Calcium in PDB 8ka0: Crystal Structure of Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+)

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+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+), PDB code: 8ka0 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)	29.62 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	136.222, 48.931, 178.603, 90, 95.7, 90
R / Rfree (%)	21.7 / 26.3

The binding sites of Calcium 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+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+) (pdb code 8ka0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium 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+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+), PDB code: 8ka0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 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+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+)


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 Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:73.8 occ:1.00 O B:TYR100 2.4 56.0 1.0 OD1 B:ASP96 2.4 83.1 1.0 OD1 B:ASN98 2.4 58.7 1.0 OD2 B:ASP96 2.5 73.5 1.0 OD1 B:ASP94 2.7 36.3 1.0 CG B:ASP96 2.7 73.6 1.0 CG B:ASN98 3.3 58.3 1.0 C B:TYR100 3.5 48.2 1.0 ND2 B:ASN98 3.6 64.8 1.0 CG B:ASP94 3.9 39.6 1.0 CB B:ASP96 4.1 66.2 1.0 CB B:TYR100 4.2 51.1 1.0 CA B:TYR100 4.2 45.8 1.0 OE1 B:GLN136 4.2 60.0 1.0 N B:TYR100 4.2 40.0 1.0 N B:ASP96 4.3 62.9 1.0 N B:ASN98 4.5 49.2 1.0 N B:ILE101 4.5 38.8 1.0 CB B:ASN98 4.5 51.5 1.0 OD2 B:ASP94 4.6 35.6 1.0 N B:GLY97 4.7 58.2 1.0 CA B:ASP96 4.7 61.3 1.0 CA B:ILE101 4.7 38.1 1.0 N B:LYS95 4.9 49.6 1.0 CA B:ASN98 5.0 52.5 1.0 N B:GLY99 5.0 45.7 1.0

Calcium binding site 2 out of 8 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+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+)


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 Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:34.2 occ:1.00 OD1 B:ASP57 2.6 58.0 1.0 N B:GLY62 2.6 64.0 1.0 N B:THR63 3.0 48.2 1.0 CA B:GLY62 3.4 61.3 1.0 O B:VAL56 3.4 61.1 1.0 N B:ASN61 3.4 75.2 1.0 C B:ASN61 3.5 79.0 1.0 O B:THR63 3.5 51.3 1.0 CA B:ASP57 3.6 62.6 1.0 CG B:ASP57 3.6 67.5 1.0 C B:GLY62 3.7 52.6 1.0 OG1 B:THR63 3.7 48.9 1.0 CA B:ASN61 3.7 75.6 1.0 OD1 B:ASP59 3.7 75.8 1.0 CB B:ASN61 3.7 79.1 1.0 OD2 B:ASP59 3.9 81.6 1.0 CB B:ASP57 3.9 63.8 1.0 CA B:THR63 4.1 50.8 1.0 CG B:ASP59 4.1 85.0 1.0 C B:THR63 4.2 46.8 1.0 C B:VAL56 4.3 58.7 1.0 N B:GLY60 4.4 70.4 1.0 C B:GLY60 4.4 70.8 1.0 N B:ASP57 4.4 55.4 1.0 O B:ASN61 4.5 64.3 1.0 CB B:THR63 4.5 51.0 1.0 C B:ASP57 4.5 63.2 1.0 CA B:GLY60 4.7 63.1 1.0 O B:ASP57 4.8 57.6 1.0 OD2 B:ASP57 4.8 66.8 1.0 O B:GLY62 4.9 40.9 1.0

Calcium binding site 3 out of 8 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+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+)


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 Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1001 b:52.1 occ:1.00 O D:THR27 2.3 50.2 1.0 OD1 D:ASP21 2.5 47.8 1.0 OD2 D:ASP25 2.5 60.7 1.0 CG D:ASP25 3.2 66.3 1.0 OD1 D:ASP25 3.3 65.9 1.0 C D:THR27 3.4 61.3 1.0 CG D:ASP21 3.5 49.9 1.0 CA D:ASP21 3.5 53.3 1.0 OG1 D:THR27 3.8 63.1 1.0 OD1 D:ASP23 3.8 93.6 1.0 CB D:ASP21 3.9 50.7 1.0 N D:LYS22 3.9 60.6 1.0 C D:ASP21 4.0 53.9 1.0 CA D:ILE28 4.2 64.5 1.0 N D:ILE28 4.2 65.7 1.0 N D:THR27 4.3 56.0 1.0 CA D:THR27 4.4 61.5 1.0 O D:HOH1107 4.4 50.2 1.0 O D:PHE20 4.4 54.1 1.0 CG D:ASP23 4.4 92.3 1.0 OD2 D:ASP21 4.6 48.0 1.0 CB D:ASP25 4.6 61.5 1.0 OD2 D:ASP23 4.6 84.4 1.0 N D:ASP21 4.6 51.6 1.0 N D:ASP25 4.7 57.5 1.0 N D:ASP23 4.7 81.3 1.0 CB D:THR27 4.7 60.6 1.0 O D:ASP21 4.9 60.4 1.0 CG2 D:ILE28 4.9 63.1 1.0 C D:PHE20 5.0 51.2 1.0

