Calcium in PDB 6uki: Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0)
Protein crystallography data
The structure of Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0), PDB code: 6uki
was solved by
J.R.Horton,
X.Cheng,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.97 /
2.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.411,
94.998,
97.868,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18 /
22.4
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0)
(pdb code 6uki). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0), PDB code: 6uki:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6uki
Go back to
Calcium Binding Sites List in 6uki
Calcium binding site 1 out
of 4 in the Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Ca301
b:55.4
occ:1.00
|
OP1
|
A:DC9
|
2.1
|
68.5
|
1.0
|
O
|
X:ALA47
|
2.2
|
66.5
|
1.0
|
O
|
X:HOH401
|
2.2
|
29.0
|
1.0
|
OD2
|
X:ASP34
|
2.3
|
42.9
|
1.0
|
OE1
|
X:GLU46
|
2.3
|
60.8
|
1.0
|
CD
|
X:GLU46
|
3.1
|
55.1
|
1.0
|
P
|
A:DC9
|
3.1
|
49.1
|
1.0
|
CG
|
X:ASP34
|
3.2
|
43.1
|
1.0
|
NZ
|
X:LYS48
|
3.3
|
36.2
|
1.0
|
C
|
X:ALA47
|
3.4
|
54.4
|
1.0
|
OD1
|
X:ASP34
|
3.4
|
56.5
|
1.0
|
OP2
|
A:DC9
|
3.4
|
34.5
|
1.0
|
OE2
|
X:GLU46
|
3.8
|
56.9
|
1.0
|
CG
|
X:GLU46
|
3.9
|
52.2
|
1.0
|
N
|
X:ALA47
|
3.9
|
48.0
|
1.0
|
O5'
|
A:DC9
|
4.0
|
42.7
|
1.0
|
CG
|
X:LYS48
|
4.1
|
43.0
|
1.0
|
O
|
X:HOH403
|
4.1
|
55.2
|
1.0
|
CA
|
X:ALA47
|
4.2
|
48.5
|
1.0
|
OP2
|
A:DT10
|
4.3
|
50.4
|
1.0
|
CA
|
A:CA101
|
4.3
|
54.6
|
1.0
|
OE1
|
X:GLU7
|
4.3
|
84.9
|
1.0
|
C5'
|
A:DC9
|
4.3
|
37.7
|
1.0
|
O3'
|
A:DG8
|
4.4
|
54.5
|
1.0
|
N
|
X:LYS48
|
4.4
|
50.5
|
1.0
|
CE
|
X:LYS48
|
4.4
|
46.4
|
1.0
|
CB
|
X:ASP34
|
4.6
|
33.9
|
1.0
|
CB
|
X:ALA47
|
4.6
|
41.8
|
1.0
|
CA
|
X:LYS48
|
4.6
|
45.2
|
1.0
|
C
|
X:GLU46
|
4.7
|
43.4
|
1.0
|
O
|
A:HOH202
|
4.8
|
41.4
|
1.0
|
CD
|
X:LYS48
|
4.9
|
45.0
|
1.0
|
CB
|
X:LYS48
|
4.9
|
42.5
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6uki
Go back to
Calcium Binding Sites List in 6uki
Calcium binding site 2 out
of 4 in the Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca101
b:54.6
occ:1.00
|
OD1
|
X:ASP34
|
2.3
|
56.5
|
1.0
|
O
|
X:HOH403
|
2.4
|
55.2
|
1.0
|
O3'
|
A:DG8
|
2.6
|
54.5
|
1.0
|
OP1
|
A:DC9
|
2.7
|
68.5
|
1.0
|
P
|
A:DC9
|
3.3
|
49.1
|
1.0
|
CG
|
X:ASP34
|
3.5
|
43.1
|
1.0
|
O
|
X:GLU27
|
3.6
|
75.0
|
1.0
|
C3'
|
A:DG8
|
3.9
|
56.7
|
1.0
|
OE1
|
X:GLU7
|
3.9
|
84.9
|
1.0
|
C4'
|
A:DG8
|
4.0
|
46.7
|
1.0
|
OD2
|
X:ASP34
|
4.1
|
42.9
|
1.0
|
CA
|
X:CA301
|
4.3
|
55.4
|
1.0
|
O5'
|
A:DC9
|
4.3
|
42.7
|
1.0
|
C5'
|
A:DC9
|
4.3
|
37.7
|
1.0
|
O
|
X:THR32
|
4.4
|
75.5
|
1.0
|
O
|
X:ASP29
|
4.4
|
59.8
|
1.0
|
OP2
|
A:DC9
|
4.4
|
34.5
|
1.0
|
O
|
X:GLY26
|
4.5
|
81.5
|
1.0
|
CA
|
X:ASP34
|
4.5
|
36.0
|
1.0
|
C2'
|
A:DG8
|
4.5
|
62.4
|
1.0
|
O
|
X:HOH401
|
4.6
|
29.0
|
1.0
|
CB
|
X:ASP34
|
4.6
|
33.9
|
1.0
|
N
|
X:ASP34
|
4.6
|
47.1
|
1.0
|
OE1
|
X:GLU46
|
4.7
|
60.8
|
1.0
|
C5'
|
A:DG8
|
4.8
|
40.9
|
1.0
|
C
|
X:GLU27
|
4.8
|
69.4
|
