Zinc in PDB 6ren: Crystal Structure of 3FPIZZA6-Sh with ZN2+
Protein crystallography data
The structure of Crystal Structure of 3FPIZZA6-Sh with ZN2+, PDB code: 6ren
was solved by
H.Noguchi,
D.E.Clarke,
J.L.Gryspeerdt,
S.D.Feyter,
A.R.D.Voet,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
22.09 /
1.30
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.781,
66.683,
70.534,
90.00,
97.92,
90.00
|
R / Rfree (%)
|
13.4 /
16.7
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of 3FPIZZA6-Sh with ZN2+
(pdb code 6ren). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Crystal Structure of 3FPIZZA6-Sh with ZN2+, PDB code: 6ren:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 6ren
Go back to
Zinc Binding Sites List in 6ren
Zinc binding site 1 out
of 8 in the Crystal Structure of 3FPIZZA6-Sh with ZN2+
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of 3FPIZZA6-Sh with ZN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:11.5
occ:1.00
|
NE2
|
A:HIS226
|
2.0
|
10.0
|
1.0
|
NE2
|
A:HIS142
|
2.0
|
10.4
|
1.0
|
NE2
|
A:HIS58
|
2.0
|
13.0
|
1.0
|
O
|
A:HOH639
|
2.3
|
25.1
|
1.0
|
CE1
|
A:HIS226
|
3.0
|
10.6
|
1.0
|
CE1
|
A:HIS58
|
3.0
|
12.5
|
1.0
|
CE1
|
A:HIS142
|
3.0
|
9.5
|
1.0
|
CD2
|
A:HIS226
|
3.0
|
10.5
|
1.0
|
CD2
|
A:HIS142
|
3.0
|
11.0
|
1.0
|
CD2
|
A:HIS58
|
3.1
|
12.7
|
1.0
|
O
|
A:HOH586
|
3.8
|
28.1
|
1.0
|
ND1
|
A:HIS142
|
4.1
|
10.1
|
1.0
|
ND1
|
A:HIS226
|
4.1
|
10.1
|
1.0
|
ND1
|
A:HIS58
|
4.1
|
12.7
|
1.0
|
CG
|
A:HIS226
|
4.2
|
9.2
|
1.0
|
CG
|
A:HIS142
|
4.2
|
9.5
|
1.0
|
CG
|
A:HIS58
|
4.2
|
10.7
|
1.0
|
CB
|
A:SER184
|
4.5
|
10.4
|
1.0
|
O
|
A:HOH576
|
4.5
|
21.7
|
1.0
|
|
Zinc binding site 2 out
of 8 in 6ren
Go back to
Zinc Binding Sites List in 6ren
Zinc binding site 2 out
of 8 in the Crystal Structure of 3FPIZZA6-Sh with ZN2+
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of 3FPIZZA6-Sh with ZN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:12.2
occ:1.00
|
O2
|
A:IPA306
|
2.0
|
16.4
|
1.0
|
NE2
|
A:HIS199
|
2.0
|
11.0
|
1.0
|
NE2
|
A:HIS241
|
2.0
|
12.8
|
1.0
|
ND1
|
A:HIS226
|
2.0
|
10.1
|
1.0
|
C1
|
A:IPA306
|
2.8
|
14.8
|
1.0
|
C2
|
A:IPA306
|
2.9
|
19.9
|
1.0
|
CE1
|
A:HIS226
|
3.0
|
10.6
|
1.0
