Zinc in PDB 4pcn: Phosphotriesterase Variant R22
Protein crystallography data
The structure of Phosphotriesterase Variant R22, PDB code: 4pcn
was solved by
C.J.Jackson,
E.Campbell,
M.Kaltenbach,
N.Tokuriki,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.44 /
1.54
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.900,
86.266,
88.684,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17 /
20.5
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Phosphotriesterase Variant R22
(pdb code 4pcn). 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 R22, PDB code: 4pcn:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 4pcn
Go back to
Zinc Binding Sites List in 4pcn
Zinc binding site 1 out
of 4 in the Phosphotriesterase Variant R22
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Phosphotriesterase Variant R22 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:11.4
occ:1.00
|
O
|
A:HOH655
|
2.0
|
17.7
|
1.0
|
NE2
|
A:HIS57
|
2.0
|
11.3
|
1.0
|
NE2
|
A:HIS55
|
2.1
|
12.8
|
1.0
|
OQ1
|
A:KCX169
|
2.1
|
11.9
|
1.0
|
OD1
|
A:ASP301
|
2.3
|
11.1
|
1.0
|
CE1
|
A:HIS57
|
3.0
|
10.6
|
1.0
|
CX
|
A:KCX169
|
3.0
|
15.0
|
1.0
|
CD2
|
A:HIS55
|
3.0
|
12.1
|
1.0
|
CD2
|
A:HIS57
|
3.1
|
10.7
|
1.0
|
CE1
|
A:HIS55
|
3.1
|
13.7
|
1.0
|
CG
|
A:ASP301
|
3.2
|
14.3
|
1.0
|
ZN
|
A:ZN403
|
3.3
|
14.9
|
1.0
|
OQ2
|
A:KCX169
|
3.4
|
11.9
|
1.0
|
OD2
|
A:ASP301
|
3.5
|
14.9
|
1.0
|
O
|
A:HOH630
|
3.5
|
7.8
|
1.0
|
CG2
|
A:VAL101
|
4.0
|
10.9
|
1.0
|
NZ
|
A:KCX169
|
4.0
|
16.7
|
1.0
|
ND1
|
A:HIS57
|
4.1
|
10.0
|
1.0
|
CE1
|
A:HIS230
|
4.2
|
16.5
|
1.0
|
CG
|
A:HIS57
|
4.2
|
9.2
|
1.0
|
CG
|
A:HIS55
|
4.2
|
10.6
|
1.0
|
ND1
|
A:HIS55
|
4.2
|
12.8
|
1.0
|
NE2
|
A:HIS230
|
4.2
|
15.4
|
1.0
|
CB
|
A:ASP301
|
4.5
|
10.6
|
1.0
|
O
|
A:HOH635
|
4.9
|
32.8
|
1.0
|
CA
|
A:ASP301
|
5.0
|
10.8
|
1.0
|
|
Zinc binding site 2 out
of 4 in 4pcn
Go back to
Zinc Binding Sites List in 4pcn
Zinc binding site 2 out
of 4 in the Phosphotriesterase Variant R22
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Phosphotriesterase Variant R22 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn403
b:14.9
occ:0.98
|
OQ2
|
A:KCX169
|
1.9
|
11.9
|
1.0
|
ND1
|
A:HIS201
|
2.0
|
12.6
|
1.0
|
NE2
|
A:HIS230
|
2.0
|
15.4
|
1.0
|
O
|
A:HOH655
|
2.1
|
17.7
|
1.0
|
CX
|
A:KCX169
|
2.8
|
15.0
|
1.0
|
CE1
|
A:HIS201
|
2.9
|
16.0
|
1.0
|
CE1
|
A:HIS230
|
3.0
|
16.5
|
1.0
|
CG
|
A:HIS201
|
3.0
|
14.1
|
1.0
|
CD2
|
A:HIS230
|
3.1
|
13.7
|
1.0
|
OQ1
|
A:KCX169
|
3.1
|
11.9
|
1.0
|
ZN
|
A:ZN402
|
3.3
|
11.4
|
1.0
|
CB
|
A:HIS201
|
3.5
|
9.9
|
1.0
|
O
|
A:HOH630
|
3.5
|
7.8
|
1.0
|
CE1
|
A:HIS55
|
3.7
|
13.7
|
1.0
|
NE2
|
A:HIS55
|
3.7
|
12.8
|
1.0
|
NE2
|
A:HIS201
|
4.0
|
17.3
|
1.0
|
NZ
|
A:KCX169
|
4.0
|
16.7
|
1.0
|
CD2
|
A:HIS201
|
4.1
|
15.8
|
1.0
|
ND1
|
A:HIS230
|
4.1
|
17.7
|
1.0
|
CG
|
A:HIS230
|
4.2
|
13.7
|
1.0
|
OD2
|
A:ASP301
|
4.2
|
14.9
|
1.0
|
CA
|
A:HIS201
|
4.3
|
12.8
|
1.0
|
NE1
|
A:TRP131
|
4.4
|
17.1
|
1.0
|
CE
|
A:KCX169
|
4.4
|
20.8
|
1.0
|
OD1
|
A:ASP301
|
4.7
|
11.1
