Zinc in PDB 6dkc: Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure
Enzymatic activity of Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure
All present enzymatic activity of Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure:
4.2.1.69;
Protein crystallography data
The structure of Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure, PDB code: 6dkc
was solved by
S.A.Moore,
W.Xiao,
J.Li,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
39.30 /
2.90
|
|
Space group
|
P 3 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
263.613,
263.613,
119.026,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
19.3 /
21.5
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure
(pdb code 6dkc). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the
Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure, PDB code: 6dkc:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Zinc binding site 1 out
of 9 in 6dkc
Go back to
Zinc Binding Sites List in 6dkc
Zinc binding site 1 out
of 9 in the Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:51.8
occ:0.50
|
HE2
|
A:HIS88
|
1.5
|
64.6
|
1.0
|
|
O
|
A:HOH420
|
2.0
|
47.3
|
0.5
|
|
OD2
|
A:ASP89
|
2.1
|
65.2
|
1.0
|
|
NE2
|
A:HIS55
|
2.2
|
57.8
|
1.0
|
|
NE2
|
A:HIS88
|
2.2
|
53.8
|
1.0
|
|
CG
|
A:ASP89
|
2.9
|
54.0
|
1.0
|
|
CE1
|
A:HIS55
|
3.0
|
50.0
|
1.0
|
|
CD2
|
A:HIS88
|
3.1
|
53.1
|
1.0
|
|
HE1
|
A:HIS55
|
3.1
|
60.0
|
1.0
|
|
HD2
|
A:HIS88
|
3.1
|
63.7
|
1.0
|
|
CD2
|
A:HIS55
|
3.2
|
49.1
|
1.0
|
|
HG13
|
A:VAL157
|
3.2
|
55.9
|
1.0
|
|
OD1
|
A:ASP89
|
3.2
|
53.8
|
1.0
|
|
CE1
|
A:HIS88
|
3.3
|
56.1
|
1.0
|
|
O
|
A:HOH419
|
3.4
|
54.7
|
1.0
|
|
HD21
|
A:ASN161
|
3.4
|
54.4
|
1.0
|
|
HD2
|
A:HIS55
|
3.5
|
58.9
|
1.0
|
|
HE1
|
A:HIS88
|
3.5
|
67.3
|
1.0
|
|
HG22
|
A:VAL157
|
3.5
|
51.4
|
1.0
|
|
HG12
|
A:VAL157
|
3.6
|
55.9
|
1.0
|
|
HZ2
|
A:TRP186
|
3.8
|
50.7
|
1.0
|
|
CG1
|
A:VAL157
|
3.9
|
46.5
|
1.0
|
|
ND1
|
A:HIS55
|
4.1
|
49.4
|
1.0
|
|
CG
|
A:HIS55
|
4.2
|
51.8
|
1.0
|
|
CG
|
A:HIS88
|
4.2
|
51.6
|
1.0
|
|
ND2
|
A:ASN161
|
4.2
|
45.4
|
1.0
|
|
CB
|
A:ASP89
|
4.3
|
48.7
|
1.0
|
|
HB2
|
A:ASP89
|
4.3
|
58.4
|
1.0
|
|
HG21
|
A:VAL157
|
4.3
|
51.4
|
1.0
|
|
CG2
|
A:VAL157
|
4.3
|
42.9
|
1.0
|
|
ND1
|
A:HIS88
|
4.3
|
52.9
|
1.0
|
|
HE1
|
A:PHE190
|
4.3
|
55.6
|
1.0
|
|
HG22
|
A:VAL59
|
4.5
|
59.3
|
1.0
|
|
HG11
|
