Zinc in PDB 4fsb: Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A
Protein crystallography data
The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A, PDB code: 4fsb
was solved by
K.Herzog,
K.M.Hoffmann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.06 /
1.88
|
Space group
|
I 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.020,
80.130,
77.639,
90.00,
91.71,
90.00
|
R / Rfree (%)
|
14.7 /
19.5
|
Other elements in 4fsb:
The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A
(pdb code 4fsb). 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 the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A, PDB code: 4fsb:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 4fsb
Go back to
Zinc Binding Sites List in 4fsb
Zinc binding site 1 out
of 4 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A
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 Vim-31 in Its Oxidized Form at 1.88 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:13.2
occ:1.00
|
O
|
A:HOH450
|
1.9
|
11.2
|
1.0
|
ND1
|
A:HIS114
|
2.0
|
11.5
|
1.0
|
NE2
|
A:HIS112
|
2.1
|
11.2
|
1.0
|
NE2
|
A:HIS177
|
2.1
|
10.7
|
1.0
|
O
|
A:HOH413
|
2.4
|
15.0
|
1.0
|
CE1
|
A:HIS114
|
2.9
|
11.6
|
1.0
|
CG
|
A:HIS114
|
3.0
|
11.6
|
1.0
|
CE1
|
A:HIS112
|
3.0
|
11.2
|
1.0
|
CD2
|
A:HIS177
|
3.0
|
10.1
|
1.0
|
CD2
|
A:HIS112
|
3.1
|
11.0
|
1.0
|
CE1
|
A:HIS177
|
3.2
|
10.7
|
1.0
|
CB
|
A:HIS114
|
3.4
|
12.2
|
1.0
|
OD2
|
A:OCS196
|
3.7
|
13.3
|
1.0
|
O
|
A:HOH568
|
4.0
|
24.4
|
1.0
|
O
|
A:HOH516
|
4.0
|
28.7
|
1.0
|
NE2
|
A:HIS114
|
4.1
|
11.5
|
1.0
|
OD1
|
A:ASP116
|
4.1
|
18.1
|
1.0
|
CD2
|
A:HIS114
|
4.1
|
12.0
|
1.0
|
ND1
|
A:HIS112
|
4.1
|
11.1
|
1.0
|
CG
|
A:HIS112
|
4.2
|
11.3
|
1.0
|
CG
|
A:HIS177
|
4.3
|
10.2
|
1.0
|
ND1
|
A:HIS177
|
4.3
|
10.6
|
1.0
|
SG
|
A:OCS196
|
4.6
|
13.5
|
1.0
|
OD3
|
A:OCS196
|
4.6
|
13.3
|
1.0
|
CB
|
A:OCS196
|
4.7
|
12.1
|
1.0
|
CA
|
A:HIS114
|
4.8
|
13.4
|
1.0
|
ND2
|
A:ASN208
|
4.8
|
52.5
|
1.0
|
O
|
A:HOH403
|
4.9
|
14.4
|
1.0
|
CG
|
A:ASP116
|
4.9
|
17.5
|
1.0
|
OD2
|
A:ASP116
|
4.9
|
19.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 4fsb
Go back to
Zinc Binding Sites List in 4fsb
Zinc binding site 2 out
of 4 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A
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 Vim-31 in Its Oxidized Form at 1.88 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:14.9
occ:1.00
|
O
|
A:HOH642
|
2.0
|
10.8
|
1.0
|
O
|
A:HOH640
|
2.1
|
10.5
|
1.0
|
ND1
|
A:HIS249
|
2.2
|
11.2
|
1.0
|
O
|
A:HOH641
|
2.7
|
18.1
|
1.0
|
O
|
A:HOH643
|
2.9
|
15.3
|
1.0
|
CE1
|
A:HIS249
|
3.1
|
11.0
|
1.0
|
CG
|
A:HIS249
|
3.2
|
10.6
|
1.0
|
CB
|
A:HIS249
|
3.6
|
11.0
|
1.0
|
CA
|
A:HIS249
|
3.9
|
11.1
|
1.0
|
O
|
A:HOH644
|
4.2
|
29.8
|
1.0
|
NE2
|
A:HIS249
|
4.2
|
10.4
|
1.0
|
ND2
|
A:ASN252
|
4.3
|
13.3
|
1.0
|
CD2
|
A:HIS249
|
4.3
|
10.9
|
1.0
|
CD2
|
A:LEU201
|
4.6
