Zinc in PDB 5ypk: Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex
Protein crystallography data
The structure of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex, PDB code: 5ypk
was solved by
H.Feng,
D.Wang,
W.Liu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
42.21 /
2.00
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
69.240,
73.610,
154.520,
90.00,
90.08,
90.00
|
|
R / Rfree (%)
|
18.6 /
22.9
|
Other elements in 5ypk:
The structure of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex also contains other interesting chemical elements:
Zinc Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex
(pdb code 5ypk). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the
Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex, PDB code: 5ypk:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Zinc binding site 1 out
of 16 in 5ypk
Go back to
Zinc Binding Sites List in 5ypk
Zinc binding site 1 out
of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex
 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 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:21.5
occ:1.00
|
O71
|
A:HIW303
|
2.0
|
23.2
|
0.8
|
|
NE2
|
A:HIS189
|
2.1
|
16.3
|
1.0
|
|
ND1
|
A:HIS122
|
2.1
|
22.7
|
1.0
|
|
NE2
|
A:HIS120
|
2.1
|
14.7
|
1.0
|
|
C7
|
A:HIW303
|
2.7
|
25.4
|
0.8
|
|
CD2
|
A:HIS189
|
2.9
|
12.8
|
1.0
|
|
O72
|
A:HIW303
|
2.9
|
25.8
|
0.8
|
|
CD2
|
A:HIS120
|
3.0
|
15.3
|
1.0
|
|
CG
|
A:HIS122
|
3.0
|
23.2
|
1.0
|
|
CE1
|
A:HIS120
|
3.0
|
18.7
|
1.0
|
|
CE1
|
A:HIS122
|
3.1
|
26.0
|
1.0
|
|
CE1
|
A:HIS189
|
3.2
|
21.8
|
1.0
|
|
CB
|
A:HIS122
|
3.3
|
15.8
|
1.0
|
|
SG
|
A:CYS208
|
4.0
|
19.3
|
1.0
|
|
ZN
|
A:ZN302
|
4.0
|
23.3
|
1.0
|
|
CG
|
A:HIS189
|
4.1
|
14.2
|
1.0
|
|
N4
|
A:HIW303
|
4.1
|
28.0
|
0.8
|
|
ND1
|
A:HIS120
|
4.1
|
13.4
|
1.0
|
|
CG
|
A:HIS120
|
4.1
|
14.5
|
1.0
|
|
NE2
|
A:HIS122
|
4.2
|
24.6
|
1.0
|
|
CD2
|
A:HIS122
|
4.2
|
21.1
|
1.0
|
|
CB
|
A:CYS208
|
4.2
|
12.5
|
1.0
|
|
C6
|
A:HIW303
|
4.2
