Zinc in PDB 6dka: Yeast DDI2 Cyanamide Hydratase
Protein crystallography data
The structure of Yeast DDI2 Cyanamide Hydratase, PDB code: 6dka
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)
|
29.97 /
2.90
|
Space group
|
P 3 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
263.430,
263.430,
119.214,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
19.8 /
23
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Yeast DDI2 Cyanamide Hydratase
(pdb code 6dka). 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, PDB code: 6dka:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Zinc binding site 1 out
of 9 in 6dka
Go back to
Zinc Binding Sites List in 6dka
Zinc binding site 1 out
of 9 in the Yeast DDI2 Cyanamide Hydratase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:68.9
occ:0.67
|
HE2
|
A:HIS88
|
1.5
|
52.5
|
1.0
|
N2
|
A:CNN302
|
2.0
|
69.1
|
0.7
|
OD2
|
A:ASP89
|
2.1
|
79.4
|
1.0
|
NE2
|
A:HIS55
|
2.2
|
41.0
|
1.0
|
NE2
|
A:HIS88
|
2.2
|
43.7
|
1.0
|
C
|
A:CNN302
|
2.7
|
71.5
|
0.7
|
CG
|
A:ASP89
|
3.0
|
74.6
|
1.0
|
CD2
|
A:HIS88
|
3.0
|
43.1
|
1.0
|
HD2
|
A:HIS88
|
3.0
|
51.8
|
1.0
|
CE1
|
A:HIS55
|
3.1
|
41.3
|
1.0
|
CD2
|
A:HIS55
|
3.2
|
41.3
|
1.0
|
HE1
|
A:HIS55
|
3.2
|
49.6
|
1.0
|
CE1
|
A:HIS88
|
3.3
|
44.2
|
1.0
|
OD1
|
A:ASP89
|
3.3
|
82.8
|
1.0
|
HD2
|
A:HIS55
|
3.4
|
49.6
|
1.0
|
HG13
|
A:VAL157
|
3.5
|
50.9
|
1.0
|
HD21
|
A:ASN161
|
3.5
|
56.0
|
1.0
|
HG11
|
A:VAL157
|
3.5
|
50.9
|
1.0
|
HE1
|
A:HIS88
|
3.6
|
53.0
|
1.0
|
HG22
|
A:VAL157
|
3.6
|
50.3
|
1.0
|
N1
|
A:CNN302
|
3.8
|
72.8
|
0.7
|
HN11
|
A:CNN302
|
3.9
|
87.4
|
0.7
|
HZ2
|
A:TRP186
|
3.9
|
53.2
|
1.0
|
CG1
|
A:VAL157
|
4.0
|
42.4
|
1.0
|
CG
|
A:HIS88
|
4.2
|
43.1
|
1.0
|
ND1
|
A:HIS55
|
4.2
|
42.0
|
1.0
|
HG21
|
A:VAL157
|
4.2
|
50.3
|
1.0
|
HB2
|
A:ASP89
|
4.2
|
74.4
|
1.0
|
CB
|
A:ASP89
|
4.2
|
62.0
|
1.0
|
CG
|
A:HIS55
|
4.2
|
42.1
|
1.0
|
ND1
|
A:HIS88
|
4.3
|
44.0
|
1.0
|
CG2
|
A:VAL157
|
4.3
|
41.9
|
1.0
|
ND2
|
A:ASN161
|
4.4
|
46.6
|
1.0
|
HE1
|
A:PHE190
|
4.4
|
50.5
|
1.0
|
HN12
|
A:CNN302
|
4.4
|
87.4
|
0.7
|
HG22
|
A:VAL59
|
4.5
|
57.9
|
1.0
|
HG12
|
A:VAL157
|
4.7
|
50.9
|
1.0
|
CE1
|
A:PHE190
|
4.7
|
42.0
|
1.0
|
CB
|
