Zinc in PDB 1nfg: Structure of D-Hydantoinase
Enzymatic activity of Structure of D-Hydantoinase
All present enzymatic activity of Structure of D-Hydantoinase:
3.5.2.2;
Protein crystallography data
The structure of Structure of D-Hydantoinase, PDB code: 1nfg
was solved by
Z.Xu,
Y.Yang,
W.Jiang,
E.Arnold,
J.Ding,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
14.94 /
2.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.700,
170.500,
87.300,
90.00,
95.20,
90.00
|
R / Rfree (%)
|
22 /
23.9
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of D-Hydantoinase
(pdb code 1nfg). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Structure of D-Hydantoinase, PDB code: 1nfg:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 1nfg
Go back to
Zinc Binding Sites List in 1nfg
Zinc binding site 1 out
of 8 in the Structure of D-Hydantoinase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of D-Hydantoinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:21.0
occ:1.00
|
OD1
|
A:ASP313
|
2.2
|
25.2
|
1.0
|
NE2
|
A:HIS59
|
2.3
|
31.3
|
1.0
|
NE2
|
A:HIS57
|
2.4
|
26.4
|
1.0
|
OQ2
|
A:KCX148
|
2.5
|
12.4
|
1.0
|
CG
|
A:ASP313
|
3.1
|
27.5
|
1.0
|
ZN
|
A:ZN502
|
3.2
|
22.7
|
1.0
|
CX
|
A:KCX148
|
3.2
|
17.9
|
1.0
|
OQ1
|
A:KCX148
|
3.2
|
13.7
|
1.0
|
CD2
|
A:HIS59
|
3.3
|
29.6
|
1.0
|
O
|
A:HOH579
|
3.3
|
24.0
|
1.0
|
CE1
|
A:HIS57
|
3.3
|
25.5
|
1.0
|
CE1
|
A:HIS59
|
3.3
|
29.5
|
1.0
|
O
|
A:HOH581
|
3.3
|
13.7
|
1.0
|
CD2
|
A:HIS57
|
3.4
|
25.5
|
1.0
|
OD2
|
A:ASP313
|
3.6
|
29.6
|
1.0
|
CB
|
A:ASP313
|
4.4
|
25.6
|
1.0
|
ND1
|
A:HIS59
|
4.4
|
28.8
|
1.0
|
CG
|
A:HIS59
|
4.4
|
29.6
|
1.0
|
ND1
|
A:HIS57
|
4.4
|
24.9
|
1.0
|
NZ
|
A:KCX148
|
4.5
|
14.6
|
1.0
|
CG
|
A:HIS57
|
4.5
|
24.4
|
1.0
|
CD2
|
A:HIS237
|
4.6
|
27.0
|
1.0
|
CA
|
A:ASP313
|
4.8
|
25.5
|
1.0
|
CE2
|
A:PHE91
|
4.8
|
21.4
|
1.0
|
NE2
|
A:HIS237
|
4.8
|
26.8
|
1.0
|
CD2
|
A:PHE91
|
4.9
|
23.3
|
1.0
|
O
|
A:HOH580
|
5.0
|
21.0
|
1.0
|
|
Zinc binding site 2 out
of 8 in 1nfg
Go back to
Zinc Binding Sites List in 1nfg
Zinc binding site 2 out
of 8 in the Structure of D-Hydantoinase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of D-Hydantoinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn502
b:22.7
occ:1.00
|
OQ1
|
A:KCX148
|
2.0
|
13.7
|
1.0
|
O
|
A:HOH579
|
2.2
|
24.0
|
1.0