Calcium binding site 4 out of 8 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+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+)


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 Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1002 b:70.5 occ:1.00 OD1 D:ASP96 2.4 71.8 1.0 O D:TYR100 2.4 49.6 1.0 OD1 D:ASN98 2.5 64.1 1.0 OD1 D:ASP94 2.6 51.2 1.0 CG D:ASP96 3.1 68.7 1.0 CG D:ASN98 3.4 63.2 1.0 OD2 D:ASP96 3.4 68.2 1.0 C D:TYR100 3.6 53.5 1.0 CG D:ASP94 3.8 50.1 1.0 ND2 D:ASN98 3.9 56.5 1.0 N D:ASP96 4.0 66.8 1.0 OE1 D:GLN136 4.2 59.3 1.0 CB D:ASP96 4.2 65.9 1.0 N D:TYR100 4.3 51.4 1.0 CA D:TYR100 4.3 55.3 1.0 N D:ASN98 4.4 59.2 1.0 N D:GLY97 4.4 57.3 1.0 CB D:ASN98 4.5 57.4 1.0 CA D:ASP96 4.5 64.3 1.0 OD2 D:ASP94 4.5 50.7 1.0 N D:LYS95 4.5 53.2 1.0 CB D:TYR100 4.5 63.0 1.0 N D:ILE101 4.6 44.1 1.0 C D:ASP96 4.7 57.2 1.0 C D:ASP94 4.7 49.8 1.0 CA D:ASP94 4.7 46.3 1.0 CA D:ILE101 4.7 41.6 1.0 CB D:ASP94 4.8 51.5 1.0 CA D:ASN98 4.9 58.0 1.0

Calcium binding site 5 out of 8 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+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+)


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 Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca2502 b:81.9 occ:1.00 OD1 F:ASP96 2.4 92.6 1.0 OD1 F:ASN98 2.4 66.1 1.0 O F:TYR100 2.4 40.9 1.0 OD1 F:ASP94 2.4 55.1 1.0 CG F:ASP96 3.4 76.1 1.0 C F:TYR100 3.4 42.7 1.0 CG F:ASN98 3.5 61.6 1.0 CG F:ASP94 3.6 50.7 1.0 OD2 F:ASP96 3.9 71.8 1.0 ND2 F:ASN98 4.2 67.4 1.0 N F:LYS95 4.2 57.9 1.0 N F:ASP96 4.2 69.5 1.0 CA F:ASP94 4.2 53.3 1.0 N F:TYR100 4.3 42.9 1.0 CA F:TYR100 4.3 43.8 1.0 N F:ILE101 4.4 42.5 1.0 OD2 F:ASP94 4.4 44.0 1.0 C F:ASP94 4.5 51.1 1.0 CB F:ASP94 4.5 52.1 1.0 CA F:ILE101 4.5 41.7 1.0 N F:ASN98 4.5 48.6 1.0 CB F:TYR100 4.5 46.1 1.0 CB F:ASN98 4.7 57.6 1.0 CG2 F:ILE101 4.7 44.2 1.0 CB F:ASP96 4.7 71.7 1.0 N F:GLY97 4.7 58.1 1.0 OE1 F:GLN136 4.9 70.4 1.0 CA F:ASP96 4.9 67.7 1.0

Calcium binding site 6 out of 8 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+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+)