|
27.3
|
0.8
|
|
ND1
|
A:HIS189
|
4.2
|
14.2
|
1.0
|
|
OD1
|
A:ASP124
|
4.2
|
22.2
|
1.0
|
|
CG2
|
A:THR190
|
4.5
|
17.3
|
1.0
|
|
C5
|
A:HIW303
|
4.6
|
27.6
|
0.8
|
|
O62
|
A:HIW303
|
4.7
|
25.7
|
0.8
|
|
OD2
|
A:ASP124
|
4.7
|
16.8
|
1.0
|
|
C61
|
A:HIW303
|
4.8
|
26.8
|
0.8
|
|
CA
|
A:HIS122
|
4.8
|
17.9
|
1.0
|
|
O31
|
A:HIW303
|
4.9
|
21.2
|
0.8
|
|
CG
|
A:ASP124
|
4.9
|
20.4
|
1.0
|
|
ND2
|
A:ASN220
|
5.0
|
26.0
|
1.0
|
|
Zinc binding site 2 out
of 16 in 5ypk
Go back to
Zinc Binding Sites List in 5ypk
Zinc binding site 2 out
of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex
 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 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:23.3
occ:1.00
|
NE2
|
A:HIS250
|
2.0
|
16.2
|
1.0
|
|
N4
|
A:HIW303
|
2.0
|
28.0
|
0.8
|
|
OD2
|
A:ASP124
|
2.1
|
16.8
|
1.0
|
|
SG
|
A:CYS208
|
2.3
|
19.3
|
1.0
|
|
CE1
|
A:HIS250
|
2.8
|
19.6
|
1.0
|
|
O31
|
A:HIW303
|
2.8
|
21.2
|
0.8
|
|
C3
|
A:HIW303
|
3.0
|
24.5
|
0.8
|
|
C5
|
A:HIW303
|
3.0
|
27.6
|
0.8
|
|
CD2
|
A:HIS250
|
3.2
|
18.2
|
1.0
|
|
O71
|
A:HIW303
|
3.2
|
23.2
|
0.8
|
|
CG
|
A:ASP124
|
3.2
|
20.4
|
1.0
|
|
C31
|
A:HIW303
|
3.3
|
28.2
|
0.8
|
|
CB
|
A:CYS208
|
3.4
|
12.5
|
1.0
|
|
C7
|
A:HIW303
|
3.7
|
25.4
|
0.8
|
|
OD1
|
A:ASP124
|
3.7
|
22.2
|
1.0
|
|
C1
|
A:HIW303
|
3.9
|
31.9
|
0.8
|
|
ND1
|
A:HIS250
|
4.0
|
18.6
|
1.0
|
|
C6
|
A:HIW303
|
4.0
|
27.3
|
0.8
|
|
ZN
|
A:ZN301
|
4.0
|
21.5
|
1.0
|
|
C2
|
A:HIW303
|
4.1
|
30.1
|
0.8
|
|
CB
|
A:SER249
|
4.1
|
15.0
|
1.0
|
|
CG
|
A:HIS250
|
4.2
|
20.9
|
1.0
|
|
CB
|
A:ASP124
|
4.5
|
19.0
|
1.0
|
|
CA
|
A:CYS208
|
4.5
|
17.6
|
1.0
|
|
OG
|
A:SER249
|
4.5
|
14.3
|
1.0
|
|
O62
|
A:HIW303
|
4.5
|
25.7
|
0.8
|
|
O32
|
A:HIW303
|
4.6
|
30.4
|
0.8
|
|
NE2
|
A:HIS189
|
4.6
|
16.3
|
1.0
|
|
O72
|
A:HIW303
|
4.6
|
25.8
|
0.8
|
|
CE1
|
A:HIS120
|
4.8
|
18.7
|
1.0
|
|
CE1
|
A:HIS189
|
4.8
|
21.8
|
1.0
|
|
CE
|
A:LYS125
|
4.8
|
19.4
|
1.0
|
|
NE2
|
A:HIS120
|
4.9
|
14.7
|
1.0
|
|
C61
