Zinc in PDB 2r2d: Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens
Protein crystallography data
The structure of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens, PDB code: 2r2d
was solved by
D.Liu,
P.W.Thomas,
J.Momb,
Q.Hoang,
G.A.Petsko,
D.Ringe,
W.Fast,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
18.10 /
1.75
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
79.146,
158.033,
80.439,
90.00,
104.48,
90.00
|
|
R / Rfree (%)
|
15.9 /
21.3
|
Zinc Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Zinc atom in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens
(pdb code 2r2d). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the
Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens, PDB code: 2r2d:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Zinc binding site 1 out
of 12 in 2r2d
Go back to
Zinc Binding Sites List in 2r2d
Zinc binding site 1 out
of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn277
b:24.1
occ:1.00
|
O3
|
A:PO4279
|
1.9
|
25.2
|
1.0
|
|
NE2
|
A:HIS259
|
2.0
|
22.7
|
1.0
|
|
NE2
|
A:HIS116
|
2.0
|
21.9
|
1.0
|
|
OD1
|
A:ASP213
|
2.3
|
25.0
|
1.0
|
|
OD2
|
A:ASP213
|
2.3
|
23.1
|
1.0
|
|
CG
|
A:ASP213
|
2.6
|
25.5
|
1.0
|
|
CE1
|
A:HIS259
|
3.0
|
19.9
|
1.0
|
|
CE1
|
A:HIS116
|
3.0
|
22.1
|
1.0
|
|
CD2
|
A:HIS116
|
3.0
|
20.2
|
1.0
|
|
CD2
|
A:HIS259
|
3.0
|
18.9
|
1.0
|
|
P
|
A:PO4279
|
3.1
|
24.5
|
1.0
|
|
O1
|
A:PO4279
|
3.3
|
24.0
|
1.0
|
|
OD2
|
A:ASP115
|
3.4
|
27.6
|
1.0
|
|
OD1
|
A:ASP115
|
3.8
|
35.6
|
1.0
|
|
O2
|
A:PO4279
|
3.8
|
28.3
|
1.0
|
|
CG
|
A:ASP115
|
4.0
|
26.2
|
1.0
|
|
O1
|
A:GOL280
|
4.0
|
41.0
|
1.0
|
|
CE1
|
A:TYR216
|
4.1
|
22.6
|
1.0
|
|
ND1
|
A:HIS259
|
4.1
|
21.6
|
1.0
|
|
ND1
|
A:HIS116
|
4.1
|
24.1
|
1.0
|
|
CB
|
A:ASP213
|
4.1
|
22.6
|
1.0
|
|
CG
|
A:HIS259
|
4.2
|
21.3
|
1.0
|
|
CG
|
A:HIS116
|
4.2
|
22.9
|
1.0
|
|
ZN
|
A:ZN278
|
4.3
|
23.2
|
1.0
|
|
O4
|
A:PO4279
|
4.3
|
22.8
|
1.0
|
|
CE1
|
A:HIS111
|
4.6
|
23.1
|
1.0
|
|
CD1
|
A:TYR216
|
4.7
|
21.9
|
1.0
|
|
C1
|
A:GOL280
|
4.8
|
43.4