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 Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca2503 b:49.5 occ:1.00 O F:VAL56 2.6 70.3 1.0 O F:THR63 2.7 64.2 1.0 OD1 F:ASN61 3.6 106.1 1.0 C F:VAL56 3.7 81.2 1.0 CA F:ASP57 3.7 96.8 1.0 N F:THR63 3.8 57.8 1.0 OG1 F:THR63 3.8 65.1 1.0 OD1 F:ASP57 3.8 91.5 1.0 C F:THR63 3.8 58.8 1.0 O F:HOH2621 3.9 56.8 1.0 N F:ASP57 4.1 92.5 1.0 CG1 F:VAL56 4.1 98.8 1.0 CA F:THR63 4.3 58.8 1.0 CB F:ASP57 4.4 99.2 1.0 N F:GLY62 4.4 68.4 1.0 CG F:ASP57 4.6 99.2 1.0 CB F:THR63 4.6 64.9 1.0 CG F:ASN61 4.7 98.6 1.0 C F:ASP57 4.7 96.0 1.0 N F:ALA58 4.8 93.6 1.0 C F:GLY62 4.8 62.6 1.0 CB F:ASP59 4.8 92.0 1.0 CA F:GLY62 4.9 66.3 1.0 CA F:VAL56 4.9 83.5 1.0 N F:ASP59 4.9 93.3 1.0 N F:ILE64 5.0 60.4 1.0

Calcium binding site 7 out of 8 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+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+)


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 Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca1001 b:62.9 occ:1.00 OD2 H:ASP25 2.4 69.3 1.0 O H:THR27 2.4 45.8 1.0 OD1 H:ASP21 2.6 38.3 1.0 OG1 H:THR27 2.7 44.1 1.0 C H:THR27 3.4 50.4 1.0 CG H:ASP25 3.4 67.2 1.0 OD2 H:ASP23 3.5 69.5 1.0 OD1 H:ASP25 3.7 71.5 1.0 CG H:ASP21 3.8 43.5 1.0 CA H:THR27 4.0 53.3 1.0 CA H:ASP21 4.0 46.9 1.0 N H:THR27 4.0 47.6 1.0 CB H:THR27 4.0 51.1 1.0 N H:LYS22 4.1 56.5 1.0 CG H:ASP23 4.2 73.9 1.0 C H:ASP21 4.2 50.2 1.0 N H:ASP23 4.3 60.3 1.0 N H:ILE28 4.4 46.9 1.0 N H:ASP25 4.4 60.5 1.0 CB H:ASP21 4.5 46.6 1.0 CB H:ASP25 4.6 61.1 1.0 CA H:ILE28 4.6 48.6 1.0 N H:GLY24 4.7 57.3 1.0 OD1 H:ASP23 4.7 82.5 1.0 OD2 H:ASP21 4.8 49.3 1.0 O H:PHE20 4.8 46.2 1.0 C H:ASP23 4.9 63.0 1.0 CA H:ASP25 4.9 59.6 1.0 O H:ASP21 4.9 51.5 1.0 CA H:ASP23 4.9 63.7 1.0 N H:GLY26 5.0 53.6 1.0

Calcium binding site 8 out of 8 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+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Vibrio Vulnificus Rid-Dependent Transforming Nadase Domain (Rdtnd)/Calmodulin-Binding Domain of Rho Inactivation Domain (Rid-Cbd) Complexed with CA2+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+) within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca1002 b:78.9 occ:1.00 OD1 H:ASN98 1.9 54.2 1.0 O H:TYR100 2.4 45.9 1.0 OD1 H:ASP94 2.5 44.8 1.0 OD2 H:ASP96 2.5 70.2 1.0 CG H:ASN98 2.9 51.7 1.0 CG H:ASP96 3.3 70.9 1.0 ND2 H:ASN98 3.3 47.9 1.0 C H:TYR100 3.5 44.7 1.0 OD1 H:ASP96 3.5 81.2 1.0 CG H:ASP94 3.7 42.2 1.0 N H:TYR100 4.1 47.3 1.0 N H:ASN98 4.1 46.2 1.0 CB H:ASN98 4.1 48.9 1.0 CA H:TYR100 4.2 48.2 1.0 N H:ASP96 4.2 54.0 1.0 CB H:TYR100 4.3 49.9 1.0 OD2 H:ASP94 4.4 43.5 1.0 N H:GLY97 4.5 61.1 1.0 CB H:ASP96 4.5 67.1 1.0 N H:LYS95 4.5 53.3 1.0 O H:HOH1118 4.5 42.1 1.0 CA H:ASN98 4.6 48.0 1.0 N H:ILE101 4.6 45.0 1.0 CA H:ASP96 4.7 58.1 1.0 N H:GLY99 4.7 52.2 1.0 CB H:ASP94 4.8 40.6 1.0 C H:ASP96 4.8 61.9 1.0 CA H:ASP94 4.9 43.2 1.0 C H:ASP94 4.9 46.8 1.0 CA H:ILE101 4.9 43.8 1.0 C H:ASN98 4.9 50.6 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+-Bound Calmodulin and A Nicotinamide Adenine Dinucleotide (Nad+) To Be Published.