|
CD2
|
A:HIS199
|
3.0
|
11.0
|
1.0
|
CE1
|
A:HIS241
|
3.0
|
14.2
|
1.0
|
CE1
|
A:HIS199
|
3.0
|
12.0
|
1.0
|
CD2
|
A:HIS241
|
3.1
|
12.4
|
1.0
|
CG
|
A:HIS226
|
3.1
|
9.2
|
1.0
|
CB
|
A:HIS226
|
3.6
|
10.4
|
1.0
|
C3
|
A:IPA307
|
3.9
|
30.8
|
1.0
|
ND1
|
A:HIS241
|
4.1
|
13.4
|
1.0
|
NE2
|
A:HIS226
|
4.1
|
10.0
|
1.0
|
CG
|
A:HIS199
|
4.1
|
11.2
|
1.0
|
ND1
|
A:HIS199
|
4.1
|
12.5
|
1.0
|
CG
|
A:HIS241
|
4.2
|
12.9
|
1.0
|
CD2
|
A:HIS226
|
4.2
|
10.5
|
1.0
|
O2
|
A:IPA307
|
4.2
|
29.6
|
1.0
|
C3
|
A:IPA306
|
4.3
|
23.2
|
1.0
|
C1
|
A:IPA311
|
4.4
|
25.9
|
1.0
|
CA
|
A:HIS226
|
4.5
|
10.2
|
1.0
|
C2
|
A:IPA307
|
4.7
|
29.9
|
1.0
|
O
|
A:PRO225
|
4.7
|
12.7
|
1.0
|
O
|
A:HOH576
|
4.7
|
21.7
|
1.0
|
CG2
|
A:THR224
|
4.8
|
16.5
|
1.0
|
|
Zinc binding site 3 out
of 8 in 6ren
Go back to
Zinc Binding Sites List in 6ren
Zinc binding site 3 out
of 8 in the Crystal Structure of 3FPIZZA6-Sh with ZN2+
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of 3FPIZZA6-Sh with ZN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn303
b:11.1
occ:1.00
|
O2
|
A:IPA305
|
2.0
|
15.4
|
1.0
|
NE2
|
A:HIS157
|
2.0
|
11.2
|
1.0
|
NE2
|
A:HIS115
|
2.0
|
12.2
|
1.0
|
ND1
|
A:HIS142
|
2.1
|
10.1
|
1.0
|
C2
|
A:IPA305
|
2.8
|
17.6
|
1.0
|
C1
|
A:IPA305
|
2.9
|
11.9
|
1.0
|
CE1
|
A:HIS142
|
3.0
|
9.5
|
1.0
|
CD2
|
A:HIS115
|
3.0
|
11.8
|
1.0
|
CD2
|
A:HIS157
|
3.0
|
10.4
|
1.0
|
CE1
|
A:HIS157
|
3.0
|
11.6
|
1.0
|
CE1
|
A:HIS115
|
3.1
|
12.9
|
1.0
|
CG
|
A:HIS142
|
3.1
|
9.5
|
1.0
|
CB
|
A:HIS142
|
3.6
|
9.7
|
1.0
|
O2
|
A:IPA311
|
3.9
|
29.1
|
1.0
|
C2
|
A:IPA311
|
4.1
|
27.5
|
1.0
|
NE2
|
A:HIS142
|
4.1
|
10.4
|
1.0
|
ND1
|
A:HIS157
|
4.2
|
12.3
|
1.0
|
CG
|
A:HIS115
|
4.2
|
11.0
|
1.0
|
ND1
|
A:HIS115
|
4.2
|
12.6
|
1.0
|
CG
|
A:HIS157
|
4.2
|
11.1
|
1.0
|
CD2
|
A:HIS142
|
4.2
|
11.0
|
1.0
|
C3
|
A:IPA305
|
4.3
|
18.4
|
1.0
|
C1
|
A:IPA309
|
4.4
|
25.9
|
1.0
|
O
|
A:HOH576
|
4.5
|
21.7
|
1.0
|
C3
|
A:IPA311
|
4.5
|
27.9
|
1.0
|
CA
|
A:HIS142
|
4.6
|
9.7
|
1.0
|
O
|
A:THR140
|
4.6
|
11.8
|
1.0
|
C3
|
A:IPA309
|
4.8
|
30.4
|
1.0
|
C2
|
A:IPA309
|
4.8
|
30.4
|
1.0
|
|
Zinc binding site 4 out
of 8 in 6ren
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Zinc Binding Sites List in 6ren
