Calcium in PDB 6qe7: Anti-Sigma Factor Domain-Containing Protein
Protein crystallography data
The structure of Anti-Sigma Factor Domain-Containing Protein, PDB code: 6qe7
was solved by
M.Voronov,
O.Livnah,
E.A.Bayer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.42 /
2.06
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.340,
121.670,
65.940,
90.00,
106.39,
90.00
|
R / Rfree (%)
|
18.7 /
25.5
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Anti-Sigma Factor Domain-Containing Protein
(pdb code 6qe7). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Anti-Sigma Factor Domain-Containing Protein, PDB code: 6qe7:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 6qe7
Go back to
Calcium Binding Sites List in 6qe7
Calcium binding site 1 out
of 6 in the Anti-Sigma Factor Domain-Containing Protein
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Anti-Sigma Factor Domain-Containing Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:30.9
occ:1.00
|
OE1
|
A:GLN130
|
2.3
|
31.1
|
1.0
|
OD1
|
A:ASP86
|
2.3
|
27.4
|
1.0
|
O
|
A:ALA134
|
2.3
|
27.8
|
1.0
|
O
|
A:VAL132
|
2.3
|
23.7
|
1.0
|
OD1
|
A:ASP87
|
2.4
|
30.2
|
1.0
|
O
|
A:HOH551
|
2.7
|
33.8
|
1.0
|
O
|
A:HOH570
|
2.7
|
33.2
|
1.0
|
CG
|
A:ASP86
|
3.2
|
32.6
|
1.0
|
CG
|
A:ASP87
|
3.3
|
27.8
|
1.0
|
CD
|
A:GLN130
|
3.4
|
27.2
|
1.0
|
C
|
A:VAL132
|
3.5
|
31.6
|
1.0
|
C
|
A:ALA134
|
3.5
|
26.9
|
1.0
|
OD2
|
A:ASP86
|
3.6
|
33.4
|
1.0
|
OD2
|
A:ASP87
|
3.6
|
29.3
|
1.0
|
N
|
A:VAL132
|
3.8
|
26.3
|
1.0
|
N
|
A:ALA134
|
3.9
|
31.7
|
1.0
|
NE2
|
A:GLN130
|
3.9
|
27.8
|
1.0
|
C
|
A:ARG133
|
4.1
|
33.0
|
1.0
|
N
|
A:HIS131
|
4.2
|
28.4
|
1.0
|
CA
|
A:VAL132
|
4.3
|
30.6
|
1.0
|
CA
|
A:ALA134
|
4.3
|
32.7
|
1.0
|
C
|
A:ASP86
|
4.3
|
29.4
|
1.0
|
N
|
A:ASP87
|
4.3
|
25.9
|
1.0
|
O
|
A:ASP86
|
4.4
|
27.1
|
1.0
|
N
|
A:ALA135
|
4.5
|
30.2
|
1.0
|
N
|
A:ARG133
|
4.5
|
38.8
|
1.0
|
CB
|
A:ASP86
|
4.5
|
34.7
|
1.0
|
C
|
A:HIS131
|
4.6
|
27.0
|
1.0
|
O
|
A:ARG133
|
4.6
|
35.1
|
1.0
|
CB
|
A:ASP87
|
4.6
|
28.2
|
1.0
|
CG
|
A:GLN130
