Zinc in PDB 7aez: Crystal Structure of the Metallo-Beta-Lactamase Ndm-7 with 407
Protein crystallography data
The structure of Crystal Structure of the Metallo-Beta-Lactamase Ndm-7 with 407, PDB code: 7aez
was solved by
J.Brem,
C.J.Schofield,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
27.72 /
1.02
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
41.746,
58.736,
83.897,
90,
90,
90
|
R / Rfree (%)
|
10.4 /
11.3
|
Other elements in 7aez:
The structure of Crystal Structure of the Metallo-Beta-Lactamase Ndm-7 with 407 also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase Ndm-7 with 407
(pdb code 7aez). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the
Crystal Structure of the Metallo-Beta-Lactamase Ndm-7 with 407, PDB code: 7aez:
Jump to Zinc binding site number:
1;
2;
Zinc binding site 1 out
of 2 in 7aez
Go back to
Zinc Binding Sites List in 7aez
Zinc binding site 1 out
of 2 in the Crystal Structure of the Metallo-Beta-Lactamase Ndm-7 with 407
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 the Metallo-Beta-Lactamase Ndm-7 with 407 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:7.7
occ:0.95
|
O
|
A:HOH435
|
1.9
|
8.7
|
1.0
|
NE2
|
A:HIS189
|
2.0
|
8.0
|
1.0
|
NE2
|
A:HIS120
|
2.0
|
7.5
|
1.0
|
ND1
|
A:HIS122
|
2.0
|
8.2
|
1.0
|
HB2
|
A:HIS122
|
3.0
|
8.7
|
1.0
|
CD2
|
A:HIS189
|
3.0
|
7.4
|
1.0
|
CE1
|
A:HIS120
|
3.0
|
7.3
|
1.0
|
CE1
|
A:HIS122
|
3.0
|
8.5
|
1.0
|
CE1
|
A:HIS189
|
3.0
|
8.1
|
1.0
|
CD2
|
A:HIS120
|
3.0
|
7.0
|
1.0
|
CG
|
A:HIS122
|
3.1
|
7.6
|
1.0
|
HD2
|
A:HIS189
|
3.1
|
8.9
|
1.0
|
HE1
|
A:HIS120
|
3.2
|
8.8
|
1.0
|
HE1
|
A:HIS122
|
3.2
|
10.2
|
1.0
|
HE1
|
A:HIS189
|
3.2
|
9.7
|
1.0
|
HD2
|
A:HIS120
|
3.2
|
8.3
|
1.0
|
CB
|
A:HIS122
|
3.4
|
7.3
|
1.0
|
H101
|
A:R8W301
|
3.5
|
9.8
|
0.8
|
HB3
|
A:HIS122
|
3.5
|
8.7
|
1.0
|
ZN
|
A:ZN303
|
3.5
|
9.6
|
0.8
|
HG23
|
A:THR190
|
3.8
|
9.9
|
1.0
|
SG
|
A:CYS208
|
3.9
|
8.2
|
1.0
|
O27
|
A:R8W301
|
3.9
|
7.1
|
0.8
|
OD1
|
A:ASP124
|
3.9
|
8.7
|
1.0
|
H033
|
A:R8W301
|
4.0
|
13.9
|
0.8
|
H021
|
A:R8W301
|
4.0
|
12.5
|
0.8
|
HG21
|
A:THR190
|
4.0
|
9.9
|
1.0
|
HB3
|
A:CYS208
|
4.0
|
9.2
|
1.0
|
ND1
|
A:HIS120
|
4.1
|
7.3
|
1.0
|
NE2
|
A:HIS122
|
4.1
|
8.9
|
1.0
|
ND1
|
A:HIS189
|
4.1
|
8.1
|
1.0
|
CG
|
A:HIS189
|
4.1
|
7.4
|
1.0
|
CG
|
A:HIS120
|
4.2
|
6.7
|
1.0
|
CD2
|
A:HIS122
|
4.2
|
8.5
|
1.0
|
CB
|
A:CYS208
|
4.3
|
7.7
|
1.0
|
CG2
|
A:THR190
|
4.4
|
8.3
|
1.0
|
H031
|
A:R8W301
|
4.4
|
13.9
|
0.8
|
N10
|
A:R8W301
|
4.4
|
8.2
|
0.8
|
C03
|
A:R8W301
|
4.5
|
11.6
|
0.8
|
HG3
|
A:LYS125
|
4.5
|
9.5
