Zinc in PDB 5n0h: Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement
Enzymatic activity of Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement
All present enzymatic activity of Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement:
3.5.2.6;
Protein crystallography data
The structure of Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement, PDB code: 5n0h
was solved by
J.E.Raczynska,
I.G.Shabalin,
M.Jaskolski,
W.Minor,
A.Wlodawer,
D.T.King,
N.C.J.Strynadka,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.19 /
1.90
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
106.000,
106.000,
92.580,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.5 /
20
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement
(pdb code 5n0h). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement, PDB code: 5n0h:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 5n0h
Go back to
Zinc Binding Sites List in 5n0h
Zinc binding site 1 out
of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:21.7
occ:0.70
|
NE2
|
A:HIS250
|
2.1
|
23.8
|
1.0
|
NAN
|
A:8YL301
|
2.1
|
23.6
|
0.6
|
OD2
|
A:ASP124
|
2.2
|
22.7
|
1.0
|
OAH
|
A:8YL301
|
2.2
|
20.5
|
0.6
|
SG
|
A:CYS208
|
2.3
|
23.8
|
1.0
|
O
|
A:HOH535
|
2.5
|
8.3
|
0.4
|
OAF
|
A:8YL301
|
2.7
|
20.8
|
0.6
|
CAS
|
A:8YL301
|
2.9
|
23.8
|
0.6
|
CE1
|
A:HIS250
|
2.9
|
25.1
|
1.0
|
CAP
|
A:8YL301
|
3.0
|
23.1
|
0.6
|
CD2
|
A:HIS250
|
3.2
|
26.2
|
1.0
|
CG
|
A:ASP124
|
3.2
|
20.7
|
1.0
|
CAZ
|
A:8YL301
|
3.3
|
23.7
|
0.6
|
CB
|
A:CYS208
|
3.4
|
19.9
|
1.0
|
OD1
|
A:ASP124
|
3.5
|
26.0
|
1.0
|
CAQ
|
A:8YL301
|
3.7
|
23.0
|
0.6
|
ZN
|
A:ZN303
|
4.0
|
19.3
|
1.0
|
CBA
|
A:8YL301
|
4.1
|
23.3
|
0.6
|
ND1
|
A:HIS250
|
4.1
|
26.0
|
1.0
|
CAT
|
A:8YL301
|
4.1
|
26.3
|
0.6
|
CAV
|
A:8YL301
|
4.2
|
25.3
|
0.6
|
CB
|
A:SER249
|
4.2
|
21.5
|
1.0
|
OAE
|
A:8YL301
|
4.2
|
21.6
|
0.6
|
OAJ
|
A:8YL301
|
4.2
|
23.4
|
0.6
|
CG
|
A:HIS250
|
4.2
|
25.1
|
1.0
|
NE2
|
A:HIS189
|
4.5
|
17.8
|
1.0
|
CB
|
A:ASP124
|
4.5
|
18.4
|
1.0
|
CA
|
A:CYS208
|
4.6
|
17.9
|
1.0
|
O
|
A:HOH441
|
4.6
|
27.3
|
0.4
|
OG
|
A:SER249
|
4.6
|
19.7
|
1.0
|
OAI
|
