Zinc in PDB 6bh7: Phosphotriesterase Variant R18+254S
Protein crystallography data
The structure of Phosphotriesterase Variant R18+254S, PDB code: 6bh7
was solved by
C.M.Miton,
E.C.Campbell,
C.J.Jackson,
N.Tokuriki,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.04 /
1.40
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.673,
86.012,
88.676,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.6 /
19.8
|
Other elements in 6bh7:
The structure of Phosphotriesterase Variant R18+254S also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Phosphotriesterase Variant R18+254S
(pdb code 6bh7). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Phosphotriesterase Variant R18+254S, PDB code: 6bh7:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6bh7
Go back to
Zinc Binding Sites List in 6bh7
Zinc binding site 1 out
of 4 in the Phosphotriesterase Variant R18+254S
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Phosphotriesterase Variant R18+254S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2401
b:15.0
occ:1.00
|
O
|
A:HOH2532
|
2.0
|
19.5
|
1.0
|
NE2
|
A:HIS57
|
2.0
|
13.5
|
0.8
|
NE2
|
A:HIS57
|
2.1
|
14.7
|
0.2
|
NE2
|
A:HIS55
|
2.1
|
14.3
|
1.0
|
OQ2
|
A:KCX169
|
2.1
|
15.1
|
1.0
|
OD1
|
A:ASP301
|
2.2
|
15.2
|
1.0
|
NE2
|
A:HIS55
|
2.3
|
15.1
|
0.0
|
H11
|
A:MPD2403
|
2.9
|
60.9
|
1.0
|
CE1
|
A:HIS57
|
2.9
|
14.2
|
0.8
|
CE1
|
A:HIS57
|
3.0
|
14.7
|
0.2
|
CX
|
A:KCX169
|
3.0
|
17.8
|
1.0
|
CG
|
A:ASP301
|
3.0
|
17.4
|
1.0
|
CD2
|
A:HIS55
|
3.0
|
14.0
|
1.0
|
CD2
|
A:HIS55
|
3.1
|
15.1
|
0.0
|
CD2
|
A:HIS57
|
3.1
|
13.2
|
0.8
|
HE1
|
A:HIS57
|
3.1
|
17.1
|
0.8
|
HD2
|
A:HIS55
|
3.1
|
18.1
|
0.0
|
CE1
|
A:HIS55
|
3.1
|
16.1
|
1.0
|
HE1
|
A:HIS57
|
3.1
|
17.7
|
0.2
|
CD2
|
A:HIS57
|
3.1
|
14.6
|
0.2
|
HD2
|
A:HIS55
|
3.2
|
16.8
|
1.0
|
HE1
|
A:HIS55
|
3.3
|
19.4
|
1.0
|
OD2
|
A:ASP301
|
3.3
|
19.4
|
1.0
|
H32
|
A:MPD2403
|
3.3
|
61.2
|
1.0
|
HD2
|
A:HIS57
|
3.3
|
15.9
|
0.8
|
HD2
|
A:HIS57
|
3.3
|
17.5
|
0.2
|
OQ1
|
A:KCX169
|
3.3
|
18.4
|
1.0
|
CE1
|
A:HIS55
|
3.4
|
15.1
|
0.0
|
HG23
|
A:VAL101
|
3.5
|
15.5
|
0.0
|
HG23
|
A:VAL101
|
3.6
|
15.7
|
1.0
|
HE1
|
A:HIS55
|
3.7
|
18.1
|
0.0
|
ZN
|
A:ZN2402
|
3.7
|
25.7
|
0.4
|
HG21
|
A:VAL101
|
3.8
|
15.5
|
0.0
|
H31
|
A:MPD2403
|
3.9
|
61.2
|
1.0
|
C1
|
A:MPD2403
|
3.9
|
50.8
|
1.0
|
HG21
|
A:VAL101
|
3.9
|
15.7
|