|
A:HIW303
|
5.0
|
26.8
|
0.8
|
|
Zinc binding site 3 out
of 16 in 5ypk
Go back to
Zinc Binding Sites List in 5ypk
Zinc binding site 3 out
of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex
 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 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:21.1
occ:1.00
|
O71
|
B:HIW303
|
2.0
|
25.0
|
0.9
|
|
NE2
|
B:HIS120
|
2.0
|
15.4
|
1.0
|
|
ND1
|
B:HIS122
|
2.1
|
22.6
|
1.0
|
|
NE2
|
B:HIS189
|
2.1
|
15.6
|
1.0
|
|
C7
|
B:HIW303
|
2.8
|
25.9
|
0.9
|
|
CD2
|
B:HIS189
|
2.9
|
15.3
|
1.0
|
|
CE1
|
B:HIS120
|
2.9
|
17.1
|
1.0
|
|
O72
|
B:HIW303
|
3.0
|
25.7
|
0.9
|
|
CG
|
B:HIS122
|
3.0
|
23.2
|
1.0
|
|
CD2
|
B:HIS120
|
3.0
|
16.5
|
1.0
|
|
CE1
|
B:HIS122
|
3.1
|
27.9
|
1.0
|
|
CE1
|
B:HIS189
|
3.2
|
24.4
|
1.0
|
|
CB
|
B:HIS122
|
3.3
|
16.3
|
1.0
|
|
SG
|
B:CYS208
|
3.9
|
20.0
|
1.0
|
|
ZN
|
B:ZN302
|
3.9
|
32.3
|
1.0
|
|
ND1
|
B:HIS120
|
4.0
|
16.0
|
1.0
|
|
CG
|
B:HIS120
|
4.1
|
17.7
|
1.0
|
|
CG
|
B:HIS189
|
4.1
|
17.3
|
1.0
|
|
CB
|
B:CYS208
|
4.1
|
19.1
|
1.0
|
|
CD2
|
B:HIS122
|
4.1
|
22.5
|
1.0
|
|
NE2
|
B:HIS122
|
4.2
|
28.0
|
1.0
|
|
N4
|
B:HIW303
|
4.2
|
27.2
|
0.9
|
|
ND1
|
B:HIS189
|
4.2
|
14.5
|
1.0
|
|
C6
|
B:HIW303
|
4.2
|
32.0
|
0.9
|
|
OD1
|
B:ASP124
|
4.3
|
24.9
|
1.0
|
|
O62
|
B:HIW303
|
4.3
|
29.1
|
0.9
|
|
CG2
|
B:THR190
|
4.5
|
21.2
|
1.0
|
|
C5
|
B:HIW303
|
4.7
|
27.2
|
0.9
|
|
C61
|
B:HIW303
|
4.7
|
34.7
|
0.9
|
|
CA
|
B:HIS122
|
4.7
|
21.2
|
1.0
|
|
OD2
|
B:ASP124
|
4.9
|
24.8
|
1.0
|
|
Zinc binding site 4 out
of 16 in 5ypk
Go back to
Zinc Binding Sites List in 5ypk
Zinc binding site 4 out
of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex
 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 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:32.3
occ:1.00
|
N4
|
B:HIW303
|
2.0
|
27.2
|
0.9
|
|
NE2
|
B:HIS250
|
2.1
|
25.9
|
1.0
|
|
SG
|
B:CYS208
|
2.3
|
20.0
|
1.0
|
|
OD2
|
B:ASP124
|
2.4
|
24.8
|
1.0
|
|
O31
|
B:HIW303
|
2.6
|
32.4
|
0.9
|
|