|
ND1
|
A:HIS181
|
2.4
|
21.8
|
1.0
|
NE2
|
A:HIS237
|
2.6
|
26.8
|
1.0
|
CE1
|
A:HIS181
|
3.1
|
20.9
|
1.0
|
CX
|
A:KCX148
|
3.1
|
17.9
|
1.0
|
ZN
|
A:ZN501
|
3.2
|
21.0
|
1.0
|
CD2
|
A:HIS237
|
3.2
|
27.0
|
1.0
|
O
|
A:HOH581
|
3.4
|
13.7
|
1.0
|
CG
|
A:HIS181
|
3.6
|
20.3
|
1.0
|
OQ2
|
A:KCX148
|
3.7
|
12.4
|
1.0
|
CE1
|
A:HIS237
|
3.8
|
26.6
|
1.0
|
CE2
|
A:PHE150
|
4.0
|
22.6
|
1.0
|
CB
|
A:HIS181
|
4.1
|
21.4
|
1.0
|
O
|
A:THR286
|
4.2
|
21.6
|
1.0
|
NZ
|
A:KCX148
|
4.2
|
14.6
|
1.0
|
NE2
|
A:HIS181
|
4.3
|
20.5
|
1.0
|
OD2
|
A:ASP313
|
4.4
|
29.6
|
1.0
|
CG
|
A:HIS237
|
4.5
|
27.4
|
1.0
|
CD2
|
A:HIS181
|
4.6
|
21.9
|
1.0
|
OD1
|
A:ASP313
|
4.6
|
25.2
|
1.0
|
CG2
|
A:VAL236
|
4.7
|
19.1
|
1.0
|
NE2
|
A:HIS57
|
4.7
|
26.4
|
1.0
|
CZ
|
A:PHE150
|
4.7
|
21.9
|
1.0
|
ND1
|
A:HIS237
|
4.7
|
28.3
|
1.0
|
CE1
|
A:HIS57
|
4.8
|
25.5
|
1.0
|
CD2
|
A:PHE150
|
4.8
|
22.6
|
1.0
|
OH
|
A:TYR153
|
4.8
|
44.0
|
1.0
|
CG
|
A:ASP313
|
4.9
|
27.5
|
1.0
|
CA
|
A:HIS181
|
5.0
|
21.7
|
1.0
|
|
Zinc binding site 3 out
of 8 in 1nfg
Go back to
Zinc Binding Sites List in 1nfg
Zinc binding site 3 out
of 8 in the Structure of D-Hydantoinase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of D-Hydantoinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn601
b:21.0
occ:1.00
|
OD1
|
B:ASP313
|
2.2
|
24.9
|
1.0
|
NE2
|
B:HIS59
|
2.3
|
31.0
|
1.0
|
NE2
|
B:HIS57
|
2.4
|
26.1
|
1.0
|
OQ2
|
B:KCX148
|
2.5
|
12.2
|
1.0
|
CG
|
B:ASP313
|
3.1
|
27.2
|
1.0
|
ZN
|
B:ZN602
|
3.2
|
22.7
|
1.0
|
CX
|
B:KCX148
|
3.2
|
17.6
|
1.0
|
OQ1
|
B:KCX148
|
3.2
|
13.5
|
1.0
|
CD2
|
B:HIS59
|
3.3
|
29.3
|
1.0
|
O
|
B:HOH689
|
3.3
|
24.0
|
1.0
|
CE1
|
B:HIS57
|
3.3
|
25.2
|
1.0
|
CE1
|
B:HIS59
|
3.3
|
29.2
|
1.0
|
O
|
B:HOH691
|
3.3
|
13.7
|
1.0
|
CD2
|
B:HIS57
|
3.4
|
25.2
|
1.0
|
OD2
|
B:ASP313
|
3.6
|
29.4
|
1.0
|
CB
|
B:ASP313
|
4.4
|
25.4
|
1.0
|
ND1
|
B:HIS59
|
4.4
|
28.5
|
1.0
|
CG
|
B:HIS59
|
4.4
|
29.4
|
1.0
|
ND1
|
B:HIS57
|
4.4
|
24.6
|
1.0
|
NZ
|
B:KCX148
|
4.5
|
14.3
|
1.0
|
CG
|
B:HIS57
|
4.5
|
24.2
|
1.0
|
CD2
|
B:HIS237
|
4.6
|
26.8
|
1.0
|
CA
|
B:ASP313
|
4.8
|
25.2
|
1.0
|
CE2
|
B:PHE91
|
4.8
|
21.1
|
1.0
|
NE2
|
B:HIS237
|
4.8
|
26.5
|
1.0
|
CD2
|
B:PHE91
|
4.9
|
23.0
|
1.0
|
O
|
B:HOH690
|
5.0
|
21.0
|
1.0
|
|
Zinc binding site 4 out
of 8 in 1nfg
Go back to