1.0
|
CG2
|
A:VAL101
|
4.0
|
12.9
|
0.0
|
CG2
|
A:VAL101
|
4.1
|
13.1
|
1.0
|
ND1
|
A:HIS57
|
4.1
|
13.7
|
0.8
|
C3
|
A:MPD2403
|
4.1
|
51.0
|
1.0
|
NZ
|
A:KCX169
|
4.1
|
17.6
|
1.0
|
H13
|
A:MPD2403
|
4.1
|
60.9
|
1.0
|
ND1
|
A:HIS57
|
4.1
|
14.4
|
0.2
|
HG22
|
A:VAL101
|
4.1
|
15.7
|
1.0
|
CG
|
A:HIS57
|
4.2
|
12.6
|
0.8
|
CG
|
A:HIS55
|
4.2
|
13.8
|
1.0
|
ND1
|
A:HIS55
|
4.2
|
15.2
|
1.0
|
HG22
|
A:VAL101
|
4.2
|
15.5
|
0.0
|
CG
|
A:HIS57
|
4.2
|
14.1
|
0.2
|
HZ
|
A:KCX169
|
4.3
|
21.2
|
1.0
|
CG
|
A:HIS55
|
4.3
|
15.0
|
0.0
|
H53
|
A:MPD2403
|
4.3
|
60.5
|
1.0
|
HA
|
A:ASP301
|
4.3
|
18.1
|
1.0
|
CB
|
A:ASP301
|
4.4
|
15.3
|
1.0
|
ND1
|
A:HIS55
|
4.4
|
15.1
|
0.0
|
H12
|
A:MPD2403
|
4.5
|
60.9
|
1.0
|
HB2
|
A:ASP301
|
4.7
|
18.4
|
1.0
|
C2
|
A:MPD2403
|
4.7
|
51.4
|
1.0
|
HD21
|
A:LEU106
|
4.8
|
18.2
|
0.8
|
HD1
|
A:HIS57
|
4.8
|
16.4
|
0.8
|
CA
|
A:ASP301
|
4.9
|
15.1
|
1.0
|
HE1
|
A:TRP131
|
4.9
|
22.9
|
0.0
|
HD1
|
A:HIS57
|
4.9
|
17.3
|
0.2
|
HD11
|
A:LEU106
|
4.9
|
13.6
|
0.2
|
HD1
|
A:HIS55
|
5.0
|
18.2
|
1.0
|
HE1
|
A:TRP131
|
5.0
|
22.9
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6bh7
Go back to
Zinc Binding Sites List in 6bh7
Zinc binding site 2 out
of 4 in the Phosphotriesterase Variant R18+254S
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Phosphotriesterase Variant R18+254S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2402
b:25.7
occ:0.40
|
OQ1
|
A:KCX169
|
1.9
|
18.4
|
1.0
|
ND1
|
A:HIS201
|
2.1
|
30.0
|
1.0
|
O
|
A:HOH2532
|
2.3
|
19.5
|
1.0
|
CG
|
A:HIS201
|
2.4
|
28.5
|
1.0
|
CE1
|
A:HIS201
|
2.7
|
30.6
|
1.0
|
HB3
|
A:HIS201
|
2.7
|
31.5
|
1.0
|
CX
|
A:KCX169
|
3.0
|
17.8
|
1.0
|
CB
|
A:HIS201
|
3.0
|
26.2
|
1.0
|
CD2
|
A:HIS201
|
3.1
|
30.0
|
1.0
|
HE1
|
A:HIS201
|
3.1
|
36.7
|
1.0
|
NE2
|
A:HIS201
|
3.2
|
30.3
|
1.0
|
O
|
A:HOH2628
|
3.3
|
43.4
|
1.0
|
HE1
|
A:HIS55
|
3.3
|
19.4
|
1.0
|
HB2
|
A:HIS201
|
3.4
|
31.5
|
1.0
|
OQ2
|
A:KCX169
|
3.5
|
15.1
|
1.0
|
HE1
|
A:HIS55
|
3.6
|
18.1
|
0.0
|
HE1
|
A:TRP131
|
3.6
|
22.9
|
0.0
|
HE1
|
A:TRP131
|
3.7
|
22.9
|
1.0
|
ZN
|
A:ZN2401
|
3.7
|
15.0
|
1.0
|
HD2
|
A:HIS201
|
3.8
|
36.0
|
1.0
|
HE2
|
A:HIS201
|
3.9
|
36.3
|
1.0
|
CE1
|
A:HIS55
|
4.0
|
16.1
|
1.0
|
HE2
|
A:KCX169
|
4.0
|
22.6
|
1.0
|
NE2
|
A:HIS55
|
4.1
|
15.1
|
0.0
|
CE1
|
A:HIS55
|
4.1
|
15.1
|
0.0
|
OD2
|
A:ASP301
|
4.1
|
19.4