A:VAL157
|
4.7
|
42.0
|
1.0
|
CZ2
|
A:TRP186
|
4.8
|
44.3
|
1.0
|
HB3
|
A:ASP89
|
4.8
|
74.4
|
1.0
|
HD22
|
A:ASN161
|
4.8
|
56.0
|
1.0
|
HD2
|
A:HIS137
|
4.9
|
53.2
|
1.0
|
HD1
|
A:HIS55
|
4.9
|
50.4
|
1.0
|
NE2
|
A:HIS137
|
4.9
|
44.3
|
1.0
|
HD1
|
A:PHE190
|
5.0
|
50.6
|
1.0
|
|
Zinc binding site 2 out
of 9 in 6dka
Go back to
Zinc Binding Sites List in 6dka
Zinc binding site 2 out
of 9 in the Yeast DDI2 Cyanamide Hydratase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:82.5
occ:0.67
|
HE2
|
B:HIS88
|
1.5
|
45.4
|
1.0
|
N2
|
B:CNN303
|
2.0
|
83.3
|
0.7
|
OD2
|
B:ASP89
|
2.1
|
0.4
|
1.0
|
NE2
|
B:HIS55
|
2.2
|
43.1
|
1.0
|
NE2
|
B:HIS88
|
2.2
|
37.9
|
1.0
|
C
|
B:CNN303
|
2.8
|
85.9
|
0.7
|
CG
|
B:ASP89
|
2.9
|
95.1
|
1.0
|
CD2
|
B:HIS88
|
3.0
|
37.0
|
1.0
|
HD2
|
B:HIS88
|
3.0
|
44.4
|
1.0
|
CD2
|
B:HIS55
|
3.1
|
43.2
|
1.0
|
CE1
|
B:HIS55
|
3.1
|
43.1
|
1.0
|
CE1
|
B:HIS88
|
3.3
|
38.5
|
1.0
|
HD2
|
B:HIS55
|
3.3
|
51.9
|
1.0
|
HG12
|
B:VAL157
|
3.3
|
58.3
|
1.0
|
OD1
|
B:ASP89
|
3.3
|
0.4
|
1.0
|
HE1
|
B:HIS55
|
3.3
|
51.7
|
1.0
|
HD21
|
B:ASN161
|
3.4
|
54.4
|
1.0
|
HG22
|
B:VAL157
|
3.5
|
58.5
|
1.0
|
HG11
|
B:VAL157
|
3.5
|
58.3
|
1.0
|
HE1
|
B:HIS88
|
3.5
|
46.2
|
1.0
|
CG1
|
B:VAL157
|
3.8
|
48.6
|
1.0
|
HZ2
|
B:TRP186
|
3.9
|
53.8
|
1.0
|
N1
|
B:CNN303
|
4.0
|
87.2
|
0.7
|
HG21
|
B:VAL157
|
4.1
|
58.5
|
1.0
|
HN11
|
B:CNN303
|
4.1
|
0.7
|
0.7
|
HB2
|
B:ASP89
|
4.1
|
91.8
|
1.0
|
CG
|
B:HIS88
|
4.1
|
37.1
|
1.0
|
CG2
|
B:VAL157
|
4.1
|
48.7
|
1.0
|
CB
|
B:ASP89
|
4.2
|
76.5
|
1.0
|
ND1
|
B:HIS55
|
4.2
|
43.9
|
1.0
|
CG
|
B:HIS55
|
4.2
|
44.0
|
1.0
|
ND1
|
B:HIS88
|
4.2
|
38.0
|
1.0
|
ND2
|
B:ASN161
|
4.3
|
45.4
|
1.0
|
HG21
|
B:VAL59
|
4.3
|
58.5
|
1.0
|
HE1
|
B:PHE190
|
4.4
|
45.2
|
1.0
|
HN12
|
B:CNN303
|
4.5
|
0.7
|
0.7
|
HG13
|
B:VAL157
|
4.6
|
58.3
|
1.0
|
CB
|
B:VAL157
|
4.6
|
48.0
|
1.0
|
CE1
|
B:PHE190
|
4.7
|
37.7
|
1.0
|
CZ2
|
B:TRP186
|
4.7
|
44.9
|
1.0
|
HD22
|
B:ASN161
|
4.7
|
54.4
|
1.0
|
HB3
|
B:ASP89
|
4.8
|
91.8
|
1.0
|
HH2
|
B:TRP186
|
4.8
|
55.0
|
1.0
|
HA
|
B:VAL157
|
4.9
|
56.6
|
1.0
|
HD2
|
B:HIS137
|
4.9
|
53.1
|
1.0
|
NE2
|
B:HIS137
|
4.9
|
44.3
|
1.0
|
OD1
|
B:ASN161
|
4.9
|
46.3
|
1.0
|
HD1
|
B:HIS55