C3
|
B:HIW303
|
2.9
|
30.7
|
0.9
|
|
CE1
|
B:HIS250
|
3.0
|
26.3
|
1.0
|
|
C5
|
B:HIW303
|
3.1
|
27.2
|
0.9
|
|
O71
|
B:HIW303
|
3.1
|
25.0
|
0.9
|
|
C31
|
B:HIW303
|
3.2
|
33.1
|
0.9
|
|
CD2
|
B:HIS250
|
3.2
|
24.5
|
1.0
|
|
CB
|
B:CYS208
|
3.3
|
19.1
|
1.0
|
|
CG
|
B:ASP124
|
3.5
|
24.5
|
1.0
|
|
C7
|
B:HIW303
|
3.7
|
25.9
|
0.9
|
|
OD1
|
B:ASP124
|
3.9
|
24.9
|
1.0
|
|
ZN
|
B:ZN301
|
3.9
|
21.1
|
1.0
|
|
C1
|
B:HIW303
|
4.0
|
33.4
|
0.9
|
|
C6
|
B:HIW303
|
4.1
|
32.0
|
0.9
|
|
C2
|
B:HIW303
|
4.1
|
36.9
|
0.9
|
|
ND1
|
B:HIS250
|
4.2
|
25.7
|
1.0
|
|
CB
|
B:SER249
|
4.2
|
24.2
|
1.0
|
|
CG
|
B:HIS250
|
4.3
|
32.3
|
1.0
|
|
O32
|
B:HIW303
|
4.4
|
39.9
|
0.9
|
|
CA
|
B:CYS208
|
4.4
|
17.1
|
1.0
|
|
NE2
|
B:HIS189
|
4.4
|
15.6
|
1.0
|
|
O72
|
B:HIW303
|
4.5
|
25.7
|
0.9
|
|
OG
|
B:SER249
|
4.5
|
23.2
|
1.0
|
|
CE1
|
B:HIS189
|
4.7
|
24.4
|
1.0
|
|
O62
|
B:HIW303
|
4.7
|
29.1
|
0.9
|
|
CB
|
B:ASP124
|
4.7
|
24.4
|
1.0
|
|
CE1
|
B:HIS120
|
4.7
|
17.1
|
1.0
|
|
NE2
|
B:HIS120
|
4.9
|
15.4
|
1.0
|
|
Zinc binding site 5 out
of 16 in 5ypk
Go back to
Zinc Binding Sites List in 5ypk
Zinc binding site 5 out
of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:18.1
occ:1.00
|
O71
|
C:HIW303
|
1.9
|
19.6
|
0.8
|
|
ND1
|
C:HIS122
|
2.0
|
19.8
|
1.0
|
|
NE2
|
C:HIS120
|
2.1
|
13.3
|
1.0
|
|
NE2
|
C:HIS189
|
2.2
|
17.1
|
1.0
|
|
C7
|
C:HIW303
|
2.5
|
21.6
|
0.8
|
|
O72
|
C:HIW303
|
2.6
|
24.4
|
0.8
|
|
CD2
|
C:HIS189
|
2.9
|
15.8
|
1.0
|
|
CG
|
C:HIS122
|
2.9
|
19.9
|
1.0
|
|
CD2
|
C:HIS120
|
3.0
|
11.5
|
1.0
|
|
CE1
|
C:HIS122
|
3.1
|
20.7
|
1.0
|
|
CE1
|
C:HIS120
|
3.1
|
15.9
|
1.0
|
|
CB
|
C:HIS122
|
3.2
|
18.9
|
1.0
|
|
CE1
|
C:HIS189
|
3.3
|
16.1
|
1.0
|
|
C6
|
C:HIW303
|
4.0
|
23.0
|
0.8
|
|
N4
|
C:HIW303
|
4.1
|
28.7
|
0.8
|
|
CD2
|
C:HIS122
|
4.1
|
23.8
|
1.0
|
|
NE2
|
C:HIS122
|
4.1
|
26.7
|
1.0
|
|
ND1
|
C:HIS120
|
4.1
|
16.4
|
1.0
|
|
CG
|
C:HIS120
|
4.1
|
14.2
|
1.0
|
|
CG
|
C:HIS189
|
4.2
|
17.6
|
1.0
|
|
ZN
|
C:ZN302
|
4.2
|