Zinc Binding Sites List in 1nfg
Zinc binding site 4 out
of 8 in the Structure of D-Hydantoinase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of D-Hydantoinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn602
b:22.7
occ:1.00
|
OQ1
|
B:KCX148
|
2.0
|
13.5
|
1.0
|
O
|
B:HOH689
|
2.2
|
24.0
|
1.0
|
ND1
|
B:HIS181
|
2.4
|
21.5
|
1.0
|
NE2
|
B:HIS237
|
2.6
|
26.5
|
1.0
|
CE1
|
B:HIS181
|
3.1
|
20.7
|
1.0
|
CX
|
B:KCX148
|
3.1
|
17.6
|
1.0
|
ZN
|
B:ZN601
|
3.2
|
21.0
|
1.0
|
CD2
|
B:HIS237
|
3.2
|
26.8
|
1.0
|
O
|
B:HOH691
|
3.4
|
13.7
|
1.0
|
CG
|
B:HIS181
|
3.6
|
20.1
|
1.0
|
OQ2
|
B:KCX148
|
3.7
|
12.2
|
1.0
|
CE1
|
B:HIS237
|
3.8
|
26.4
|
1.0
|
CE2
|
B:PHE150
|
4.0
|
22.4
|
1.0
|
CB
|
B:HIS181
|
4.1
|
21.2
|
1.0
|
O
|
B:THR286
|
4.2
|
21.4
|
1.0
|
NZ
|
B:KCX148
|
4.2
|
14.3
|
1.0
|
NE2
|
B:HIS181
|
4.3
|
20.2
|
1.0
|
OD2
|
B:ASP313
|
4.4
|
29.4
|
1.0
|
CG
|
B:HIS237
|
4.5
|
27.1
|
1.0
|
CD2
|
B:HIS181
|
4.6
|
21.6
|
1.0
|
OD1
|
B:ASP313
|
4.6
|
24.9
|
1.0
|
CG2
|
B:VAL236
|
4.7
|
18.8
|
1.0
|
NE2
|
B:HIS57
|
4.7
|
26.1
|
1.0
|
CZ
|
B:PHE150
|
4.7
|
21.6
|
1.0
|
ND1
|
B:HIS237
|
4.7
|
28.0
|
1.0
|
CE1
|
B:HIS57
|
4.8
|
25.2
|
1.0
|
CD2
|
B:PHE150
|
4.8
|
22.4
|
1.0
|
OH
|
B:TYR153
|
4.8
|
43.8
|
1.0
|
CG
|
B:ASP313
|
4.9
|
27.2
|
1.0
|
CA
|
B:HIS181
|
5.0
|
21.4
|
1.0
|
|
Zinc binding site 5 out
of 8 in 1nfg
Go back to
Zinc Binding Sites List in 1nfg
Zinc binding site 5 out
of 8 in the Structure of D-Hydantoinase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Structure of D-Hydantoinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn701
b:21.0
occ:1.00
|
OD1
|
C:ASP313
|
2.2
|
24.9
|
1.0
|
NE2
|
C:HIS59
|
2.3
|
31.0
|
1.0
|
NE2
|
C:HIS57
|
2.4
|
26.1
|
1.0
|
OQ2
|
C:KCX148
|
2.5
|
12.2
|
1.0
|
CG
|
C:ASP313
|
3.1
|
27.2
|
1.0
|
ZN
|
C:ZN702
|
3.2
|
22.7
|
1.0
|
CX
|
C:KCX148
|
3.2
|
17.6
|
1.0
|
OQ1
|
C:KCX148
|
3.2
|
13.5
|
1.0
|
CD2
|
C:HIS59
|
3.3
|
29.3
|
1.0
|
O
|
C:HOH782
|
3.3
|
24.0
|
1.0
|
CE1
|
C:HIS57
|
3.3
|
25.2
|
1.0
|
CE1
|
C:HIS59
|
3.3
|
29.2
|
1.0
|
O
|
C:HOH784
|
3.3
|
13.7
|
1.0
|
CD2
|
C:HIS57
|
3.4
|
25.2
|
1.0
|
OD2
|
C:ASP313
|
3.6
|
29.4
|
1.0
|
CB
|
C:ASP313
|
4.4
|
25.4
|
1.0
|
ND1
|
C:HIS59
|
4.4
|
28.5
|
1.0
|
CG
|
C:HIS59
|
4.4
|
29.4
|
1.0
|
ND1
|
C:HIS57
|
4.4
|
24.6
|
1.0
|
NZ
|
C:KCX148
|
4.5
|
14.3
|
1.0
|
CG
