Calcium in PDB 6qdi: Anti-Sigma Factor Domain-Containing Protein From Clostridium Clariflavum

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

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 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 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 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 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

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