|
1.0
|
|
NE2
|
A:HIS111
|
4.8
|
20.1
|
1.0
|
|
CA
|
A:ASP213
|
5.0
|
21.6
|
1.0
|
|
Zinc binding site 2 out
of 12 in 2r2d
Go back to
Zinc Binding Sites List in 2r2d
Zinc binding site 2 out
of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn278
b:23.2
occ:1.00
|
O1
|
A:PO4279
|
1.9
|
24.0
|
1.0
|
|
NE2
|
A:HIS111
|
2.0
|
20.1
|
1.0
|
|
NE2
|
A:HIS191
|
2.1
|
21.6
|
1.0
|
|
ND1
|
A:HIS113
|
2.2
|
22.3
|
1.0
|
|
OD1
|
A:ASP213
|
2.5
|
25.0
|
1.0
|
|
CD2
|
A:HIS111
|
2.9
|
22.0
|
1.0
|
|
CD2
|
A:HIS191
|
3.0
|
22.5
|
1.0
|
|
CE1
|
A:HIS111
|
3.1
|
23.1
|
1.0
|
|
CE1
|
A:HIS191
|
3.1
|
23.2
|
1.0
|
|
CG
|
A:HIS113
|
3.1
|
20.3
|
1.0
|
|
P
|
A:PO4279
|
3.1
|
24.5
|
1.0
|
|
CE1
|
A:HIS113
|
3.2
|
23.1
|
1.0
|
|
O2
|
A:PO4279
|
3.3
|
28.3
|
1.0
|
|
CB
|
A:HIS113
|
3.4
|
20.5
|
1.0
|
|
CG
|
A:ASP213
|
3.6
|
25.5
|
1.0
|
|
CB
|
A:ASP213
|
4.0
|
22.6
|
1.0
|
|
O3
|
A:PO4279
|
4.0
|
25.2
|
1.0
|
|
CG
|
A:HIS111
|
4.1
|
22.6
|
1.0
|
|
CG
|
A:HIS191
|
4.1
|
22.4
|
1.0
|
|
ND1
|
A:HIS111
|
4.2
|
22.7
|
1.0
|
|
ND1
|
A:HIS191
|
4.2
|
23.6
|
1.0
|
|
ZN
|
A:ZN277
|
4.3
|
24.1
|
1.0
|
|
NE2
|
A:HIS113
|
4.3
|
21.9
|
1.0
|
|
CD2
|
A:HIS113
|
4.3
|
20.8
|
1.0
|
|
O4
|
A:PO4279
|
4.3
|
22.8
|
1.0
|
|
CD2
|
A:HIS116
|
4.4
|
20.2
|
1.0
|
|
NE2
|
A:HIS116
|
4.6
|
21.9
|
1.0
|
|
OD2
|
A:ASP213
|
4.7
|
23.1
|
1.0
|
|
O
|
A:HOH326
|
4.8
|
26.9
|
1.0
|
|
CA
|
A:HIS113
|
4.9
|
20.9
|
1.0
|
|
Zinc binding site 3 out
of 12 in 2r2d
Go back to
Zinc Binding Sites List in 2r2d
Zinc binding site 3 out
of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn277
b:27.6
occ:1.00
|
O4
|
B:PO4279
|
1.8
|
26.7
|
1.0
|
|
NE2
|
B:HIS259
|
2.0
|
25.8
|
1.0
|
|
NE2
|
B:HIS116
|
2.0
|
22.5
|
1.0
|
|
OD1
|
B:ASP213
|
2.3
|
26.9
|
1.0
|
|
OD2
|
B:ASP213
|
2.4
|
25.9
|
1.0
|
|
CG
|
B:ASP213
|
2.7
|
26.7
|
1.0
|
|
CE1
|
B:HIS116
|
2.9
|
25.2
|
1.0
|
|
CD2
|
B:HIS259
|
3.0
|
25.3
|
1.0
|
|
CE1
|
B:HIS259
|
3.0
|
27.8
|
1.0
|
|
CD2
|
B:HIS116
|
3.1
|
23.0
|
1.0
|
|
P
|
B:PO4279
|
3.1
|
26.5
|
1.0
|
|
O3
|
B:PO4279
|
3.4
|
27.7
|
