Zinc in PDB 6dr8: Metallo-Beta-Lactamase From Cronobacter Sakazakii (Enterobacter Sakazakii) Harldq Motif Mutant S60/R118H/Q121H/K254H
Protein crystallography data
The structure of Metallo-Beta-Lactamase From Cronobacter Sakazakii (Enterobacter Sakazakii) Harldq Motif Mutant S60/R118H/Q121H/K254H, PDB code: 6dr8
was solved by
M.Monteiro Pedroso,
D.Waite,
M.Natasa,
R.Mcgeary,
L.Guddat,
P.Hugenholtz,
G.Schenk,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
34.58 /
1.48
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
43.767,
69.151,
77.523,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
13.2 /
16.7
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Metallo-Beta-Lactamase From Cronobacter Sakazakii (Enterobacter Sakazakii) Harldq Motif Mutant S60/R118H/Q121H/K254H
(pdb code 6dr8). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the
Metallo-Beta-Lactamase From Cronobacter Sakazakii (Enterobacter Sakazakii) Harldq Motif Mutant S60/R118H/Q121H/K254H, PDB code: 6dr8:
Jump to Zinc binding site number:
1;
2;
Zinc binding site 1 out
of 2 in 6dr8
Go back to
Zinc Binding Sites List in 6dr8
Zinc binding site 1 out
of 2 in the Metallo-Beta-Lactamase From Cronobacter Sakazakii (Enterobacter Sakazakii) Harldq Motif Mutant S60/R118H/Q121H/K254H
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Metallo-Beta-Lactamase From Cronobacter Sakazakii (Enterobacter Sakazakii) Harldq Motif Mutant S60/R118H/Q121H/K254H within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn405
b:32.6
occ:0.45
|
O3
|
A:PO4402
|
1.9
|
15.3
|
0.6
|
O1
|
A:PO4402
|
2.0
|
26.8
|
0.4
|
NE2
|
A:HIS121
|
2.1
|
11.7
|
1.0
|
O1
|
A:PO4402
|
2.1
|
29.6
|
0.6
|
O3
|
A:PO4402
|
2.2
|
16.1
|
0.4
|
OD2
|
A:ASP120
|
2.2
|
19.7
|
0.8
|
P
|
A:PO4402
|
2.3
|
11.3
|
0.6
|
P
|
A:PO4402
|
2.4
|
34.0
|
0.4
|
NE2
|
A:HIS254
|
2.5
|
22.7
|
0.5
|
HD2
|
A:HIS254
|
2.6
|
26.8
|
0.5
|
CE1
|
A:HIS121
|
2.7
|
11.0
|
1.0
|
HE1
|
A:HIS121
|
2.8
|
13.2
|
1.0
|
CD2
|
A:HIS254
|
2.8
|
22.4
|
0.5
|
O2
|
A:PO4402
|
3.0
|
17.7
|
0.6
|
CG
|
A:ASP120
|
3.0
|
18.0
|
1.0
|
CD2
|
A:HIS121
|
3.1
|
11.5
|
1.0
|
O2
|
A:PO4402
|
3.1
|
17.0
|
0.4
|
OD1
|
A:ASP120
|
3.3
|
17.8
|
0.8
|
HH12
|
A:ARG257
|
3.4
|
21.5
|
1.0
|
HD2
|
A:HIS121
|
3.5
|
13.8
|
1.0
|
O4
|
A:PO4402
|
3.7
|
12.4
|
0.6
|
CE1
|
A:HIS254
|
3.7
|
23.4
|
0.5
|
O4
|
A:PO4402
|
3.8
|
28.5
|
0.4
|
ND1
|
A:HIS121
|
3.8
|
10.0
|
1.0
|
HE1
|
A:HIS116
|
3.8
|
8.2
|
1.0
|
CG
|
A:HIS121
|
4.0
|
8.9
|
1.0
|
HE1
|
A:HIS254
|
4.1
|
28.1
|
0.5
|
CG
|
A:HIS254
|
4.2
|
20.5
|
0.5
|
NH1
|
A:ARG257
|
4.2
|
17.9
|
1.0
|
O
|
A:HOH501
|
4.2
|
35.5
|
1.0
|
HB2
|
A:ASP120
|
4.2
|
18.2
|
1.0
|
CB
|
A:ASP120
|
4.3
|
15.2
|
1.0
|
HH22
|
A:ARG257
|
4.3
|
20.3
|
1.0
|
HD2
|
A:HIS254
|
4.4
|
23.6
|
0.5
|
HD22
|
A:LEU70
|
4.4
|
27.3
|
1.0
|
CE1
|
A:HIS116
|
4.4
|
6.9
|
1.0
|
HB2
|
A:HIS254
|
4.5
|
17.6
|
0.5
|
ZN
|
A:ZN406
|
4.5
|
9.0
|
1.0
|
HD1
|
A:HIS121
|
4.5
|
12.0
|
1.0
|
