Calcium in PDB 6qdi: Anti-Sigma Factor Domain-Containing Protein From Clostridium Clariflavum
Protein crystallography data
The structure of Anti-Sigma Factor Domain-Containing Protein From Clostridium Clariflavum, PDB code: 6qdi
was solved by
M.Voronov,
E.A.Bayer,
O.Livnah,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.97 /
1.13
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.600,
41.430,
73.310,
90.00,
100.35,
90.00
|
R / Rfree (%)
|
14.6 /
17.1
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Anti-Sigma Factor Domain-Containing Protein From Clostridium Clariflavum
(pdb code 6qdi). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Anti-Sigma Factor Domain-Containing Protein From Clostridium Clariflavum, PDB code: 6qdi:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6qdi
Go back to
Calcium Binding Sites List in 6qdi
Calcium binding site 1 out
of 4 in the Anti-Sigma Factor Domain-Containing Protein From Clostridium Clariflavum
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 From Clostridium Clariflavum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca403
b:6.9
occ:1.00
|
O
|
A:THR133
|
2.3
|
8.3
|
1.0
|
OD1
|
A:ASP87
|
2.3
|
7.6
|
1.0
|
OD1
|
A:ASN131
|
2.3
|
7.0
|
1.0
|
O
|
A:ASN135
|
2.4
|
7.3
|
1.0
|
OD1
|
A:ASN88
|
2.5
|
6.9
|
1.0
|
O2
|
A:EDO402
|
2.5
|
10.6
|
1.0
|
O1
|
A:EDO402
|
2.5
|
8.9
|
1.0
|
C2
|
A:EDO402
|
3.3
|
14.1
|
1.0
|
CG
|
A:ASP87
|
3.3
|
7.1
|
1.0
|
C1
|
A:EDO402
|
3.3
|
12.6
|
1.0
|
CG
|
A:ASN88
|
3.3
|
7.0
|
1.0
|
CG
|
A:ASN131
|
3.5
|
6.3
|
1.0
|
C
|
A:THR133
|
3.5
|
8.1
|
1.0
|
C
|
A:ASN135
|
3.6
|
7.0
|
1.0
|
OD2
|
A:ASP87
|
3.6
|
8.0
|
1.0
|
ND2
|
A:ASN88
|
3.7
|
8.9
|
1.0
|
C
|
A:GLY134
|
3.8
|
8.2
|
1.0
|
N
|
A:ASN135
|
4.0
|
8.1
|
1.0
|
ND2
|
A:ASN131
|
4.1
|
7.4
|
1.0
|
O
|
A:GLY134
|
4.1
|
8.5
|
1.0
|
CA
|
A:GLY134
|
4.2
|
8.8
|
1.0
|
N
|
A:ASN132
|
4.3
|
6.2
|
1.0
|
N
|
A:GLY134
|
4.3
|
9.1
|
1.0
|
C
|
A:ASP87
|
4.3
|
6.0
|
1.0
|
CA
|
A:ASN135
|
4.4
|
7.6
|
1.0
|
O
|
A:ASN132
|
4.4
|
7.5
|
1.0
|
O
|
A:ASP87
|
4.4
|
6.5
|
1.0
|
C
|
A:ASN132
|
4.4
|
6.5
|
1.0
|
N
|
A:ASN88
|
4.5
|
6.3
|
1.0
|
N
|
A:THR133
|
4.5
|
6.7
|
1.0
|
CB
|
A:ASP87
|
4.5
|
6.8
|
1.0
|
N
|
A:GLY136
|
4.6
|
7.3
|
1.0
|
CB
|
A:ASN88
|
4.6
|
6.5
|
1.0
|
CA
|
A:THR133
|
4.6
|
7.8
|
1.0
|
CB
|
A:ASN131
|
4.7
|
6.5
|
1.0
|
CA
|
A:ASN131