1.0
|
|
OD2
|
B:ASP115
|
3.5
|
33.5
|
1.0
|
|
OD1
|
B:ASP115
|
3.6
|
35.2
|
1.0
|
|
O2
|
B:PO4279
|
3.8
|
29.4
|
1.0
|
|
CG
|
B:ASP115
|
3.9
|
29.9
|
1.0
|
|
O1
|
B:GOL281
|
4.0
|
51.7
|
1.0
|
|
ND1
|
B:HIS116
|
4.1
|
26.5
|
1.0
|
|
ND1
|
B:HIS259
|
4.1
|
25.3
|
1.0
|
|
CG
|
B:HIS259
|
4.1
|
26.8
|
1.0
|
|
CE1
|
B:TYR216
|
4.1
|
25.8
|
1.0
|
|
CB
|
B:ASP213
|
4.1
|
25.4
|
1.0
|
|
CG
|
B:HIS116
|
4.2
|
24.7
|
1.0
|
|
ZN
|
B:ZN278
|
4.3
|
26.3
|
1.0
|
|
O1
|
B:PO4279
|
4.3
|
28.9
|
1.0
|
|
CE1
|
B:HIS111
|
4.7
|
21.5
|
1.0
|
|
CD1
|
B:TYR216
|
4.7
|
22.6
|
1.0
|
|
NE2
|
B:HIS111
|
4.9
|
21.7
|
1.0
|
|
CA
|
B:ASP213
|
4.9
|
25.2
|
1.0
|
|
Zinc binding site 4 out
of 12 in 2r2d
Go back to
Zinc Binding Sites List in 2r2d
Zinc binding site 4 out
of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn278
b:26.3
occ:1.00
|
O3
|
B:PO4279
|
1.9
|
27.7
|
1.0
|
|
NE2
|
B:HIS111
|
2.1
|
21.7
|
1.0
|
|
NE2
|
B:HIS191
|
2.1
|
21.6
|
1.0
|
|
ND1
|
B:HIS113
|
2.2
|
24.7
|
1.0
|
|
OD1
|
B:ASP213
|
2.6
|
26.9
|
1.0
|
|
CD2
|
B:HIS111
|
3.0
|
22.3
|
1.0
|
|
CD2
|
B:HIS191
|
3.0
|
22.1
|
1.0
|
|
P
|
B:PO4279
|
3.1
|
26.5
|
1.0
|
|
CE1
|
B:HIS111
|
3.1
|
21.5
|
1.0
|
|
CE1
|
B:HIS191
|
3.1
|
23.0
|
1.0
|
|
CG
|
B:HIS113
|
3.1
|
22.4
|
1.0
|
|
CE1
|
B:HIS113
|
3.3
|
24.6
|
1.0
|
|
O2
|
B:PO4279
|
3.3
|
29.4
|
1.0
|
|
CB
|
B:HIS113
|
3.4
|
23.9
|
1.0
|
|
CG
|
B:ASP213
|
3.6
|
26.7
|
1.0
|
|
O4
|
B:PO4279
|
3.9
|
26.7
|
1.0
|
|
CB
|
B:ASP213
|
4.0
|
25.4
|
1.0
|
|
CG
|
B:HIS111
|
4.2
|
23.1
|
1.0
|
|
O1
|
B:PO4279
|
4.2
|
28.9
|
1.0
|
|
CG
|
B:HIS191
|
4.2
|
22.6
|
1.0
|
|
ND1
|
B:HIS111
|
4.2
|
22.6
|
1.0
|
|
ND1
|
B:HIS191
|
4.2
|
23.1
|
1.0
|
|
CD2
|
B:HIS113
|
4.3
|
23.2
|
1.0
|
|
ZN
|
B:ZN277
|
4.3
|
27.6
|
1.0
|
|
CD2
|
B:HIS116
|
4.3
|
23.0
|
1.0
|
|
NE2
|
B:HIS113
|
4.3
|
24.1
|
1.0
|
|
NE2
|
B:HIS116
|
4.6
|
22.5
|
1.0
|
|
O
|
B:HOH350
|
4.7
|
31.3
|
1.0
|
|
OD2
|
B:ASP213
|
4.8
|
25.9
|
1.0
|
|
CA
|
B:HIS113
|
4.8
|
24.3
|
1.0
|
|
Zinc binding site 5 out
of 12 in 2r2d
Go back to
Zinc Binding Sites List in 2r2d
