Calcium in PDB 8k9z: 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

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, PDB code: 8k9z 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)	48.51 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	243.374, 49.778, 135.746, 90, 119.35, 90
R / Rfree (%)	26.5 / 30.4

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 (pdb code 8k9z). 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, PDB code: 8k9z:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:63.3 occ:1.00 OD2 B:ASP25 2.4 68.7 1.0 OD1 B:ASP21 2.4 37.6 1.0 OD2 B:ASP23 2.4 78.2 1.0 O B:THR27 2.5 51.1 1.0 OD1 B:ASP25 2.5 66.0 1.0 OD1 B:ASP23 2.6 85.0 1.0 OG1 B:THR27 2.6 59.7 1.0 CG B:ASP25 2.8 62.5 1.0 CG B:ASP23 2.8 75.0 1.0 CG B:ASP21 3.6 40.4 1.0 C B:THR27 3.6 49.8 1.0 N B:THR27 4.0 53.2 1.0 CB B:THR27 4.0 53.8 1.0 CB B:ASP23 4.1 61.9 1.0 CA B:THR27 4.2 53.6 1.0 OD2 B:ASP21 4.2 37.3 1.0 CB B:ASP25 4.2 60.6 1.0 N B:ASP25 4.4 58.5 1.0 N B:ASP23 4.4 51.9 1.0 N B:GLY26 4.6 59.8 1.0 CA B:ASP23 4.7 54.1 1.0 CB B:ASP21 4.7 40.6 1.0 N B:ILE28 4.7 44.7 1.0 CA B:ASP25 4.7 59.7 1.0 C B:ASP23 4.8 50.4 1.0 N B:GLY24 4.9 55.4 1.0 CA B:ASP21 4.9 38.4 1.0 CA B:ILE28 5.0 40.0 1.0 C B:ASP25 5.0 63.1 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:76.4 occ:1.00 OD1 B:ASN98 2.5 76.5 1.0 O B:GLY97 2.5 77.2 1.0 OD1 B:ASP96 2.6 95.0 1.0 OD2 B:ASP96 2.6 95.2 1.0 OD1 B:ASP94 2.6 68.8 1.0 O B:TYR100 2.6 63.7 1.0 CG B:ASP96 2.9 93.4 1.0 CG B:ASN98 3.5 77.0 1.0 C B:GLY97 3.7 73.8 1.0 C B:TYR100 3.7 65.1 1.0 CG B:ASP94 3.7 64.3 1.0 N B:ASP96 4.1 83.1 1.0 CB B:ASP96 4.1 93.3 1.0 N B:GLY97 4.2 73.4 1.0 C B:ASP96 4.2 79.2 1.0 N B:TYR100 4.3 74.7 1.0 ND2 B:ASN98 4.3 78.5 1.0 CA B:ASP96 4.3 87.5 1.0 CB B:ASN98 4.3 76.9 1.0 CB B:ASP94 4.5 58.6 1.0 CA B:ASP94 4.5 53.9 1.0 CA B:TYR100 4.5 72.2 1.0 CA B:GLY97 4.5 72.6 1.0 OD2 B:ASP94 4.6 67.7 1.0 O B:ASP96 4.6 81.6 1.0 N B:ILE101 4.6 58.9 1.0 N B:ASN98 4.7 73.2 1.0 N B:LYS95 4.7 63.5 1.0 C B:ASP94 4.8 58.1 1.0 CA B:ILE101 4.8 59.5 1.0 N B:GLY99 4.8 77.1 1.0 CA B:ASN98 4.8 75.8 1.0 CB B:TYR100 4.9 74.0 