Calcium in PDB 5x9a: Crystal Structure of Calaxin with Calcium

The structure of Crystal Structure of Calaxin with Calcium, PDB code: 5x9a was solved by T.Shojima, F.Hou, Y.Takahashi, M.Okai, K.Mizuno, K.Inaba, T.Miyakawa, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.77 / 1.85
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	65.540, 65.540, 113.540, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.9

The binding sites of Calcium atom in the Crystal Structure of Calaxin with Calcium (pdb code 5x9a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Calaxin with Calcium, PDB code: 5x9a:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Crystal Structure of Calaxin with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Calaxin with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:17.2 occ:1.00 O A:HOH448 2.2 28.5 1.0 OD2 A:ASP73 2.2 21.5 1.0 OD1 A:ASP71 2.3 15.5 1.0 O A:TYR77 2.3 18.9 1.0 OE1 A:GLU82 2.4 14.8 1.0 OD1 A:ASP75 2.4 21.1 1.0 OE2 A:GLU82 2.7 15.7 1.0 CD A:GLU82 2.8 14.5 1.0 CG A:ASP75 3.3 26.4 1.0 CG A:ASP73 3.4 25.0 1.0 CG A:ASP71 3.4 18.3 1.0 C A:TYR77 3.5 14.9 1.0 OD2 A:ASP75 3.8 22.8 1.0 OD1 A:ASP73 3.9 23.1 1.0 CA A:ASP71 4.2 15.5 1.0 N A:TYR77 4.2 20.0 1.0 N A:ASP75 4.2 19.5 1.0 OD2 A:ASP71 4.3 17.0 1.0 CB A:ASP71 4.3 15.6 1.0 N A:ASP73 4.4 19.6 1.0 CB A:ASP75 4.4 23.4 1.0 N A:SER79 4.4 16.8 1.0 CG A:GLU82 4.4 14.7 1.0 CA A:TYR77 4.4 17.5 1.0 N A:ILE78 4.4 16.1 1.0 C A:ASP71 4.4 16.8 1.0 CA A:ILE78 4.5 14.0 1.0 CB A:ASP73 4.6 23.3 1.0 CA A:ASP75 4.7 22.5 1.0 N A:SER74 4.7 20.6 1.0 N A:LYS72 4.7 17.2 1.0 CB A:TYR77 4.8 21.7 1.0 N A:SER76 4.8 21.2 1.0 CA A:ASP73 4.8 23.3 1.0 O A:HOH454 4.8 29.9 1.0 C A:ASP73 4.9 23.3 1.0 C A:ASP75 4.9 20.9 1.0 C A:ILE78 4.9 14.8 1.0 O A:ASP71 5.0 18.7 1.0

Calcium binding site 2 out of 7 in the Crystal Structure of Calaxin with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Calaxin with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:24.9 occ:1.00 O A:HOH474 2.3 26.6 1.0 OD1 A:ASP107 2.3 21.0 1.0 OD1 A:ASP111 2.3 25.6 1.0 O A:TYR113 2.3 28.2 1.0 OE2 A:GLU118 2.4 25.5 1.0 OE1 A:GLU118 2.4 24.8 1.0 OD1 A:ASN109 2.4 20.4 1.0 CD A:GLU118 2.8 26.6 1.0 CG A:ASP111 3.3 27.9 1.0 CG A:ASN109 3.3 30.0 1.0 CG A:ASP107 3.4 18.2 1.0 C A:TYR113 3.6 25.8 1.0 OD2 A:ASP111 3.7 26.0 1.0 ND2 A:ASN109 3.8 33.6 1.0 N A:ASP111 4.1 28.6 1.0 N A:ASN109 4.2 25.4 1.0 OD2 A:ASP107 4.2 18.9 1.0 CA A:ASP107 4.2 18.3 1.0 N A:TYR113 4.2 23.1 1.0 CG A:GLU118 4.3 23.5 1.0 C A:ASP107 4.3 18.7 1.0 CA A:TYR113 4.4 26.2 1.0 CB A:ASP107 4.4 19.9 1.0 N A:LEU108 4.4 20.9 1.0 CB A:ASP111 4.4 28.5 1.0 N A:GLY110 4.5 24.1 1.0 N A:ILE114 4.5 21.6 1.0 CB A:ASN109 4.5 25.8 1.0 N A:SER115 4.5 23.6 1.0 CA A:ILE114 4.5 20.5 1.0 CA A:ASP111 4.7 29.6 1.0 CA A:ASN109 4.7 24.0 1.0 CB A:TYR113 4.7 26.1 1.0 O A:HOH426 4.8 25.6 1.0 C A:ASN109 4.8 24.1 1.0 O A:ASP107 4.8 21.8 1.0 N A:GLY112 4.9 28.8 1.0 C A:ILE114 5.0 27.2 1.0

