Cobalt in PDB 7qaz: Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex
Protein crystallography data
The structure of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex, PDB code: 7qaz
was solved by
A.W.H.Li,
A.J.Doherty,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
56.98 /
2.11
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
227.91,
39.62,
79.77,
90,
90,
90
|
R / Rfree (%)
|
21 /
26.1
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex
(pdb code 7qaz). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the
Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex, PDB code: 7qaz:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
7;
Cobalt binding site 1 out
of 7 in 7qaz
Go back to
Cobalt Binding Sites List in 7qaz
Cobalt binding site 1 out
of 7 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co401
b:38.4
occ:1.00
|
O
|
A:HOH521
|
1.9
|
28.4
|
1.0
|
O2B
|
A:DZ4402
|
2.2
|
34.6
|
1.0
|
O1A
|
A:DZ4402
|
2.2
|
37.3
|
1.0
|
O3G
|
A:DZ4402
|
2.3
|
31.0
|
1.0
|
OD1
|
A:ASP179
|
2.4
|
38.1
|
1.0
|
OD1
|
A:ASP177
|
2.4
|
33.0
|
1.0
|
OD2
|
A:ASP177
|
2.8
|
37.5
|
1.0
|
CG
|
A:ASP177
|
2.9
|
35.2
|
1.0
|
OD2
|
A:ASP179
|
3.0
|
42.9
|
1.0
|
CG
|
A:ASP179
|
3.0
|
37.7
|
1.0
|
PB
|
A:DZ4402
|
3.2
|
30.6
|
1.0
|
PA
|
A:DZ4402
|
3.2
|
45.4
|
1.0
|
PG
|
A:DZ4402
|
3.4
|
28.5
|
1.0
|
N3A
|
A:DZ4402
|
3.5
|
32.6
|
1.0
|
O
|
A:HOH501
|
3.6
|
37.6
|
1.0
|
O3B
|
A:DZ4402
|
3.6
|
38.9
|
1.0
|
O5'
|
A:DZ4402
|
3.7
|
43.6
|
1.0
|
NE
|
A:ARG223
|
4.2
|
35.7
|
1.0
|
O1G
|
A:DZ4402
|
4.2
|
30.6
|
1.0
|
CB
|
A:ASP177
|
4.4
|
31.8
|
1.0
|
CB
|
A:ASP179
|
4.4
|
28.9
|
1.0
|
O1B
|
A:DZ4402
|
4.5
|
35.3
|
1.0
|
O2G
|
A:DZ4402
|
4.5
|
34.4
|
1.0
|
O2A
|
A:DZ4402
|
4.6
|
44.1
|
1.0
|
NH2
|
A:ARG223
|
4.6
|
32.8
|
1.0
|
NE2
|
A:HIS226
|
4.6
|
33.4
|
1.0
|
O
|
A:ILE178
|
4.6
|
37.2
|
1.0
|
OG1
|
A:THR220
|
4.7
|
31.1
|
1.0
|
CZ
|
A:ARG223
|
4.7
|
38.9
|
1.0
|
CA
|
A:ASP179
|
4.9
|
35.8
|
1.0
|
CG2
|
A:THR220
|
4.9
|
29.6
|
1.0
|
CD
|
A:ARG223
|
4.9
|
30.7
|
1.0
|
|
Cobalt binding site 2 out
of 7 in 7qaz
Go back to
Cobalt Binding Sites List in 7qaz
Cobalt binding site 2 out
of 7 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co401
b:60.9
occ:1.00
|
O3'
|
B:GTP405
|
2.1
|
55.1
|
1.0
|
OD2
|
B:ASP179
|
2.2
|
43.7
|
1.0
|
OD2
|
B:ASP177
|
2.3
|
36.7
|
1.0
|
O1A
|
B:DZ4404
|
2.7
|
34.6
|
1.0
|
OE1
|
B:GLU260
|
2.7
|
47.0
|
1.0
|
O
|
B:HOH574
|
2.8
|
51.3
|
1.0
|
CG
|
B:ASP177
|
3.4
|
31.7
|
1.0
|
CG
|
