
|
0.5
|
C12
|
A:O0L306
|
3.8
|
9.0
|
1.0
|
O
|
A:O0L306
|
3.9
|
9.3
|
1.0
|
ZN
|
A:ZN303
|
4.0
|
6.1
|
1.0
|
C
|
A:O0L306
|
4.1
|
9.1
|
1.0
|
N1
|
A:O0L306
|
4.2
|
6.9
|
1.0
|
ND1
|
A:HIS250
|
4.3
|
6.5
|
1.0
|
CG
|
A:HIS250
|
4.3
|
6.1
|
1.0
|
CB
|
A:SER249
|
4.3
|
6.1
|
1.0
|
N
|
A:O0L306
|
4.4
|
8.5
|
1.0
|
NE2
|
A:HIS189
|
4.4
|
5.3
|
1.0
|
CB
|
A:ASP124
|
4.4
|
5.1
|
0.5
|
CB
|
A:ASP124
|
4.5
|
6.6
|
0.5
|
CA
|
A:CYS208
|
4.6
|
5.5
|
1.0
|
CE1
|
A:HIS189
|
4.6
|
5.4
|
1.0
|
OG
|
A:SER249
|
4.6
|
6.1
|
1.0
|
C4
|
A:O0L306
|
4.7
|
10.8
|
1.0
|
C6
|
A:O0L306
|
4.7
|
13.8
|
1.0
|
CE1
|
A:HIS120
|
4.9
|
6.2
|
1.0
|
NE2
|
A:HIS120
|
4.9
|
5.8
|
1.0
|
|
Zinc binding site 3 out
of 4 in 7uox
Go back to
Zinc Binding Sites List in 7uox
Zinc binding site 3 out
of 4 in the NDM1-Inhibitor Co-Structure
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:6.2
occ:1.00
|
O
|
B:HOH408
|
1.9
|
6.3
|
1.0
|
NE2
|
B:HIS120
|
2.0
|
6.4
|
1.0
|
NE2
|
B:HIS189
|
2.0
|
5.2
|
1.0
|
ND1
|
B:HIS122
|
2.0
|
5.2
|
1.0
|
CD2
|
B:HIS189
|
3.0
|
4.9
|
1.0
|
CD2
|
B:HIS120
|
3.0
|
5.9
|
1.0
|
CE1
|
B:HIS122
|
3.0
|
5.7
|
1.0
|
CE1
|
B:HIS120
|
3.0
|
7.1
|
1.0
|
CG
|
B:HIS122
|
3.0
|
4.9
|
1.0
|
CE1
|
B:HIS189
|
3.1
|
5.1
|
1.0
|
CB
|
B:HIS122
|
3.3
|
4.8
|
1.0
|
O
|
B:O0L306
|
3.5
|
9.2
|
1.0
|
OD1
|
B:ASP124
|
3.9
|
4.3
|
0.5
|
OD1
|
B:ASP124
|
4.0
|
6.2
|
0.5
|
ZN
|
B:ZN303
|
4.0
|
4.7
|
1.0
|
SG
|
B:CYS208
|
4.1
|
3.4
|
0.5
|
CG
|
B:HIS189
|
4.1
|
4.6
|
1.0
|
NE2
|
B:HIS122
|
4.1
|
6.0
|
1.0
|
CG
|
B:HIS120
|
4.1
|
5.5
|
1.0
|
ND1
|
B:HIS120
|
4.1
|
6.8
|
1.0
|
CD2
|
B:HIS122
|
4.1
|
5.5
|
1.0
|
SG
|
B:CYS208
|
4.2
|
10.8
|
0.5
|
ND1
|
B:HIS189
|
4.2
|
5.0
|
1.0
|
N3
|
B:O0L306
|
4.3
|
6.8
|
1.0
|
CB
|
B:CYS208
|
4.3
|
3.7
|
0.5
|
CB
|
B:CYS208
|
4.3
|
7.6
|
0.5
|
CG2
|
B:THR190
|
4.3
|
5.5
|
1.0
|
OXT
|
B:ACT301
|
4.4
|
8.6
|
1.0
|
C
|
B:O0L306
|
4.7
|
8.9
|
1.0
|
O
|
B:ACT301
|
4.7
|
9.3
|
1.0
|
N2
|
B:O0L306
|
4.7
|
6.5
|
1.0
|
CA
|
B:HIS122
|
4.8
|
4.5
|
1.0
|
CG
|
B:ASP124
|
4.8
|
5.4
|
0.5
|
OD2
|
B:ASP124
|
4.8
|
4.7
|
0.5
|
OD2
|
B:ASP124
|
4.8
|
9.2
|
0.5
|
CG
|
B:ASP124
|
4.8
|
4.9
|
0.5
|
O
|
B:HOH418
|
4.8
|
13.9
|
1.0
|
C
|
B:ACT301
|
4.9
|
7.6
|
1.0
|
C13
|
B:O0L306
|
4.9
|
8.1
|
1.0
|
|
Zinc binding site 4 out
of 4 in 7uox
Go back to