25.4
|
1.0
|
|
SG
|
C:CYS208
|
4.2
|
20.5
|
1.0
|
|
OD1
|
C:ASP124
|
4.3
|
23.7
|
1.0
|
|
ND1
|
C:HIS189
|
4.3
|
14.1
|
1.0
|
|
CG2
|
C:THR190
|
4.4
|
14.7
|
1.0
|
|
CB
|
C:CYS208
|
4.4
|
15.1
|
1.0
|
|
O62
|
C:HIW303
|
4.5
|
24.5
|
0.8
|
|
C61
|
C:HIW303
|
4.5
|
28.6
|
0.8
|
|
C5
|
C:HIW303
|
4.5
|
30.2
|
0.8
|
|
CA
|
C:HIS122
|
4.7
|
18.4
|
1.0
|
|
OD2
|
C:ASP124
|
4.8
|
25.4
|
1.0
|
|
CG
|
C:ASP124
|
5.0
|
22.3
|
1.0
|
|
Zinc binding site 6 out
of 16 in 5ypk
Go back to
Zinc Binding Sites List in 5ypk
Zinc binding site 6 out
of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn302
b:25.4
occ:1.00
|
N4
|
C:HIW303
|
1.9
|
28.7
|
0.8
|
|
NE2
|
C:HIS250
|
2.1
|
24.1
|
1.0
|
|
OD2
|
C:ASP124
|
2.1
|
25.4
|
1.0
|
|
SG
|
C:CYS208
|
2.4
|
20.5
|
1.0
|
|
C5
|
C:HIW303
|
2.8
|
30.2
|
0.8
|
|
O31
|
C:HIW303
|
2.8
|
24.4
|
0.8
|
|
C3
|
C:HIW303
|
2.9
|
27.6
|
0.8
|
|
CE1
|
C:HIS250
|
3.0
|
19.8
|
1.0
|
|
O71
|
C:HIW303
|
3.1
|
19.6
|
0.8
|
|
CD2
|
C:HIS250
|
3.2
|
23.3
|
1.0
|
|
CG
|
C:ASP124
|
3.3
|
22.3
|
1.0
|
|
C31
|
C:HIW303
|
3.3
|
25.2
|
0.8
|
|
CB
|
C:CYS208
|
3.3
|
15.1
|
1.0
|
|
C7
|
C:HIW303
|
3.6
|
21.6
|
0.8
|
|
C1
|
C:HIW303
|
3.7
|
26.6
|
0.8
|
|
OD1
|
C:ASP124
|
3.8
|
23.7
|
1.0
|
|
C6
|
C:HIW303
|
3.9
|
23.0
|
0.8
|
|
C2
|
C:HIW303
|
4.0
|
29.1
|
0.8
|
|
ND1
|
C:HIS250
|
4.1
|
25.0
|
1.0
|
|
ZN
|
C:ZN301
|
4.2
|
18.1
|
1.0
|
|
CB
|
C:SER249
|
4.2
|
20.9
|
1.0
|
|
CG
|
C:HIS250
|
4.2
|
24.6
|
1.0
|
|
O62
|
C:HIW303
|
4.4
|
24.5
|
0.8
|
|
OG
|
C:SER249
|
4.4
|
17.3
|
1.0
|
|
CA
|
C:CYS208
|
4.5
|
16.8
|
1.0
|
|
O72
|
C:HIW303
|
4.5
|
24.4
|
0.8
|
|
CB
|
C:ASP124
|
4.5
|
19.9
|
1.0
|
|
NE2
|
C:HIS189
|
4.5
|
17.1
|
1.0
|
|
O32
|
C:HIW303
|
4.5
|
28.3
|
0.8
|
|
CE1
|
C:HIS120
|
4.7
|
15.9
|
1.0
|
|
CE1
|
C:HIS189
|
4.8
|
16.1
|
1.0
|
|
C61
|
C:HIW303
|
4.8
|
28.6
|
0.8
|
|
CE
|
C:LYS125
|
4.9
|
26.0
|
1.0
|
|
NE2
|
C:HIS120
|
4.9
|
13.3
|
1.0
|
|
S21
|
C:HIW303
|
5.0
|
37.0
|
0.8
|
|
Zinc binding site 7 out
of 16 in 5ypk