Zinc binding site 5 out
of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn277
b:24.7
occ:1.00
|
O1
|
C:PO4279
|
1.9
|
25.6
|
1.0
|
|
NE2
|
C:HIS116
|
2.0
|
22.5
|
1.0
|
|
NE2
|
C:HIS259
|
2.1
|
23.5
|
1.0
|
|
OD1
|
C:ASP213
|
2.3
|
25.5
|
1.0
|
|
OD2
|
C:ASP213
|
2.4
|
24.2
|
1.0
|
|
CG
|
C:ASP213
|
2.6
|
21.9
|
1.0
|
|
CE1
|
C:HIS116
|
2.9
|
22.5
|
1.0
|
|
CD2
|
C:HIS259
|
3.0
|
20.4
|
1.0
|
|
CE1
|
C:HIS259
|
3.1
|
23.7
|
1.0
|
|
CD2
|
C:HIS116
|
3.1
|
21.5
|
1.0
|
|
P
|
C:PO4279
|
3.1
|
23.4
|
1.0
|
|
O3
|
C:PO4279
|
3.3
|
21.6
|
1.0
|
|
OD2
|
C:ASP115
|
3.4
|
30.8
|
1.0
|
|
OD1
|
C:ASP115
|
3.6
|
35.5
|
1.0
|
|
O1
|
C:GOL281
|
3.8
|
40.2
|
1.0
|
|
O4
|
C:PO4279
|
3.8
|
25.6
|
1.0
|
|
CG
|
C:ASP115
|
3.9
|
26.5
|
1.0
|
|
CE1
|
C:TYR216
|
4.1
|
22.1
|
1.0
|
|
ND1
|
C:HIS116
|
4.1
|
24.3
|
1.0
|
|
CB
|
C:ASP213
|
4.1
|
22.7
|
1.0
|
|
ND1
|
C:HIS259
|
4.2
|
21.8
|
1.0
|
|
CG
|
C:HIS259
|
4.2
|
22.7
|
1.0
|
|
CG
|
C:HIS116
|
4.2
|
23.4
|
1.0
|
|
ZN
|
C:ZN278
|
4.2
|
23.5
|
1.0
|
|
O2
|
C:PO4279
|
4.3
|
23.9
|
1.0
|
|
CE1
|
C:HIS111
|
4.6
|
21.0
|
1.0
|
|
NE2
|
C:HIS111
|
4.7
|
22.0
|
1.0
|
|
CD1
|
C:TYR216
|
4.8
|
21.1
|
1.0
|
|
C1
|
C:GOL281
|
4.9
|
43.0
|
1.0
|
|
CA
|
C:ASP213
|
5.0
|
21.7
|
1.0
|
|
Zinc binding site 6 out
of 12 in 2r2d
Go back to
Zinc Binding Sites List in 2r2d
Zinc binding site 6 out
of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn278
b:23.5
occ:1.00
|
O3
|
C:PO4279
|
1.9
|
21.6
|
1.0
|
|
NE2
|
C:HIS191
|
2.1
|
20.5
|
1.0
|
|
NE2
|
C:HIS111
|
2.1
|
22.0
|
1.0
|
|
ND1
|
C:HIS113
|
2.2
|
22.2
|
1.0
|
|
OD1
|
C:ASP213
|
2.5
|
25.5
|
1.0
|
|
CD2
|
C:HIS111
|
3.0
|
22.4
|
1.0
|
|
CD2
|
C:HIS191
|
3.0
|
22.4
|
1.0
|
|
CE1
|
C:HIS191
|
3.0
|
22.6
|
1.0
|
|
P
|
C:PO4279
|
3.1
|
23.4
|
1.0
|
|
CG
|
C:HIS113
|
3.1
|
21.6
|
1.0
|
|
CE1
|
C:HIS113
|
3.2
|
22.6
|
1.0
|
|
CE1
|
C:HIS111
|
3.2
|
21.0
|
1.0
|
|
O4
|
C:PO4279
|
3.3
|
25.6
|
1.0
|
|
CB
|
C:HIS113
|
3.3
|
21.0
|
1.0
|
|
CG
|
C:ASP213
|
3.6
|
21.9
|
1.0
|
|
O1
|
C:PO4279
|
4.0
|
25.6
|
1.0