|
4.7
|
6.1
|
1.0
|
CA
|
A:GLY136
|
4.8
|
7.3
|
1.0
|
O
|
A:HOH604
|
4.8
|
22.1
|
1.0
|
CA
|
A:ASP87
|
4.8
|
6.0
|
1.0
|
C
|
A:ASN131
|
4.9
|
6.3
|
1.0
|
CA
|
A:ASN88
|
5.0
|
6.0
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6qdi
Go back to
Calcium Binding Sites List in 6qdi
Calcium binding site 2 out
of 4 in the Anti-Sigma Factor Domain-Containing Protein From Clostridium Clariflavum
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 From Clostridium Clariflavum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca404
b:7.3
occ:0.95
|
O
|
A:GLY287
|
2.3
|
8.1
|
1.0
|
O
|
A:ALA289
|
2.3
|
7.5
|
1.0
|
OD1
|
A:ASP240
|
2.4
|
7.8
|
1.0
|
OD2
|
A:ASP241
|
2.4
|
7.9
|
1.0
|
OD1
|
A:ASN285
|
2.4
|
7.8
|
1.0
|
O1
|
A:EDO401
|
2.5
|
10.3
|
1.0
|
O2
|
A:EDO401
|
2.6
|
9.9
|
1.0
|
C1
|
A:EDO401
|
3.3
|
12.4
|
1.0
|
C2
|
A:EDO401
|
3.4
|
13.0
|
1.0
|
CG
|
A:ASP240
|
3.4
|
7.7
|
1.0
|
CG
|
A:ASP241
|
3.4
|
7.8
|
1.0
|
C
|
A:GLY287
|
3.5
|
8.1
|
1.0
|
CG
|
A:ASN285
|
3.5
|
7.0
|
1.0
|
C
|
A:ALA289
|
3.5
|
7.1
|
1.0
|
OD2
|
A:ASP240
|
3.8
|
8.5
|
1.0
|
CB
|
A:ASP241
|
3.8
|
7.7
|
1.0
|
N
|
A:ALA289
|
3.9
|
7.8
|
1.0
|
C
|
A:LEU288
|
4.0
|
7.6
|
1.0
|
N
|
A:GLY287
|
4.0
|
8.3
|
1.0
|
ND2
|
A:ASN285
|
4.1
|
6.9
|
1.0
|
O
|
A:HOH621
|
4.2
|
20.8
|
1.0
|
C
|
A:ASP240
|
4.2
|
6.7
|
1.0
|
O
|
A:ASP240
|
4.3
|
6.9
|
1.0
|
CA
|
A:ALA289
|
4.3
|
7.4
|
1.0
|
O
|
A:LEU288
|
4.3
|
8.1
|
1.0
|
N
|
A:ASP241
|
4.3
|
6.6
|
1.0
|
CA
|
A:GLY287
|
4.4
|
8.5
|
1.0
|
N
|
A:THR286
|
4.4
|
7.2
|
1.0
|
N
|
A:LEU288
|
4.4
|
8.0
|
1.0
|
CA
|
A:LEU288
|
4.5
|
8.3
|
1.0
|
N
|
A:GLY290
|
4.5
|
6.5
|
1.0
|
OD1
|
A:ASP241
|
4.6
|
9.3
|
1.0
|
CB
|
A:LEU288
|
4.6
|
9.4
|
1.0
|
CB
|
A:ASP240
|
4.6
|
7.9
|
1.0
|
CB
|
A:ASN285
|
4.6
|
7.2
|
1.0
|
CA
|
A:ASN285
|
4.6
|
6.8
|
1.0
|
CA
|
A:ASP241
|
4.7
|
7.4
|
1.0
|
CA
|
A:GLY290
|
4.7
|
6.4
|
1.0
|
CA
|
A:ASP240
|
4.9
|
7.1
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6qdi
Go back to
Calcium Binding Sites List in 6qdi
Calcium binding site 3 out
of 4 in the Anti-Sigma Factor Domain-Containing Protein From Clostridium Clariflavum
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 From Clostridium Clariflavum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca405
b:7.4
occ:0.90
|
O
|
A:LYS216
|
2.3
|
8.3
|
1.0
|
O
|
A:ASP182
|
2.3
|
8.2
|
1.0
|