|
4.6
|
26.4
|
1.0
|
CA
|
A:ARG133
|
4.7
|
31.2
|
1.0
|
CA
|
A:ALA135
|
4.7
|
27.0
|
1.0
|
CB
|
A:ARG133
|
4.7
|
30.3
|
1.0
|
CA
|
A:GLN130
|
4.8
|
24.8
|
1.0
|
CA
|
A:HIS131
|
4.8
|
28.3
|
1.0
|
CA
|
A:ASP87
|
4.8
|
28.1
|
1.0
|
CA
|
A:ASP86
|
4.9
|
32.8
|
1.0
|
C
|
A:GLN130
|
5.0
|
25.5
|
1.0
|
CB
|
A:GLN130
|
5.0
|
24.3
|
1.0
|
|
Calcium binding site 2 out
of 6 in 6qe7
Go back to
Calcium Binding Sites List in 6qe7
Calcium binding site 2 out
of 6 in the Anti-Sigma Factor Domain-Containing Protein
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Anti-Sigma Factor Domain-Containing Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:27.8
occ:1.00
|
O
|
A:ASN29
|
2.3
|
22.6
|
1.0
|
OG1
|
A:THR62
|
2.4
|
26.9
|
1.0
|
O
|
A:HOH579
|
2.4
|
28.6
|
1.0
|
O
|
A:THR62
|
2.4
|
22.0
|
1.0
|
O
|
A:HOH519
|
2.4
|
25.6
|
1.0
|
O
|
A:HOH521
|
2.5
|
28.5
|
1.0
|
O
|
A:HOH627
|
2.5
|
28.3
|
1.0
|
O
|
A:ASP61
|
2.6
|
24.1
|
1.0
|
C
|
A:THR62
|
3.3
|
26.8
|
1.0
|
C
|
A:ASN29
|
3.4
|
24.0
|
1.0
|
CB
|
A:THR62
|
3.5
|
25.8
|
1.0
|
C
|
A:ASP61
|
3.6
|
25.5
|
1.0
|
CA
|
A:THR62
|
3.8
|
27.2
|
1.0
|
N
|
A:THR62
|
4.1
|
24.3
|
1.0
|
CA
|
A:ASN29
|
4.3
|
27.0
|
1.0
|
N
|
A:TYR63
|
4.3
|
20.7
|
1.0
|
N
|
A:ASN30
|
4.3
|
26.2
|
1.0
|
O
|
A:HOH569
|
4.4
|
43.0
|
1.0
|
O
|
A:GLY59
|
4.4
|
29.6
|
1.0
|
O
|
A:LYS60
|
4.4
|
27.7
|
1.0
|
CA
|
A:ASN30
|
4.5
|
26.3
|
1.0
|
OD1
|
A:ASN30
|
4.6
|
25.7
|
1.0
|
OD1
|
A:ASN29
|
4.6
|
29.3
|
1.0
|
O
|
A:HOH651
|
4.6
|
39.2
|
1.0
|
CB
|
A:ASN29
|
4.6
|
27.6
|
1.0
|
CG2
|
A:THR62
|
4.7
|
29.4
|
1.0
|
CA
|
A:TYR63
|
4.7
|
21.7
|
1.0
|
O
|
A:HOH658
|
4.9
|
36.9
|
1.0
|
CB
|
A:TYR63
|
4.9
|
21.4
|
1.0
|
CA
|
A:ASP61
|
4.9
|
28.6
|
1.0
|
|
Calcium binding site 3 out
of 6 in 6qe7
Go back to
Calcium Binding Sites List in 6qe7
Calcium binding site 3 out
of 6 in the Anti-Sigma Factor Domain-Containing Protein
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Anti-Sigma Factor Domain-Containing Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca401
b:35.0
occ:1.00
|
OD1
|