Zinc binding site 4 out
of 8 in the Crystal Structure of 3FPIZZA6-Sh with ZN2+
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of 3FPIZZA6-Sh with ZN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn304
b:14.9
occ:1.00
|
O2
|
A:IPA310
|
2.0
|
23.1
|
1.0
|
NE2
|
A:HIS73
|
2.0
|
15.0
|
1.0
|
NE2
|
A:HIS31
|
2.1
|
15.3
|
1.0
|
ND1
|
A:HIS58
|
2.1
|
12.7
|
1.0
|
CE1
|
A:HIS58
|
3.0
|
12.5
|
1.0
|
C2
|
A:IPA310
|
3.0
|
27.8
|
1.0
|
CD2
|
A:HIS31
|
3.0
|
15.3
|
1.0
|
CD2
|
A:HIS73
|
3.0
|
15.2
|
1.0
|
CE1
|
A:HIS73
|
3.0
|
15.5
|
1.0
|
CE1
|
A:HIS31
|
3.1
|
14.7
|
1.0
|
CG
|
A:HIS58
|
3.1
|
10.7
|
1.0
|
C3
|
A:IPA310
|
3.3
|
27.3
|
1.0
|
CB
|
A:HIS58
|
3.5
|
10.9
|
1.0
|
O2
|
A:IPA309
|
4.0
|
34.0
|
1.0
|
C1
|
A:IPA309
|
4.1
|
25.9
|
1.0
|
NE2
|
A:HIS58
|
4.1
|
13.0
|
1.0
|
ND1
|
A:HIS73
|
4.1
|
15.1
|
1.0
|
CG
|
A:HIS73
|
4.2
|
13.8
|
1.0
|
CG
|
A:HIS31
|
4.2
|
14.7
|
1.0
|
ND1
|
A:HIS31
|
4.2
|
17.1
|
1.0
|
CD2
|
A:HIS58
|
4.2
|
12.7
|
1.0
|
O
|
A:THR56
|
4.3
|
16.4
|
1.0
|
C1
|
A:IPA310
|
4.3
|
30.2
|
1.0
|
O2
|
A:IPA307
|
4.4
|
29.6
|
1.0
|
C2
|
A:IPA309
|
4.5
|
30.4
|
1.0
|
CA
|
A:HIS58
|
4.6
|
10.6
|
1.0
|
CB
|
A:THR56
|
4.7
|
17.0
|
1.0
|
C1
|
A:IPA307
|
4.8
|
31.2
|
1.0
|
O
|
A:HOH576
|
4.9
|
21.7
|
1.0
|
O
|
A:PRO57
|
5.0
|
17.8
|
1.0
|
|
Zinc binding site 5 out
of 8 in 6ren
Go back to
Zinc Binding Sites List in 6ren
Zinc binding site 5 out
of 8 in the Crystal Structure of 3FPIZZA6-Sh with ZN2+
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of 3FPIZZA6-Sh with ZN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:15.1
occ:1.00
|
NE2
|
B:HIS226
|
2.0
|
13.2
|
1.0
|
NE2
|
B:HIS142
|
2.0
|
13.5
|
1.0
|
O
|
B:HOH591
|
2.1
|
24.1
|
1.0
|
NE2
|
B:HIS58
|
2.1
|
15.4
|
1.0
|
CE1
|
B:HIS142
|
3.0
|
14.4
|
1.0
|
CE1
|
B:HIS226
|
3.0
|
12.7
|
1.0
|
CD2
|
B:HIS226
|
3.0
|
12.6
|
1.0
|
CE1
|
B:HIS58
|
3.0
|
16.0
|
1.0
|
CD2
|
B:HIS58
|
3.1
|
14.2
|
1.0
|
CD2
|
B:HIS142
|
3.1
|
13.0
|
1.0
|
ND1
|
B:HIS226
|
4.1
|
12.9
|
1.0
|
ND1
|
B:HIS142
|
4.1
|
14.0
|
1.0
|
ND1
|
B:HIS58
|
4.2
|
14.9
|
1.0
|
CG
|
B:HIS226
|
4.2
|
13.0
|
1.0
|
CG
|
B:HIS58
|
4.2
|
13.7
|
1.0
|
CG
|
B:HIS142
|
4.2
|
12.7
|
1.0
|
O
|
B:HOH576
|
4.5
|
29.8
|
1.0