Calcium binding site 3 out of 7 in the Crystal Structure of Calaxin with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Calaxin with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:32.4 occ:1.00 OD1 A:ASP156 2.2 27.7 1.0 O A:HOH436 2.2 36.5 1.0 OD1 A:ASP152 2.2 30.2 1.0 O A:HOH425 2.4 37.7 1.0 OD1 A:ASP163 2.4 28.6 1.0 O A:ARG158 2.5 28.7 1.0 OD1 A:ASP154 2.8 49.2 1.0 CG A:ASP156 3.2 40.5 1.0 CG A:ASP152 3.3 31.3 1.0 CG A:ASP163 3.5 32.0 1.0 CG A:ASP154 3.5 45.2 1.0 C A:ARG158 3.7 32.9 1.0 OD2 A:ASP156 3.7 37.9 1.0 OD2 A:ASP163 3.9 28.8 1.0 OD2 A:ASP154 4.0 48.4 1.0 O A:HOH449 4.0 41.2 1.0 OD2 A:ASP152 4.1 38.2 1.0 N A:ASP154 4.2 45.4 1.0 CA A:ASP152 4.2 29.3 1.0 N A:ASP156 4.2 40.6 1.0 CB A:ASP152 4.2 32.0 1.0 N A:SER160 4.3 29.6 1.0 C A:ASP152 4.4 31.1 1.0 N A:ARG158 4.4 31.4 1.0 N A:HIS153 4.4 36.2 1.0 N A:HIS155 4.5 39.2 1.0 CB A:ASP156 4.5 37.8 1.0 CB A:ASP154 4.5 45.8 1.0 CA A:LEU159 4.5 26.0 1.0 N A:LEU159 4.5 29.4 1.0 CA A:ARG158 4.6 35.8 1.0 CA A:ASP154 4.6 43.7 1.0 C A:ASP154 4.6 41.3 1.0 CA A:ASP156 4.8 38.7 1.0 CB A:ASP163 4.8 30.6 1.0 CB A:ARG158 4.9 36.6 1.0 C A:LEU159 4.9 29.6 1.0 OG A:SER160 4.9 29.9 1.0 CB A:SER160 5.0 33.5 1.0

Calcium binding site 4 out of 7 in the Crystal Structure of Calaxin with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Calaxin with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:29.8 occ:1.00 O A:HOH470 2.3 37.2 1.0 O A:HOH480 2.4 39.0 1.0 O B:ASP135 2.4 30.5 1.0 OD2 A:ASP142 2.5 28.6 1.0 O B:HOH511 2.5 38.4 1.0 OD1 A:ASP142 2.5 27.9 1.0 CG A:ASP142 2.9 27.5 1.0 OE2 A:GLU138 2.9 76.9 1.0 C B:ASP135 3.6 30.2 1.0 CD A:GLU138 4.0 72.8 1.0 CB A:ASP142 4.3 24.3 1.0 CA B:PRO136 4.4 30.7 1.0 N B:PRO136 4.5 31.4 1.0 CA B:ASP135 4.5 31.7 1.0 CB B:ASP135 4.5 32.4 1.0 CG A:GLU138 4.5 62.1 1.0 OD1 B:ASP135 4.5 29.6 1.0 N B:ASP137 4.6 24.6 1.0 C B:PRO136 4.6 28.0 1.0 N B:GLU138 4.6 24.1 1.0 O A:GLU138 4.7 31.5 1.0 N B:ASP135 4.7 30.0 1.0 CB B:GLU138 4.8 29.3 1.0 CG B:GLU138 4.8 31.3 1.0

Calcium binding site 5 out of 7 in the Crystal Structure of Calaxin with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Calaxin with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:12.3 occ:1.00 O B:HOH507 2.2 22.3 1.0 O B:TYR77 2.2 13.8 1.0 OD1 B:ASP71 2.3 12.7 1.0 OD1 B:ASP73 2.4 15.8 1.0 OD1 B:ASP75 2.4 14.6 1.0 OE1 B:GLU82 2.4 13.0 1.0 OE2 B:GLU82 2.6 14.5 1.0 CD B:GLU82 2.9 12.2 1.0 CG B:ASP75 3.3 17.6 1.0 CG B:ASP73 3.4 18.9 1.0 C B:TYR77 3.5 12.8 1.0 CG B:ASP71 3.5 14.2 1.0 OD2 B:ASP75 3.8 16.9 1.0 OD2 B:ASP73 3.9 19.1 1.0 N B:TYR77 4.2 12.8 1.0 CA B:ASP71 4.2 12.5 1.0 N B:ASP75 4.2 16.8 1.0 OD2 B:ASP71 4.3 13.2 1.0 CA B:TYR77 4.4 13.5 1.0 CB B:ASP71 4.4 14.2 1.0 CG B:GLU82 4.4 10.8 1.0 N B:ILE78 4.4 13.2 1.0 N B:ASP73 4.4 17.2 1.0 C B:ASP71 4.4 15.1 1.0 N B:SER79 4.4 13.4 1.0 CA B:ILE78 4.5 12.3 1.0 CB B:ASP75 4.5 17.6 1.0 N B:LYS72 4.6 14.8 1.0 CB B:ASP73 4.7 19.8 1.0 CA B:ASP75 4.7 15.7 1.0 N B:SER74 4.7 15.1 1.0 N B:SER76 4.8 15.1 1.0 CB B:TYR77 4.8 16.3 1.0 CA B:ASP73 4.9 17.3 1.0 O B:HOH417 4.9 20.3 1.0 C B:ASP75 4.9 15.1 1.0 C B:ILE78 5.0 13.2 1.0 C B:ASP73 5.0 16.4 1.0