B:ASP86
|
2.1
|
28.5
|
1.0
|
O
|
B:VAL132
|
2.2
|
34.5
|
1.0
|
OE1
|
B:GLN130
|
2.3
|
34.8
|
1.0
|
O
|
B:ALA134
|
2.4
|
39.9
|
1.0
|
OD1
|
B:ASP87
|
2.4
|
41.3
|
1.0
|
O
|
B:HOH512
|
2.6
|
36.8
|
1.0
|
O
|
B:HOH532
|
2.7
|
45.8
|
1.0
|
CG
|
B:ASP86
|
3.2
|
41.1
|
1.0
|
CG
|
B:ASP87
|
3.2
|
42.6
|
1.0
|
C
|
B:VAL132
|
3.4
|
41.4
|
1.0
|
CD
|
B:GLN130
|
3.4
|
36.9
|
1.0
|
OD2
|
B:ASP87
|
3.4
|
42.2
|
1.0
|
C
|
B:ALA134
|
3.6
|
44.2
|
1.0
|
OD2
|
B:ASP86
|
3.7
|
41.1
|
1.0
|
N
|
B:VAL132
|
3.7
|
37.7
|
1.0
|
NE2
|
B:GLN130
|
3.9
|
34.4
|
1.0
|
N
|
B:ALA134
|
4.1
|
33.4
|
1.0
|
C
|
B:ARG133
|
4.2
|
36.3
|
1.0
|
CA
|
B:VAL132
|
4.2
|
42.8
|
1.0
|
C
|
B:ASP86
|
4.3
|
36.5
|
1.0
|
N
|
B:HIS131
|
4.3
|
44.6
|
1.0
|
N
|
B:ASP87
|
4.4
|
37.2
|
1.0
|
O
|
B:ASP86
|
4.4
|
31.4
|
1.0
|
N
|
B:ARG133
|
4.4
|
43.4
|
1.0
|
CB
|
B:ASP86
|
4.4
|
41.8
|
1.0
|
CA
|
B:ALA134
|
4.5
|
39.5
|
1.0
|
CB
|
B:ASP87
|
4.5
|
37.2
|
1.0
|
O
|
B:ARG133
|
4.5
|
41.5
|
1.0
|
C
|
B:HIS131
|
4.6
|
37.4
|
1.0
|
N
|
B:ALA135
|
4.6
|
36.7
|
1.0
|
CB
|
B:ARG133
|
4.7
|
62.9
|
1.0
|
CA
|
B:ARG133
|
4.7
|
54.1
|
1.0
|
CG
|
B:GLN130
|
4.7
|
34.4
|
1.0
|
O
|
B:GLN105
|
4.7
|
42.0
|
1.0
|
CA
|
B:ALA135
|
4.8
|
36.9
|
1.0
|
CA
|
B:ASP87
|
4.8
|
39.3
|
1.0
|
CA
|
B:ASP86
|
4.8
|
38.9
|
1.0
|
CA
|
B:HIS131
|
4.9
|
41.9
|
1.0
|
CA
|
B:GLN130
|
4.9
|
36.1
|
1.0
|
|
Calcium binding site 4 out
of 6 in 6qe7
Go back to
Calcium Binding Sites List in 6qe7
Calcium binding site 4 out
of 6 in the Anti-Sigma Factor Domain-Containing Protein
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Anti-Sigma Factor Domain-Containing Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca402
b:40.9
occ:1.00
|
O
|
B:THR62
|
2.2
|
29.6
|
1.0
|
O
|
B:HOH570
|
2.3
|
38.6
|
1.0
|
OG1
|
B:THR62
|
2.3
|
41.0
|
1.0
|
O
|
B:HOH517
|
2.4
|
38.6
|
1.0
|
O
|
B:ASN29
|
2.4
|
43.8
|
1.0
|
O
|
B:HOH529
|
2.4
|
38.5
|
1.0
|
O
|
B:HOH593
|
2.5
|
42.1
|
1.0
|
O
|
B:ASP61
|
2.6
|
38.5
|
1.0
|
C
|
B:THR62
|
3.1
|
37.2
|
1.0
|
CB
|
B:THR62
|
3.3
|
37.5
|
1.0
|
C
|
B:ASN29