A:8YL301
|
4.6
|
20.2
|
0.6
|
CE1
|
A:HIS189
|
4.7
|
17.1
|
1.0
|
CAU
|
A:8YL301
|
4.8
|
24.0
|
0.6
|
CE1
|
A:HIS120
|
4.8
|
16.8
|
1.0
|
NE2
|
A:HIS120
|
4.9
|
16.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 5n0h
Go back to
Zinc Binding Sites List in 5n0h
Zinc binding site 2 out
of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn303
b:19.3
occ:1.00
|
ND1
|
A:HIS122
|
2.0
|
15.3
|
1.0
|
OAF
|
A:8YL301
|
2.0
|
20.8
|
0.6
|
NE2
|
A:HIS120
|
2.1
|
16.1
|
1.0
|
NE2
|
A:HIS189
|
2.1
|
17.8
|
1.0
|
O
|
A:HOH535
|
2.2
|
8.3
|
0.4
|
CAQ
|
A:8YL301
|
2.8
|
23.0
|
0.6
|
OAI
|
A:8YL301
|
3.0
|
20.2
|
0.6
|
CG
|
A:HIS122
|
3.0
|
15.3
|
1.0
|
CD2
|
A:HIS189
|
3.0
|
16.4
|
1.0
|
CD2
|
A:HIS120
|
3.0
|
15.0
|
1.0
|
CE1
|
A:HIS120
|
3.0
|
16.8
|
1.0
|
CE1
|
A:HIS122
|
3.0
|
18.3
|
1.0
|
CE1
|
A:HIS189
|
3.1
|
17.1
|
1.0
|
CB
|
A:HIS122
|
3.3
|
13.3
|
1.0
|
ZN
|
A:ZN302
|
4.0
|
21.7
|
0.7
|
ND1
|
A:HIS120
|
4.1
|
16.6
|
1.0
|
SG
|
A:CYS208
|
4.1
|
23.8
|
1.0
|
NE2
|
A:HIS122
|
4.1
|
18.2
|
1.0
|
CD2
|
A:HIS122
|
4.1
|
17.5
|
1.0
|
CBA
|
A:8YL301
|
4.1
|
23.3
|
0.6
|
CG
|
A:HIS120
|
4.2
|
14.4
|
1.0
|
OD1
|
A:ASP124
|
4.2
|
26.0
|
1.0
|
CG
|
A:HIS189
|
4.2
|
16.9
|
1.0
|
ND1
|
A:HIS189
|
4.2
|
15.9
|
1.0
|
CB
|
A:CYS208
|
4.2
|
19.9
|
1.0
|
NAN
|
A:8YL301
|
4.3
|
23.6
|
0.6
|
CAU
|
A:8YL301
|
4.4
|
24.0
|
0.6
|
OAJ
|
A:8YL301
|
4.4
|
23.4
|
0.6
|
CG2
|
A:THR190
|
4.4
|
18.3
|
1.0
|
OAH
|
A:8YL301
|
4.6
|
20.5
|
0.6
|
CA
|
A:HIS122
|
4.8
|
13.6
|
1.0
|
CAZ
|
A:8YL301
|
4.9
|
23.7
|
0.6
|
CAP
|
A:8YL301
|
4.9
|
23.1
|
0.6
|
CAS
|
A:8YL301
|
4.9
|
23.8
|
0.6
|
OD2
|
A:ASP124
|
5.0
|
22.7
|
1.0
|
|
Zinc binding site 3 out
of 4 in 5n0h
Go back to
Zinc Binding Sites List in 5n0h
Zinc binding site 3 out
of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:22.7
occ:0.60
|
NE2
|
B:HIS250
|
2.0
|
29.4
|
1.0
|
O
|
B:HOH542
|
2.2
|
24.2
|
1.0
|
OD2
|
B:ASP124
|
2.2
|
23.4
|
1.0
|
SG
|
B:CYS208
|
2.3
|
25.6
|
1.0
|
CE1
|
B:HIS250
|
2.9
|
27.2
|
1.0
|
O
|
B:HOH534
|
2.9
|
45.3
|
1.0
|
CD2
|
B:HIS250
|
3.1
|
28.1
|
1.0
|
CG
|
B:ASP124
|
3.2
|
19.3
|
1.0
|
CB
|
B:CYS208
|
3.4
|
18.9