|
C:HIS57
|
4.5
|
24.2
|
1.0
|
CD2
|
C:HIS237
|
4.6
|
26.8
|
1.0
|
CA
|
C:ASP313
|
4.8
|
25.2
|
1.0
|
CE2
|
C:PHE91
|
4.8
|
21.1
|
1.0
|
NE2
|
C:HIS237
|
4.8
|
26.5
|
1.0
|
CD2
|
C:PHE91
|
4.9
|
23.0
|
1.0
|
O
|
C:HOH783
|
5.0
|
21.0
|
1.0
|
|
Zinc binding site 6 out
of 8 in 1nfg
Go back to
Zinc Binding Sites List in 1nfg
Zinc binding site 6 out
of 8 in the Structure of D-Hydantoinase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Structure of D-Hydantoinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn702
b:22.7
occ:1.00
|
OQ1
|
C:KCX148
|
2.0
|
13.5
|
1.0
|
O
|
C:HOH782
|
2.2
|
24.0
|
1.0
|
ND1
|
C:HIS181
|
2.4
|
21.5
|
1.0
|
NE2
|
C:HIS237
|
2.6
|
26.5
|
1.0
|
CE1
|
C:HIS181
|
3.1
|
20.7
|
1.0
|
CX
|
C:KCX148
|
3.1
|
17.6
|
1.0
|
ZN
|
C:ZN701
|
3.2
|
21.0
|
1.0
|
CD2
|
C:HIS237
|
3.2
|
26.8
|
1.0
|
O
|
C:HOH784
|
3.4
|
13.7
|
1.0
|
CG
|
C:HIS181
|
3.6
|
20.1
|
1.0
|
OQ2
|
C:KCX148
|
3.7
|
12.2
|
1.0
|
CE1
|
C:HIS237
|
3.8
|
26.4
|
1.0
|
CE2
|
C:PHE150
|
4.0
|
22.4
|
1.0
|
CB
|
C:HIS181
|
4.1
|
21.2
|
1.0
|
O
|
C:THR286
|
4.2
|
21.4
|
1.0
|
NZ
|
C:KCX148
|
4.2
|
14.3
|
1.0
|
NE2
|
C:HIS181
|
4.3
|
20.2
|
1.0
|
OD2
|
C:ASP313
|
4.4
|
29.4
|
1.0
|
CG
|
C:HIS237
|
4.5
|
27.1
|
1.0
|
CD2
|
C:HIS181
|
4.6
|
21.6
|
1.0
|
OD1
|
C:ASP313
|
4.6
|
24.9
|
1.0
|
CG2
|
C:VAL236
|
4.7
|
18.8
|
1.0
|
NE2
|
C:HIS57
|
4.7
|
26.1
|
1.0
|
CZ
|
C:PHE150
|
4.7
|
21.6
|
1.0
|
ND1
|
C:HIS237
|
4.7
|
28.0
|
1.0
|
CE1
|
C:HIS57
|
4.8
|
25.2
|
1.0
|
CD2
|
C:PHE150
|
4.8
|
22.4
|
1.0
|
OH
|
C:TYR153
|
4.8
|
43.8
|
1.0
|
CG
|
C:ASP313
|
4.9
|
27.2
|
1.0
|
CA
|
C:HIS181
|
5.0
|
21.4
|
1.0
|
|
Zinc binding site 7 out
of 8 in 1nfg
Go back to
Zinc Binding Sites List in 1nfg
Zinc binding site 7 out
of 8 in the Structure of D-Hydantoinase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Structure of D-Hydantoinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn801
b:21.0
occ:1.00
|
OD1
|
D:ASP313
|
2.2
|
24.9
|
1.0
|
NE2
|
D:HIS59
|
2.3
|
31.0
|
1.0
|
NE2
|
D:HIS57
|
2.4
|
26.1
|
1.0
|
OQ2
|
D:KCX148
|
2.5
|
12.2
|
1.0
|
CG
|
D:ASP313
|
3.1
|
27.2
|
1.0
|
ZN
|
D:ZN802
|
3.2
|
22.7
|
1.0
|
CX
|
D:KCX148
|
3.2
|
17.6
|
1.0
|
OQ1
|
D:KCX148
|
3.2
|
13.5
|
1.0
|
CD2
|
D:HIS59
|
3.3
|
29.3
|
1.0
|
O
|
D:HOH3085
|
3.3
|
24.0
|
1.0
|
CE1
|
D:HIS57
|
3.3
|
25.2
|
1.0
|
CE1