Go back to
Zinc Binding Sites List in 5ypk
Zinc binding site 7 out
of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn301
b:19.4
occ:1.00
|
O72
|
D:HIW303
|
2.0
|
25.7
|
0.8
|
|
NE2
|
D:HIS120
|
2.1
|
14.0
|
1.0
|
|
ND1
|
D:HIS122
|
2.1
|
21.2
|
1.0
|
|
NE2
|
D:HIS189
|
2.1
|
17.2
|
1.0
|
|
CD2
|
D:HIS189
|
2.9
|
16.6
|
1.0
|
|
C7
|
D:HIW303
|
3.0
|
30.6
|
0.8
|
|
CG
|
D:HIS122
|
3.0
|
18.6
|
1.0
|
|
CD2
|
D:HIS120
|
3.0
|
16.8
|
1.0
|
|
CE1
|
D:HIS120
|
3.0
|
18.5
|
1.0
|
|
CE1
|
D:HIS122
|
3.1
|
20.5
|
1.0
|
|
CE1
|
D:HIS189
|
3.3
|
18.8
|
1.0
|
|
O71
|
D:HIW303
|
3.3
|
31.3
|
0.8
|
|
CB
|
D:HIS122
|
3.3
|
19.4
|
1.0
|
|
ZN
|
D:ZN302
|
3.9
|
26.2
|
1.0
|
|
SG
|
D:CYS208
|
4.0
|
18.3
|
1.0
|
|
ND1
|
D:HIS120
|
4.1
|
17.8
|
1.0
|
|
CG
|
D:HIS120
|
4.1
|
13.1
|
1.0
|
|
CG
|
D:HIS189
|
4.1
|
14.5
|
1.0
|
|
N4
|
D:HIW303
|
4.1
|
36.3
|
0.8
|
|
CB
|
D:CYS208
|
4.1
|
11.0
|
1.0
|
|
CD2
|
D:HIS122
|
4.2
|
22.1
|
1.0
|
|
NE2
|
D:HIS122
|
4.2
|
23.2
|
1.0
|
|
OD1
|
D:ASP124
|
4.2
|
24.1
|
1.0
|
|
ND1
|
D:HIS189
|
4.3
|
21.3
|
1.0
|
|
C6
|
D:HIW303
|
4.3
|
27.6
|
0.8
|
|
CG2
|
D:THR190
|
4.4
|
20.7
|
1.0
|
|
C5
|
D:HIW303
|
4.6
|
33.0
|
0.8
|
|
OD2
|
D:ASP124
|
4.7
|
23.5
|
1.0
|
|
O62
|
D:HIW303
|
4.7
|
27.7
|
0.8
|
|
CA
|
D:HIS122
|
4.7
|
18.1
|
1.0
|
|
C61
|
D:HIW303
|
4.8
|
29.8
|
0.8
|
|
CG
|
D:ASP124
|
4.9
|
20.4
|
1.0
|
|
Zinc binding site 8 out
of 16 in 5ypk
Go back to
Zinc Binding Sites List in 5ypk
Zinc binding site 8 out
of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn302
b:26.2
occ:1.00
|
OD2
|
D:ASP124
|
2.0
|
23.5
|
1.0
|
|
N4
|
D:HIW303
|
2.1
|
36.3
|
0.8
|
|
NE2
|
D:HIS250
|
2.1
|
26.3
|
1.0
|
|
SG
|
D:CYS208
|
2.3
|
18.3
|
1.0
|
|
C5
|
D:HIW303
|
2.8
|
33.0
|
0.8
|
|
CE1
|
D:HIS250
|
2.9
|
25.2
|
1.0
|
|
C3
|
D:HIW303
|
3.1
|
31.2
|
0.8
|
|
O72
|
D:HIW303
|
3.1
|
25.7
|
0.8
|
|
CG
|
D:ASP124
|
3.1
|
20.4
|
1.0
|
|
O32
|
D:HIW303
|
3.1
|
33.9
|
0.8
|
|
CD2
|
D:HIS250
|
3.2
|
21.0
|
1.0
|
|
CB
|
D:CYS208
|
3.4
|