A:VAL157
|
4.6
|
55.9
|
1.0
|
|
CZ2
|
A:TRP186
|
4.7
|
42.3
|
1.0
|
|
CB
|
A:VAL157
|
4.7
|
43.7
|
1.0
|
|
CE1
|
A:PHE190
|
4.7
|
46.3
|
1.0
|
|
HD22
|
A:ASN161
|
4.7
|
54.4
|
1.0
|
|
HB3
|
A:ASP89
|
4.8
|
58.4
|
1.0
|
|
HD1
|
A:HIS55
|
4.8
|
59.3
|
1.0
|
|
OD1
|
A:ASN161
|
4.9
|
51.1
|
1.0
|
|
HH2
|
A:TRP186
|
4.9
|
52.3
|
1.0
|
|
HD2
|
A:HIS137
|
4.9
|
56.3
|
1.0
|
|
NE2
|
A:HIS137
|
4.9
|
47.4
|
1.0
|
|
HG
|
A:SER56
|
4.9
|
54.3
|
1.0
|
|
HA
|
A:VAL157
|
5.0
|
54.5
|
1.0
|
|
HD1
|
A:PHE190
|
5.0
|
56.8
|
1.0
|
|
Zinc binding site 2 out
of 9 in 6dkc
Go back to
Zinc Binding Sites List in 6dkc
Zinc binding site 2 out
of 9 in the Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:59.8
occ:0.50
|
HE2
|
B:HIS88
|
1.5
|
77.9
|
1.0
|
|
O
|
B:HOH420
|
2.0
|
76.0
|
0.5
|
|
OD2
|
B:ASP89
|
2.1
|
67.3
|
1.0
|
|
NE2
|
B:HIS55
|
2.2
|
48.6
|
1.0
|
|
NE2
|
B:HIS88
|
2.2
|
64.9
|
1.0
|
|
CD2
|
B:HIS88
|
2.9
|
61.8
|
1.0
|
|
HD2
|
B:HIS88
|
3.0
|
74.2
|
1.0
|
|
CG
|
B:ASP89
|
3.0
|
55.5
|
1.0
|
|
CE1
|
B:HIS55
|
3.1
|
47.7
|
1.0
|
|
HG11
|
B:VAL157
|
3.2
|
61.5
|
1.0
|
|
CD2
|
B:HIS55
|
3.2
|
46.2
|
1.0
|
|
HE1
|
B:HIS55
|
3.2
|
57.2
|
1.0
|
|
HD21
|
B:ASN161
|
3.3
|
60.6
|
1.0
|
|
OD1
|
B:ASP89
|
3.3
|
56.4
|
1.0
|
|
CE1
|
B:HIS88
|
3.3
|
66.2
|
1.0
|
|
HG13
|
B:VAL157
|
3.4
|
61.5
|
1.0
|
|
HD2
|
B:HIS55
|
3.4
|
55.5
|
1.0
|
|
O
|
B:HOH416
|
3.4
|
67.5
|
1.0
|
|
HG23
|
B:VAL157
|
3.4
|
60.0
|
1.0
|
|
HE1
|
B:HIS88
|
3.6
|
79.5
|
1.0
|
|
CG1
|
B:VAL157
|
3.7
|
51.2
|
1.0
|
|
HZ2
|
B:TRP186
|
3.8
|
55.0
|
1.0
|
|
ND2
|
B:ASN161
|
4.1
|
50.5
|
1.0
|
|
CG
|
B:HIS88
|
4.1
|
60.6
|
1.0
|
|
ND1
|
B:HIS55
|
4.2
|
47.3
|
1.0
|
|
HB2
|
B:ASP89
|
4.2
|
60.3
|
1.0
|
|
CG2
|
B:VAL157
|
4.3
|
50.0
|
1.0
|
|
CG
|
B:HIS55
|
4.3
|
47.1
|
1.0
|
|
CB
|
B:ASP89
|
4.3
|
50.2
|
1.0
|
|
ND1
|
B:HIS88
|
4.3
|
62.5
|
1.0
|
|
HE1
|
B:PHE190
|
4.3
|
48.4
|
1.0
|
|
HG12
|
B:VAL157
|
4.4
|
61.5
|
1.0
|
|
HG21
|
B:VAL59
|
4.4
|
57.5
|
1.0
|
|
HG22
|
B:VAL157
|
4.5
|
60.0
|
1.0
|
|
HD22
|
B:ASN161
|
4.6
|
60.6
|
1.0
|
|
CB
|
B:VAL157
|
4.6
|
47.7
|
1.0
|
|
CZ2
|
B:TRP186
|
4.6
|
45.8
|
1.0
|
|
CE1
|
B:PHE190
|
4.6
|
40.4
|
1.0
|
|
HH2
|
B:TRP186
|
4.7
|
57.9
|
1.0
|
|
OD1
|
B:ASN161
|
4.8
|
51.0
|
1.0
|
|
NE2
|
B:HIS137
|
4.8
|
45.1
|
1.0
|
|
HD2
|
B:HIS137
|
4.8
|
52.8
|
1.0
|
|
HB3
|
B:ASP89
|
4.8
|
60.3
|
1.0
|
|
CG
|
B:ASN161