|
1.0
|
H13
|
A:MPD2403
|
4.1
|
60.9
|
1.0
|
NZ
|
A:KCX169
|
4.2
|
17.6
|
1.0
|
NE2
|
A:HIS55
|
4.2
|
14.3
|
1.0
|
CA
|
A:HIS201
|
4.4
|
24.3
|
1.0
|
NE1
|
A:TRP131
|
4.4
|
19.1
|
0.0
|
NE1
|
A:TRP131
|
4.4
|
19.1
|
1.0
|
HD1
|
A:TRP131
|
4.4
|
21.4
|
1.0
|
H11
|
A:MPD2403
|
4.5
|
60.9
|
1.0
|
CE
|
A:KCX169
|
4.5
|
18.8
|
1.0
|
C
|
A:HIS201
|
4.6
|
29.1
|
1.0
|
HE3
|
A:KCX169
|
4.6
|
22.6
|
1.0
|
H32
|
A:MPD2403
|
4.6
|
61.2
|
1.0
|
HD1
|
A:TRP131
|
4.7
|
22.6
|
0.0
|
HM2
|
A:MPD2403
|
4.7
|
60.8
|
1.0
|
C1
|
A:MPD2403
|
4.8
|
50.8
|
1.0
|
CD1
|
A:TRP131
|
4.8
|
17.9
|
1.0
|
O
|
A:HIS201
|
4.8
|
29.8
|
1.0
|
HA
|
A:HIS201
|
4.9
|
29.1
|
1.0
|
HZ
|
A:KCX169
|
4.9
|
21.2
|
1.0
|
CG
|
A:ASP301
|
4.9
|
17.4
|
1.0
|
CD1
|
A:TRP131
|
5.0
|
18.8
|
0.0
|
OD1
|
A:ASP301
|
5.0
|
15.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6bh7
Go back to
Zinc Binding Sites List in 6bh7
Zinc binding site 3 out
of 4 in the Phosphotriesterase Variant R18+254S
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Phosphotriesterase Variant R18+254S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn2401
b:18.3
occ:1.00
|
O2
|
G:CAC2403
|
1.8
|
18.5
|
0.8
|
NE2
|
G:HIS57
|
2.0
|
18.1
|
1.0
|
NE2
|
G:HIS55
|
2.1
|
18.8
|
1.0
|
OQ2
|
G:KCX169
|
2.1
|
19.0
|
1.0
|
OD1
|
G:ASP301
|
2.3
|
20.4
|
1.0
|
CE1
|
G:HIS57
|
2.9
|
17.4
|
1.0
|
CD2
|
G:HIS55
|
3.0
|
19.2
|
1.0
|
CX
|
G:KCX169
|
3.0
|
18.7
|
1.0
|
HE1
|
G:HIS57
|
3.1
|
20.9
|
1.0
|
CE1
|
G:HIS55
|
3.1
|
19.7
|
1.0
|
CD2
|
G:HIS57
|
3.1
|
18.7
|
1.0
|
HD2
|
G:HIS55
|
3.1
|
23.0
|
1.0
|
CG
|
G:ASP301
|
3.1
|
21.5
|
1.0
|
AS
|
G:CAC2403
|
3.2
|
19.0
|
0.8
|
HE1
|
G:HIS55
|
3.3
|
23.7
|
1.0
|
HD2
|
G:HIS57
|
3.3
|
22.4
|
1.0
|
OD2
|
G:ASP301
|
3.4
|
22.1
|
1.0
|
HG23
|
G:VAL101
|
3.4
|
22.4
|
1.0
|
OQ1
|
G:KCX169
|
3.4
|
18.8
|
1.0
|
HE1
|
G:HIS230
|
3.5
|
25.2
|
1.0
|
C1
|
G:CAC2403
|
3.7
|
19.4
|
0.8
|
HG21
|
G:VAL101
|
3.9
|
22.4
|
1.0
|
ZN
|
G:ZN2402
|
3.9
|
18.4
|
0.8
|
CG2
|
G:VAL101
|
4.0
|
18.7
|
1.0
|
O1
|
G:CAC2403
|
4.0
|
16.7
|
0.8
|
HG22
|
G:VAL101
|
4.1
|
22.4
|
1.0
|
ND1
|
G:HIS57
|
4.1
|
17.7
|
1.0
|
NZ
|
G:KCX169
|
4.1
|
18.7
|
1.0
|
CG
|
G:HIS55
|
4.1
|
18.8
|
1.0
|
ND1
|
G:HIS55
|
4.2
|
19.6
|
1.0
|
CG
|
G:HIS57
|
4.2
|
18.6
|
1.0
|
CE1
|
G:HIS230
|
4.2
|
21.0
|
1.0
|
HZ
|
G:KCX169
|
4.3
|
22.5
|
1.0
|
NE2
|
G:HIS230
|
4.5
|
21.0
