Calcium in PDB 6s58: Avaii Restriction Endonuclease in the Absence of Nucleic Acids
Protein crystallography data
The structure of Avaii Restriction Endonuclease in the Absence of Nucleic Acids, PDB code: 6s58
was solved by
M.Kisiala,
M.Kowalska,
H.Korza,
H.Czapinska,
M.Bochtler,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
51.37 /
2.32
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.231,
102.733,
121.197,
90.00,
90.67,
90.00
|
R / Rfree (%)
|
21.6 /
25.8
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Avaii Restriction Endonuclease in the Absence of Nucleic Acids
(pdb code 6s58). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
Avaii Restriction Endonuclease in the Absence of Nucleic Acids, PDB code: 6s58:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 6s58
Go back to
Calcium Binding Sites List in 6s58
Calcium binding site 1 out
of 5 in the Avaii Restriction Endonuclease in the Absence of Nucleic Acids
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Avaii Restriction Endonuclease in the Absence of Nucleic Acids within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca301
b:56.6
occ:1.00
|
O
|
A:HOH408
|
2.3
|
59.3
|
1.0
|
O
|
A:HOH411
|
2.3
|
53.9
|
1.0
|
O
|
A:HOH429
|
2.3
|
46.1
|
1.0
|
O
|
A:HOH406
|
2.3
|
50.6
|
1.0
|
OD1
|
A:ASP147
|
2.5
|
46.7
|
1.0
|
CG
|
A:ASP147
|
3.8
|
44.8
|
1.0
|
OE2
|
A:GLU123
|
4.0
|
53.5
|
1.0
|
O
|
A:VAL146
|
4.1
|
49.1
|
1.0
|
O
|
A:VAL143
|
4.3
|
51.5
|
1.0
|
O
|
A:CYS138
|
4.3
|
48.2
|
1.0
|
O
|
A:HOH425
|
4.4
|
46.0
|
1.0
|
CA
|
A:ASP147
|
4.4
|
45.9
|
1.0
|
CB
|
A:ASP147
|
4.5
|
45.1
|
1.0
|
O
|
A:GLY140
|
4.5
|
52.9
|
1.0
|
OD2
|
A:ASP147
|
4.7
|
49.1
|
1.0
|
OE1
|
A:GLU123
|
4.7
|
55.0
|
1.0
|
C
|
A:VAL146
|
4.7
|
46.3
|
1.0
|
CD
|
A:GLU123
|
4.8
|
50.1
|
1.0
|
O
|
A:HOH431
|
4.8
|
48.1
|
1.0
|
N
|
A:ASP147
|
4.9
|
45.2
|
1.0
|
|
Calcium binding site 2 out
of 5 in 6s58
Go back to
Calcium Binding Sites List in 6s58
Calcium binding site 2 out
of 5 in the Avaii Restriction Endonuclease in the Absence of Nucleic Acids
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Avaii Restriction Endonuclease in the Absence of Nucleic Acids within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca302
b:85.5
occ:1.00
|
CG
|
A:GLN161
|
3.7
|
51.6
|
1.0
|
CD
|
A:GLN161
|
3.8
|
53.6
|
1.0
|
O
|
A:ASN170
|
3.9
|
82.7
|
1.0
|
OD2
|
A:ASP147
|
3.9
|
49.1
|
1.0
|
O
|
A:VAL162
|
4.0
|
52.9
|
1.0
|
NE2
|
A:GLN161
|
4.1
|
52.7
|
1.0
|
OD1
|
A:ASP147
|
4.2
|
46.7
|
1.0
|
OE1
|
A:GLN161
|
4.3
|
55.5
|
1.0
|
CG
|
A:ASP147
|
4.5
|
44.8
|
1.0
|
O
|
A:HOH431
|
4.5
|
48.1
|
1.0
|
O
|
A:ALA145
|
4.6
|
55.7
|
1.0
|
ND2
|
A:ASN170
|
4.9
|
96.2
|
1.0
|
CG
|
A:LYS163
|
4.9
|
61.6
|
1.0
|
OD1
|
A:ASN170
|
4.9
|
0.4
|
1.0
|
C
|
A:VAL162
|
5.0
|
50.8
|
1.0
|
CG
|
A:ASN170
|
5.0
|
99.1
|
1.0
|
|
Calcium binding site 3 out
of 5 in 6s58
Go back to
Calcium Binding Sites List in 6s58
Calcium binding site 3 out
of 5 in the Avaii Restriction Endonuclease in the Absence of Nucleic Acids