ND1
|
A:HIS254
|
4.5
|
23.4
|
0.5
|
HH11
|
A:ARG257
|
4.5
|
21.5
|
1.0
|
NE2
|
A:HIS116
|
4.6
|
7.3
|
1.0
|
O
|
A:HOH583
|
4.7
|
38.5
|
1.0
|
HB2
|
A:SER214
|
4.8
|
13.1
|
1.0
|
HD21
|
A:ASN253
|
4.9
|
12.2
|
1.0
|
HB3
|
A:ASP120
|
4.9
|
18.2
|
1.0
|
NH2
|
A:ARG257
|
4.9
|
16.9
|
1.0
|
ND2
|
A:ASN253
|
5.0
|
10.2
|
1.0
|
O
|
A:ASN253
|
5.0
|
11.2
|
1.0
|
OD1
|
A:ASN253
|
5.0
|
10.8
|
1.0
|
CZ
|
A:ARG257
|
5.0
|
17.4
|
1.0
|
HB2
|
A:HIS118
|
5.0
|
8.6
|
1.0
|
|
Zinc binding site 2 out
of 2 in 6dr8
Go back to
Zinc Binding Sites List in 6dr8
Zinc binding site 2 out
of 2 in the Metallo-Beta-Lactamase From Cronobacter Sakazakii (Enterobacter Sakazakii) Harldq Motif Mutant S60/R118H/Q121H/K254H
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Metallo-Beta-Lactamase From Cronobacter Sakazakii (Enterobacter Sakazakii) Harldq Motif Mutant S60/R118H/Q121H/K254H within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn406
b:9.0
occ:1.00
|
O2
|
A:PO4402
|
1.9
|
17.7
|
0.6
|
O2
|
A:PO4402
|
2.0
|
17.0
|
0.4
|
ND1
|
A:HIS118
|
2.0
|
7.8
|
1.0
|
NE2
|
A:HIS116
|
2.0
|
7.3
|
1.0
|
NE2
|
A:HIS192
|
2.0
|
7.1
|
1.0
|
CE1
|
A:HIS118
|
2.9
|
8.6
|
1.0
|
CE1
|
A:HIS116
|
2.9
|
6.9
|
1.0
|
CE1
|
A:HIS192
|
3.0
|
7.6
|
1.0
|
CD2
|
A:HIS116
|
3.0
|
6.9
|
1.0
|
HE1
|
A:HIS118
|
3.0
|
10.3
|
1.0
|
CD2
|
A:HIS192
|
3.0
|
7.2
|
1.0
|
CG
|
A:HIS118
|
3.1
|
6.9
|
1.0
|
HB2
|
A:HIS118
|
3.1
|
8.6
|
1.0
|
HE1
|
A:HIS116
|
3.1
|
8.2
|
1.0
|
P
|
A:PO4402
|
3.1
|
11.3
|
0.6
|
P
|
A:PO4402
|
3.2
|
34.0
|
0.4
|
HE1
|
A:HIS192
|
3.2
|
9.1
|
1.0
|
HD2
|
A:HIS192
|
3.2
|
8.6
|
1.0
|
HD2
|
A:HIS116
|
3.2
|
8.3
|
1.0
|
O3
|
A:PO4402
|
3.4
|
16.1
|
0.4
|
CB
|
A:HIS118
|
3.5
|
7.1
|
1.0
|
O3
|
A:PO4402
|
3.6
|
15.3
|
0.6
|
O4
|
A:PO4402
|
3.7
|
12.4
|
0.6
|
HB3
|
A:HIS118
|
3.7
|
8.6
|
1.0
|
O
|
A:HOH583
|
3.8
|
38.5
|
1.0
|
O4
|
A:PO4402
|
3.8
|
28.5
|
0.4
|
HD2
|
A:HIS121
|
3.9
|
13.8
|
1.0
|
ND1
|
A:HIS116
|
4.0
|
7.7
|
1.0
|
NE2
|
A:HIS118
|
4.0
|
9.7
|
1.0
|
CG
|
A:HIS116
|
4.1
|
7.8
|
1.0
|
ND1
|
A:HIS192
|
4.1
|
7.3
|
1.0
|
CD2
|
A:HIS118
|
4.1
|
8.6
|
1.0
|
CG
|
A:HIS192
|
4.2
|
6.8
|
1.0
|
O1
|
A:PO4402
|
4.3
|
29.6
|
0.6
|
O1
|
A:PO4402
|
4.3
|
26.8
|
0.4
|
ZN
|
A:ZN405
|
4.5
|
32.6
|
0.5
|
HG
|
A:SER214
|
4.5
|
15.7
|
1.0
|
CD2
|
A:HIS121
|
4.6
|
11.5
|
1.0
|
HB3
|
A:SER214
|
4.6
|
13.1
|
1.0
|
OD1
|
A:ASP120
|
4.6
|
17.8
|
0.8
|
HG
|
A:LEU193
|
4.6
|
11.4
|
1.0
|
NE2
|
A:HIS121
|
4.7
|
11.7
|
1.0
|
HD1
|
A:HIS116
|
4.7
|
9.3
|
1.0
|
HE2
|
A:HIS118
|
4.8
|
11.6
|
1.0
|
HB2
|
A:SER214
|
4.8
|
13.1
|
1.0
|
HD1
|
A:HIS192
|
4.9
|
8.7
|
1.0
|
CA
|
A:HIS118
|
4.9
|
6.9
|
1.0
|
HD11
|
A:LEU193
|
5.0
|
10.3
|
1.0
|
|
Reference:
M.Monteiro Pedroso,
D.Waite,
M.Natasa,
R.Mcgeary,
L.Guddat,
P.Hugenholtz,
G.Schenk.
Evolution and Diversity of B3-Type Metallo-Beta-Lactamases, Emerging Contributors to the Spread of Antibiotic Resistance. To Be Published.
Page generated: Mon Oct 28 19:44:37 2024
|