|
1.0
|
CB
|
G:ASP301
|
4.5
|
20.9
|
1.0
|
HA
|
G:ASP301
|
4.5
|
24.8
|
1.0
|
HD21
|
G:LEU106
|
4.6
|
24.3
|
0.8
|
HB2
|
G:ASP301
|
4.6
|
25.1
|
1.0
|
C2
|
G:CAC2403
|
4.8
|
19.6
|
0.8
|
HD1
|
G:HIS57
|
4.8
|
21.2
|
1.0
|
HD11
|
G:LEU106
|
4.9
|
14.8
|
0.2
|
HD1
|
G:HIS55
|
5.0
|
23.6
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6bh7
Go back to
Zinc Binding Sites List in 6bh7
Zinc binding site 4 out
of 4 in the Phosphotriesterase Variant R18+254S
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Phosphotriesterase Variant R18+254S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn2402
b:18.4
occ:0.83
|
OQ1
|
G:KCX169
|
1.9
|
18.8
|
1.0
|
O1
|
G:CAC2403
|
1.9
|
16.7
|
0.8
|
NE2
|
G:HIS230
|
2.0
|
21.0
|
1.0
|
ND1
|
G:HIS201
|
2.1
|
19.6
|
1.0
|
CD2
|
G:HIS230
|
2.9
|
21.4
|
1.0
|
CE1
|
G:HIS201
|
3.0
|
21.2
|
1.0
|
HB2
|
G:HIS201
|
3.0
|
24.9
|
1.0
|
CX
|
G:KCX169
|
3.0
|
18.7
|
1.0
|
HD2
|
G:HIS230
|
3.1
|
25.6
|
1.0
|
O2
|
G:CAC2403
|
3.1
|
18.5
|
0.8
|
CE1
|
G:HIS230
|
3.1
|
21.0
|
1.0
|
AS
|
G:CAC2403
|
3.1
|
19.0
|
0.8
|
HE1
|
G:HIS201
|
3.1
|
25.4
|
1.0
|
CG
|
G:HIS201
|
3.1
|
20.6
|
1.0
|
HE1
|
G:TRP131
|
3.1
|
23.5
|
1.0
|
HE1
|
G:HIS230
|
3.3
|
25.2
|
1.0
|
OQ2
|
G:KCX169
|
3.4
|
19.0
|
1.0
|
CB
|
G:HIS201
|
3.5
|
20.7
|
1.0
|
HE1
|
G:HIS55
|
3.6
|
23.7
|
1.0
|
NE1
|
G:TRP131
|
3.9
|
19.6
|
1.0
|
HA
|
G:HIS201
|
3.9
|
25.1
|
1.0
|
ZN
|
G:ZN2401
|
3.9
|
18.3
|
1.0
|
O
|
G:HOH2642
|
4.0
|
28.2
|
1.0
|
NE2
|
G:HIS201
|
4.1
|
23.1
|
1.0
|
CG
|
G:HIS230
|
4.1
|
21.0
|
1.0
|
ND1
|
G:HIS230
|
4.1
|
21.1
|
1.0
|
NZ
|
G:KCX169
|
4.2
|
18.7
|
1.0
|
CD2
|
G:HIS201
|
4.2
|
22.6
|
1.0
|
HD1
|
G:TRP131
|
4.2
|
23.2
|
1.0
|
CE1
|
G:HIS55
|
4.2
|
19.7
|
1.0
|
HE2
|
G:KCX169
|
4.2
|
22.5
|
1.0
|
C2
|
G:CAC2403
|
4.3
|
19.6
|
0.8
|
HB3
|
G:HIS201
|
4.3
|
24.9
|
1.0
|
CA
|
G:HIS201
|
4.3
|
21.0
|
1.0
|
NE2
|
G:HIS55
|
4.4
|
18.8
|
1.0
|
CD1
|
G:TRP131
|
4.5
|
19.3
|
1.0
|
HE3
|
G:KCX169
|
4.6
|
22.5
|
1.0
|
CE
|
G:KCX169
|
4.6
|
18.8
|
1.0
|
C1
|
G:CAC2403
|
4.6
|
19.4
|
0.8
|
OD2
|
G:ASP301
|
4.8
|
22.1
|
1.0
|
HE2
|
G:HIS201
|
4.9
|
27.7
|
1.0
|
HD1
|
G:HIS230
|
4.9
|
25.3
|
1.0
|
HZ
|
G:KCX169
|
5.0
|
22.5
|
1.0
|
|
Reference:
C.M.Miton,
E.C.Campbell,
C.J.Jackson,
N.Tokuriki.
Phosphotriesterase Variant R18+254S To Be Published.
Page generated: Mon Oct 28 17:57:06 2024
|