Magnesium in PDB 5ypx: Crystal Structure of Calaxin with Magnesium

The structure of Crystal Structure of Calaxin with Magnesium, PDB code: 5ypx 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)	42.76 / 2.64
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	65.258, 65.258, 113.203, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 21.2

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

Magnesium binding site 1 out of 5 in the Crystal Structure of Calaxin with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Calaxin with Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:25.9 occ:1.00 OD1 A:ASP73 2.0 33.1 1.0 O A:TYR77 2.2 30.3 1.0 OE1 A:GLU82 2.2 41.2 1.0 OD1 A:ASP71 2.3 33.2 1.0 OD1 A:ASP75 2.4 39.0 1.0 CG A:ASP73 2.9 33.5 1.0 OD2 A:ASP75 2.9 40.5 1.0 CG A:ASP75 2.9 35.0 1.0 OD2 A:ASP73 3.0 32.0 1.0 CD A:GLU82 3.0 39.6 1.0 OE2 A:GLU82 3.2 40.6 1.0 C A:TYR77 3.4 32.4 1.0 CG A:ASP71 3.5 30.6 1.0 N A:TYR77 4.1 36.7 1.0 N A:SER79 4.1 23.9 1.0 CB A:ASP75 4.3 32.8 1.0 N A:ASP75 4.3 34.4 1.0 CA A:TYR77 4.3 37.3 1.0 CB A:ASP73 4.3 32.6 1.0 N A:ILE78 4.3 30.2 1.0 OD2 A:ASP71 4.4 26.8 1.0 CA A:ILE78 4.4 28.4 1.0 CG A:GLU82 4.4 39.7 1.0 CA A:ASP71 4.5 30.3 1.0 CB A:ASP71 4.5 28.4 1.0 CB A:TYR77 4.6 38.4 1.0 OG A:SER79 4.6 23.5 1.0 N A:SER74 4.7 31.8 1.0 CA A:ASP75 4.7 31.8 1.0 C A:ILE78 4.7 27.2 1.0 N A:ASP73 4.8 37.0 1.0 C A:ASP71 4.8 29.2 1.0 N A:SER76 4.8 33.9 1.0 C A:ASP73 4.8 32.4 1.0 CA A:ASP73 4.9 32.9 1.0 CB A:SER79 4.9 22.2 1.0 C A:ASP75 4.9 32.1 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Calaxin with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Calaxin with Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:29.8 occ:1.00 OD1 A:ASP107 2.3 54.2 1.0 O A:TYR113 2.3 43.7 1.0 OE2 A:GLU118 2.3 37.3 1.0 OD1 A:ASP111 2.4 55.9 1.0 OE1 A:GLU118 2.5 37.5 1.0 OD1 A:ASN109 2.7 49.6 1.0 CD A:GLU118 2.8 38.4 1.0 CG A:ASP111 2.9 59.3 1.0 OD2 A:ASP111 3.0 57.1 1.0 CG A:ASN109 3.4 55.8 1.0 CG A:ASP107 3.5 46.1 1.0 C A:TYR113 3.5 48.5 1.0 ND2 A:ASN109 3.6 54.9 1.0 N A:ASP111 4.2 57.5 1.0 N A:ASN109 4.2 51.7 1.0 CB A:ASP111 4.2 53.7 1.0 N A:TYR113 4.2 49.3 1.0 CA A:ASP107 4.2 43.0 1.0 OD2 A:ASP107 4.3 48.4 1.0 C A:ASP107 4.3 41.0 1.0 N A:LEU108 4.3 41.9 1.0 CG A:GLU118 4.3 40.1 1.0 CA A:TYR113 4.4 49.9 1.0 CB A:ASP107 4.4 44.7 1.0 N A:ILE114 4.5 48.5 1.0 N A:GLY110 4.5 53.6 1.0 CA A:ILE114 4.6 52.9 1.0 CA A:ASP111 4.6 55.1 1.0 CB A:ASN109 4.6 49.8 1.0 N A:SER115 4.7 48.9 1.0 CA A:ASN109 4.7 50.7 1.0 CB A:TYR113 4.8 52.6 1.0 C A:ASN109 4.8 50.0 1.0 O A:ASP107 4.8 37.5 1.0 N A:GLY112 4.9 54.8 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Calaxin with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Calaxin with Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:26.6 occ:1.00 OE1 B:GLU82 2.1 31.1 1.0 O B:TYR77 2.1 30.5 1.0 OD1 B:ASP71 2.1 29.1 1.0 OD1 B:ASP73 2.2 43.6 1.0 OD1 B:ASP75 2.3 25.1 1.0 OD2 B:ASP73 2.6 37.7 1.0 CG B:ASP73 2.8 35.3 1.0 CD B:GLU82 2.9 31.6 1.0 CG B:ASP75 3.1 25.8 