Calcium in PDB 4p5f: The Crystal Structure of Type III Effector Protein Xopq Complexed with Adenosine Diphosphate Ribose

The structure of The Crystal Structure of Type III Effector Protein Xopq Complexed with Adenosine Diphosphate Ribose, PDB code: 4p5f was solved by S.Yu, I.Hwang, S.Rhee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.30 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.999, 73.808, 201.943, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 25.3

The binding sites of Calcium atom in the The Crystal Structure of Type III Effector Protein Xopq Complexed with Adenosine Diphosphate Ribose (pdb code 4p5f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The Crystal Structure of Type III Effector Protein Xopq Complexed with Adenosine Diphosphate Ribose, PDB code: 4p5f:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the The Crystal Structure of Type III Effector Protein Xopq Complexed with Adenosine Diphosphate Ribose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of Type III Effector Protein Xopq Complexed with Adenosine Diphosphate Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:10.9 occ:1.00 OD1 A:ASP123 2.4 12.3 1.0 O A:ILE232 2.4 10.6 1.0 OD2 A:ASP399 2.5 13.0 1.0 OD1 A:ASP116 2.5 13.9 1.0 O A:HOH700 2.5 16.7 1.0 O A:HOH699 2.5 9.3 1.0 OD2 A:ASP123 2.9 15.5 1.0 O A:HOH701 2.9 15.6 1.0 CG A:ASP123 3.0 12.1 1.0 CG A:ASP399 3.5 12.4 1.0 CG A:ASP116 3.6 11.7 1.0 C A:ILE232 3.7 9.8 1.0 OD1 A:ASP399 3.8 12.5 1.0 OD2 A:ASP116 3.9 13.2 1.0 NZ A:LYS119 4.4 15.1 1.0 CB A:ILE232 4.4 8.6 1.0 CB A:ASP123 4.4 8.4 1.0 N A:ALA233 4.5 9.0 1.0 CA A:ALA233 4.6 8.4 1.0 OD1 A:ASN280 4.6 11.3 1.0 N A:ASP116 4.6 13.0 1.0 CE A:LYS119 4.6 17.4 1.0 CA A:ILE232 4.6 9.4 1.0 O A:ASP116 4.6 11.0 1.0 CB A:ALA233 4.7 8.8 1.0 N A:ASP123 4.7 11.1 1.0 CG1 A:ILE232 4.8 7.8 1.0 CB A:ASP399 4.8 11.7 1.0 ND2 A:ASN280 4.8 9.3 1.0 CB A:ASP122 4.8 12.8 1.0 OD1 A:ASP120 4.9 20.6 1.0 CB A:ASP116 4.9 11.0 1.0 CA A:ASP123 4.9 13.0 1.0 O A:HOH698 4.9 13.3 1.0 CD1 A:ILE232 5.0 10.2 1.0 C A:ASP116 5.0 12.9 1.0

Calcium binding site 2 out of 3 in the The Crystal Structure of Type III Effector Protein Xopq Complexed with Adenosine Diphosphate Ribose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of Type III Effector Protein Xopq Complexed with Adenosine Diphosphate Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:18.7 occ:1.00 O B:ILE232 2.3 17.3 1.0 OD1 B:ASP123 2.4 18.1 1.0 OD2 B:ASP399 2.4 21.4 1.0 O2D B:AR6503 2.5 19.8 1.0 OD1 B:ASP116 2.5 18.6 1.0 OD2 B:ASP123 2.6 18.8 1.0 O1D B:AR6503 2.7 28.8 1.0 CG B:ASP123 2.8 21.5 1.0 O3D B:AR6503 3.0 20.1 1.0 CG B:ASP399 3.5 20.1 1.0 C2D B:AR6503 3.5 28.3 1.0 C B:ILE232 3.5 21.6 1.0 CG B:ASP116 3.6 22.8 1.0 C1D B:AR6503 3.6 33.0 1.0 OD1 B:ASP399 3.8 23.6 1.0 C3D B:AR6503 3.8 23.2 1.0 OD2 B:ASP116 4.0 25.1 1.0 OD1 B:ASP122 4.2 18.0 1.0 CB B:ILE232 4.3 18.6 1.0 CB B:ASP123 4.3 14.7 1.0 N B:ALA233 4.4 20.2 1.0 CA B:ALA233 4.4 19.4 1.0 N B:ASP116 4.5 16.2 1.0 CB B:ALA233 4.5 16.8 1.0 CA B:ILE232 4.5 18.6 1.0 O B:HOH686 4.5 20.4 1.0 CG1 B:ILE232 4.6 14.4 1.0 OD1 B:ASN280 4.6 19.9 1.0 ND2 B:ASN280 4.7 21.3 1.0 O B:ASP116 4.8 20.8 1.0 OD2 B:ASP122 4.8 20.7 1.0 CB B:ASP399 4.8 14.9 1.0 O4D B:AR6503 4.8 27.9 1.0 C4D B:AR6503 4.8 22.9 1.0 CG B:ASP122 4.9 23.2 1.0 CB B:ASP116 4.9 18.4 1.0 CA B:ASP123 4.9 19.2 1.0 N B:ASP123 4.9 17.2 1.0

Calcium binding site 3 out of 3 in the The Crystal Structure of Type III Effector Protein Xopq Complexed with Adenosine Diphosphate Ribose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of Type III Effector Protein Xopq Complexed with Adenosine Diphosphate Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:43.0 occ:1.00 NE2 B:HIS286 2.3 42.1 1.0 O B:HOH683 2.5 32.7 1.0 CE1 B:HIS286 3.1 36.0 1.0 O B:HOH684 3.1 32.1 1.0 CD2 B:HIS286 3.3 35.3 1.0 ND1 B:HIS286 4.2 41.8 1.0 CG B:HIS286 4.3 35.2 1.0

S.Yu, I.Hwang, S.Rhee. The Crystal Structure of Type III Effector Protein Xopq From Xanthomonas Oryzae Complexed with Adenosine Diphosphate Ribose. Proteins V. 82 2910 2014.
ISSN: ESSN 1097-0134
PubMed: 25079351
DOI: 10.1002/PROT.24656