|
1.0
|
OD2
|
A:ASP124
|
4.6
|
10.1
|
1.0
|
HG2
|
A:LYS125
|
4.6
|
9.5
|
1.0
|
CG
|
A:ASP124
|
4.7
|
8.3
|
1.0
|
HG22
|
A:THR190
|
4.7
|
9.9
|
1.0
|
C02
|
A:R8W301
|
4.8
|
10.4
|
0.8
|
C25
|
A:R8W301
|
4.8
|
7.5
|
0.8
|
CA
|
A:HIS122
|
4.9
|
7.0
|
1.0
|
HD1
|
A:HIS120
|
4.9
|
8.7
|
1.0
|
HE2
|
A:HIS122
|
4.9
|
10.7
|
1.0
|
HD1
|
A:HIS189
|
4.9
|
9.7
|
1.0
|
|
Zinc binding site 2 out
of 2 in 7aez
Go back to
Zinc Binding Sites List in 7aez
Zinc binding site 2 out
of 2 in the Crystal Structure of the Metallo-Beta-Lactamase Ndm-7 with 407
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 the Metallo-Beta-Lactamase Ndm-7 with 407 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn303
b:9.6
occ:0.75
|
O
|
A:HOH435
|
2.0
|
8.7
|
1.0
|
OD2
|
A:ASP124
|
2.1
|
10.1
|
1.0
|
NE2
|
A:HIS250
|
2.1
|
8.8
|
1.0
|
O27
|
A:R8W301
|
2.2
|
7.1
|
0.8
|
SG
|
A:CYS208
|
2.3
|
8.2
|
1.0
|
H101
|
A:R8W301
|
2.8
|
9.8
|
0.8
|
C25
|
A:R8W301
|
3.1
|
7.5
|
0.8
|
CG
|
A:ASP124
|
3.1
|
8.3
|
1.0
|
CE1
|
A:HIS250
|
3.1
|
8.6
|
1.0
|
CD2
|
A:HIS250
|
3.1
|
8.9
|
1.0
|
N10
|
A:R8W301
|
3.1
|
8.2
|
0.8
|
HB3
|
A:CYS208
|
3.2
|
9.2
|
1.0
|
CB
|
A:CYS208
|
3.3
|
7.7
|
1.0
|
HD2
|
A:HIS250
|
3.3
|
10.7
|
1.0
|
HE1
|
A:HIS250
|
3.3
|
10.4
|
1.0
|
C11
|
A:R8W301
|
3.3
|
7.3
|
0.8
|
OD1
|
A:ASP124
|
3.4
|
8.7
|
1.0
|
ZN
|
A:ZN302
|
3.5
|
7.7
|
0.9
|
HB3
|
A:SER249
|
3.9
|
10.1
|
1.0
|
H021
|
A:R8W301
|
4.0
|
12.5
|
0.8
|
HB2
|
A:SER249
|
4.0
|
10.1
|
1.0
|
HG
|
A:SER249
|
4.1
|
10.5
|
1.0
|
HE1
|
A:HIS120
|
4.1
|
8.8
|
1.0
|
HE3
|
A:LYS125
|
4.1
|
10.9
|
1.0
|
NE2
|
A:HIS189
|
4.2
|
8.0
|
1.0
|
O26
|
A:R8W301
|
4.2
|
8.4
|
0.8
|
ND1
|
A:HIS250
|
4.2
|
8.6
|
1.0
|
C09
|
A:R8W301
|
4.2
|
8.6
|
0.8
|
HE1
|
A:HIS189
|
4.2
|
9.7
|
1.0
|
CG
|
A:HIS250
|
4.2
|
8.8
|
1.0
|
CB
|
A:SER249
|
4.4
|
8.4
|
1.0
|
CE1
|
A:HIS189
|
4.4
|
8.1
|
1.0
|
CB
|
A:ASP124
|
4.4
|
7.7
|
1.0
|
C12
|
A:R8W301
|
4.5
|
8.4
|
0.8
|
HG2
|
A:LYS125
|
4.5
|
9.5
|
1.0
|
HB2
|
A:ASP124
|
4.5
|
9.2
|
1.0
|
HD2
|
A:LYS125
|
4.6
|
10.2
|
1.0
|
CA
|
A:CYS208
|
4.6
|
7.8
|
1.0
|
NE2
|
A:HIS120
|
4.6
|
7.5
|
1.0
|
HZ1
|
A:LYS211
|
4.6
|
12.1
|
1.0
|
HB3
|
A:ASP124
|
4.7
|
9.2
|
1.0
|
H141
|
A:R8W301
|
4.7
|
12.9
|
0.8
|
CE1
|
A:HIS120
|
4.7
|
7.3
|
1.0
|
OG
|
A:SER249
|
4.7
|
8.8
|
1.0
|
C02
|
A:R8W301
|
4.9
|
10.4
|
0.8
|
C08
|
A:R8W301
|
5.0
|
8.4
|
0.8
|
CE
|
A:LYS125
|
5.0
|
9.1
|
1.0
|
HD1
|
A:HIS250
|
5.0
|
10.3
|
1.0
|
C04
|
A:R8W301
|
5.0
|
9.3
|
0.8
|
|
Reference:
J.Brem,
C.J.Schofield.
Not Available Yet To Be Published.
Page generated: Tue Oct 29 16:46:27 2024
|