|
5.0
|
52.7
|
1.0
|
HG23
|
B:VAL157
|
5.0
|
58.5
|
1.0
|
|
Zinc binding site 3 out
of 9 in 6dka
Go back to
Zinc Binding Sites List in 6dka
Zinc binding site 3 out
of 9 in the Yeast DDI2 Cyanamide Hydratase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:62.7
occ:0.67
|
N2
|
C:CNN302
|
2.0
|
63.8
|
0.7
|
OD2
|
C:ASP89
|
2.1
|
70.4
|
1.0
|
NE2
|
C:HIS55
|
2.2
|
35.4
|
1.0
|
NE2
|
C:HIS88
|
2.2
|
33.2
|
1.0
|
C
|
C:CNN302
|
2.3
|
67.0
|
0.7
|
CG
|
C:ASP89
|
2.9
|
65.4
|
1.0
|
CD2
|
C:HIS88
|
3.0
|
33.2
|
1.0
|
CE1
|
C:HIS55
|
3.0
|
35.3
|
1.0
|
HD2
|
C:HIS88
|
3.0
|
39.8
|
1.0
|
HE1
|
C:HIS55
|
3.2
|
42.4
|
1.0
|
CD2
|
C:HIS55
|
3.2
|
35.5
|
1.0
|
HN11
|
C:CNN302
|
3.2
|
82.8
|
0.7
|
OD1
|
C:ASP89
|
3.2
|
71.3
|
1.0
|
N1
|
C:CNN302
|
3.2
|
69.0
|
0.7
|
HG23
|
C:VAL157
|
3.2
|
43.6
|
1.0
|
CE1
|
C:HIS88
|
3.3
|
33.3
|
1.0
|
HD21
|
C:ASN161
|
3.3
|
45.2
|
1.0
|
HD2
|
C:HIS55
|
3.4
|
42.7
|
1.0
|
HG12
|
C:VAL157
|
3.5
|
45.9
|
1.0
|
HE1
|
C:HIS88
|
3.6
|
40.0
|
1.0
|
HG11
|
C:VAL157
|
3.6
|
45.9
|
1.0
|
HN12
|
C:CNN302
|
3.9
|
82.8
|
0.7
|
HZ2
|
C:TRP186
|
3.9
|
37.1
|
1.0
|
CG1
|
C:VAL157
|
4.0
|
38.2
|
1.0
|
ND1
|
C:HIS55
|
4.1
|
35.6
|
1.0
|
CG
|
C:HIS88
|
4.2
|
33.5
|
1.0
|
ND2
|
C:ASN161
|
4.2
|
37.7
|
1.0
|
CG2
|
C:VAL157
|
4.2
|
36.4
|
1.0
|
CG
|
C:HIS55
|
4.2
|
36.0
|
1.0
|
CB
|
C:ASP89
|
4.3
|
55.2
|
1.0
|
ND1
|
C:HIS88
|
4.3
|
33.5
|
1.0
|
HB2
|
C:ASP89
|
4.3
|
66.2
|
1.0
|
HE1
|
C:PHE190
|
4.4
|
42.4
|
1.0
|
HG21
|
C:VAL59
|
4.4
|
47.4
|
1.0
|
HG21
|
C:VAL157
|
4.6
|
43.6
|
1.0
|
HD22
|
C:ASN161
|
4.6
|
45.2
|
1.0
|
HH2
|
C:TRP186
|
4.7
|
37.1
|
1.0
|
CZ2
|
C:TRP186
|
4.7
|
30.9
|
1.0
|
CB
|
C:VAL157
|
4.7
|
37.0
|
1.0
|
CE1
|
C:PHE190
|
4.7
|
35.4
|
1.0
|
HG22
|
C:VAL157
|
4.8
|
43.6
|
1.0
|
HG13
|
C:VAL157
|
4.8
|
45.9
|
1.0
|
HB3
|
C:ASP89
|
4.8
|
66.2
|
1.0
|
HD2
|
C:HIS137
|
4.8
|
50.2
|
1.0
|
NE2
|
C:HIS137
|
4.9
|
41.9
|
1.0
|
HD1
|
C:HIS55
|
4.9
|
42.8
|
1.0
|
HA
|
C:VAL157
|
4.9
|
43.9
|
1.0
|
OD1
|
C:ASN161
|
5.0
|
37.7
|
1.0
|
|
Zinc binding site 4 out
of 9 in 6dka
Go back to
Zinc Binding Sites List in 6dka
Zinc binding site 4 out
of 9 in the Yeast DDI2 Cyanamide Hydratase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn302