Calcium binding site 6 out of 7 in the Crystal Structure of Calaxin with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Calaxin with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:16.6 occ:1.00 O B:TYR113 2.2 20.5 1.0 OD1 B:ASN109 2.2 18.8 1.0 OD1 B:ASP107 2.3 14.7 1.0 OD1 B:ASP111 2.3 19.1 1.0 O B:HOH488 2.4 19.1 1.0 OE1 B:GLU118 2.4 15.4 1.0 OE2 B:GLU118 2.5 15.6 1.0 CD B:GLU118 2.8 15.1 1.0 CG B:ASP111 3.2 24.2 1.0 CG B:ASN109 3.3 17.0 1.0 C B:TYR113 3.4 16.3 1.0 CG B:ASP107 3.4 18.5 1.0 OD2 B:ASP111 3.6 24.8 1.0 ND2 B:ASN109 3.9 21.6 1.0 N B:ASN109 4.1 16.8 1.0 N B:TYR113 4.1 19.0 1.0 N B:ASP111 4.2 21.8 1.0 OD2 B:ASP107 4.2 17.1 1.0 CA B:ASP107 4.2 15.2 1.0 C B:ASP107 4.3 14.9 1.0 N B:LEU108 4.3 14.6 1.0 CA B:TYR113 4.3 18.0 1.0 CG B:GLU118 4.3 16.2 1.0 N B:ILE114 4.4 15.8 1.0 CB B:ASP107 4.4 16.6 1.0 CB B:ASP111 4.4 22.9 1.0 CB B:ASN109 4.4 19.0 1.0 N B:SER115 4.5 18.3 1.0 CA B:ILE114 4.5 16.0 1.0 N B:GLY110 4.5 18.8 1.0 CA B:ASN109 4.7 17.1 1.0 CA B:ASP111 4.7 22.3 1.0 CB B:TYR113 4.7 18.6 1.0 O B:ASP107 4.8 13.6 1.0 N B:GLY112 4.8 19.9 1.0 C B:ASN109 4.8 17.5 1.0 O B:HOH454 4.9 26.4 1.0 OG B:SER115 4.9 19.4 1.0 C B:ASP111 5.0 21.0 1.0 C B:ILE114 5.0 17.9 1.0

Calcium binding site 7 out of 7 in the Crystal Structure of Calaxin with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Calaxin with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:23.0 occ:1.00 O B:HOH476 2.1 31.3 1.0 OD1 B:ASP152 2.2 31.3 1.0 OD1 B:ASP156 2.2 32.4 1.0 O B:ARG158 2.4 18.7 1.0 O B:HOH404 2.4 40.2 1.0 OD1 B:ASP163 2.5 24.5 1.0 OD1 B:ASP154 2.5 41.4 1.0 CG B:ASP156 3.3 34.5 1.0 CG B:ASP152 3.3 27.4 1.0 CG B:ASP154 3.5 42.8 1.0 CG B:ASP163 3.6 25.8 1.0 C B:ARG158 3.6 22.0 1.0 OD2 B:ASP156 3.7 35.8 1.0 OD2 B:ASP154 4.0 47.1 1.0 OD2 B:ASP163 4.0 26.0 1.0 OD2 B:ASP152 4.1 30.9 1.0 N B:ASP154 4.3 33.5 1.0 N B:ASP156 4.3 31.0 1.0 CB B:ASP152 4.3 27.9 1.0 N B:ARG158 4.3 24.2 1.0 CA B:ASP152 4.3 26.4 1.0 CA B:LEU159 4.4 18.8 1.0 N B:SER160 4.4 19.2 1.0 N B:LEU159 4.5 19.8 1.0 CB B:ASP156 4.5 32.1 1.0 N B:HIS153 4.5 34.9 1.0 CA B:ARG158 4.6 24.9 1.0 C B:ASP152 4.6 34.5 1.0 CB B:ASP154 4.7 37.8 1.0 N B:HIS155 4.7 37.1 1.0 CG B:ARG158 4.8 30.9 1.0 CA B:ASP154 4.8 36.4 1.0 CA B:ASP156 4.8 29.5 1.0 CB B:ASP163 4.8 22.3 1.0 C B:ASP154 4.8 38.1 1.0 C B:LEU159 4.9 18.2 1.0 OG B:SER160 5.0 18.2 1.0

T.Shojima, F.Hou, Y.Takahashi, Y.Matsumura, M.Okai, A.Nakamura, K.Mizuno, K.Inaba, M.Kojima, T.Miyakawa, M.Tanokura. Crystal Structure of A CA2+-Dependent Regulator of Flagellar Motility Reveals the Open-Closed Structural Transition Sci Rep V. 8 2014 2018.
ISSN: ESSN 2045-2322
PubMed: 29386625
DOI: 10.1038/S41598-018-19898-7