|
4.9
|
50.7
|
1.0
|
|
HD1
|
B:HIS55
|
4.9
|
56.8
|
1.0
|
|
HA
|
B:VAL157
|
5.0
|
58.0
|
1.0
|
|
HD1
|
B:PHE190
|
5.0
|
52.5
|
1.0
|
|
CD1
|
B:PHE190
|
5.0
|
43.8
|
1.0
|
|
Zinc binding site 3 out
of 9 in 6dkc
Go back to
Zinc Binding Sites List in 6dkc
Zinc binding site 3 out
of 9 in the Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:44.0
occ:0.50
|
O
|
C:HOH405
|
2.0
|
52.7
|
0.5
|
|
OD2
|
C:ASP89
|
2.1
|
52.1
|
1.0
|
|
NE2
|
C:HIS55
|
2.2
|
49.4
|
1.0
|
|
NE2
|
C:HIS88
|
2.2
|
34.5
|
1.0
|
|
CG
|
C:ASP89
|
3.0
|
43.6
|
1.0
|
|
CE1
|
C:HIS55
|
3.0
|
42.4
|
1.0
|
|
CD2
|
C:HIS88
|
3.0
|
33.9
|
1.0
|
|
HE1
|
C:HIS55
|
3.1
|
50.9
|
1.0
|
|
O
|
C:HOH419
|
3.1
|
56.4
|
1.0
|
|
HD2
|
C:HIS88
|
3.1
|
40.7
|
1.0
|
|
CD2
|
C:HIS55
|
3.2
|
40.5
|
1.0
|
|
HD21
|
C:ASN161
|
3.2
|
45.0
|
1.0
|
|
OD1
|
C:ASP89
|
3.2
|
44.0
|
1.0
|
|
CE1
|
C:HIS88
|
3.3
|
36.1
|
1.0
|
|
HG12
|
C:VAL157
|
3.3
|
64.4
|
1.0
|
|
HG23
|
C:VAL157
|
3.4
|
52.2
|
1.0
|
|
HG11
|
C:VAL157
|
3.4
|
64.4
|
1.0
|
|
HD2
|
C:HIS55
|
3.5
|
48.6
|
1.0
|
|
HE1
|
C:HIS88
|
3.6
|
43.3
|
1.0
|
|
HZ2
|
C:TRP186
|
3.7
|
44.4
|
1.0
|
|
CG1
|
C:VAL157
|
3.8
|
53.7
|
1.0
|
|
ND1
|
C:HIS55
|
4.1
|
39.4
|
1.0
|
|
ND2
|
C:ASN161
|
4.1
|
37.5
|
1.0
|
|
CG
|
C:HIS55
|
4.2
|
40.5
|
1.0
|
|
CG
|
C:HIS88
|
4.2
|
34.4
|
1.0
|
|
CG2
|
C:VAL157
|
4.2
|
43.5
|
1.0
|
|
CB
|
C:ASP89
|
4.3
|
40.0
|
1.0
|
|
ND1
|
C:HIS88
|
4.3
|
34.7
|
1.0
|
|
HB2
|
C:ASP89
|
4.3
|
48.0
|
1.0
|
|
HE1
|
C:PHE190
|
4.4
|
40.8
|
1.0
|
|
CZ2
|
C:TRP186
|
4.5
|
37.0
|
1.0
|
|
HG21
|
C:VAL157
|
4.5
|
52.2
|
1.0
|
|
HD22
|
C:ASN161
|
4.5
|
45.0
|
1.0
|
|
HH2
|
C:TRP186
|
4.6
|
45.6
|
1.0
|
|
HG13
|
C:VAL157
|
4.6
|
64.4
|
1.0
|
|
HG21
|
C:VAL59
|
4.6
|
40.8
|
1.0
|
|
CB
|
C:VAL157
|
4.7
|
47.8
|
1.0
|
|
CE1
|
C:PHE190
|
4.7
|
34.0
|
1.0
|
|
OD1
|
C:ASN161
|
4.8
|
32.4
|
1.0
|
|
HD1
|
C:HIS55
|
4.8
|
47.3
|
1.0
|
|
HB3
|
C:ASP89
|
4.8
|
48.0
|
1.0
|
|
HD2
|
C:HIS137
|
4.9
|
52.6
|
1.0
|
|
CG
|
C:ASN161
|
4.9
|
33.6
|
1.0
|
|
HA
|
C:VAL157
|
4.9
|
54.2
|
1.0
|
|
HG22
|
C:VAL157
|
4.9
|
52.2
|
1.0
|
|
NE2
|
C:HIS137
|
4.9
|
43.5
|
1.0
|
|
HD1
|
C:PHE190
|
5.0
|
42.8
|
1.0
|
|
CH2
|
C:TRP186
|
5.0
|
38.0
|
1.0
|
|
Zinc binding site 4 out
of 9 in 6dkc
Go back to
Zinc Binding Sites List in 6dkc
Zinc binding site 4 out
of 9 in the Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn302