B:ASP179
|
3.4
|
43.4
|
1.0
|
O
|
B:HOH502
|
3.4
|
36.5
|
1.0
|
C3'
|
B:GTP405
|
3.5
|
53.0
|
1.0
|
CO
|
B:CO402
|
3.6
|
35.1
|
1.0
|
CD
|
B:GLU260
|
3.6
|
46.3
|
1.0
|
PA
|
B:DZ4404
|
3.8
|
31.6
|
1.0
|
O2'
|
B:GTP405
|
3.8
|
47.9
|
1.0
|
O5'
|
B:DZ4404
|
4.0
|
43.7
|
1.0
|
OD1
|
B:ASP177
|
4.0
|
34.5
|
1.0
|
C5'
|
B:DZ4404
|
4.1
|
32.9
|
1.0
|
NH2
|
B:ARG223
|
4.1
|
39.2
|
1.0
|
OD1
|
B:ASP179
|
4.1
|
48.4
|
1.0
|
C4'
|
B:GTP405
|
4.1
|
55.6
|
1.0
|
C2'
|
B:GTP405
|
4.2
|
50.2
|
1.0
|
CG
|
B:GLU260
|
4.3
|
37.0
|
1.0
|
CB
|
B:GLU260
|
4.3
|
33.9
|
1.0
|
CB
|
B:ASP177
|
4.3
|
36.1
|
1.0
|
CB
|
B:ASP179
|
4.4
|
38.3
|
1.0
|
O2A
|
B:DZ4404
|
4.4
|
41.6
|
1.0
|
OE2
|
B:GLU260
|
4.5
|
54.0
|
1.0
|
O2B
|
B:DZ4404
|
4.8
|
33.0
|
1.0
|
O
|
B:ASP177
|
4.8
|
31.2
|
1.0
|
C5'
|
B:GTP405
|
4.9
|
61.3
|
1.0
|
CZ
|
B:ARG223
|
5.0
|
40.9
|
1.0
|
|
Cobalt binding site 3 out
of 7 in 7qaz
Go back to
Cobalt Binding Sites List in 7qaz
Cobalt binding site 3 out
of 7 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 3 of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co402
b:35.1
occ:1.00
|
O1G
|
B:DZ4404
|
2.1
|
33.2
|
1.0
|
O2B
|
B:DZ4404
|
2.2
|
33.0
|
1.0
|
OD1
|
B:ASP179
|
2.2
|
48.4
|
1.0
|
O1A
|
B:DZ4404
|
2.5
|
34.6
|
1.0
|
OD1
|
B:ASP177
|
2.5
|
34.5
|
1.0
|
O
|
B:HOH530
|
2.5
|
31.5
|
1.0
|
OD2
|
B:ASP179
|
2.8
|
43.7
|
1.0
|
CG
|
B:ASP179
|
2.8
|
43.4
|
1.0
|
OD2
|
B:ASP177
|
2.9
|
36.7
|
1.0
|
CG
|
B:ASP177
|
3.0
|
31.7
|
1.0
|
PB
|
B:DZ4404
|
3.2
|
33.3
|
1.0
|
PG
|
B:DZ4404
|
3.3
|
32.6
|
1.0
|
PA
|
B:DZ4404
|
3.4
|
31.6
|
1.0
|
O3B
|
B:DZ4404
|
3.6
|
37.7
|
1.0
|
N3A
|
B:DZ4404
|
3.6
|
26.3
|
1.0
|
CO
|
B:CO401
|
3.6
|
60.9
|
1.0
|
O5'
|
B:DZ4404
|
3.9
|
43.7
|
1.0
|
NE2
|
B:HIS226
|
4.1
|
31.4
|
1.0
|
O2G
|
B:DZ4404
|
4.2
|
33.8
|
1.0
|
CB
|
B:ASP179
|
4.3
|
38.3
|
1.0
|
NE
|
B:ARG223
|
4.3
|
38.5
|
1.0
|
O3G
|
B:DZ4404
|
4.4
|
35.9
|
1.0
|
CB
|
B:ASP177
|
4.5
|
36.1
|
1.0
|
O1B
|
B:DZ4404
|
4.5
|
36.1
|
1.0
|
CD2
|
B:HIS226
|
4.6
|
27.2
|
1.0
|
O
|
B:ILE178
|
4.6
|
40.1
|
1.0
|
NH2
|
B:ARG223
|
4.6
|
39.2
|
1.0
|
OG1
|
B:THR220
|
4.7
|
31.3
|
1.0
|
O2A
|
B:DZ4404
|
4.8
|
41.6
|
1.0
|
CA
|
B:ASP179
|
4.8
|
38.7
|
1.0
|
O3'
|
B:GTP405
|
4.8
|
55.1
|
1.0
|
CZ
|
B:ARG223
|
4.9
|
40.9
|
1.0
|
C5'
|
B:DZ4404
|
5.0
|
32.9
|
1.0
|
|
Cobalt binding site 4 out
of 7 in 7qaz
Go back to
Cobalt Binding Sites List in 7qaz
Cobalt binding site 4 out
of 7 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 4 of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co403