Zinc Binding Sites List in 7uox
Zinc binding site 4 out
of 4 in the NDM1-Inhibitor Co-Structure
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of NDM1-Inhibitor Co-Structure within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn303
b:4.7
occ:1.00
|
OD2
|
B:ASP124
|
2.1
|
4.7
|
0.5
|
NE2
|
B:HIS250
|
2.2
|
6.0
|
1.0
|
N3
|
B:O0L306
|
2.2
|
6.8
|
1.0
|
OD2
|
B:ASP124
|
2.2
|
9.2
|
0.5
|
SG
|
B:CYS208
|
2.2
|
10.8
|
0.5
|
SG
|
B:CYS208
|
2.4
|
3.4
|
0.5
|
O
|
B:HOH408
|
2.6
|
6.3
|
1.0
|
N2
|
B:O0L306
|
3.0
|
6.5
|
1.0
|
CG
|
B:ASP124
|
3.1
|
5.4
|
0.5
|
CE1
|
B:HIS250
|
3.2
|
5.8
|
1.0
|
CD2
|
B:HIS250
|
3.2
|
6.4
|
1.0
|
CG
|
B:ASP124
|
3.2
|
4.9
|
0.5
|
C13
|
B:O0L306
|
3.3
|
8.1
|
1.0
|
OD1
|
B:ASP124
|
3.4
|
4.3
|
0.5
|
CB
|
B:CYS208
|
3.4
|
3.7
|
0.5
|
CB
|
B:CYS208
|
3.5
|
7.6
|
0.5
|
OD1
|
B:ASP124
|
3.6
|
6.2
|
0.5
|
C12
|
B:O0L306
|
3.8
|
8.6
|
1.0
|
O
|
B:O0L306
|
3.9
|
9.2
|
1.0
|
ZN
|
B:ZN302
|
4.0
|
6.2
|
1.0
|
C
|
B:O0L306
|
4.1
|
8.9
|
1.0
|
N1
|
B:O0L306
|
4.2
|
7.0
|
1.0
|
ND1
|
B:HIS250
|
4.3
|
6.1
|
1.0
|
CB
|
B:SER249
|
4.3
|
6.4
|
1.0
|
CG
|
B:HIS250
|
4.3
|
6.2
|
1.0
|
N
|
B:O0L306
|
4.4
|
8.0
|
1.0
|
NE2
|
B:HIS189
|
4.4
|
5.2
|
1.0
|
CB
|
B:ASP124
|
4.4
|
5.2
|
0.5
|
CB
|
B:ASP124
|
4.5
|
5.9
|
0.5
|
CE1
|
B:HIS189
|
4.6
|
5.1
|
1.0
|
CA
|
B:CYS208
|
4.6
|
4.4
|
0.5
|
CA
|
B:CYS208
|
4.6
|
6.5
|
0.5
|
OG
|
B:SER249
|
4.6
|
6.0
|
1.0
|
C4
|
B:O0L306
|
4.7
|
11.0
|
1.0
|
C6
|
B:O0L306
|
4.7
|
12.8
|
1.0
|
CE1
|
B:HIS120
|
4.9
|
7.1
|
1.0
|
NE2
|
B:HIS120
|
4.9
|
6.4
|
1.0
|
O
|
B:HOH418
|
5.0
|
13.9
|
1.0
|
|
Reference:
M.Mandal,
L.Xiao,
W.Pan,
G.Scapin,
G.Li,
H.Tang,
S.W.Yang,
J.Pan,
Y.Root,
R.K.De Jesus,
C.Yang,
W.Prosise,
P.Dayananth,
A.Mirza,
A.G.Therien,
K.Young,
A.Flattery,
C.Garlisi,
R.Zhang,
D.Chu,
P.Sheth,
I.Chu,
J.Wu,
C.Markgraf,
H.Y.Kim,
R.Painter,
T.W.Mayhood,
E.Dinunzio,
D.F.Wyss,
A.V.Buevich,
T.Fischmann,
A.Pasternak,
S.Dong,
J.D.Hicks,
A.Villafania,
L.Liang,
N.Murgolo,
T.Black,
W.K.Hagmann,
J.Tata,
E.R.Parmee,
A.E.Weber,
J.Su,
H.Tang.
Rapid Evolution of A Fragment-Like Molecule to Pan-Metallo-Beta-Lactamase Inhibitors: Initial Leads Toward Clinical Candidates. J.Med.Chem. V. 65 16234 2022.
ISSN: ISSN 0022-2623
PubMed: 36475645
DOI: 10.1021/ACS.JMEDCHEM.2C00766
Page generated: Wed Oct 30 12:16:27 2024
|