b:58.8
occ:0.50
|
O
|
D:HOH429
|
2.0
|
73.1
|
0.5
|
|
OD2
|
D:ASP89
|
2.1
|
65.3
|
1.0
|
|
NE2
|
D:HIS55
|
2.2
|
55.6
|
1.0
|
|
NE2
|
D:HIS88
|
2.2
|
39.8
|
1.0
|
|
CD2
|
D:HIS88
|
2.9
|
37.0
|
1.0
|
|
CG
|
D:ASP89
|
3.0
|
51.7
|
1.0
|
|
HD2
|
D:HIS88
|
3.0
|
44.4
|
1.0
|
|
CE1
|
D:HIS55
|
3.0
|
54.0
|
1.0
|
|
HG12
|
D:VAL157
|
3.0
|
60.2
|
1.0
|
|
HE1
|
D:HIS55
|
3.2
|
64.8
|
1.0
|
|
CD2
|
D:HIS55
|
3.2
|
50.9
|
1.0
|
|
OD1
|
D:ASP89
|
3.2
|
49.8
|
1.0
|
|
HG13
|
D:VAL157
|
3.3
|
60.2
|
1.0
|
|
CE1
|
D:HIS88
|
3.3
|
40.6
|
1.0
|
|
HG23
|
D:VAL157
|
3.3
|
57.3
|
1.0
|
|
HD21
|
D:ASN161
|
3.4
|
54.3
|
1.0
|
|
HD2
|
D:HIS55
|
3.4
|
61.0
|
1.0
|
|
O
|
D:HOH409
|
3.5
|
64.7
|
1.0
|
|
CG1
|
D:VAL157
|
3.6
|
50.1
|
1.0
|
|
HE1
|
D:HIS88
|
3.6
|
48.7
|
1.0
|
|
HZ2
|
D:TRP186
|
3.9
|
49.0
|
1.0
|
|
ND1
|
D:HIS55
|
4.1
|
52.3
|
1.0
|
|
CG
|
D:HIS88
|
4.2
|
37.9
|
1.0
|
|
CG2
|
D:VAL157
|
4.2
|
47.8
|
1.0
|
|
ND2
|
D:ASN161
|
4.2
|
45.2
|
1.0
|
|
HB2
|
D:ASP89
|
4.2
|
54.8
|
1.0
|
|
CB
|
D:ASP89
|
4.3
|
45.7
|
1.0
|
|
CG
|
D:HIS55
|
4.3
|
51.3
|
1.0
|
|
ND1
|
D:HIS88
|
4.3
|
36.3
|
1.0
|
|
HG11
|
D:VAL157
|
4.3
|
60.2
|
1.0
|
|
HG21
|
D:VAL157
|
4.4
|
57.3
|
1.0
|
|
HE1
|
D:PHE190
|
4.4
|
62.4
|
1.0
|
|
HG23
|
D:VAL59
|
4.5
|
54.8
|
1.0
|
|
CB
|
D:VAL157
|
4.5
|
48.0
|
1.0
|
|
CE1
|
D:PHE190
|
4.7
|
52.0
|
1.0
|
|
HD22
|
D:ASN161
|
4.7
|
54.3
|
1.0
|
|
CZ2
|
D:TRP186
|
4.7
|
40.9
|
1.0
|
|
HD2
|
D:HIS137
|
4.8
|
50.9
|
1.0
|
|
HH2
|
D:TRP186
|
4.8
|
48.5
|
1.0
|
|
HA
|
D:VAL157
|
4.8
|
57.3
|
1.0
|
|
HB3
|
D:ASP89
|
4.8
|
54.8
|
1.0
|
|
OD1
|
D:ASN161
|
4.8
|
39.1
|
1.0
|
|
NE2
|
D:HIS137
|
4.9
|
42.7
|
1.0
|
|
HD1
|
D:HIS55
|
4.9
|
62.8
|
1.0
|
|
HG22
|
D:VAL157
|
4.9
|
57.3
|
1.0
|
|
CG
|
D:ASN161
|
5.0
|
40.9
|
1.0
|
|
Zinc binding site 5 out
of 9 in 6dkc
Go back to
Zinc Binding Sites List in 6dkc
Zinc binding site 5 out
of 9 in the Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn301
b:53.6
occ:0.50
|
O
|
E:HOH416
|
2.0
|
66.4
|
0.5
|
|
OD2
|
E:ASP89
|
2.1
|
56.0
|
1.0
|
|
NE2
|
E:HIS55
|
2.2
|
48.5
|
1.0
|
|
NE2
|
E:HIS88
|
2.2
|
48.6
|
1.0
|
|
CD2
|
E:HIS88
|
2.9
|
40.5
|
1.0
|
|
HD2
|
E:HIS88
|
2.9
|
48.6
|
1.0
|
|
CG
|
E:ASP89
|
2.9
|
42.7
|
1.0
|
|
CE1
|
E:HIS55
|
3.0
|
43.8
|
1.0
|
|
HE1
|
E:HIS55
|
3.2
|
52.5
|
1.0
|
|
CD2
|
E:HIS55
|
3.2
|
41.4
|
1.0
|
|
OD1
|
E:ASP89
|
3.2
|