b:71.1
occ:0.67
|
N2
|
D:CNN303
|
2.0
|
74.1
|
0.7
|
OD2
|
D:ASP89
|
2.1
|
82.4
|
1.0
|
NE2
|
D:HIS55
|
2.2
|
73.1
|
1.0
|
NE2
|
D:HIS88
|
2.2
|
35.8
|
1.0
|
C
|
D:CNN303
|
2.5
|
79.1
|
0.7
|
CG
|
D:ASP89
|
2.9
|
77.2
|
1.0
|
CD2
|
D:HIS88
|
3.0
|
35.1
|
1.0
|
HD2
|
D:HIS88
|
3.0
|
42.1
|
1.0
|
CE1
|
D:HIS55
|
3.1
|
74.6
|
1.0
|
CD2
|
D:HIS55
|
3.1
|
74.6
|
1.0
|
HG13
|
D:VAL157
|
3.2
|
57.4
|
1.0
|
OD1
|
D:ASP89
|
3.2
|
85.5
|
1.0
|
CE1
|
D:HIS88
|
3.3
|
36.1
|
1.0
|
HE1
|
D:HIS55
|
3.3
|
89.5
|
1.0
|
HD2
|
D:HIS55
|
3.3
|
89.5
|
1.0
|
N1
|
D:CNN303
|
3.4
|
82.5
|
0.7
|
HG11
|
D:VAL157
|
3.5
|
57.4
|
1.0
|
HD21
|
D:ASN161
|
3.5
|
54.4
|
1.0
|
HG22
|
D:VAL157
|
3.5
|
56.7
|
1.0
|
HE1
|
D:HIS88
|
3.5
|
43.3
|
1.0
|
HN12
|
D:CNN303
|
3.7
|
99.0
|
0.7
|
CG1
|
D:VAL157
|
3.8
|
47.8
|
1.0
|
HN11
|
D:CNN303
|
3.8
|
99.0
|
0.7
|
HZ2
|
D:TRP186
|
4.0
|
51.1
|
1.0
|
HG21
|
D:VAL157
|
4.0
|
56.7
|
1.0
|
CG2
|
D:VAL157
|
4.2
|
47.2
|
1.0
|
CG
|
D:HIS88
|
4.2
|
35.1
|
1.0
|
ND1
|
D:HIS55
|
4.2
|
75.0
|
1.0
|
HB2
|
D:ASP89
|
4.2
|
76.3
|
1.0
|
CB
|
D:ASP89
|
4.2
|
63.6
|
1.0
|
CG
|
D:HIS55
|
4.2
|
69.5
|
1.0
|
ND1
|
D:HIS88
|
4.3
|
35.6
|
1.0
|
ND2
|
D:ASN161
|
4.4
|
45.3
|
1.0
|
HG21
|
D:VAL59
|
4.4
|
53.0
|
1.0
|
HE1
|
D:PHE190
|
4.5
|
63.9
|
1.0
|
HG12
|
D:VAL157
|
4.5
|
57.4
|
1.0
|
CB
|
D:VAL157
|
4.6
|
47.5
|
1.0
|
HB3
|
D:ASP89
|
4.8
|
76.3
|
1.0
|
CZ2
|
D:TRP186
|
4.8
|
42.6
|
1.0
|
CE1
|
D:PHE190
|
4.8
|
53.2
|
1.0
|
HH2
|
D:TRP186
|
4.8
|
52.0
|
1.0
|
HA
|
D:VAL157
|
4.9
|
57.7
|
1.0
|
HD22
|
D:ASN161
|
4.9
|
54.4
|
1.0
|
HD1
|
D:HIS55
|
5.0
|
90.0
|
1.0
|
HD2
|
D:HIS137
|
5.0
|
52.0
|
1.0
|
|
Zinc binding site 5 out
of 9 in 6dka
Go back to
Zinc Binding Sites List in 6dka
Zinc binding site 5 out
of 9 in the Yeast DDI2 Cyanamide Hydratase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn301
b:67.7
occ:0.67
|
N2
|
E:CNN302
|
2.0
|
68.9
|
0.7
|
OD2
|
E:ASP89
|
2.1
|
67.7
|
1.0
|
NE2
|
E:HIS55
|
2.2
|
39.9
|
1.0
|
NE2
|
E:HIS88
|
2.2
|
62.8
|
1.0
|
C
|
E:CNN302
|
2.5
|
72.5
|
0.7
|
CG
|
E:ASP89
|
2.9
|
62.4
|
1.0
|
CD2
|
E:HIS88
|
3.0
|
63.0
|
1.0
|
CE1
|
E:HIS55
|
3.0
|
40.1
|
1.0
|
HD2
|
E:HIS88
|
3.0
|
75.7
|
1.0
|
OD1