1.0
|
C
|
X:SER33
|
4.9
|
55.0
|
1.0
|
CD
|
X:GLU7
|
4.9
|
83.8
|
1.0
|
OE2
|
X:GLU46
|
5.0
|
56.9
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6uki
Go back to
Calcium Binding Sites List in 6uki
Calcium binding site 3 out
of 4 in the Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Ca301
b:52.5
occ:1.00
|
OP1
|
D:DC9
|
2.2
|
51.5
|
1.0
|
O
|
Y:HOH402
|
2.2
|
32.8
|
1.0
|
O
|
Y:ALA47
|
2.3
|
54.5
|
1.0
|
OD2
|
Y:ASP34
|
2.3
|
56.7
|
1.0
|
O
|
D:HOH201
|
2.5
|
55.9
|
1.0
|
OE1
|
Y:GLU46
|
2.7
|
46.1
|
1.0
|
CG
|
Y:ASP34
|
3.1
|
51.1
|
1.0
|
OE2
|
Y:GLU46
|
3.1
|
76.2
|
1.0
|
CD
|
Y:GLU46
|
3.2
|
60.5
|
1.0
|
OD1
|
Y:ASP34
|
3.4
|
45.6
|
1.0
|
P
|
D:DC9
|
3.4
|
51.0
|
1.0
|
C
|
Y:ALA47
|
3.4
|
52.5
|
1.0
|
N
|
Y:ALA47
|
3.7
|
52.3
|
1.0
|
OP2
|
D:DC9
|
3.7
|
35.7
|
1.0
|
CA
|
Y:ALA47
|
4.0
|
51.2
|
1.0
|
O5'
|
D:DC9
|
4.2
|
48.7
|
1.0
|
O
|
Y:HOH401
|
4.2
|
41.9
|
1.0
|
NZ
|
Y:LYS48
|
4.3
|
37.7
|
1.0
|
CA
|
D:CA101
|
4.3
|
63.0
|
1.0
|
CB
|
Y:ALA47
|
4.4
|
34.5
|
1.0
|
CE
|
Y:LYS48
|
4.4
|
44.9
|
1.0
|
CB
|
Y:ASP34
|
4.4
|
39.5
|
1.0
|
OE2
|
Y:GLU7
|
4.4
|
59.7
|
1.0
|
CD
|
Y:LYS48
|
4.4
|
55.4
|
1.0
|
C
|
Y:GLU46
|
4.5
|
48.0
|
1.0
|
N
|
Y:LYS48
|
4.5
|
53.4
|
1.0
|
CG
|
Y:GLU46
|
4.5
|
54.0
|
1.0
|
C5'
|
D:DC9
|
4.6
|
45.9
|
1.0
|
OP2
|
D:DT10
|
4.6
|
39.8
|
1.0
|
O3'
|
D:DG8
|
4.6
|
72.2
|
1.0
|
CG
|
Y:LYS48
|
4.6
|
53.9
|
1.0
|
CA
|
Y:GLU46
|
4.8
|
42.5
|
1.0
|
CB
|
Y:GLU46
|
4.8
|
36.0
|
1.0
|
CA
|
Y:LYS48
|
4.8
|
53.2
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6uki
Go back to
Calcium Binding Sites List in 6uki
Calcium binding site 4 out
of 4 in the Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Hhai Endonuclease in Complex with Dna in Space Group P212121 (pH 6.0) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca101
b:63.0
occ:1.00
|
O
|
Y:HOH401
|
2.2
|
41.9
|
1.0
|
OD1
|
Y:ASP34
|
2.4
|
45.6
|
1.0
|
O3'
|
D:DG8
|
2.6
|
72.2
|
1.0
|
OP1
|
D:DC9
|
2.9
|
51.5
|
1.0
|
P
|
D:DC9
|
3.3
|
51.0
|
1.0
|
CG
|
Y:ASP34
|
3.6
|
51.1
|
1.0
|
C3'
|
D:DG8
|
3.8
|
61.6
|
1.0
|
C4'
|
D:DG8
|
3.9
|
47.4
|
1.0
|
O
|
Y:ASP29
|
3.9
|
68.8
|
1.0
|
OE2
|
Y:GLU46
|
3.9
|
76.2
|
1.0
|
O
|
Y:THR32
|
4.1
|
67.9
|
1.0
|
OP2
|
D:DC9
|
4.2
|
35.7
|
1.0
|
OD2
|
Y:ASP34
|
4.3
|
56.7
|
1.0
|
CA
|
Y:CA301
|
4.3
|
52.5
|
1.0
|
C5'
|
D:DG8
|
4.4
|
48.3
|
1.0
|
N
|
Y:ASP34
|
4.4
|
33.4
|
1.0
|
OE2
|
Y:GLU7
|
4.5
|
59.7
|
1.0
|
C
|
Y:SER33
|
4.5
|
42.8
|
1.0
|
O5'
|
D:DC9
|
4.5
|
48.7
|
1.0
|
CA
|
Y:ASP34
|
4.5
|
45.1
|
1.0
|
C5'
|
D:DC9
|
4.7
|
45.9
|
1.0
|
CB
|
Y:ASP34
|
4.7
|
39.5
|
1.0
|
C2'
|
D:DG8
|
4.7
|
63.3
|
1.0
|
CA
|
Y:SER33
|
4.8
|
41.2
|
1.0
|
O
|
Y:HOH402
|
4.8
|
32.8
|
1.0
|
O
|
Y:SER33
|
4.9
|
57.3
|
1.0
|
CD
|
Y:GLU46
|
5.0
|
60.5
|
1.0
|
|
Reference:
J.R.Horton,
J.Yang,
X.Zhang,
T.Petronzio,
A.Fomenkov,
G.G.Wilson,
R.J.Roberts,
X.Cheng.
Structure of Hhai Endonuclease with Cognate Dna at An Atomic Resolution of 1.0 Angstrom Nucleic Acids Res. 2019.
ISSN: ESSN 1362-4962
Page generated: Tue Jul 16 15:56:04 2024
|