11.0
|
1.0
|
|
C31
|
D:HIW303
|
3.5
|
34.5
|
0.8
|
|
OD1
|
D:ASP124
|
3.6
|
24.1
|
1.0
|
|
C1
|
D:HIW303
|
3.7
|
33.8
|
0.8
|
|
C7
|
D:HIW303
|
3.7
|
30.6
|
0.8
|
|
C6
|
D:HIW303
|
3.9
|
27.6
|
0.8
|
|
ZN
|
D:ZN301
|
3.9
|
19.4
|
1.0
|
|
C2
|
D:HIW303
|
4.1
|
36.7
|
0.8
|
|
CB
|
D:SER249
|
4.1
|
16.7
|
1.0
|
|
ND1
|
D:HIS250
|
4.1
|
24.9
|
1.0
|
|
CG
|
D:HIS250
|
4.3
|
25.3
|
1.0
|
|
CB
|
D:ASP124
|
4.3
|
19.7
|
1.0
|
|
O62
|
D:HIW303
|
4.4
|
27.7
|
0.8
|
|
OG
|
D:SER249
|
4.4
|
18.5
|
1.0
|
|
CA
|
D:CYS208
|
4.5
|
13.3
|
1.0
|
|
NE2
|
D:HIS189
|
4.5
|
17.2
|
1.0
|
|
CE1
|
D:HIS120
|
4.7
|
18.5
|
1.0
|
|
CE
|
D:LYS125
|
4.7
|
19.8
|
1.0
|
|
O71
|
D:HIW303
|
4.7
|
31.3
|
0.8
|
|
NE2
|
D:HIS120
|
4.8
|
14.0
|
1.0
|
|
O31
|
D:HIW303
|
4.8
|
34.7
|
0.8
|
|
C61
|
D:HIW303
|
4.8
|
29.8
|
0.8
|
|
CE1
|
D:HIS189
|
4.8
|
18.8
|
1.0
|
|
Zinc binding site 9 out
of 16 in 5ypk
Go back to
Zinc Binding Sites List in 5ypk
Zinc binding site 9 out
of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn301
b:24.4
occ:1.00
|
ND1
|
E:HIS122
|
2.0
|
17.3
|
1.0
|
|
NE2
|
E:HIS189
|
2.0
|
30.1
|
1.0
|
|
NE2
|
E:HIS120
|
2.1
|
22.7
|
1.0
|
|
O71
|
E:HIW303
|
2.4
|
25.0
|
0.9
|
|
O72
|
E:HIW303
|
2.6
|
35.7
|
0.9
|
|
C7
|
E:HIW303
|
2.8
|
33.8
|
0.9
|
|
CD2
|
E:HIS189
|
2.8
|
22.4
|
1.0
|
|
CE1
|
E:HIS122
|
2.9
|
23.9
|
1.0
|
|
CE1
|
E:HIS120
|
3.0
|
26.5
|
1.0
|
|
CG
|
E:HIS122
|
3.0
|
26.7
|
1.0
|
|
CD2
|
E:HIS120
|
3.1
|
21.3
|
1.0
|
|
CE1
|
E:HIS189
|
3.2
|
29.7
|
1.0
|
|
CB
|
E:HIS122
|
3.4
|
25.6
|
1.0
|
|
ZN
|
E:ZN302
|
3.9
|
37.4
|
1.0
|
|
SG
|
E:CYS208
|
4.0
|
34.1
|
1.0
|
|
CG
|
E:HIS189
|
4.1
|
26.6
|
1.0
|
|
NE2
|
E:HIS122
|
4.1
|
23.6
|
1.0
|
|
ND1
|
E:HIS120
|
4.1
|
21.7
|
1.0
|
|
CD2
|
E:HIS122
|
4.1
|
28.1
|
1.0
|
|
ND1
|
E:HIS189
|
4.2
|
25.8
|
1.0
|
|
CG
|
E:HIS120
|
4.2
|
24.4
|
1.0
|
|
CB
|
E:CYS208
|
4.3
|
22.2
|
1.0
|
|
OD1
|
E:ASP124
|
4.3
|
26.9
|
1.0
|
|
C6
|
E:HIW303
|
4.3
|
36.5
|
0.9
|
|
N4
|
E:HIW303
|
4.4
|
37.1
|
0.9
|
|