42.8
|
1.0
|
|
HG13
|
E:VAL157
|
3.3
|
67.7
|
1.0
|
|
HD21
|
E:ASN161
|
3.3
|
39.8
|
1.0
|
|
O
|
E:HOH429
|
3.3
|
55.5
|
1.0
|
|
CE1
|
E:HIS88
|
3.3
|
43.4
|
1.0
|
|
HG12
|
E:VAL157
|
3.4
|
67.7
|
1.0
|
|
HD2
|
E:HIS55
|
3.4
|
49.7
|
1.0
|
|
HG23
|
E:VAL157
|
3.5
|
64.4
|
1.0
|
|
HE1
|
E:HIS88
|
3.7
|
52.1
|
1.0
|
|
CG1
|
E:VAL157
|
3.8
|
56.4
|
1.0
|
|
HZ2
|
E:TRP186
|
3.9
|
50.7
|
1.0
|
|
ND1
|
E:HIS55
|
4.1
|
43.0
|
1.0
|
|
CG
|
E:HIS88
|
4.2
|
41.1
|
1.0
|
|
HE1
|
E:PHE190
|
4.2
|
44.7
|
1.0
|
|
ND2
|
E:ASN161
|
4.2
|
33.2
|
1.0
|
|
CG
|
E:HIS55
|
4.2
|
43.7
|
1.0
|
|
CB
|
E:ASP89
|
4.3
|
33.3
|
1.0
|
|
HB2
|
E:ASP89
|
4.3
|
40.0
|
1.0
|
|
ND1
|
E:HIS88
|
4.3
|
41.6
|
1.0
|
|
CG2
|
E:VAL157
|
4.3
|
53.7
|
1.0
|
|
HG23
|
E:VAL59
|
4.5
|
44.4
|
1.0
|
|
HG11
|
E:VAL157
|
4.5
|
67.7
|
1.0
|
|
CE1
|
E:PHE190
|
4.6
|
37.2
|
1.0
|
|
HD22
|
E:ASN161
|
4.6
|
39.8
|
1.0
|
|
CB
|
E:VAL157
|
4.7
|
52.5
|
1.0
|
|
HH2
|
E:TRP186
|
4.7
|
51.5
|
1.0
|
|
CZ2
|
E:TRP186
|
4.7
|
42.3
|
1.0
|
|
HG22
|
E:VAL157
|
4.7
|
64.4
|
1.0
|
|
NE2
|
E:HIS137
|
4.8
|
38.9
|
1.0
|
|
HB3
|
E:ASP89
|
4.8
|
40.0
|
1.0
|
|
OD1
|
E:ASN161
|
4.9
|
36.9
|
1.0
|
|
HA
|
E:VAL157
|
4.9
|
57.2
|
1.0
|
|
HD1
|
E:HIS55
|
4.9
|
51.6
|
1.0
|
|
HD2
|
E:HIS137
|
4.9
|
46.0
|
1.0
|
|
HD1
|
E:PHE190
|
5.0
|
49.3
|
1.0
|
|
CG
|
E:ASN161
|
5.0
|
33.5
|
1.0
|
|
Zinc binding site 6 out
of 9 in 6dkc
Go back to
Zinc Binding Sites List in 6dkc
Zinc binding site 6 out
of 9 in the Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn302
b:57.6
occ:0.50
|
O
|
F:HOH418
|
2.0
|
70.6
|
0.5
|
|
OD2
|
F:ASP89
|
2.1
|
68.7
|
1.0
|
|
NE2
|
F:HIS55
|
2.2
|
62.5
|
1.0
|
|
NE2
|
F:HIS88
|
2.2
|
47.2
|
1.0
|
|
HG12
|
F:VAL157
|
2.9
|
59.1
|
1.0
|
|
CE1
|
F:HIS55
|
2.9
|
53.4
|
1.0
|
|
CG
|
F:ASP89
|
3.0
|
59.5
|
1.0
|
|
HE1
|
F:HIS55
|
3.0
|
64.1
|
1.0
|
|
CD2
|
F:HIS88
|
3.1
|
43.9
|
1.0
|
|
HD2
|
F:HIS88
|
3.1
|
52.7
|
1.0
|
|
OD1
|
F:ASP89
|
3.2
|
61.5
|
1.0
|
|
CD2
|
F:HIS55
|
3.3
|
50.5
|
1.0
|
|
CE1
|
F:HIS88
|
3.3
|
46.2
|
1.0
|
|
HD21
|
F:ASN161
|
3.3
|
53.5
|
1.0
|
|
HG11
|
F:VAL157
|
3.3
|
59.1
|
1.0
|
|
O
|
F:HOH412
|
3.5
|
50.2
|
0.9
|
|
HE1
|
F:HIS88
|
3.5
|
55.5
|
1.0
|
|
CG1
|
F:VAL157
|
3.5
|
49.2
|
1.0
|
|
HG22
|
F:VAL157
|
3.5
|
58.2
|
1.0
|
|
HD2
|
F:HIS55
|
3.6
|
60.6
|
1.0
|
|
HZ2
|
F:TRP186
|
3.9
|
44.8
|
1.0
|
|
ND1
|
F:HIS55
|
4.1