|
|
CB
|
C:ASP213
|
4.0
|
22.7
|
1.0
|
|
ND1
|
C:HIS191
|
4.1
|
21.3
|
1.0
|
|
CG
|
C:HIS111
|
4.2
|
22.5
|
1.0
|
|
CG
|
C:HIS191
|
4.2
|
21.5
|
1.0
|
|
O2
|
C:PO4279
|
4.2
|
23.9
|
1.0
|
|
ZN
|
C:ZN277
|
4.2
|
24.7
|
1.0
|
|
CD2
|
C:HIS113
|
4.3
|
24.0
|
1.0
|
|
NE2
|
C:HIS113
|
4.3
|
24.5
|
1.0
|
|
ND1
|
C:HIS111
|
4.3
|
22.2
|
1.0
|
|
CD2
|
C:HIS116
|
4.4
|
21.5
|
1.0
|
|
NE2
|
C:HIS116
|
4.6
|
22.5
|
1.0
|
|
OD2
|
C:ASP213
|
4.7
|
24.2
|
1.0
|
|
O
|
C:HOH319
|
4.7
|
29.3
|
1.0
|
|
CA
|
C:HIS113
|
4.8
|
22.0
|
1.0
|
|
Zinc binding site 7 out
of 12 in 2r2d
Go back to
Zinc Binding Sites List in 2r2d
Zinc binding site 7 out
of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn277
b:30.7
occ:1.00
|
O4
|
D:PO4279
|
1.9
|
31.9
|
1.0
|
|
NE2
|
D:HIS116
|
2.0
|
28.6
|
1.0
|
|
NE2
|
D:HIS259
|
2.1
|
31.8
|
1.0
|
|
OD2
|
D:ASP213
|
2.2
|
29.5
|
1.0
|
|
OD1
|
D:ASP213
|
2.2
|
31.1
|
1.0
|
|
CG
|
D:ASP213
|
2.6
|
30.2
|
1.0
|
|
CD2
|
D:HIS259
|
2.9
|
28.6
|
1.0
|
|
CE1
|
D:HIS116
|
3.0
|
28.9
|
1.0
|
|
CD2
|
D:HIS116
|
3.1
|
29.6
|
1.0
|
|
P
|
D:PO4279
|
3.1
|
29.6
|
1.0
|
|
CE1
|
D:HIS259
|
3.1
|
29.1
|
1.0
|
|
O2
|
D:PO4279
|
3.3
|
30.1
|
1.0
|
|
OD2
|
D:ASP115
|
3.4
|
34.4
|
1.0
|
|
OD1
|
D:ASP115
|
3.6
|
40.0
|
1.0
|
|
O1
|
D:PO4279
|
3.8
|
30.5
|
1.0
|
|
CG
|
D:ASP115
|
3.9
|
32.1
|
1.0
|
|
O1
|
D:GOL280
|
4.0
|
47.5
|
1.0
|
|
CE1
|
D:TYR216
|
4.1
|
29.5
|
1.0
|
|
CB
|
D:ASP213
|
4.1
|
30.8
|
1.0
|
|
ND1
|
D:HIS116
|
4.1
|
28.7
|
1.0
|
|
CG
|
D:HIS259
|
4.1
|
30.1
|
1.0
|
|
ND1
|
D:HIS259
|
4.2
|
28.2
|
1.0
|
|
CG
|
D:HIS116
|
4.2
|
29.1
|
1.0
|
|
O3
|
D:PO4279
|
4.3
|
29.4
|
1.0
|
|
ZN
|
D:ZN278
|
4.3
|
28.8
|
1.0
|
|
CE1
|
D:HIS111
|
4.7
|
24.5
|
1.0
|
|
C1
|
D:GOL280
|
4.8
|
48.7
|
1.0
|
|
CD1
|
D:TYR216
|
4.8
|
28.5
|
1.0
|
|
NE2
|
D:HIS111
|
4.9
|
24.2
|
1.0
|
|
CA
|
D:ASP213
|
4.9
|
29.7
|
1.0
|
|
Zinc binding site 8 out
of 12 in 2r2d
Go back to
Zinc Binding Sites List in 2r2d
Zinc binding site 8 out
of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn278
b:28.8
occ:1.00
|