|
3.5
|
39.6
|
1.0
|
C
|
B:ASP61
|
3.6
|
40.0
|
1.0
|
CA
|
B:THR62
|
3.6
|
38.8
|
1.0
|
N
|
B:THR62
|
4.0
|
42.0
|
1.0
|
N
|
B:TYR63
|
4.2
|
35.2
|
1.0
|
CA
|
B:ASN29
|
4.3
|
40.0
|
1.0
|
O
|
B:GLY59
|
4.4
|
44.9
|
1.0
|
N
|
B:ASN30
|
4.4
|
40.4
|
1.0
|
O
|
B:LYS60
|
4.4
|
40.3
|
1.0
|
CA
|
B:ASN30
|
4.5
|
37.7
|
1.0
|
OD1
|
B:ASN30
|
4.5
|
37.0
|
1.0
|
OD1
|
B:ASN29
|
4.6
|
41.3
|
1.0
|
CB
|
B:TYR63
|
4.6
|
41.3
|
1.0
|
CG2
|
B:THR62
|
4.6
|
40.0
|
1.0
|
CA
|
B:TYR63
|
4.7
|
37.2
|
1.0
|
CB
|
B:ASN29
|
4.7
|
38.9
|
1.0
|
CA
|
B:ASP61
|
4.8
|
46.6
|
1.0
|
C
|
B:GLY59
|
5.0
|
48.7
|
1.0
|
|
Calcium binding site 5 out
of 6 in 6qe7
Go back to
Calcium Binding Sites List in 6qe7
Calcium binding site 5 out
of 6 in the Anti-Sigma Factor Domain-Containing Protein
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Anti-Sigma Factor Domain-Containing Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca401
b:37.2
occ:1.00
|
O
|
C:ALA134
|
2.1
|
34.9
|
1.0
|
O
|
C:VAL132
|
2.3
|
41.9
|
1.0
|
OD1
|
C:ASP86
|
2.3
|
42.9
|
1.0
|
O
|
C:HOH551
|
2.3
|
36.1
|
1.0
|
OE1
|
C:GLN130
|
2.4
|
43.4
|
1.0
|
O
|
C:HOH538
|
2.5
|
31.4
|
1.0
|
OD1
|
C:ASP87
|
2.7
|
38.2
|
1.0
|
CG
|
C:ASP86
|
3.2
|
38.3
|
1.0
|
C
|
C:ALA134
|
3.3
|
41.4
|
1.0
|
CD
|
C:GLN130
|
3.5
|
39.3
|
1.0
|
CG
|
C:ASP87
|
3.5
|
34.5
|
1.0
|
C
|
C:VAL132
|
3.5
|
51.9
|
1.0
|
OD2
|
C:ASP86
|
3.6
|
46.9
|
1.0
|
OD2
|
C:ASP87
|
3.7
|
44.4
|
1.0
|
NE2
|
C:GLN130
|
3.9
|
40.0
|
1.0
|
N
|
C:ALA134
|
3.9
|
40.7
|
1.0
|
N
|
C:VAL132
|
3.9
|
41.2
|
1.0
|
C
|
C:ARG133
|
4.1
|
45.9
|
1.0
|
CA
|
C:ALA134
|
4.2
|
42.3
|
1.0
|
C
|
C:ASP86
|
4.3
|
36.3
|
1.0
|
O
|
C:ARG133
|
4.3
|
41.4
|
1.0
|
N
|
C:HIS131
|
4.3
|
40.5
|
1.0
|
CA
|
C:VAL132
|
4.3
|
48.6
|
1.0
|
N
|
C:ALA135
|
4.3
|
41.5
|
1.0
|
O
|
C:ASP86
|
4.3
|
36.4
|
1.0
|
CB
|
C:ASP86
|
4.4
|
42.6
|
1.0
|
N
|
C:ARG133
|
4.4
|
46.6
|
1.0
|
N
|
C:ASP87
|
4.4
|
38.8
|
1.0
|
CA
|
C:ARG133
|
4.6
|
44.8
|
1.0
|
CA
|
C:ALA135
|
4.7
|
44.4
|
1.0
|
CB
|
C:ASP87
|
4.7
|
34.4
|
1.0
|
C
|
C:HIS131
|
4.7
|