|
50.6
|
1.0
|
|
ND2
|
F:ASN161
|
4.1
|
44.6
|
1.0
|
|
HG21
|
F:VAL157
|
4.2
|
58.2
|
1.0
|
|
HG13
|
F:VAL157
|
4.2
|
59.1
|
1.0
|
|
CG2
|
F:VAL157
|
4.2
|
48.5
|
1.0
|
|
CG
|
F:HIS88
|
4.3
|
43.6
|
1.0
|
|
CG
|
F:HIS55
|
4.3
|
51.1
|
1.0
|
|
CB
|
F:ASP89
|
4.3
|
53.2
|
1.0
|
|
HG21
|
F:VAL59
|
4.3
|
53.5
|
1.0
|
|
ND1
|
F:HIS88
|
4.3
|
42.5
|
1.0
|
|
HB2
|
F:ASP89
|
4.4
|
63.9
|
1.0
|
|
HE1
|
F:PHE190
|
4.4
|
53.8
|
1.0
|
|
CB
|
F:VAL157
|
4.5
|
47.5
|
1.0
|
|
OD1
|
F:ASN161
|
4.7
|
40.1
|
1.0
|
|
HD22
|
F:ASN161
|
4.7
|
53.5
|
1.0
|
|
CE1
|
F:PHE190
|
4.7
|
44.8
|
1.0
|
|
CZ2
|
F:TRP186
|
4.7
|
37.3
|
1.0
|
|
HA
|
F:VAL157
|
4.8
|
58.9
|
1.0
|
|
HD1
|
F:HIS55
|
4.8
|
60.8
|
1.0
|
|
HB3
|
F:ASP89
|
4.8
|
63.9
|
1.0
|
|
CG
|
F:ASN161
|
4.9
|
42.3
|
1.0
|
|
HD2
|
F:HIS137
|
4.9
|
57.5
|
1.0
|
|
HH2
|
F:TRP186
|
4.9
|
42.1
|
1.0
|
|
NE2
|
F:HIS137
|
4.9
|
47.8
|
1.0
|
|
Zinc binding site 7 out
of 9 in 6dkc
Go back to
Zinc Binding Sites List in 6dkc
Zinc binding site 7 out
of 9 in the Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn301
b:69.4
occ:0.50
|
HE2
|
G:HIS55
|
1.6
|
75.2
|
1.0
|
|
O
|
G:HOH416
|
2.0
|
69.5
|
0.5
|
|
OD2
|
G:ASP89
|
2.1
|
82.8
|
1.0
|
|
NE2
|
G:HIS88
|
2.2
|
56.8
|
1.0
|
|
NE2
|
G:HIS55
|
2.2
|
62.6
|
1.0
|
|
CG
|
G:ASP89
|
2.9
|
71.7
|
1.0
|
|
CD2
|
G:HIS88
|
3.0
|
53.0
|
1.0
|
|
HD2
|
G:HIS88
|
3.0
|
63.5
|
1.0
|
|
CE1
|
G:HIS55
|
3.1
|
63.7
|
1.0
|
|
CD2
|
G:HIS55
|
3.1
|
64.0
|
1.0
|
|
HD21
|
G:ASN161
|
3.2
|
82.0
|
1.0
|
|
OD1
|
G:ASP89
|
3.2
|
75.5
|
1.0
|
|
HE1
|
G:HIS55
|
3.3
|
76.4
|
1.0
|
|
CE1
|
G:HIS88
|
3.3
|
55.9
|
1.0
|
|
HG13
|
G:VAL157
|
3.3
|
90.7
|
1.0
|
|
HG22
|
G:VAL157
|
3.3
|
86.7
|
1.0
|
|
HD2
|
G:HIS55
|
3.3
|
76.8
|
1.0
|
|
HG12
|
G:VAL157
|
3.4
|
90.7
|
1.0
|
|
O
|
G:HOH408
|
3.6
|
70.6
|
1.0
|
|
HE1
|
G:HIS88
|
3.6
|
67.1
|
1.0
|
|
CG1
|
G:VAL157
|
3.8
|
75.6
|
1.0
|
|
HZ2
|
G:TRP186
|
3.8
|
83.2
|
1.0
|
|
ND2
|
G:ASN161
|
4.0
|
68.3
|
1.0
|
|
ND1
|
G:HIS55
|
4.1
|
65.1
|
1.0
|
|
CG2
|
G:VAL157
|
4.1
|
72.2
|
1.0
|
|
CG
|
G:HIS55
|
4.2
|
64.6
|
1.0
|
|
CG
|
G:HIS88
|
4.2
|
53.3
|
1.0
|
|
HE1
|
G:PHE190
|
4.2
|
81.9
|
1.0
|
|
HG21
|
G:VAL157
|
4.2
|
86.7
|
1.0
|
|
CB
|
G:ASP89
|
4.3
|
62.7
|
1.0
|
|
HB2
|
G:ASP89
|
4.3
|
75.3
|
1.0
|
|
ND1
|
G:HIS88
|
4.3
|
55.0
|
1.0
|
|
HD22
|
G:ASN161
|
4.5
|
82.0
|
1.0
|
|
HG23
|
G:VAL59
|
4.5
|