O2
|
D:PO4279
|
1.9
|
30.1
|
1.0
|
|
NE2
|
D:HIS191
|
2.0
|
26.5
|
1.0
|
|
NE2
|
D:HIS111
|
2.1
|
24.2
|
1.0
|
|
ND1
|
D:HIS113
|
2.2
|
27.8
|
1.0
|
|
OD1
|
D:ASP213
|
2.6
|
31.1
|
1.0
|
|
CD2
|
D:HIS191
|
3.0
|
28.0
|
1.0
|
|
CD2
|
D:HIS111
|
3.0
|
24.8
|
1.0
|
|
CE1
|
D:HIS191
|
3.0
|
27.1
|
1.0
|
|
P
|
D:PO4279
|
3.1
|
29.6
|
1.0
|
|
CG
|
D:HIS113
|
3.1
|
25.8
|
1.0
|
|
O1
|
D:PO4279
|
3.2
|
30.5
|
1.0
|
|
CE1
|
D:HIS111
|
3.2
|
24.5
|
1.0
|
|
CE1
|
D:HIS113
|
3.2
|
28.4
|
1.0
|
|
CB
|
D:HIS113
|
3.4
|
25.9
|
1.0
|
|
CG
|
D:ASP213
|
3.6
|
30.2
|
1.0
|
|
O4
|
D:PO4279
|
4.0
|
31.9
|
1.0
|
|
CB
|
D:ASP213
|
4.0
|
30.8
|
1.0
|
|
ND1
|
D:HIS191
|
4.1
|
29.9
|
1.0
|
|
CG
|
D:HIS191
|
4.1
|
27.7
|
1.0
|
|
O3
|
D:PO4279
|
4.2
|
29.4
|
1.0
|
|
CG
|
D:HIS111
|
4.2
|
25.5
|
1.0
|
|
ND1
|
D:HIS111
|
4.3
|
24.9
|
1.0
|
|
CD2
|
D:HIS113
|
4.3
|
26.7
|
1.0
|
|
ZN
|
D:ZN277
|
4.3
|
30.7
|
1.0
|
|
NE2
|
D:HIS113
|
4.3
|
27.5
|
1.0
|
|
CD2
|
D:HIS116
|
4.4
|
29.6
|
1.0
|
|
NE2
|
D:HIS116
|
4.6
|
28.6
|
1.0
|
|
O
|
D:HOH335
|
4.7
|
36.7
|
1.0
|
|
OD2
|
D:ASP213
|
4.7
|
29.5
|
1.0
|
|
CA
|
D:HIS113
|
4.8
|
26.0
|
1.0
|
|
Zinc binding site 9 out
of 12 in 2r2d
Go back to
Zinc Binding Sites List in 2r2d
Zinc binding site 9 out
of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn277
b:32.8
occ:1.00
|
O1
|
E:PO4279
|
1.8
|
35.8
|
1.0
|
|
NE2
|
E:HIS116
|
2.1
|
27.0
|
1.0
|
|
NE2
|
E:HIS259
|
2.1
|
34.0
|
1.0
|
|
OD2
|
E:ASP213
|
2.3
|
31.4
|
1.0
|
|
OD1
|
E:ASP213
|
2.3
|
27.0
|
1.0
|
|
CG
|
E:ASP213
|
2.7
|
29.2
|
1.0
|
|
CD2
|
E:HIS259
|
3.0
|
32.0
|
1.0
|
|
CD2
|
E:HIS116
|
3.0
|
27.1
|
1.0
|
|
CE1
|
E:HIS116
|
3.1
|
28.4
|
1.0
|
|
CE1
|
E:HIS259
|
3.1
|
31.6
|
1.0
|
|
P
|
E:PO4279
|
3.2
|
33.9
|
1.0
|
|
OD2
|
E:ASP115
|
3.4
|
36.6
|
1.0
|
|
O3
|
E:PO4279
|
3.5
|
32.3
|
1.0
|
|
OD1
|
E:ASP115
|
3.7
|
42.1
|
1.0
|
|
O4
|
E:PO4279
|
3.9
|
36.3
|
1.0
|
|
CG
|
E:ASP115
|
3.9
|
35.7
|
1.0
|
|
O1
|
E:GOL281
|
4.0
|
49.7
|
1.0
|
|
CG
|
E:HIS259
|
4.1
|
34.2
|
1.0
|
|
CB
|
E:ASP213
|
4.2
|
26.2
|
1.0
|
|