|
14.9
|
1.0
|
O
|
A:HIS249
|
4.7
|
12.0
|
1.0
|
C
|
A:HIS249
|
4.8
|
10.9
|
1.0
|
N
|
A:HIS249
|
4.9
|
11.4
|
1.0
|
CB
|
A:ASN252
|
5.0
|
13.9
|
1.0
|
O
|
A:LEU201
|
5.0
|
17.6
|
1.0
|
|
Zinc binding site 3 out
of 4 in 4fsb
Go back to
Zinc Binding Sites List in 4fsb
Zinc binding site 3 out
of 4 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A
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 the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:16.3
occ:1.00
|
O
|
B:HOH620
|
2.0
|
12.2
|
1.0
|
O
|
B:HOH623
|
2.1
|
12.8
|
1.0
|
ND1
|
B:HIS249
|
2.1
|
11.6
|
1.0
|
O
|
B:HOH624
|
2.7
|
26.2
|
1.0
|
CE1
|
B:HIS249
|
3.0
|
11.8
|
1.0
|
O
|
B:HOH621
|
3.1
|
16.6
|
1.0
|
CG
|
B:HIS249
|
3.1
|
11.6
|
1.0
|
CB
|
B:HIS249
|
3.6
|
11.5
|
1.0
|
CA
|
B:HIS249
|
3.8
|
12.6
|
1.0
|
NE2
|
B:HIS249
|
4.2
|
11.3
|
1.0
|
O
|
B:HOH622
|
4.2
|
21.0
|
1.0
|
CD2
|
B:HIS249
|
4.3
|
11.0
|
1.0
|
ND2
|
B:ASN252
|
4.3
|
15.4
|
1.0
|
O
|
B:HIS249
|
4.6
|
13.8
|
1.0
|
CD2
|
B:LEU201
|
4.7
|
13.5
|
1.0
|
C
|
B:HIS249
|
4.7
|
12.7
|
1.0
|
N
|
B:HIS249
|
4.9
|
13.2
|
1.0
|
CB
|
B:ASN252
|
5.0
|
15.1
|
1.0
|
|
Zinc binding site 4 out
of 4 in 4fsb
Go back to
Zinc Binding Sites List in 4fsb
Zinc binding site 4 out
of 4 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A
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 the Metallo-Beta-Lactamase Vim-31 in Its Oxidized Form at 1.88 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:12.5
occ:1.00
|
ND1
|
B:HIS114
|
2.0
|
14.5
|
1.0
|
O
|
B:HOH448
|
2.0
|
11.0
|
1.0
|
NE2
|
B:HIS177
|
2.1
|
11.1
|
1.0
|
NE2
|
B:HIS112
|
2.2
|
13.1
|
1.0
|
O
|
B:HOH407
|
2.4
|
12.6
|
1.0
|
CE1
|
B:HIS114
|
3.0
|
15.1
|
1.0
|
CD2
|
B:HIS177
|
3.0
|
11.2
|
1.0
|
CG
|
B:HIS114
|
3.0
|
13.9
|
1.0
|
CE1
|
B:HIS112
|
3.1
|
13.4
|
1.0
|
CE1
|
B:HIS177
|
3.1
|
10.6
|
1.0
|
CD2
|
B:HIS112
|
3.2
|
13.4
|
1.0
|
CB
|
B:HIS114
|
3.4
|
13.2
|
1.0
|
OD2
|
B:OCS196
|
3.6
|
14.5
|
1.0
|
O
|
B:HOH475
|
4.0
|
32.7
|
1.0
|
NE2
|
B:HIS114
|
4.1
|
16.3
|
1.0
|
OD1
|
B:ASP116
|
4.1
|
16.2
|
1.0
|
CD2
|
B:HIS114
|
4.2
|
14.6
|
1.0
|
O
|
B:HOH480
|
4.2
|
24.4
|
1.0
|
CG
|
B:HIS177
|
4.2
|
10.7
|
1.0
|
ND1
|
B:HIS177
|
4.2
|
11.8
|
1.0
|
ND1
|
B:HIS112
|
4.2
|
12.5
|
1.0
|
CG
|
B:HIS112
|
4.3
|
12.9
|
1.0
|
SG
|
B:OCS196
|
4.6
|
14.5
|
1.0
|
CB
|
B:OCS196
|
4.6
|
13.3
|
1.0
|
OD3
|
B:OCS196
|
4.7
|
14.0
|
1.0
|
CA
|
B:HIS114
|
4.8
|
13.1
|
1.0
|
O
|
B:HOH425
|
4.9
|
15.4
|
1.0
|
CG
|
B:ASP116
|
5.0
|
15.6
|
1.0
|
OD2
|
B:ASP116
|
5.0
|
18.4
|
1.0
|
|
Reference:
M.B.Kupper,
K.Herzog,
S.Bennink,
P.Schlomer,
P.Bogaerts,
Y.Glupczynski,
R.Fischer,
C.Bebrone,
K.M.Hoffmann.
The Three-Dimensional Structure of Vim-31 - A Metallo-Beta-Lactamase From Enterobacter Cloacae in Its Native and Oxidized Form. Febs J. V. 282 2352 2015.
ISSN: ISSN 1742-464X
PubMed: 25825035
DOI: 10.1111/FEBS.13283
Page generated: Sat Oct 26 22:52:34 2024
|