b:87.2
occ:1.00
|
OD1
|
B:ASP296
|
2.2
|
50.1
|
1.0
|
O3G
|
B:DZ4406
|
2.6
|
72.4
|
1.0
|
O1A
|
B:DZ4406
|
2.8
|
67.7
|
1.0
|
O2B
|
B:DZ4406
|
3.0
|
73.4
|
1.0
|
CG
|
B:ASP296
|
3.3
|
47.6
|
1.0
|
O3B
|
B:DZ4406
|
3.5
|
78.1
|
1.0
|
PG
|
B:DZ4406
|
3.6
|
77.8
|
1.0
|
PB
|
B:DZ4406
|
3.7
|
80.9
|
1.0
|
OD2
|
B:ASP296
|
3.8
|
57.8
|
1.0
|
PA
|
B:DZ4406
|
4.0
|
68.0
|
1.0
|
N3A
|
B:DZ4406
|
4.0
|
74.0
|
1.0
|
O1G
|
B:DZ4406
|
4.2
|
76.9
|
1.0
|
NZ
|
B:LYS202
|
4.2
|
50.2
|
1.0
|
O
|
B:HOH504
|
4.3
|
52.1
|
1.0
|
ND2
|
B:ASN295
|
4.4
|
50.3
|
1.0
|
CB
|
B:ASP296
|
4.6
|
38.0
|
1.0
|
O2G
|
B:DZ4406
|
4.8
|
70.0
|
1.0
|
CA
|
B:ASP296
|
4.8
|
34.2
|
1.0
|
O2A
|
B:DZ4406
|
4.9
|
66.0
|
1.0
|
|
Cobalt binding site 5 out
of 7 in 7qaz
Go back to
Cobalt Binding Sites List in 7qaz
Cobalt binding site 5 out
of 7 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 5 of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co401
b:55.5
occ:1.00
|
OD2
|
C:ASP179
|
1.9
|
38.2
|
1.0
|
OD2
|
C:ASP177
|
2.2
|
32.8
|
1.0
|
O2A
|
C:DZ4403
|
2.4
|
29.9
|
1.0
|
OE1
|
C:GLU260
|
2.7
|
50.5
|
1.0
|
CG
|
C:ASP179
|
3.0
|
28.9
|
1.0
|
PA
|
C:DZ4403
|
3.3
|
31.8
|
1.0
|
CG
|
C:ASP177
|
3.3
|
34.5
|
1.0
|
O5'
|
C:DZ4403
|
3.4
|
31.9
|
1.0
|
OD1
|
C:ASP179
|
3.5
|
29.4
|
1.0
|
CO
|
C:CO402
|
3.5
|
29.3
|
1.0
|
O1A
|
C:DZ4403
|
3.6
|
34.2
|
1.0
|
O
|
C:HOH578
|
3.6
|
35.9
|
1.0
|
CD
|
C:GLU260
|
3.7
|
46.2
|
1.0
|
C5'
|
C:DZ4403
|
3.8
|
34.5
|
1.0
|
NH2
|
C:ARG223
|
3.8
|
34.7
|
1.0
|
OD1
|
C:ASP177
|
3.9
|
28.5
|
1.0
|
CB
|
C:ASP179
|
4.3
|
27.7
|
1.0
|
CG
|
C:GLU260
|
4.3
|
32.2
|
1.0
|
CB
|
C:ASP177
|
4.5
|
26.9
|
1.0
|
O2B
|
C:DZ4403
|
4.7
|
27.4
|
1.0
|
OE2
|
C:GLU260
|
4.7
|
54.8
|
1.0
|
CZ
|
C:ARG223
|
4.7
|
33.7
|
1.0
|
O3G
|
C:DZ4403
|
4.7
|
25.8
|
1.0
|
CB
|
C:GLU260
|
4.8
|
31.1
|
1.0
|
N3A
|
C:DZ4403
|
4.8
|
28.5
|
1.0
|
|
Cobalt binding site 6 out
of 7 in 7qaz
Go back to
Cobalt Binding Sites List in 7qaz
Cobalt binding site 6 out
of 7 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 6 of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co402
b:29.3
occ:1.00
|
OD1
|
C:ASP179
|
1.9
|
29.4
|
1.0
|
O
|
C:HOH529
|
2.0
|
24.4
|
1.0
|
O2B
|
C:DZ4403
|
2.0
|
27.4
|
1.0
|
O2A
|
C:DZ4403
|
2.1
|
29.9
|
1.0
|
OD1
|
C:ASP177
|
2.1
|
28.5
|
1.0
|
O3G
|
C:DZ4403
|
2.2
|
25.8
|
1.0
|
CG
|
C:ASP179
|
2.9
|
28.9
|
1.0
|
CG
|
C:ASP177
|
2.9
|
34.5
|
1.0
|
OD2
|
C:ASP177
|
3.1
