Zinc in PDB 4p62: Directed Evolution of A B3 Metallo-Beta-Lactamase Aim-1
Protein crystallography data
The structure of Directed Evolution of A B3 Metallo-Beta-Lactamase Aim-1, PDB code: 4p62
was solved by
C.-F.D.Hou,
C.Collyer,
D.L.Ollis,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
66.21 /
1.89
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.453,
76.453,
240.270,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
17.5 /
20
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Directed Evolution of A B3 Metallo-Beta-Lactamase Aim-1
(pdb code 4p62). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the
Directed Evolution of A B3 Metallo-Beta-Lactamase Aim-1, PDB code: 4p62:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 4p62
Go back to
Zinc Binding Sites List in 4p62
Zinc binding site 1 out
of 3 in the Directed Evolution of A B3 Metallo-Beta-Lactamase Aim-1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Directed Evolution of A B3 Metallo-Beta-Lactamase Aim-1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:11.4
occ:1.00
|
O
|
A:HOH581
|
1.9
|
13.7
|
1.0
|
NE2
|
A:HIS104
|
2.0
|
10.2
|
1.0
|
ND1
|
A:HIS106
|
2.1
|
11.7
|
1.0
|
NE2
|
A:HIS182
|
2.1
|
9.6
|
1.0
|
CD2
|
A:HIS182
|
2.9
|
9.8
|
1.0
|
CE1
|
A:HIS106
|
2.9
|
11.3
|
1.0
|
O
|
A:HOH605
|
2.9
|
20.6
|
1.0
|
CE1
|
A:HIS104
|
3.0
|
9.9
|
1.0
|
CD2
|
A:HIS104
|
3.0
|
9.8
|
1.0
|
CG
|
A:HIS106
|
3.1
|
11.2
|
1.0
|
O
|
A:HOH464
|
3.2
|
20.9
|
1.0
|
CE1
|
A:HIS182
|
3.2
|
9.3
|
1.0
|
ZN
|
A:ZN302
|
3.5
|
12.5
|
1.0
|
CB
|
A:HIS106
|
3.5
|
10.5
|
1.0
|
ND1
|
A:HIS104
|
4.0
|
10.1
|
1.0
|
NE2
|
A:HIS106
|
4.1
|
12.4
|
1.0
|
CG
|
A:HIS104
|
4.1
|
9.8
|
1.0
|
CG
|
A:HIS182
|
4.2
|
9.8
|
1.0
|
CD2
|
A:HIS109
|
4.2
|
9.8
|
1.0
|
CD2
|
A:HIS106
|
4.2
|
11.4
|
1.0
|
OD1
|
A:ASP108
|
4.2
|
11.7
|
1.0
|
ND1
|
A:HIS182
|
4.3
|
9.8
|
1.0
|
NE2
|
A:HIS109
|
4.3
|
9.7
|
1.0
|
NE2
|
A:GLN145
|
4.3
|
14.5
|
1.0
|
O
|
A:HOH512
|
4.5
|
21.2
|
1.0
|
OG
|
A:SER207
|
4.7
|
10.0
|
1.0
|
O
|
A:HOH462
|
4.8
|
9.9
|
1.0
|
OD2
|
A:ASP108
|
4.8
|
11.1
|
1.0
|
CB
|
A:SER207
|
4.9
|
10.9
|
1.0
|
CG2
|
A:THR183
|
4.9
|
11.2
|
1.0
|
CG
|
A:ASP108
|
5.0
|
11.7
|
1.0
|
CA
|
A:HIS106
|
5.0
|
10.4
|
1.0
|
|
Zinc binding site 2 out
of 3 in 4p62
Go back to
Zinc Binding Sites List in 4p62
Zinc binding site 2 out