|
E:ASP89
|
3.1
|
70.0
|
1.0
|
HE1
|
E:HIS55
|
3.2
|
48.1
|
1.0
|
CD2
|
E:HIS55
|
3.2
|
40.1
|
1.0
|
HG23
|
E:VAL157
|
3.2
|
47.4
|
1.0
|
CE1
|
E:HIS88
|
3.3
|
63.0
|
1.0
|
HD21
|
E:ASN161
|
3.4
|
48.3
|
1.0
|
HD2
|
E:HIS55
|
3.4
|
48.1
|
1.0
|
N1
|
E:CNN302
|
3.4
|
75.2
|
0.7
|
HG12
|
E:VAL157
|
3.5
|
49.9
|
1.0
|
HE1
|
E:HIS88
|
3.6
|
75.6
|
1.0
|
HG11
|
E:VAL157
|
3.6
|
49.9
|
1.0
|
HN11
|
E:CNN302
|
3.6
|
90.2
|
0.7
|
HZ2
|
E:TRP186
|
3.9
|
53.5
|
1.0
|
HN12
|
E:CNN302
|
3.9
|
90.2
|
0.7
|
CG1
|
E:VAL157
|
4.0
|
41.6
|
1.0
|
ND1
|
E:HIS55
|
4.1
|
40.6
|
1.0
|
CG
|
E:HIS88
|
4.2
|
55.9
|
1.0
|
CG2
|
E:VAL157
|
4.2
|
39.5
|
1.0
|
CG
|
E:HIS55
|
4.2
|
40.8
|
1.0
|
ND2
|
E:ASN161
|
4.2
|
40.2
|
1.0
|
CB
|
E:ASP89
|
4.2
|
49.8
|
1.0
|
ND1
|
E:HIS88
|
4.3
|
62.8
|
1.0
|
HB2
|
E:ASP89
|
4.3
|
59.7
|
1.0
|
HE1
|
E:PHE190
|
4.3
|
47.8
|
1.0
|
HG22
|
E:VAL59
|
4.4
|
48.6
|
1.0
|
HG21
|
E:VAL157
|
4.6
|
47.4
|
1.0
|
HG22
|
E:VAL157
|
4.7
|
47.4
|
1.0
|
CB
|
E:VAL157
|
4.7
|
40.2
|
1.0
|
CE1
|
E:PHE190
|
4.7
|
39.9
|
1.0
|
HD22
|
E:ASN161
|
4.7
|
48.3
|
1.0
|
CZ2
|
E:TRP186
|
4.7
|
44.6
|
1.0
|
HH2
|
E:TRP186
|
4.8
|
53.8
|
1.0
|
HG13
|
E:VAL157
|
4.8
|
49.9
|
1.0
|
HB3
|
E:ASP89
|
4.8
|
59.7
|
1.0
|
HD1
|
E:HIS55
|
4.9
|
48.7
|
1.0
|
HA
|
E:VAL157
|
4.9
|
48.3
|
1.0
|
OD1
|
E:ASN161
|
4.9
|
39.3
|
1.0
|
HD2
|
E:HIS137
|
4.9
|
50.2
|
1.0
|
NE2
|
E:HIS137
|
5.0
|
41.9
|
1.0
|
HD1
|
E:PHE190
|
5.0
|
47.9
|
1.0
|
|
Zinc binding site 6 out
of 9 in 6dka
Go back to
Zinc Binding Sites List in 6dka
Zinc binding site 6 out
of 9 in the Yeast DDI2 Cyanamide Hydratase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn302
b:69.3
occ:0.67
|
N2
|
F:CNN303
|
2.0
|
70.7
|
0.7
|
OD2
|
F:ASP89
|
2.1
|
85.3
|
1.0
|
NE2
|
F:HIS55
|
2.2
|
43.7
|
1.0
|
NE2
|
F:HIS88
|
2.2
|
41.0
|
1.0
|
C
|
F:CNN303
|
2.5
|
73.9
|
0.7
|
CG
|
F:ASP89
|
3.0
|
80.8
|
1.0
|
CD2
|
F:HIS88
|
3.0
|
41.0
|
1.0
|
CE1
|
F:HIS55
|
3.1
|
43.8
|
1.0
|
HD2
|
F:HIS88
|
3.1
|
49.2
|
1.0
|
CD2
|
F:HIS55
|
3.2
|
43.5
|
1.0
|
HE1
|
F:HIS55
|
3.2
|
52.6
|
1.0
|
HG12
|
F:VAL157
|
3.2
|
54.8
|
1.0
|
CE1
|
F:HIS88
|
3.2
|
41.3
|
1.0
|
OD1
|
F:ASP89
|
3.3
|
89.3
|
1.0
|
HG23
|
F:VAL157
|
3.3
|
55.3
|