|
32.8
|
1.0
|
PB
|
C:DZ4403
|
3.2
|
30.2
|
1.0
|
OD2
|
C:ASP179
|
3.2
|
38.2
|
1.0
|
PA
|
C:DZ4403
|
3.3
|
31.8
|
1.0
|
PG
|
C:DZ4403
|
3.3
|
30.6
|
1.0
|
CO
|
C:CO401
|
3.5
|
55.5
|
1.0
|
O3B
|
C:DZ4403
|
3.6
|
28.8
|
1.0
|
N3A
|
C:DZ4403
|
3.7
|
28.5
|
1.0
|
O1G
|
C:DZ4403
|
4.0
|
28.3
|
1.0
|
NE2
|
C:HIS226
|
4.3
|
24.4
|
1.0
|
CB
|
C:ASP179
|
4.3
|
27.7
|
1.0
|
O1A
|
C:DZ4403
|
4.3
|
34.2
|
1.0
|
C5'
|
C:DZ4403
|
4.4
|
34.5
|
1.0
|
O5'
|
C:DZ4403
|
4.4
|
31.9
|
1.0
|
CB
|
C:ASP177
|
4.4
|
26.9
|
1.0
|
OG1
|
C:THR220
|
4.4
|
28.2
|
1.0
|
O1B
|
C:DZ4403
|
4.5
|
25.0
|
1.0
|
O
|
C:ILE178
|
4.5
|
34.0
|
1.0
|
O2G
|
C:DZ4403
|
4.5
|
30.5
|
1.0
|
NE
|
C:ARG223
|
4.6
|
39.2
|
1.0
|
CA
|
C:ASP179
|
4.7
|
29.5
|
1.0
|
CD2
|
C:HIS226
|
4.7
|
28.0
|
1.0
|
C
|
C:ILE178
|
4.8
|
33.4
|
1.0
|
NH2
|
C:ARG223
|
4.9
|
34.7
|
1.0
|
CG2
|
C:THR220
|
4.9
|
29.1
|
1.0
|
CB
|
C:THR220
|
4.9
|
27.9
|
1.0
|
N
|
C:ASP179
|
4.9
|
32.0
|
1.0
|
C
|
C:ASP177
|
5.0
|
25.4
|
1.0
|
CA
|
C:ASP177
|
5.0
|
28.8
|
1.0
|
CG
|
C:ARG223
|
5.0
|
33.5
|
1.0
|
|
Cobalt binding site 7 out
of 7 in 7qaz
Go back to
Cobalt Binding Sites List in 7qaz
Cobalt binding site 7 out
of 7 in the Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 7 of Prim-Pol Domain of Crispr-Associated Prim-Pol (Capp) From Marinitoga Sp. 1137 - Primer Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co101
b:88.1
occ:1.00
|
O
|
B:HOH617
|
2.2
|
51.5
|
1.0
|
O2B
|
B:GTP405
|
2.2
|
71.2
|
1.0
|
N7
|
B:GTP405
|
2.4
|
54.7
|
1.0
|
O
|
B:HOH510
|
2.6
|
61.5
|
1.0
|
O6
|
B:GTP405
|
3.1
|
52.0
|
1.0
|
C5
|
B:GTP405
|
3.3
|
53.8
|
1.0
|
C8
|
B:GTP405
|
3.5
|
55.8
|
1.0
|
PB
|
B:GTP405
|
3.5
|
85.7
|
1.0
|
C6
|
B:GTP405
|
3.6
|
49.1
|
1.0
|
O3G
|
B:GTP405
|
3.8
|
78.4
|
1.0
|
O
|
B:HOH588
|
4.0
|
57.8
|
1.0
|
O3B
|
B:GTP405
|
4.1
|
79.9
|
1.0
|
O3A
|
B:GTP405
|
4.2
|
76.9
|
1.0
|
O2G
|
B:GTP405
|
4.2
|
81.6
|
1.0
|
PG
|
B:GTP405
|
4.2
|
88.6
|
1.0
|
C4
|
B:GTP405
|
4.5
|
51.8
|
1.0
|
N9
|
B:GTP405
|
4.6
|
55.9
|
1.0
|
O1B
|
B:GTP405
|
4.7
|
77.2
|
1.0
|
O
|
D:HOH203
|
4.8
|
49.1
|
1.0
|
N6
|
B:DZ4404
|
4.8
|
40.0
|
1.0
|
N1
|
B:GTP405
|
5.0
|
46.0
|
1.0
|
|
Reference:
A.W.H.Li,
K.Zabrady,
L.J.Bainbridge,
M.Zabrady,
S.Naseem-Khan,
M.B.Berger,
P.Kolesar,
G.A.Cisneros,
A.J.Doherty.
Molecular Basis For the Initiation of Dna Primer Synthesis. Nature V. 605 767 2022.
ISSN: ESSN 1476-4687
PubMed: 35508653
DOI: 10.1038/S41586-022-04695-0
Page generated: Tue Jul 30 19:22:44 2024
|