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Avaii Restriction Endonuclease in the Absence of Nucleic Acids within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca301
b:80.3
occ:1.00
|
O
|
C:HOH412
|
2.3
|
78.2
|
1.0
|
O
|
C:HOH405
|
2.4
|
73.9
|
1.0
|
OD1
|
C:ASP147
|
2.4
|
53.8
|
1.0
|
O
|
C:HOH406
|
2.7
|
60.4
|
1.0
|
CG
|
C:ASP147
|
3.6
|
55.7
|
1.0
|
OE2
|
C:GLU123
|
3.8
|
71.5
|
1.0
|
OE1
|
C:GLU123
|
4.1
|
66.1
|
1.0
|
O
|
C:GLY140
|
4.3
|
66.8
|
1.0
|
CD
|
C:GLU123
|
4.3
|
66.3
|
1.0
|
O
|
C:CYS138
|
4.4
|
57.3
|
1.0
|
O
|
C:HOH409
|
4.4
|
72.9
|
1.0
|
O
|
C:VAL146
|
4.4
|
68.6
|
1.0
|
OD2
|
C:ASP147
|
4.5
|
59.4
|
1.0
|
CB
|
C:ASP147
|
4.5
|
57.2
|
1.0
|
CA
|
C:ASP147
|
4.5
|
58.9
|
1.0
|
O
|
C:VAL143
|
4.8
|
58.1
|
1.0
|
O
|
C:HOH415
|
4.9
|
67.0
|
1.0
|
C
|
C:VAL146
|
4.9
|
64.5
|
1.0
|
|
Calcium binding site 4 out
of 5 in 6s58
Go back to
Calcium Binding Sites List in 6s58
Calcium binding site 4 out
of 5 in the Avaii Restriction Endonuclease in the Absence of Nucleic Acids
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Avaii Restriction Endonuclease in the Absence of Nucleic Acids within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca301
b:84.1
occ:1.00
|
OE1
|
D:GLU123
|
2.7
|
70.7
|
1.0
|
OD1
|
D:ASP147
|
2.9
|
80.4
|
1.0
|
CD
|
D:GLU123
|
3.5
|
69.2
|
1.0
|
CG
|
D:ASP147
|
3.6
|
79.1
|
1.0
|
OE2
|
D:GLU123
|
3.9
|
70.9
|
1.0
|
CA
|
D:CA302
|
4.1
|
0.6
|
1.0
|
CB
|
D:ASP147
|
4.1
|
76.5
|
1.0
|
O
|
D:CYS138
|
4.3
|
59.5
|
1.0
|
OD2
|
D:ASP147
|
4.4
|
79.4
|
1.0
|
CA
|
D:ASP147
|
4.5
|
75.4
|
1.0
|
O
|
D:GLY140
|
4.5
|
73.4
|
1.0
|
CG
|
D:GLU123
|
4.7
|
67.0
|
1.0
|
NE1
|
D:TRP137
|
4.9
|
51.6
|
1.0
|
O
|
D:VAL146
|
5.0
|
78.4
|
1.0
|
|
Calcium binding site 5 out
of 5 in 6s58
Go back to
Calcium Binding Sites List in 6s58
Calcium binding site 5 out
of 5 in the Avaii Restriction Endonuclease in the Absence of Nucleic Acids
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Avaii Restriction Endonuclease in the Absence of Nucleic Acids within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca302
b:0.6
occ:1.00
|
O
|
D:VAL162
|
2.7
|
74.3
|
1.0
|
OD2
|
D:ASP147
|
2.7
|
79.4
|
1.0
|
OE2
|
D:GLU123
|
3.2
|
70.9
|
1.0
|
CG
|
D:ASP147
|
3.4
|
79.1
|
1.0
|
OD1
|
D:ASP147
|
3.4
|
80.4
|
1.0
|
CD
|
D:LYS163
|
3.8
|
0.4
|
1.0
|
CE
|
D:LYS163
|
3.9
|
0.7
|
1.0
|
C
|
D:VAL162
|
3.9
|
80.4
|
1.0
|
NZ
|
D:LYS163
|
3.9
|
0.5
|
1.0
|
CD
|
D:GLU123
|
3.9
|
69.2
|
1.0
|
CA
|
D:CA301
|
4.1
|
84.1
|
1.0
|
OE1
|
D:GLU123
|
4.4
|
70.7
|
1.0
|
CG2
|
D:VAL162
|
4.6
|
74.8
|
1.0
|
CB
|
D:ASP147
|
4.7
|
76.5
|
1.0
|
CA
|
D:LYS163
|
4.7
|
86.9
|
1.0
|
N
|
D:VAL162
|
4.7
|
82.5
|
1.0
|
N
|
D:LYS163
|
4.8
|
82.9
|
1.0
|
CG
|
D:GLU123
|
4.8
|
67.0
|
1.0
|
CG
|
D:LYS163
|
4.8
|
97.1
|
1.0
|
CA
|
D:VAL162
|
4.9
|
80.4
|
1.0
|
|
Reference:
M.Kisiala,
M.Kowalska,
M.Pastor,
H.Korza,
H.Czapinska,
M.Bochtler.
Restriction Endonucleases That Cleave Rna/Dna Heteroduplexes Bind Dsdna in A-Like Conformation Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
Page generated: Tue Jul 16 14:31:19 2024
|