1.0
|
HD2
|
F:HIS55
|
3.4
|
52.2
|
1.0
|
N1
|
F:CNN303
|
3.4
|
75.5
|
0.7
|
HD21
|
F:ASN161
|
3.5
|
58.9
|
1.0
|
HE1
|
F:HIS88
|
3.5
|
49.6
|
1.0
|
HG13
|
F:VAL157
|
3.5
|
54.8
|
1.0
|
HN12
|
F:CNN303
|
3.8
|
90.6
|
0.7
|
HN11
|
F:CNN303
|
3.8
|
90.6
|
0.7
|
CG1
|
F:VAL157
|
3.8
|
45.6
|
1.0
|
HZ2
|
F:TRP186
|
4.0
|
53.6
|
1.0
|
ND1
|
F:HIS55
|
4.2
|
44.0
|
1.0
|
CG
|
F:HIS88
|
4.2
|
41.0
|
1.0
|
CG2
|
F:VAL157
|
4.2
|
46.0
|
1.0
|
CG
|
F:HIS55
|
4.3
|
43.5
|
1.0
|
HG21
|
F:VAL59
|
4.3
|
62.3
|
1.0
|
ND1
|
F:HIS88
|
4.3
|
41.1
|
1.0
|
CB
|
F:ASP89
|
4.3
|
67.3
|
1.0
|
HB2
|
F:ASP89
|
4.3
|
80.8
|
1.0
|
ND2
|
F:ASN161
|
4.3
|
49.0
|
1.0
|
HE1
|
F:PHE190
|
4.4
|
57.3
|
1.0
|
HG11
|
F:VAL157
|
4.6
|
54.8
|
1.0
|
HG21
|
F:VAL157
|
4.6
|
55.3
|
1.0
|
CB
|
F:VAL157
|
4.6
|
45.9
|
1.0
|
CE1
|
F:PHE190
|
4.8
|
47.7
|
1.0
|
CZ2
|
F:TRP186
|
4.8
|
44.7
|
1.0
|
HD22
|
F:ASN161
|
4.8
|
58.9
|
1.0
|
HG22
|
F:VAL157
|
4.8
|
55.3
|
1.0
|
HB3
|
F:ASP89
|
4.8
|
80.8
|
1.0
|
HA
|
F:VAL157
|
4.8
|
56.3
|
1.0
|
HH2
|
F:TRP186
|
4.9
|
53.9
|
1.0
|
OD1
|
F:ASN161
|
4.9
|
48.4
|
1.0
|
HD1
|
F:HIS55
|
4.9
|
52.8
|
1.0
|
|
Zinc binding site 7 out
of 9 in 6dka
Go back to
Zinc Binding Sites List in 6dka
Zinc binding site 7 out
of 9 in the Yeast DDI2 Cyanamide Hydratase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn301
b:0.6
occ:0.67
|
HE2
|
G:HIS55
|
1.5
|
72.0
|
1.0
|
N2
|
G:CNN302
|
2.0
|
0.2
|
0.7
|
OD2
|
G:ASP89
|
2.1
|
0.9
|
1.0
|
NE2
|
G:HIS88
|
2.2
|
53.8
|
1.0
|
NE2
|
G:HIS55
|
2.2
|
60.0
|
1.0
|
C
|
G:CNN302
|
2.6
|
0.3
|
0.7
|
CG
|
G:ASP89
|
3.0
|
0.9
|
1.0
|
CD2
|
G:HIS55
|
3.0
|
61.3
|
1.0
|
CD2
|
G:HIS88
|
3.0
|
52.3
|
1.0
|
CE1
|
G:HIS55
|
3.1
|
60.6
|
1.0
|
HD2
|
G:HIS88
|
3.1
|
62.8
|
1.0
|
HD2
|
G:HIS55
|
3.2
|
73.6
|
1.0
|
CE1
|
G:HIS88
|
3.2
|
53.9
|
1.0
|
HD21
|
G:ASN161
|
3.3
|
81.7
|
1.0
|
OD1
|
G:ASP89
|
3.3
|
0.9
|
1.0
|
HE1
|
G:HIS55
|
3.4
|
72.8
|
1.0
|
HG22
|
G:VAL157
|
3.5
|
78.8
|
1.0
|
HE1
|
G:HIS88
|
3.5
|
64.6
|
1.0
|
HG12
|
G:VAL157
|
3.5
|
81.6
|
1.0
|
HN11
|
G:CNN302
|
3.5
|
0.9
|
0.7
|
N1
|
G:CNN302
|
3.6
|
0.9
|
0.7
|
HG11
|
G:VAL157
|
3.6
|
81.6
|
1.0
|
HZ2
|
G:TRP186
|
3.8
|
95.3
|
1.0
|
CG1
|
G:VAL157
|
4.0
|
68.0
|