61.9
|
1.0
|
|
HG11
|
G:VAL157
|
4.6
|
90.7
|
1.0
|
|
CB
|
G:VAL157
|
4.6
|
72.1
|
1.0
|
|
CE1
|
G:PHE190
|
4.6
|
68.3
|
1.0
|
|
CZ2
|
G:TRP186
|
4.7
|
69.3
|
1.0
|
|
HB3
|
G:ASP89
|
4.8
|
75.3
|
1.0
|
|
HA
|
G:VAL157
|
4.8
|
83.1
|
1.0
|
|
HH2
|
G:TRP186
|
4.8
|
84.5
|
1.0
|
|
OD1
|
G:ASN161
|
4.8
|
67.5
|
1.0
|
|
HD1
|
G:HIS55
|
4.9
|
78.1
|
1.0
|
|
CG
|
G:ASN161
|
4.9
|
66.1
|
1.0
|
|
HG23
|
G:VAL157
|
4.9
|
86.7
|
1.0
|
|
NE2
|
G:HIS137
|
4.9
|
66.0
|
1.0
|
|
HD2
|
G:HIS137
|
4.9
|
78.7
|
1.0
|
|
HD1
|
G:PHE190
|
5.0
|
84.4
|
1.0
|
|
Zinc binding site 8 out
of 9 in 6dkc
Go back to
Zinc Binding Sites List in 6dkc
Zinc binding site 8 out
of 9 in the Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn500
b:0.5
occ:0.50
|
OD2
|
H:ASP89
|
2.1
|
0.2
|
1.0
|
|
NE2
|
H:HIS55
|
2.2
|
86.8
|
1.0
|
|
NE2
|
H:HIS88
|
2.2
|
93.3
|
1.0
|
|
CG
|
H:ASP89
|
2.8
|
1.0
|
1.0
|
|
CD2
|
H:HIS88
|
2.9
|
93.7
|
1.0
|
|
HD2
|
H:HIS88
|
2.9
|
0.4
|
1.0
|
|
OD1
|
H:ASP89
|
2.9
|
0.5
|
1.0
|
|
CE1
|
H:HIS55
|
3.1
|
86.1
|
1.0
|
|
CD2
|
H:HIS55
|
3.2
|
87.0
|
1.0
|
|
HG12
|
H:VAL157
|
3.2
|
0.2
|
1.0
|
|
HE1
|
H:HIS55
|
3.2
|
0.3
|
1.0
|
|
CE1
|
H:HIS88
|
3.3
|
93.3
|
1.0
|
|
HD2
|
H:HIS55
|
3.4
|
0.4
|
1.0
|
|
HG22
|
H:VAL157
|
3.4
|
0.0
|
1.0
|
|
HD21
|
H:ASN161
|
3.6
|
0.1
|
1.0
|
|
HE1
|
H:HIS88
|
3.7
|
0.0
|
1.0
|
|
HG11
|
H:VAL157
|
3.7
|
0.2
|
1.0
|
|
CG1
|
H:VAL157
|
3.9
|
0.0
|
1.0
|
|
HZ2
|
H:TRP186
|
3.9
|
0.1
|
1.0
|
|
CG
|
H:HIS88
|
4.1
|
96.1
|
1.0
|
|
HG21
|
H:VAL157
|
4.1
|
0.0
|
1.0
|
|
CG2
|
H:VAL157
|
4.1
|
0.8
|
1.0
|
|
CB
|
H:ASP89
|
4.2
|
0.6
|
1.0
|
|
ND1
|
H:HIS55
|
4.2
|
85.6
|
1.0
|
|
ND1
|
H:HIS88
|
4.3
|
94.4
|
1.0
|
|
HB2
|
H:ASP89
|
4.3
|
1.0
|
1.0
|
|
CG
|
H:HIS55
|
4.3
|
86.5
|
1.0
|
|
HE1
|
H:PHE190
|
4.3
|
86.1
|
1.0
|
|
ND2
|
H:ASN161
|
4.5
|
96.8
|
1.0
|
|
NE2
|
H:HIS137
|
4.5
|
0.3
|
1.0
|
|
HG22
|
H:VAL59
|
4.6
|
0.8
|
1.0
|
|
CB
|
H:VAL157
|
4.6
|
0.2
|
1.0
|
|
HH2
|
H:TRP186
|
4.7
|
0.6
|
1.0
|
|
HG13
|
H:VAL157
|
4.7
|
0.2
|
1.0
|
|
HD2
|
H:HIS137
|
4.7
|
0.0
|
1.0
|
|
HB3
|
H:ASP89
|
4.7
|
1.0
|
1.0
|
|
CZ2
|
H:TRP186
|
4.7
|
88.4
|
1.0
|
|
CE1
|
H:PHE190
|
4.8
|
71.8
|
1.0
|
|
HA
|
H:VAL157
|
4.8
|
0.8
|
1.0
|
|
HG23
|
H:VAL59
|
4.8
|
0.8
|
1.0
|
|
CD2
|
H:HIS137
|
4.9
|
0.8
|
1.0
|
|
HD22
|
H:ASN161
|
4.9
|
0.1
|
1.0
|
|
HG23
|
H:VAL157
|
5.0
|
0.0
|
1.0
|
|
HD1
|