|
CB
|
B:SER184
|
4.7
|
13.4
|
1.0
|
|
Zinc binding site 6 out
of 8 in 6ren
Go back to
Zinc Binding Sites List in 6ren
Zinc binding site 6 out
of 8 in the Crystal Structure of 3FPIZZA6-Sh with ZN2+
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of 3FPIZZA6-Sh with ZN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:17.7
occ:1.00
|
O2
|
B:IPA307
|
2.0
|
23.4
|
1.0
|
NE2
|
B:HIS73
|
2.1
|
16.2
|
1.0
|
NE2
|
B:HIS31
|
2.1
|
16.3
|
1.0
|
ND1
|
B:HIS58
|
2.1
|
14.9
|
1.0
|
C2
|
B:IPA307
|
3.0
|
26.4
|
1.0
|
CE1
|
B:HIS58
|
3.0
|
16.0
|
1.0
|
CD2
|
B:HIS31
|
3.0
|
15.7
|
1.0
|
CE1
|
B:HIS73
|
3.0
|
20.7
|
1.0
|
C1
|
B:IPA307
|
3.1
|
25.7
|
1.0
|
CE1
|
B:HIS31
|
3.1
|
17.8
|
1.0
|
CD2
|
B:HIS73
|
3.1
|
19.4
|
1.0
|
CG
|
B:HIS58
|
3.1
|
13.7
|
1.0
|
CB
|
B:HIS58
|
3.5
|
14.1
|
1.0
|
NE2
|
B:HIS58
|
4.1
|
15.4
|
1.0
|
ND1
|
B:HIS73
|
4.1
|
23.3
|
1.0
|
CG
|
B:HIS31
|
4.2
|
16.4
|
1.0
|
ND1
|
B:HIS31
|
4.2
|
18.8
|
1.0
|
C3
|
B:IPA310
|
4.2
|
27.6
|
1.0
|
CG
|
B:HIS73
|
4.2
|
21.5
|
1.0
|
CD2
|
B:HIS58
|
4.2
|
14.2
|
1.0
|
C3
|
B:IPA307
|
4.3
|
27.0
|
1.0
|
C1
|
B:IPA310
|
4.3
|
25.0
|
1.0
|
O2
|
B:IPA308
|
4.4
|
32.3
|
1.0
|
C2
|
B:IPA310
|
4.4
|
29.2
|
1.0
|
C3
|
B:IPA308
|
4.5
|
28.4
|
1.0
|
CA
|
B:HIS58
|
4.6
|
13.6
|
1.0
|
O
|
B:THR56
|
4.7
|
26.0
|
1.0
|
O
|
B:HOH576
|
4.9
|
29.8
|
1.0
|
C2
|
B:IPA308
|
5.0
|
29.9
|
1.0
|
|
Zinc binding site 7 out
of 8 in 6ren
Go back to
Zinc Binding Sites List in 6ren
Zinc binding site 7 out
of 8 in the Crystal Structure of 3FPIZZA6-Sh with ZN2+
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Crystal Structure of 3FPIZZA6-Sh with ZN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn303
b:13.9
occ:1.00
|
O2
|
B:IPA305
|
1.9
|
18.5
|
1.0
|
ND1
|
B:HIS226
|
2.0
|
12.9
|
1.0
|
NE2
|
B:HIS241
|
2.0
|
15.2
|
1.0
|
NE2
|
B:HIS199
|
2.0
|
13.1
|
1.0
|
C2
|
B:IPA305
|
2.8
|
19.9
|
1.0
|
C3
|
B:IPA305
|
2.9
|
16.0
|
1.0
|
CE1
|
B:HIS226
|
2.9
|
12.7
|
1.0
|
CD2
|
B:HIS199
|
3.0
|
11.9
|
1.0
|
CE1
|
B:HIS241
|
3.0
|
17.5
|
1.0
|
CE1
|
B:HIS199
|
3.1
|
14.0
|
1.0
|
CD2
|
B:HIS241
|
3.1
|
15.6
|
1.0
|
CG
|
B:HIS226
|
3.1
|
13.0
|
1.0
|
O2
|
B:IPA309
|
3.4
|
34.2
|
1.0
|
CB
|
B:HIS226
|
3.6
|
12.5
|
1.0
|
NE2
|