1.0
|
ND2
|
G:ASN161
|
4.1
|
68.1
|
1.0
|
CG
|
G:HIS55
|
4.1
|
63.4
|
1.0
|
ND1
|
G:HIS55
|
4.2
|
62.5
|
1.0
|
CG
|
G:HIS88
|
4.2
|
51.8
|
1.0
|
CG2
|
G:VAL157
|
4.2
|
65.7
|
1.0
|
HB2
|
G:ASP89
|
4.3
|
0.5
|
1.0
|
ND1
|
G:HIS88
|
4.3
|
52.8
|
1.0
|
HG21
|
G:VAL157
|
4.3
|
78.8
|
1.0
|
CB
|
G:ASP89
|
4.3
|
0.2
|
1.0
|
HN12
|
G:CNN302
|
4.3
|
0.9
|
0.7
|
HG21
|
G:VAL59
|
4.3
|
69.7
|
1.0
|
HE1
|
G:PHE190
|
4.5
|
74.0
|
1.0
|
HD22
|
G:ASN161
|
4.6
|
81.7
|
1.0
|
CZ2
|
G:TRP186
|
4.6
|
79.4
|
1.0
|
HH2
|
G:TRP186
|
4.6
|
96.8
|
1.0
|
CB
|
G:VAL157
|
4.7
|
66.2
|
1.0
|
HG13
|
G:VAL157
|
4.8
|
81.6
|
1.0
|
CE1
|
G:PHE190
|
4.8
|
61.6
|
1.0
|
HA
|
G:VAL157
|
4.8
|
79.9
|
1.0
|
HB3
|
G:ASP89
|
4.8
|
0.5
|
1.0
|
OD1
|
G:ASN161
|
4.9
|
70.4
|
1.0
|
HD1
|
G:HIS55
|
4.9
|
75.0
|
1.0
|
CG
|
G:ASN161
|
5.0
|
69.0
|
1.0
|
|
Zinc binding site 8 out
of 9 in 6dka
Go back to
Zinc Binding Sites List in 6dka
Zinc binding site 8 out
of 9 in the Yeast DDI2 Cyanamide Hydratase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn301
b:0.7
occ:0.65
|
OD2
|
H:ASP89
|
2.1
|
0.7
|
1.0
|
NE2
|
H:HIS55
|
2.2
|
80.9
|
1.0
|
NE2
|
H:HIS88
|
2.2
|
0.7
|
1.0
|
HD2
|
H:HIS88
|
2.8
|
0.9
|
1.0
|
CD2
|
H:HIS88
|
2.8
|
0.4
|
1.0
|
CG
|
H:ASP89
|
2.9
|
0.8
|
1.0
|
OD1
|
H:ASP89
|
3.0
|
0.9
|
1.0
|
CD2
|
H:HIS55
|
3.1
|
81.0
|
1.0
|
CE1
|
H:HIS55
|
3.2
|
80.2
|
1.0
|
HG13
|
H:VAL157
|
3.3
|
0.3
|
1.0
|
HD2
|
H:HIS55
|
3.3
|
97.3
|
1.0
|
HE1
|
H:HIS55
|
3.3
|
96.3
|
1.0
|
CE1
|
H:HIS88
|
3.4
|
0.9
|
1.0
|
HG22
|
H:VAL157
|
3.4
|
0.1
|
1.0
|
HG11
|
H:VAL157
|
3.6
|
0.3
|
1.0
|
HD21
|
H:ASN161
|
3.7
|
0.5
|
1.0
|
HE1
|
H:HIS88
|
3.7
|
0.5
|
1.0
|
CG1
|
H:VAL157
|
3.9
|
0.6
|
1.0
|
HZ2
|
H:TRP186
|
3.9
|
0.1
|
1.0
|
HG21
|
H:VAL157
|
4.1
|
0.1
|
1.0
|
CG
|
H:HIS88
|
4.1
|
0.4
|
1.0
|
CG2
|
H:VAL157
|
4.1
|
0.8
|
1.0
|
ND1
|
H:HIS55
|
4.2
|
80.0
|
1.0
|
CB
|
H:ASP89
|
4.2
|
0.7
|
1.0
|
CG
|
H:HIS55
|
4.3
|
80.9
|
1.0
|
ND1
|
H:HIS88
|
4.3
|
0.8
|
1.0
|
HB2
|
H:ASP89
|
4.3
|
0.9
|
1.0
|
HG21
|
H:VAL59
|
4.3
|
0.9
|
1.0
|
HE1
|
H:PHE190
|
4.4
|
88.1
|
1.0
|
ND2
|
H:ASN161
|
4.5
|
91.3
|
1.0
|
CB
|
H:VAL157
|
4.6
|
0.3
|
1.0
|
HH2
|
H:TRP186
|
4.6
|
0.3
|
1.0
|
HG12
|
H:VAL157
|
4.7