|
1.0
|
CG
|
A:ASP301
|
4.8
|
14.3
|
1.0
|
CD1
|
A:TRP131
|
4.9
|
19.4
|
1.0
|
ND1
|
A:HIS55
|
4.9
|
12.8
|
1.0
|
|
Zinc binding site 3 out
of 4 in 4pcn
Go back to
Zinc Binding Sites List in 4pcn
Zinc binding site 3 out
of 4 in the Phosphotriesterase Variant R22
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Phosphotriesterase Variant R22 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn405
b:13.3
occ:0.86
|
OQ1
|
B:KCX169
|
1.9
|
15.3
|
1.0
|
O
|
B:HOH725
|
1.9
|
16.2
|
1.0
|
ND1
|
B:HIS201
|
2.0
|
11.9
|
1.0
|
NE2
|
B:HIS230
|
2.0
|
12.2
|
1.0
|
CX
|
B:KCX169
|
2.9
|
14.4
|
1.0
|
CE1
|
B:HIS201
|
2.9
|
15.8
|
1.0
|
O
|
B:HOH701
|
2.9
|
23.1
|
1.0
|
CD2
|
B:HIS230
|
2.9
|
16.2
|
1.0
|
CE1
|
B:HIS230
|
3.1
|
13.9
|
1.0
|
CG
|
B:HIS201
|
3.1
|
15.3
|
1.0
|
OQ2
|
B:KCX169
|
3.2
|
15.7
|
1.0
|
ZN
|
B:ZN406
|
3.2
|
12.8
|
0.9
|
CB
|
B:HIS201
|
3.5
|
15.4
|
1.0
|
CE1
|
B:HIS55
|
3.6
|
13.9
|
1.0
|
O2
|
B:MPD403
|
3.6
|
23.6
|
1.0
|
NE2
|
B:HIS55
|
3.7
|
11.8
|
1.0
|
NE2
|
B:HIS201
|
4.0
|
18.6
|
1.0
|
NZ
|
B:KCX169
|
4.1
|
22.5
|
1.0
|
OD2
|
B:ASP301
|
4.1
|
12.9
|
1.0
|
CG
|
B:HIS230
|
4.1
|
12.1
|
1.0
|
ND1
|
B:HIS230
|
4.1
|
12.3
|
1.0
|
CD2
|
B:HIS201
|
4.1
|
20.2
|
1.0
|
CA
|
B:HIS201
|
4.3
|
15.8
|
1.0
|
CE
|
B:KCX169
|
4.5
|
25.7
|
1.0
|
OD1
|
B:ASP301
|
4.6
|
12.2
|
1.0
|
CG
|
B:ASP301
|
4.6
|
12.3
|
1.0
|
NE1
|
B:TRP131
|
4.7
|
16.8
|
1.0
|
C2
|
B:MPD403
|
4.7
|
35.9
|
1.0
|
ND1
|
B:HIS55
|
4.8
|
13.5
|
1.0
|
CD1
|
B:TRP131
|
4.9
|
17.2
|
1.0
|
CD2
|
B:HIS55
|
4.9
|
10.5
|
1.0
|
CM
|
B:MPD403
|
5.0
|
28.1
|
1.0
|
|
Zinc binding site 4 out
of 4 in 4pcn
Go back to
Zinc Binding Sites List in 4pcn
Zinc binding site 4 out
of 4 in the Phosphotriesterase Variant R22
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Phosphotriesterase Variant R22 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn406
b:12.8
occ:0.95
|
O
|
B:HOH725
|
2.0
|
16.2
|
1.0
|
NE2
|
B:HIS57
|
2.0
|
11.9
|
1.0
|
NE2
|
B:HIS55
|
2.1
|
11.8
|
1.0
|
OQ2
|
B:KCX169
|
2.2
|
15.7
|
1.0
|
OD1
|
B:ASP301
|
2.2
|
12.2
|
1.0
|
CE1
|
B:HIS57
|
2.9
|
10.8
|
1.0
|
CX
|
B:KCX169
|
3.0
|
14.4
|
1.0
|
CD2
|
B:HIS55
|
3.0
|
10.5
|
1.0
|
CD2
|
B:HIS57
|
3.1
|
12.0
|
1.0
|
CG
|
B:ASP301
|
3.1
|
12.3
|
1.0
|
CE1
|
B:HIS55
|
3.2
|
13.9
|
1.0
|
ZN
|
B:ZN405
|
3.2
|
13.3
|
0.9
|
OQ1
|
B:KCX169
|
3.4
|
15.3
|
1.0
|
O
|
B:HOH701
|
3.4
|
23.1
|
1.0
|
OD2
|
B:ASP301
|
3.4
|
12.9
|
1.0
|
CM
|
B:MPD403
|
3.6
|
28.1
|
1.0
|
CG2
|
B:VAL101
|
4.1
|
13.8
|
1.0
|
O2
|
B:MPD403
|
4.1
|
23.6
|
1.0
|
ND1
|
B:HIS57
|
4.1
|
11.5
|
1.0
|
NZ
|
B:KCX169
|
4.1
|
22.5
|
1.0
|
NE2
|
B:HIS230
|
4.1
|
12.2
|
1.0
|
CE1
|
B:HIS230
|
4.2
|
13.9
|
1.0
|
CG
|
B:HIS57
|
4.2
|
13.2
|
1.0
|
CG
|
B:HIS55
|
4.2
|
9.9
|
1.0
|
ND1
|
B:HIS55
|
4.3
|
13.5
|
1.0
|
C2
|
B:MPD403
|
4.4
|
35.9
|
1.0
|
CB
|
B:ASP301
|
4.4
|
10.8
|
1.0
|
CA
|
B:ASP301
|
4.9
|
10.1
|
1.0
|
|
Reference:
C.J.Jackson,
E.Campbell,
M.Kaltenbach,
N.Tokuriki.
Phosphotriesterase Variant R22 To Be Published.
Page generated: Sun Oct 27 05:50:12 2024
|