B:HIS226
|
4.1
|
13.2
|
1.0
|
ND1
|
B:HIS241
|
4.1
|
19.8
|
1.0
|
CG
|
B:HIS199
|
4.1
|
12.4
|
1.0
|
C3
|
B:IPA308
|
4.2
|
28.4
|
1.0
|
ND1
|
B:HIS199
|
4.2
|
14.4
|
1.0
|
CG
|
B:HIS241
|
4.2
|
17.4
|
1.0
|
CD2
|
B:HIS226
|
4.2
|
12.6
|
1.0
|
C1
|
B:IPA305
|
4.2
|
23.1
|
1.0
|
C1
|
B:IPA308
|
4.3
|
29.1
|
1.0
|
CG2
|
B:THR224
|
4.5
|
23.9
|
1.0
|
CA
|
B:HIS226
|
4.5
|
11.4
|
1.0
|
C2
|
B:IPA309
|
4.6
|
30.8
|
1.0
|
O
|
B:HOH576
|
4.6
|
29.8
|
1.0
|
C3
|
B:IPA309
|
4.8
|
27.5
|
1.0
|
C2
|
B:IPA308
|
4.9
|
29.9
|
1.0
|
O
|
B:PRO225
|
4.9
|
18.9
|
1.0
|
|
Zinc binding site 8 out
of 8 in 6ren
Go back to
Zinc Binding Sites List in 6ren
Zinc binding site 8 out
of 8 in the Crystal Structure of 3FPIZZA6-Sh with ZN2+
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Crystal Structure of 3FPIZZA6-Sh with ZN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn304
b:15.6
occ:1.00
|
O2
|
B:IPA306
|
2.0
|
22.2
|
1.0
|
NE2
|
B:HIS157
|
2.0
|
14.9
|
1.0
|
NE2
|
B:HIS115
|
2.0
|
16.5
|
1.0
|
ND1
|
B:HIS142
|
2.1
|
14.0
|
1.0
|
C2
|
B:IPA306
|
3.0
|
25.9
|
1.0
|
CE1
|
B:HIS142
|
3.0
|
14.4
|
1.0
|
CD2
|
B:HIS115
|
3.0
|
15.4
|
1.0
|
CE1
|
B:HIS157
|
3.0
|
16.9
|
1.0
|
CD2
|
B:HIS157
|
3.0
|
15.1
|
1.0
|
CE1
|
B:HIS115
|
3.1
|
15.2
|
1.0
|
CG
|
B:HIS142
|
3.1
|
12.7
|
1.0
|
C1
|
B:IPA306
|
3.1
|
25.2
|
1.0
|
CB
|
B:HIS142
|
3.5
|
12.6
|
1.0
|
C1
|
B:IPA309
|
4.0
|
27.4
|
1.0
|
ND1
|
B:HIS157
|
4.1
|
17.0
|
1.0
|
NE2
|
B:HIS142
|
4.1
|
13.5
|
1.0
|
ND1
|
B:HIS115
|
4.1
|
17.0
|
1.0
|
CG
|
B:HIS115
|
4.2
|
15.7
|
1.0
|
CG
|
B:HIS157
|
4.2
|
16.1
|
1.0
|
CD2
|
B:HIS142
|
4.2
|
13.0
|
1.0
|
C3
|
B:IPA306
|
4.3
|
26.6
|
1.0
|
C2
|
B:IPA309
|
4.4
|
30.8
|
1.0
|
CG2
|
B:THR140
|
4.5
|
22.9
|
1.0
|
O2
|
B:IPA310
|
4.5
|
32.4
|
1.0
|
CA
|
B:HIS142
|
4.5
|
12.3
|
1.0
|
C1
|
B:IPA310
|
4.5
|
25.0
|
1.0
|
O
|
B:HOH576
|
4.9
|
29.8
|
1.0
|
O
|
B:THR140
|
4.9
|
17.7
|
1.0
|
C2
|
B:IPA310
|
5.0
|
29.2
|
1.0
|
|
Reference:
D.E.Clarke,
H.Noguchi,
J.A.G.Gryspeerdt,
S.De Feyter,
A.R.D.Voet.
Artificial Beta-Propeller Protein-Based Hydrolases. Chem.Commun.(Camb.) V. 55 8880 2019.
ISSN: ESSN 1364-548X
PubMed: 31321399
DOI: 10.1039/C9CC04388H
Page generated: Tue Oct 29 06:29:57 2024
|