of 3 in the Directed Evolution of A B3 Metallo-Beta-Lactamase Aim-1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Directed Evolution of A B3 Metallo-Beta-Lactamase Aim-1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:12.5
occ:1.00
|
O
|
A:HOH581
|
1.9
|
13.7
|
1.0
|
NE2
|
A:HIS250
|
2.0
|
11.9
|
1.0
|
OD2
|
A:ASP108
|
2.0
|
11.1
|
1.0
|
NE2
|
A:HIS109
|
2.1
|
9.7
|
1.0
|
O
|
A:HOH605
|
2.5
|
20.6
|
1.0
|
CG
|
A:ASP108
|
2.9
|
11.7
|
1.0
|
CD2
|
A:HIS250
|
2.9
|
11.7
|
1.0
|
CE1
|
A:HIS250
|
3.0
|
12.3
|
1.0
|
CE1
|
A:HIS109
|
3.0
|
9.8
|
1.0
|
CD2
|
A:HIS109
|
3.0
|
9.8
|
1.0
|
OD1
|
A:ASP108
|
3.2
|
11.7
|
1.0
|
ZN
|
A:ZN301
|
3.5
|
11.4
|
1.0
|
O
|
A:HOH464
|
3.8
|
20.9
|
1.0
|
ND1
|
A:HIS250
|
4.1
|
12.3
|
1.0
|
CG
|
A:HIS250
|
4.1
|
12.2
|
1.0
|
ND1
|
A:HIS109
|
4.1
|
9.8
|
1.0
|
CG
|
A:HIS109
|
4.1
|
9.8
|
1.0
|
NE2
|
A:HIS104
|
4.1
|
10.2
|
1.0
|
CE1
|
A:HIS104
|
4.2
|
9.9
|
1.0
|
CB
|
A:ASP108
|
4.3
|
11.3
|
1.0
|
O
|
A:HOH462
|
4.3
|
9.9
|
1.0
|
OG
|
A:SER207
|
4.5
|
10.0
|
1.0
|
CD1
|
A:ILE58
|
4.6
|
13.4
|
1.0
|
O
|
A:HOH512
|
4.7
|
21.2
|
1.0
|
NE2
|
A:HIS182
|
4.9
|
9.6
|
1.0
|
|
Zinc binding site 3 out
of 3 in 4p62
Go back to
Zinc Binding Sites List in 4p62
Zinc binding site 3 out
of 3 in the Directed Evolution of A B3 Metallo-Beta-Lactamase Aim-1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Directed Evolution of A B3 Metallo-Beta-Lactamase Aim-1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn303
b:38.8
occ:1.00
|
OD1
|
A:ASP242
|
2.3
|
21.6
|
1.0
|
O
|
A:HOH408
|
2.4
|
26.5
|
1.0
|
OD1
|
A:ASP244
|
2.7
|
21.5
|
1.0
|
O
|
A:HOH402
|
2.9
|
35.1
|
1.0
|
CG
|
A:ASP242
|
3.3
|
20.7
|
1.0
|
OD2
|
A:ASP242
|
3.6
|
23.0
|
1.0
|
CG
|
A:ASP244
|
3.7
|
19.1
|
1.0
|
O1
|
A:EDO304
|
3.7
|
26.7
|
1.0
|
OD2
|
A:ASP244
|
4.0
|
19.1
|
1.0
|
O
|
A:HOH445
|
4.2
|
13.7
|
1.0
|
N
|
A:CYS243
|
4.4
|
16.6
|
1.0
|
CG2
|
A:THR271
|
4.5
|
14.4
|
1.0
|
CB
|
A:ASP242
|
4.6
|
18.2
|
1.0
|
O
|
A:HOH424
|
4.7
|
27.8
|
1.0
|
O
|
A:CYS243
|
4.8
|
21.2
|
1.0
|
C
|
A:CYS243
|
4.8
|
17.2
|
1.0
|
CA
|
A:ASP242
|
4.8
|
16.5
|
1.0
|
C
|
A:ASP242
|
4.9
|
16.4
|
1.0
|
N
|
A:ASP244
|
4.9
|
15.5
|
1.0
|
|
Reference:
C.-F.D.Hou,
C.Collyer,
D.L.Ollis.
Directed Evolution of A B3 Metallo-Beta-Lactamase Aim-1 To Be Published.
Page generated: Sun Oct 27 04:16:17 2024
|