H:HIS55
|
5.0
|
0.7
|
1.0
|
|
HD1
|
H:PHE190
|
5.0
|
84.8
|
1.0
|
|
Zinc binding site 9 out
of 9 in 6dkc
Go back to
Zinc Binding Sites List in 6dkc
Zinc binding site 9 out
of 9 in the Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Yeast DDI2 Cyanamide Hydratase, T157V Mutant, Apo Structure within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn500
b:95.9
occ:0.50
|
OD2
|
I:ASP89
|
2.1
|
0.1
|
1.0
|
|
NE2
|
I:HIS88
|
2.2
|
0.4
|
1.0
|
|
NE2
|
I:HIS55
|
2.2
|
0.2
|
1.0
|
|
CD2
|
I:HIS88
|
2.9
|
0.7
|
1.0
|
|
HD2
|
I:HIS88
|
2.9
|
0.1
|
1.0
|
|
CG
|
I:ASP89
|
3.0
|
0.1
|
1.0
|
|
CD2
|
I:HIS55
|
3.1
|
0.7
|
1.0
|
|
CE1
|
I:HIS55
|
3.2
|
0.4
|
1.0
|
|
HD21
|
I:ASN161
|
3.2
|
0.5
|
1.0
|
|
HD2
|
I:HIS55
|
3.2
|
0.6
|
1.0
|
|
HG22
|
I:VAL157
|
3.3
|
0.1
|
1.0
|
|
OD1
|
I:ASP89
|
3.3
|
0.4
|
1.0
|
|
CE1
|
I:HIS88
|
3.3
|
0.7
|
1.0
|
|
HE1
|
I:HIS55
|
3.4
|
0.2
|
1.0
|
|
HG12
|
I:VAL157
|
3.4
|
0.5
|
1.0
|
|
HZ
|
I:PHE190
|
3.6
|
0.5
|
1.0
|
|
HZ2
|
I:TRP186
|
3.6
|
0.6
|
1.0
|
|
HE1
|
I:HIS88
|
3.7
|
0.9
|
1.0
|
|
HE1
|
I:PHE190
|
3.8
|
0.4
|
1.0
|
|
HG11
|
I:VAL157
|
3.9
|
0.5
|
1.0
|
|
ND2
|
I:ASN161
|
4.0
|
0.3
|
1.0
|
|
CG1
|
I:VAL157
|
4.1
|
0.2
|
1.0
|
|
CG2
|
I:VAL157
|
4.1
|
0.8
|
1.0
|
|
HG21
|
I:VAL157
|
4.1
|
0.1
|
1.0
|
|
CZ
|
I:PHE190
|
4.2
|
0.7
|
1.0
|
|
ND1
|
I:HIS55
|
4.2
|
0.2
|
1.0
|
|
CG
|
I:HIS55
|
4.2
|
0.8
|
1.0
|
|
CG
|
I:HIS88
|
4.2
|
0.8
|
1.0
|
|
HH2
|
I:TRP186
|
4.2
|
0.3
|
1.0
|
|
CE1
|
I:PHE190
|
4.3
|
0.8
|
1.0
|
|
ND1
|
I:HIS88
|
4.3
|
0.1
|
1.0
|
|
CB
|
I:ASP89
|
4.3
|
0.5
|
1.0
|
|
HB2
|
I:ASP89
|
4.4
|
0.8
|
1.0
|
|
CZ2
|
I:TRP186
|
4.4
|
0.0
|
1.0
|
|
HD22
|
I:ASN161
|
4.5
|
0.5
|
1.0
|
|
HG22
|
I:VAL59
|
4.5
|
0.3
|
1.0
|
|
HA
|
I:VAL157
|
4.6
|
0.8
|
1.0
|
|
CB
|
I:VAL157
|
4.6
|
0.2
|
1.0
|
|
CH2
|
I:TRP186
|
4.7
|
0.6
|
1.0
|
|
OD1
|
I:ASN161
|
4.8
|
0.1
|
1.0
|
|
HG23
|
I:VAL157
|
4.8
|
0.1
|
1.0
|
|
HB3
|
I:ASP89
|
4.9
|
0.8
|
1.0
|
|
CG
|
I:ASN161
|
4.9
|
0.3
|
1.0
|
|
HG13
|
I:VAL157
|
4.9
|
0.5
|
1.0
|
|
HD1
|
I:HIS55
|
4.9
|
0.5
|
1.0
|
|
Reference:
J.Li,
Y.Jia,
A.Lin,
M.Hanna,
L.Chelico,
W.Xiao,
S.A.Moore.
Structure of DDI2, A Highly Inducible Detoxifying Metalloenzyme Fromsaccharomyces Cerevisiae. J.Biol.Chem. V. 294 10674 2019.
ISSN: ESSN 1083-351X
PubMed: 31152065
DOI: 10.1074/JBC.RA118.006394
Page generated: Mon Oct 28 19:36:52 2024
|