|
0.3
|
1.0
|
CZ2
|
H:TRP186
|
4.7
|
84.3
|
1.0
|
HB3
|
H:ASP89
|
4.8
|
0.9
|
1.0
|
NE2
|
H:HIS137
|
4.8
|
90.3
|
1.0
|
HA
|
H:VAL157
|
4.8
|
0.2
|
1.0
|
CE1
|
H:PHE190
|
4.8
|
73.4
|
1.0
|
HD1
|
H:PHE190
|
4.9
|
87.9
|
1.0
|
HG23
|
H:VAL157
|
5.0
|
0.1
|
1.0
|
HD2
|
H:HIS137
|
5.0
|
0.0
|
1.0
|
HD22
|
H:ASN161
|
5.0
|
0.5
|
1.0
|
|
Zinc binding site 9 out
of 9 in 6dka
Go back to
Zinc Binding Sites List in 6dka
Zinc binding site 9 out
of 9 in the Yeast DDI2 Cyanamide Hydratase
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn500
b:0.4
occ:0.65
|
OD2
|
I:ASP89
|
2.1
|
0.6
|
1.0
|
NE2
|
I:HIS88
|
2.2
|
0.5
|
1.0
|
NE2
|
I:HIS55
|
2.2
|
0.1
|
1.0
|
CE1
|
I:HIS55
|
3.0
|
0.3
|
1.0
|
CG
|
I:ASP89
|
3.0
|
0.7
|
1.0
|
CD2
|
I:HIS88
|
3.0
|
0.8
|
1.0
|
HE1
|
I:HIS55
|
3.1
|
0.0
|
1.0
|
HD2
|
I:HIS88
|
3.1
|
0.0
|
1.0
|
HD21
|
I:ASN161
|
3.1
|
0.8
|
1.0
|
OD1
|
I:ASP89
|
3.2
|
0.4
|
1.0
|
CD2
|
I:HIS55
|
3.3
|
0.9
|
1.0
|
CE1
|
I:HIS88
|
3.3
|
0.1
|
1.0
|
HG23
|
I:VAL157
|
3.4
|
0.3
|
1.0
|
HE1
|
I:HIS88
|
3.5
|
0.2
|
1.0
|
HD2
|
I:HIS55
|
3.5
|
0.1
|
1.0
|
HZ2
|
I:TRP186
|
3.6
|
0.8
|
1.0
|
HG13
|
I:VAL157
|
3.7
|
0.7
|
1.0
|
HE1
|
I:PHE190
|
3.9
|
0.5
|
1.0
|
ND2
|
I:ASN161
|
4.0
|
0.5
|
1.0
|
ND1
|
I:HIS55
|
4.1
|
0.1
|
1.0
|
HG11
|
I:VAL157
|
4.2
|
0.7
|
1.0
|
CG
|
I:HIS88
|
4.2
|
0.5
|
1.0
|
CG2
|
I:VAL157
|
4.3
|
0.1
|
1.0
|
CG
|
I:HIS55
|
4.3
|
0.7
|
1.0
|
ND1
|
I:HIS88
|
4.3
|
0.4
|
1.0
|
CB
|
I:ASP89
|
4.3
|
0.7
|
1.0
|
HG22
|
I:VAL59
|
4.4
|
0.5
|
1.0
|
HG21
|
I:VAL157
|
4.4
|
0.3
|
1.0
|
HB2
|
I:ASP89
|
4.4
|
0.1
|
1.0
|
CG1
|
I:VAL157
|
4.4
|
0.1
|
1.0
|
HD22
|
I:ASN161
|
4.4
|
0.8
|
1.0
|
CE1
|
I:PHE190
|
4.4
|
0.4
|
1.0
|
CZ2
|
I:TRP186
|
4.5
|
0.5
|
1.0
|
HH2
|
I:TRP186
|
4.5
|
0.9
|
1.0
|
OD1
|
I:ASN161
|
4.8
|
1.0
|
1.0
|
HA
|
I:VAL157
|
4.8
|
0.9
|
1.0
|
HD1
|
I:HIS55
|
4.8
|
0.4
|
1.0
|
HB3
|
I:ASP89
|
4.8
|
0.1
|
1.0
|
CG
|
I:ASN161
|
4.8
|
0.5
|
1.0
|
CB
|
I:VAL157
|
4.9
|
0.4
|
1.0
|
CH2
|
I:TRP186
|
4.9
|
0.2
|
1.0
|
HZ
|
I:PHE190
|
4.9
|
0.4
|
1.0
|
HG23
|
I:VAL59
|
4.9
|
0.5
|
1.0
|
HG22
|
I:VAL157
|
5.0
|
0.3
|
1.0
|
CZ
|
I:PHE190
|
5.0
|
0.7
|
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 19:36:53 2024
|