|
D:HIS59
|
3.3
|
29.2
|
1.0
|
O
|
D:HOH3087
|
3.3
|
13.7
|
1.0
|
CD2
|
D:HIS57
|
3.4
|
25.2
|
1.0
|
OD2
|
D:ASP313
|
3.6
|
29.4
|
1.0
|
CB
|
D:ASP313
|
4.4
|
25.4
|
1.0
|
ND1
|
D:HIS59
|
4.4
|
28.5
|
1.0
|
CG
|
D:HIS59
|
4.4
|
29.4
|
1.0
|
ND1
|
D:HIS57
|
4.4
|
24.6
|
1.0
|
NZ
|
D:KCX148
|
4.5
|
14.3
|
1.0
|
CG
|
D:HIS57
|
4.5
|
24.2
|
1.0
|
CD2
|
D:HIS237
|
4.6
|
26.8
|
1.0
|
CA
|
D:ASP313
|
4.8
|
25.2
|
1.0
|
CE2
|
D:PHE91
|
4.8
|
21.1
|
1.0
|
NE2
|
D:HIS237
|
4.8
|
26.5
|
1.0
|
CD2
|
D:PHE91
|
4.9
|
23.0
|
1.0
|
O
|
D:HOH3086
|
5.0
|
21.0
|
1.0
|
|
Zinc binding site 8 out
of 8 in 1nfg
Go back to
Zinc Binding Sites List in 1nfg
Zinc binding site 8 out
of 8 in the Structure of D-Hydantoinase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Structure of D-Hydantoinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn802
b:22.7
occ:1.00
|
OQ1
|
D:KCX148
|
2.0
|
13.5
|
1.0
|
O
|
D:HOH3085
|
2.2
|
24.0
|
1.0
|
ND1
|
D:HIS181
|
2.4
|
21.5
|
1.0
|
NE2
|
D:HIS237
|
2.6
|
26.5
|
1.0
|
CE1
|
D:HIS181
|
3.1
|
20.7
|
1.0
|
CX
|
D:KCX148
|
3.1
|
17.6
|
1.0
|
ZN
|
D:ZN801
|
3.2
|
21.0
|
1.0
|
CD2
|
D:HIS237
|
3.2
|
26.8
|
1.0
|
O
|
D:HOH3087
|
3.4
|
13.7
|
1.0
|
CG
|
D:HIS181
|
3.6
|
20.1
|
1.0
|
OQ2
|
D:KCX148
|
3.7
|
12.2
|
1.0
|
CE1
|
D:HIS237
|
3.8
|
26.4
|
1.0
|
CE2
|
D:PHE150
|
4.0
|
22.4
|
1.0
|
CB
|
D:HIS181
|
4.1
|
21.2
|
1.0
|
O
|
D:THR286
|
4.2
|
21.4
|
1.0
|
NZ
|
D:KCX148
|
4.2
|
14.3
|
1.0
|
NE2
|
D:HIS181
|
4.3
|
20.2
|
1.0
|
OD2
|
D:ASP313
|
4.4
|
29.4
|
1.0
|
CG
|
D:HIS237
|
4.5
|
27.1
|
1.0
|
CD2
|
D:HIS181
|
4.6
|
21.6
|
1.0
|
OD1
|
D:ASP313
|
4.6
|
24.9
|
1.0
|
CG2
|
D:VAL236
|
4.7
|
18.8
|
1.0
|
NE2
|
D:HIS57
|
4.7
|
26.1
|
1.0
|
CZ
|
D:PHE150
|
4.7
|
21.6
|
1.0
|
ND1
|
D:HIS237
|
4.7
|
28.0
|
1.0
|
CE1
|
D:HIS57
|
4.8
|
25.2
|
1.0
|
CD2
|
D:PHE150
|
4.8
|
22.4
|
1.0
|
OH
|
D:TYR153
|
4.8
|
43.8
|
1.0
|
CG
|
D:ASP313
|
4.9
|
27.2
|
1.0
|
CA
|
D:HIS181
|
5.0
|
21.4
|
1.0
|
|
Reference:
Z.Xu,
Y.Liu,
Y.Yang,
W.Jiang,
E.Arnold,
J.Ding.
Crystal Structure of D-Hydantoinase From Burkholderia Pickettii at A Resolution of 2.7 Angstroms: Insights Into the Molecular Basis of Enzyme Thermostability. J.Bacteriol. V. 185 4038 2003.
ISSN: ISSN 0021-9193
PubMed: 12837777
DOI: 10.1128/JB.185.14.4038-4049.2003
Page generated: Wed Oct 16 17:15:44 2024
|