O
|
A:HOH825
|
2.4
|
10.6
|
1.0
|
O
|
A:HOH619
|
2.4
|
8.6
|
1.0
|
O
|
A:HOH791
|
2.4
|
12.2
|
1.0
|
OD2
|
A:ASP214
|
2.4
|
12.7
|
1.0
|
OD1
|
A:ASP214
|
2.5
|
9.4
|
1.0
|
CG
|
A:ASP214
|
2.8
|
9.9
|
1.0
|
C
|
A:LYS216
|
3.5
|
7.5
|
1.0
|
C
|
A:ASP182
|
3.5
|
7.3
|
1.0
|
CB
|
A:LYS216
|
4.0
|
8.6
|
1.0
|
CA
|
A:LYS216
|
4.2
|
8.0
|
1.0
|
CB
|
A:ASP214
|
4.3
|
10.0
|
1.0
|
OD1
|
A:ASP182
|
4.4
|
9.3
|
1.0
|
CA
|
A:ASP182
|
4.4
|
7.0
|
1.0
|
O
|
A:HOH684
|
4.4
|
22.9
|
1.0
|
N
|
A:LYS216
|
4.4
|
7.9
|
1.0
|
N
|
A:GLU183
|
4.5
|
7.5
|
1.0
|
O
|
A:ASN212
|
4.5
|
8.6
|
1.0
|
CA
|
A:GLU183
|
4.5
|
7.8
|
1.0
|
N
|
A:PHE217
|
4.6
|
7.1
|
1.0
|
O
|
A:HOH642
|
4.7
|
10.7
|
1.0
|
O
|
A:HOH571
|
4.7
|
12.2
|
1.0
|
CB
|
A:ASN212
|
4.7
|
9.9
|
1.0
|
CG
|
A:ASP182
|
4.7
|
8.5
|
1.0
|
CA
|
A:PHE217
|
4.7
|
6.9
|
1.0
|
CB
|
A:PHE217
|
4.8
|
7.0
|
1.0
|
CB
|
A:ASP182
|
4.8
|
7.7
|
1.0
|
ND2
|
A:ASN212
|
4.9
|
18.0
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6qdi
Go back to
Calcium Binding Sites List in 6qdi
Calcium binding site 4 out
of 4 in the Anti-Sigma Factor Domain-Containing Protein From Clostridium Clariflavum
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 From Clostridium Clariflavum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca406
b:7.3
occ:1.00
|
O
|
A:SER63
|
2.3
|
9.0
|
1.0
|
O
|
A:HOH656
|
2.4
|
8.3
|
1.0
|
O
|
A:ASP29
|
2.4
|
8.4
|
1.0
|
O
|
A:HOH654
|
2.5
|
8.6
|
1.0
|
OD2
|
A:ASP61
|
2.5
|
8.2
|
1.0
|
O
|
A:HOH792
|
2.5
|
11.4
|
1.0
|
OD1
|
A:ASP61
|
2.5
|
7.5
|
1.0
|
OG
|
A:SER63
|
2.5
|
6.5
|
1.0
|
CG
|
A:ASP61
|
2.9
|
7.3
|
1.0
|
C
|
A:SER63
|
3.4
|
7.6
|
1.0
|
C
|
A:ASP29
|
3.6
|
6.8
|
1.0
|
CB
|
A:SER63
|
3.6
|
6.6
|
1.0
|
CA
|
A:SER63
|
3.9
|
6.6
|
1.0
|
N
|
A:SER63
|
4.1
|
7.4
|
1.0
|
O
|
A:HOH587
|
4.3
|
10.9
|
1.0
|
CB
|
A:ASP61
|
4.4
|
8.0
|
1.0
|
CD1
|
A:TRP202
|
4.4
|
7.1
|
1.0
|
N
|
A:ASN30
|
4.4
|
6.9
|
1.0
|
CA
|
A:ASP29
|
4.5
|
7.3
|
1.0
|
CA
|
A:ASN30
|
4.5
|
6.5
|
1.0
|
OD1
|
A:ASP29
|
4.6
|
9.9
|
1.0
|
N
|
A:TYR64
|
4.6
|
6.2
|
1.0
|
O
|
A:HOH540
|
4.6
|
7.7
|
1.0
|
O
|
A:ARG59
|
4.6
|
9.7
|
1.0
|
OD1
|
A:ASN30
|
4.6
|
6.5
|
1.0
|
CG
|
A:ASP29
|
4.7
|
10.5
|
1.0
|
CB
|
A:ARG59
|
4.7
|
13.5
|
1.0
|
CB
|
A:ASP29
|
4.8
|
9.0
|
1.0
|
CA
|
A:TYR64
|
4.9
|
6.0
|
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 13:45:53 2024
|