CG2
|
E:THR190
|
4.4
|
26.7
|
1.0
|
|
OD2
|
E:ASP124
|
4.8
|
36.6
|
1.0
|
|
CA
|
E:HIS122
|
4.9
|
23.9
|
1.0
|
|
CG
|
E:ASP124
|
5.0
|
28.8
|
1.0
|
|
O31
|
E:HIW303
|
5.0
|
33.7
|
0.9
|
|
Zinc binding site 10 out
of 16 in 5ypk
Go back to
Zinc Binding Sites List in 5ypk
Zinc binding site 10 out
of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI2 Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn302
b:37.4
occ:1.00
|
NE2
|
E:HIS250
|
2.2
|
34.4
|
1.0
|
|
OD2
|
E:ASP124
|
2.3
|
36.6
|
1.0
|
|
SG
|
E:CYS208
|
2.4
|
34.1
|
1.0
|
|
O71
|
E:HIW303
|
2.5
|
25.0
|
0.9
|
|
N4
|
E:HIW303
|
2.5
|
37.1
|
0.9
|
|
CE1
|
E:HIS250
|
2.9
|
32.4
|
1.0
|
|
O31
|
E:HIW303
|
3.2
|
33.7
|
0.9
|
|
C7
|
E:HIW303
|
3.3
|
33.8
|
0.9
|
|
CD2
|
E:HIS250
|
3.3
|
34.3
|
1.0
|
|
CG
|
E:ASP124
|
3.4
|
28.8
|
1.0
|
|
CB
|
E:CYS208
|
3.4
|
22.2
|
1.0
|
|
C5
|
E:HIW303
|
3.5
|
39.8
|
0.9
|
|
C3
|
E:HIW303
|
3.5
|
42.3
|
0.9
|
|
C31
|
E:HIW303
|
3.8
|
38.9
|
0.9
|
|
OD1
|
E:ASP124
|
3.8
|
26.9
|
1.0
|
|
ZN
|
E:ZN301
|
3.9
|
24.4
|
1.0
|
|
C6
|
E:HIW303
|
3.9
|
36.5
|
0.9
|
|
ND1
|
E:HIS250
|
4.1
|
36.1
|
1.0
|
|
O72
|
E:HIW303
|
4.2
|
35.7
|
0.9
|
|
C61
|
E:HIW303
|
4.3
|
37.8
|
0.9
|
|
CB
|
E:SER249
|
4.3
|
26.5
|
1.0
|
|
CG
|
E:HIS250
|
4.4
|
33.4
|
1.0
|
|
NE2
|
E:HIS189
|
4.4
|
30.1
|
1.0
|
|
CA
|
E:CYS208
|
4.6
|
23.8
|
1.0
|
|
CB
|
E:ASP124
|
4.6
|
24.7
|
1.0
|
|
C2
|
E:HIW303
|
4.6
|
41.9
|
0.9
|
|
OG
|
E:SER249
|
4.6
|
27.6
|
1.0
|
|
CE1
|
E:HIS189
|
4.6
|
29.7
|
1.0
|
|
C1
|
E:HIW303
|
4.7
|
41.0
|
0.9
|
|
CE1
|
E:HIS120
|
4.7
|
26.5
|
1.0
|
|
NE2
|
E:HIS120
|
4.8
|
22.7
|
1.0
|
|
Reference:
H.Feng,
X.Liu,
S.Wang,
J.Fleming,
D.C.Wang,
W.Liu.
The Mechanism of Ndm-1-Catalyzed Carbapenem Hydrolysis Is Distinct From That of Penicillin or Cephalosporin Hydrolysis. Nat Commun V. 8 2242 2017.
ISSN: ESSN 2041-1723
PubMed: 29269938
DOI: 10.1038/S41467-017-02339-W
Page generated: Mon Oct 28 16:14:32 2024
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