ND1
|
E:HIS116
|
4.2
|
28.0
|
1.0
|
|
CE1
|
E:TYR216
|
4.2
|
28.1
|
1.0
|
|
CG
|
E:HIS116
|
4.2
|
27.7
|
1.0
|
|
ND1
|
E:HIS259
|
4.2
|
33.1
|
1.0
|
|
ZN
|
E:ZN278
|
4.3
|
29.3
|
1.0
|
|
O2
|
E:PO4279
|
4.3
|
35.8
|
1.0
|
|
CE1
|
E:HIS111
|
4.6
|
25.8
|
1.0
|
|
CD1
|
E:TYR216
|
4.8
|
28.0
|
1.0
|
|
NE2
|
E:HIS111
|
4.8
|
24.4
|
1.0
|
|
C1
|
E:GOL281
|
4.8
|
52.6
|
1.0
|
|
CA
|
E:ASP213
|
5.0
|
27.5
|
1.0
|
|
Zinc binding site 10 out
of 12 in 2r2d
Go back to
Zinc Binding Sites List in 2r2d
Zinc binding site 10 out
of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn278
b:29.3
occ:1.00
|
O3
|
E:PO4279
|
1.9
|
32.3
|
1.0
|
|
NE2
|
E:HIS191
|
2.1
|
28.8
|
1.0
|
|
NE2
|
E:HIS111
|
2.1
|
24.4
|
1.0
|
|
ND1
|
E:HIS113
|
2.1
|
27.1
|
1.0
|
|
OD1
|
E:ASP213
|
2.5
|
27.0
|
1.0
|
|
CD2
|
E:HIS111
|
2.9
|
24.3
|
1.0
|
|
CD2
|
E:HIS191
|
2.9
|
26.8
|
1.0
|
|
CE1
|
E:HIS113
|
3.0
|
30.9
|
1.0
|
|
P
|
E:PO4279
|
3.1
|
33.9
|
1.0
|
|
CG
|
E:HIS113
|
3.1
|
26.6
|
1.0
|
|
CE1
|
E:HIS191
|
3.1
|
27.4
|
1.0
|
|
CE1
|
E:HIS111
|
3.1
|
25.8
|
1.0
|
|
O4
|
E:PO4279
|
3.3
|
36.3
|
1.0
|
|
CB
|
E:HIS113
|
3.4
|
28.2
|
1.0
|
|
CG
|
E:ASP213
|
3.6
|
29.2
|
1.0
|
|
O1
|
E:PO4279
|
3.8
|
35.8
|
1.0
|
|
CB
|
E:ASP213
|
4.0
|
26.2
|
1.0
|
|
CG
|
E:HIS191
|
4.1
|
26.4
|
1.0
|
|
CG
|
E:HIS111
|
4.1
|
25.8
|
1.0
|
|
NE2
|
E:HIS113
|
4.1
|
29.0
|
1.0
|
|
ND1
|
E:HIS191
|
4.2
|
28.8
|
1.0
|
|
ND1
|
E:HIS111
|
4.2
|
26.8
|
1.0
|
|
CD2
|
E:HIS113
|
4.2
|
28.4
|
1.0
|
|
O2
|
E:PO4279
|
4.2
|
35.8
|
1.0
|
|
ZN
|
E:ZN277
|
4.3
|
32.8
|
1.0
|
|
CD2
|
E:HIS116
|
4.4
|
27.1
|
1.0
|
|
NE2
|
E:HIS116
|
4.7
|
27.0
|
1.0
|
|
OD2
|
E:ASP213
|
4.7
|
31.4
|
1.0
|
|
O
|
E:HOH347
|
4.8
|
36.9
|
1.0
|
|
CA
|
E:HIS113
|
4.9
|
27.5
|
1.0
|
|
Reference:
D.Liu,
P.W.Thomas,
J.Momb,
Q.Q.Hoang,
G.A.Petsko,
D.Ringe,
W.Fast.
Structure and Specificity of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens. Biochemistry V. 46 11789 2007.
ISSN: ISSN 0006-2960
PubMed: 17900178
DOI: 10.1021/BI7012849
Page generated: Wed Dec 16 03:51:28 2020
|