44.9
|
1.0
|
CB
|
C:ARG133
|
4.7
|
40.4
|
1.0
|
CB
|
C:ALA134
|
4.8
|
41.8
|
1.0
|
CG
|
C:GLN130
|
4.8
|
40.6
|
1.0
|
CA
|
C:ASP86
|
4.8
|
37.9
|
1.0
|
CA
|
C:GLN130
|
4.9
|
37.1
|
1.0
|
CA
|
C:ASP87
|
4.9
|
36.8
|
1.0
|
CA
|
C:HIS131
|
5.0
|
40.4
|
1.0
|
O
|
C:GLN105
|
5.0
|
42.2
|
1.0
|
|
Calcium binding site 6 out
of 6 in 6qe7
Go back to
Calcium Binding Sites List in 6qe7
Calcium binding site 6 out
of 6 in the Anti-Sigma Factor Domain-Containing Protein
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Anti-Sigma Factor Domain-Containing Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca402
b:37.4
occ:1.00
|
O
|
C:HOH536
|
2.2
|
40.7
|
1.0
|
O
|
C:THR62
|
2.3
|
41.2
|
1.0
|
OG1
|
C:THR62
|
2.3
|
36.3
|
1.0
|
O
|
C:ASN29
|
2.3
|
41.1
|
1.0
|
O
|
C:HOH524
|
2.4
|
52.5
|
1.0
|
O
|
C:HOH568
|
2.4
|
41.0
|
1.0
|
O
|
C:ASP61
|
2.5
|
34.6
|
1.0
|
O
|
C:HOH642
|
2.8
|
48.2
|
1.0
|
C
|
C:THR62
|
3.1
|
37.0
|
1.0
|
CB
|
C:THR62
|
3.3
|
43.6
|
1.0
|
C
|
C:ASP61
|
3.5
|
34.6
|
1.0
|
C
|
C:ASN29
|
3.5
|
37.3
|
1.0
|
CA
|
C:THR62
|
3.6
|
39.1
|
1.0
|
N
|
C:THR62
|
3.9
|
33.8
|
1.0
|
N
|
C:TYR63
|
4.1
|
39.2
|
1.0
|
O
|
C:LYS60
|
4.2
|
39.1
|
1.0
|
CA
|
C:ASN29
|
4.3
|
43.5
|
1.0
|
O
|
C:HOH520
|
4.3
|
38.6
|
1.0
|
O
|
C:GLY59
|
4.5
|
41.6
|
1.0
|
N
|
C:ASN30
|
4.5
|
36.5
|
1.0
|
CA
|
C:ASN30
|
4.5
|
35.2
|
1.0
|
CB
|
C:ASN29
|
4.6
|
45.8
|
1.0
|
OD1
|
C:ASN29
|
4.6
|
40.1
|
1.0
|
CA
|
C:TYR63
|
4.6
|
41.7
|
1.0
|
CB
|
C:TYR63
|
4.6
|
41.6
|
1.0
|
OD1
|
C:ASN30
|
4.6
|
40.7
|
1.0
|
CG2
|
C:THR62
|
4.6
|
49.2
|
1.0
|
CA
|
C:ASP61
|
4.8
|
40.1
|
1.0
|
C
|
C:LYS60
|
4.9
|
43.6
|
1.0
|
|
Reference:
I.R.Grinberg,
O.Yaniv,
L.O.De Ora,
I.Munoz-Gutierrez,
A.Hershko,
O.Livnah,
E.A.Bayer,
I.Borovok,
F.Frolow,
R.Lamed,
M.Voronov-Goldman.
Distinctive Ligand-Binding Specificities of Tandem PA14 Biomass-Sensory Elements From Clostridium Thermocellum and Clostridium Clariflavum. Proteins V. 87 917 2019.
ISSN: ESSN 1097-0134
PubMed: 31162722
DOI: 10.1002/PROT.25753
Page generated: Tue Jul 16 13:47:14 2024
|