Magnesium in PDB 8ka1: Crystal Structure of Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Free Calmodulin

The structure of Crystal Structure of Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Free Calmodulin, PDB code: 8ka1 was solved by Y.Lee, S.Choi, J.Hwang, M.H.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.53 / 2.82
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	106.032, 88.081, 136.954, 90, 90.14, 90
R / Rfree (%)	27.1 / 34.2

The binding sites of Magnesium atom in the Crystal Structure of Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Free Calmodulin (pdb code 8ka1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Free Calmodulin, PDB code: 8ka1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Free Calmodulin


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 Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Free Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg201 b:27.7 occ:1.00 O F:TYR100 2.1 38.2 1.0 OD1 F:ASN98 2.1 35.8 1.0 OD1 F:ASP96 2.2 50.9 1.0 OD1 F:ASP94 2.3 38.9 1.0 CG F:ASN98 3.2 38.5 1.0 C F:TYR100 3.2 37.8 1.0 CG F:ASP96 3.3 53.6 1.0 ND2 F:ASN98 3.6 40.6 1.0 CG F:ASP94 3.6 43.2 1.0 OD2 F:ASP96 3.6 53.5 1.0 N F:ILE101 4.1 36.0 1.0 CA F:ILE101 4.1 36.7 1.0 N F:ASN98 4.2 42.7 1.0 CA F:TYR100 4.2 38.6 1.0 N F:TYR100 4.3 38.0 1.0 CA F:ASP94 4.3 44.0 1.0 OD2 F:ASP94 4.4 48.4 1.0 O F:ASN98 4.4 53.9 1.0 N F:GLY97 4.4 42.5 1.0 CB F:ASN98 4.5 38.3 1.0 N F:ASP96 4.5 53.9 1.0 CB F:ASP94 4.5 44.0 1.0 C F:ASP94 4.6 44.0 1.0 CB F:ASP96 4.6 54.1 1.0 CB F:TYR100 4.6 39.4 1.0 CG2 F:ILE101 4.7 38.3 1.0 CA F:ASN98 4.7 41.8 1.0 N F:LYS95 4.7 53.0 1.0 C F:ASN98 4.7 45.5 1.0 C F:ASP96 4.8 45.7 1.0 CA F:ASP96 4.8 52.2 1.0 OE1 F:GLN136 4.8 35.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Free Calmodulin


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 Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Free Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg202 b:56.5 occ:1.00 O F:THR27 2.1 55.8 1.0 OD1 F:ASP25 2.1 64.7 1.0 OD1 F:ASP21 2.3 51.3 1.0 OG1 F:THR27 2.4 65.7 1.0 CG F:ASP25 2.9 67.4 1.0 C F:THR27 3.2 59.1 1.0 OD2 F:ASP25 3.2 62.4 1.0 OD1 F:ASP23 3.3 70.5 1.0 CG F:ASP23 3.5 70.0 1.0 CG F:ASP21 3.6 50.1 1.0 CB F:ASP23 3.6 66.9 1.0 CB F:THR27 3.7 64.6 1.0 N F:THR27 3.8 66.5 1.0 CA F:THR27 3.8 65.1 1.0 OD2 F:ASP23 4.1 68.5 1.0 CA F:ASP21 4.2 47.2 1.0 N F:ILE28 4.2 57.0 1.0 N F:ASP23 4.2 63.2 1.0 N F:ASP25 4.2 63.0 1.0 CB F:ASP25 4.2 65.9 1.0 CB F:ASP21 4.3 48.6 1.0 N F:GLY24 4.3 61.0 1.0 CA F:ASP23 4.3 64.3 1.0 CA F:ILE28 4.5 57.0 1.0 OD2 F:ASP21 4.5 48.0 1.0 C F:ASP21 4.6 50.6 1.0 C F:ASP23 4.7 61.1 1.0 N F:GLY26 4.7 64.9 1.0 CA F:ASP25 4.7 65.1 1.0 N F:LYS22 4.8 55.0 1.0 C F:ASP25 4.9 65.0 1.0 CG2 F:THR27 4.9 63.5 1.0 C F:GLY26 5.0 63.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Free Calmodulin


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 Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Free Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg203 b:39.0 occ:1.00 OD1 F:ASP132 2.0 54.4 1.0 O F:GLN136 2.2 33.4 1.0 OD2 F:ASP132 2.3 57.4 1.0 OD1 F:ASP134 2.3 44.1 1.0 OD1 F:ASP130 2.4 45.3 1.0 CG F:ASP132 2.4 57.7 1.0 C F:GLN136 3.3 32.1 1.0 CG F:ASP134 3.5 44.9 1.0 CG F:ASP130 3.7 50.1 1.0 N F:GLN136 3.7 36.9 1.0 CB F:ASP132 3.9 56.0 1.0 CA F:ASP130 3.9 49.9 1.0 OD2 F:ASP134 4.0 44.6 1.0 CA F:GLN136 4.0 33.7 1.0 O F:ALA129 4.1 45.8 1.0 N F:GLY135 4.2 34.6 1.0 N F:ASP134 4.2 45.1 1.0 N F:GLY133 4.3 53.6 1.0 N F:ASP132 4.3 60.7 1.0 CB F:ASP130 4.4 48.5 1.0 N F:VAL137 4.4 32.5 1.0 C F:ASP130 4.4 52.9 1.0 CB F:GLN136 4.4 33.7 1.0 CA F:ASP132 4.5 57.2 1.0 N F:ILE131 4.6 61.0 1.0 OD2 F:ASP130 4.6 55.3 1.0 C F:GLY135 4.7 36.6 1.0 CB F:ASP134 4.7 43.0 1.0 CA F:VAL137 4.7 32.9 1.0 CA F:ASP134 4.8 40.4 1.0 C F:ASP134 4.8 36.1 1.0 C F:ASP132 4.8 56.6 1.0 N F:ASP130 4.9 48.9 1.0 C F:ALA129 4.9 44.1 1.0 CA F:GLY135 4.9 34.4 1.0

Y.Lee, S.Choi, J.Hwang, M.H.Kim. Crystal Structure of Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Free Calmodulin To Be Published.