1.0 OE2 B:GLU82 3.1 33.9 1.0 OD2 B:ASP75 3.2 34.2 1.0 C B:TYR77 3.3 30.1 1.0 CG B:ASP71 3.4 31.0 1.0 N B:TYR77 4.0 29.2 1.0 N B:SER79 4.0 24.9 1.0 CA B:TYR77 4.1 33.8 1.0 OD2 B:ASP71 4.2 30.9 1.0 CB B:ASP73 4.2 32.4 1.0 N B:ILE78 4.3 28.7 1.0 CG B:GLU82 4.3 28.4 1.0 CA B:ILE78 4.4 29.0 1.0 CB B:ASP71 4.4 29.1 1.0 CB B:ASP75 4.4 22.8 1.0 CB B:TYR77 4.4 36.4 1.0 CA B:ASP71 4.4 30.5 1.0 N B:ASP75 4.4 23.1 1.0 N B:ASP73 4.6 30.4 1.0 C B:ILE78 4.7 26.6 1.0 OG B:SER79 4.7 27.4 1.0 C B:ASP71 4.7 33.4 1.0 CB B:SER79 4.8 23.5 1.0 N B:SER74 4.8 28.6 1.0 CA B:ASP73 4.8 31.8 1.0 CA B:ASP75 4.9 23.0 1.0 N B:LYS72 4.9 34.5 1.0 CB B:GLU82 4.9 26.9 1.0 N B:SER76 5.0 24.2 1.0 C B:ASP73 5.0 30.7 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Calaxin with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Calaxin with Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:20.9 occ:1.00 OD1 B:ASN109 2.1 41.8 1.0 OD1 B:ASP107 2.2 39.4 1.0 O B:TYR113 2.2 34.3 1.0 OE2 B:GLU118 2.2 35.2 1.0 OE1 B:GLU118 2.4 37.7 1.0 OD1 B:ASP111 2.5 38.1 1.0 CD B:GLU118 2.7 34.5 1.0 CG B:ASN109 3.1 37.1 1.0 CG B:ASP111 3.3 38.1 1.0 CG B:ASP107 3.4 33.4 1.0 C B:TYR113 3.5 41.7 1.0 OD2 B:ASP111 3.6 36.0 1.0 ND2 B:ASN109 3.7 37.7 1.0 N B:ASN109 4.1 31.7 1.0 CG B:GLU118 4.1 34.7 1.0 OD2 B:ASP107 4.2 36.3 1.0 CB B:ASN109 4.2 32.9 1.0 CA B:ASP107 4.2 31.5 1.0 N B:TYR113 4.3 39.7 1.0 C B:ASP107 4.3 30.5 1.0 N B:LEU108 4.3 31.9 1.0 N B:ASP111 4.4 42.9 1.0 CA B:TYR113 4.4 43.4 1.0 N B:ILE114 4.4 36.3 1.0 CB B:ASP107 4.4 32.6 1.0 N B:SER115 4.5 38.3 1.0 CB B:ASP111 4.5 40.9 1.0 CA B:ILE114 4.5 36.4 1.0 CA B:ASN109 4.5 33.4 1.0 N B:GLY110 4.5 39.4 1.0 C B:ASN109 4.7 34.2 1.0 O B:ASP107 4.7 31.1 1.0 OG B:SER115 4.9 34.1 1.0 CA B:ASP111 4.9 38.6 1.0 N B:GLY112 5.0 37.9 1.0 CB B:TYR113 5.0 47.5 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Calaxin with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Calaxin with Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:56.5 occ:1.00 O B:ARG158 1.9 48.2 1.0 OD2 B:ASP163 2.0 52.1 1.0 OD1 B:ASP156 2.0 66.5 1.0 OD1 B:ASP154 2.2 60.1 1.0 OD1 B:ASP152 2.4 54.3 1.0 CG B:ASP156 3.0 70.7 1.0 CG B:ASP163 3.1 51.4 1.0 C B:ARG158 3.1 49.8 1.0 CG B:ASP154 3.2 56.6 1.0 CG B:ASP152 3.3 54.4 1.0 OD2 B:ASP156 3.3 63.2 1.0 OD2 B:ASP154 3.6 60.9 1.0 OD1 B:ASP163 3.6 50.7 1.0 CA B:LEU159 3.8 43.0 1.0 N B:LEU159 3.9 45.3 1.0 OD2 B:ASP152 3.9 58.1 1.0 N B:SER160 4.0 43.8 1.0 N B:ARG158 4.1 55.7 1.0 CA B:ARG158 4.2 53.8 1.0 CB B:ASP163 4.2 48.1 1.0 CB B:ASP152 4.3 48.1 1.0 N B:ASP156 4.3 64.1 1.0 CG B:ARG158 4.3 60.0 1.0 CB B:ASP156 4.4 66.0 1.0 C B:LEU159 4.4 41.6 1.0 CA B:ASP152 4.5 54.1 1.0 CB B:ASP154 4.6 55.6 1.0 N B:ASP154 4.7 59.2 1.0 N B:HIS155 4.7 63.4 1.0 CA B:ASP156 4.7 59.8 1.0 N B:SER157 4.7 60.7 1.0 C B:ASP156 4.8 62.3 1.0 C B:ASP154 4.8 61.1 1.0 CD2 B:LEU159 4.8 41.2 1.0 OG B:SER160 4.8 46.7 1.0 CA B:ASP154 4.9 60.3 1.0 CB B:ARG158 4.9 58.2 1.0 C B:ASP152 4.9 57.2 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