|
1.0
|
OD1
|
B:ASP124
|
3.6
|
22.1
|
1.0
|
O
|
B:HOH528
|
3.8
|
41.9
|
1.0
|
ZN
|
B:ZN302
|
3.8
|
18.3
|
0.9
|
ND1
|
B:HIS250
|
4.1
|
30.9
|
1.0
|
CG
|
B:HIS250
|
4.1
|
28.4
|
1.0
|
CB
|
B:SER249
|
4.2
|
21.7
|
1.0
|
O
|
B:HOH504
|
4.3
|
30.1
|
1.0
|
NE2
|
B:HIS189
|
4.5
|
16.7
|
1.0
|
CB
|
B:ASP124
|
4.5
|
16.4
|
1.0
|
OG
|
B:SER249
|
4.6
|
19.1
|
1.0
|
CE1
|
B:HIS120
|
4.6
|
16.7
|
1.0
|
CE1
|
B:HIS189
|
4.7
|
15.3
|
1.0
|
NE2
|
B:HIS120
|
4.7
|
16.6
|
1.0
|
CA
|
B:CYS208
|
4.7
|
15.8
|
1.0
|
|
Zinc binding site 4 out
of 4 in 5n0h
Go back to
Zinc Binding Sites List in 5n0h
Zinc binding site 4 out
of 4 in the Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Ndm-1 in Complex with Hydrolyzed Meropenem - New Refinement within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:18.3
occ:0.90
|
NE2
|
B:HIS120
|
2.1
|
16.6
|
1.0
|
ND1
|
B:HIS122
|
2.1
|
18.5
|
1.0
|
O
|
B:HOH542
|
2.1
|
24.2
|
1.0
|
NE2
|
B:HIS189
|
2.1
|
16.7
|
1.0
|
O
|
B:HOH528
|
2.7
|
41.9
|
1.0
|
CD2
|
B:HIS120
|
3.0
|
15.3
|
1.0
|
CE1
|
B:HIS120
|
3.0
|
16.7
|
1.0
|
CE1
|
B:HIS122
|
3.0
|
16.9
|
1.0
|
CD2
|
B:HIS189
|
3.0
|
15.3
|
1.0
|
CG
|
B:HIS122
|
3.0
|
15.7
|
1.0
|
CE1
|
B:HIS189
|
3.1
|
15.3
|
1.0
|
CB
|
B:HIS122
|
3.4
|
14.2
|
1.0
|
ZN
|
B:ZN301
|
3.8
|
22.7
|
0.6
|
SG
|
B:CYS208
|
4.0
|
25.6
|
1.0
|
NE2
|
B:HIS122
|
4.1
|
17.8
|
1.0
|
ND1
|
B:HIS120
|
4.1
|
16.3
|
1.0
|
CG
|
B:HIS120
|
4.1
|
14.6
|
1.0
|
CD2
|
B:HIS122
|
4.2
|
17.3
|
1.0
|
CG
|
B:HIS189
|
4.2
|
15.6
|
1.0
|
ND1
|
B:HIS189
|
4.2
|
14.6
|
1.0
|
OD1
|
B:ASP124
|
4.2
|
22.1
|
1.0
|
CB
|
B:CYS208
|
4.3
|
18.9
|
1.0
|
CG2
|
B:THR190
|
4.5
|
17.9
|
1.0
|
O
|
B:HOH534
|
4.7
|
45.3
|
1.0
|
OD2
|
B:ASP124
|
4.8
|
23.4
|
1.0
|
CA
|
B:HIS122
|
4.8
|
13.7
|
1.0
|
ND2
|
B:ASN220
|
4.9
|
51.5
|
1.0
|
CG
|
B:ASP124
|
5.0
|
19.3
|
1.0
|
|
Reference:
J.E.Raczynska,
I.G.Shabalin,
W.Minor,
A.Wlodawer,
M.Jaskolski.
A Close Look Onto Structural Models and Primary Ligands of Metallo-Beta-Lactamases. Drug Resist. Updat. V. 40 1 2018.
ISSN: ESSN 1532-2084
PubMed: 30466711
DOI: 10.1016/J.DRUP.2018.08.001
Page generated: Sun Oct 27 22:26:09 2024
|