1.0 C B:ASN98 4.9 74.4 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:45.2 occ:1.00 OD1 B:ASN61 2.5 74.9 1.0 OG1 B:THR63 2.5 66.4 1.0 O B:THR63 2.6 45.4 1.0 OD2 B:ASP59 2.7 39.5 1.0 C B:THR63 3.4 48.6 1.0 OD1 B:ASP59 3.4 48.0 1.0 CB B:THR63 3.4 59.9 1.0 CG B:ASP59 3.5 42.2 1.0 CG B:ASN61 3.6 67.1 1.0 CA B:THR63 3.7 53.0 1.0 N B:THR63 3.8 52.9 1.0 OE2 B:GLU68 3.9 33.5 1.0 OE1 B:GLU68 4.2 36.5 1.0 ND2 B:ASN61 4.4 69.4 1.0 O B:VAL56 4.5 43.3 1.0 CD B:GLU68 4.5 35.6 1.0 N B:ILE64 4.6 46.0 1.0 OD1 B:ASP57 4.6 47.4 1.0 CB B:ASN61 4.7 59.6 1.0 CG2 B:THR63 4.8 58.8 1.0 CB B:ASP59 5.0 41.8 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1004 b:72.6 occ:1.00 OD2 B:ASP132 2.4 81.1 1.0 OD1 B:ASP132 2.5 76.3 1.0 OD1 B:ASP134 2.5 59.8 1.0 OD2 B:ASP134 2.5 55.5 1.0 O B:GLN136 2.5 66.8 1.0 OD2 B:ASP130 2.5 66.9 1.0 CG B:ASP132 2.6 76.7 1.0 CG B:ASP134 2.8 57.7 1.0 CB B:ASP130 2.9 71.8 1.0 CG B:ASP130 3.1 66.6 1.0 CB B:ASP132 3.7 73.0 1.0 C B:GLN136 3.7 69.6 1.0 CA B:ASP130 4.0 69.2 1.0 C B:ASP130 4.0 64.2 1.0 N B:ASP132 4.1 66.9 1.0 O B:ASP130 4.1 52.8 1.0 O B:ASP134 4.2 75.0 1.0 O B:ASP132 4.2 89.4 1.0 CB B:ASP134 4.3 61.5 1.0 CA B:ASP132 4.3 71.7 1.0 OD1 B:ASP130 4.4 60.6 1.0 C B:ASP132 4.5 77.8 1.0 CA B:VAL137 4.5 61.9 1.0 N B:VAL137 4.5 69.2 1.0 N B:ILE131 4.7 64.9 1.0 C B:ASP134 4.7 71.5 1.0 N B:ASP134 4.7 74.0 1.0 O B:GLY135 4.8 66.4 1.0 CA B:GLN136 4.8 65.6 1.0 CA B:ASP134 4.8 68.6 1.0 N B:GLN136 5.0 65.9 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1001 b:49.4 occ:1.00 OD2 D:ASP25 2.4 48.2 1.0 OD1 D:ASP21 2.4 39.5 1.0 O D:THR27 2.5 48.4 1.0 OD1 D:ASP23 2.5 60.1 1.0 CB D:ASP25 2.8 51.4 1.0 CG D:ASP25 3.0 47.5 1.0 CG D:ASP23 3.5 59.2 1.0 CG D:ASP21 3.6 41.3 1.0 C D:THR27 3.7 43.7 1.0 OD2 D:ASP23 3.9 60.9 1.0 OG1 D:THR27 4.1 39.0 1.0 CA D:ASP25 4.1 53.4 1.0 OD1 D:ASP25 4.2 47.5 1.0 OD2 D:ASP21 4.4 37.5 1.0 N D:THR27 4.4 42.3 1.0 CA D:ASP21 4.4 42.8 1.0 N D:ASP25 4.5 61.2 1.0 CB D:ASP21 4.5 43.7 1.0 N D:LYS22 4.6 54.0 1.0 CA D:THR27 4.6 42.5 1.0 N D:ILE28 4.6 44.8 1.0 CB D:ASP23 4.6 60.7 1.0 N D:ASP23 4.6 69.8 1.0 CA D:ILE28 4.7 47.4 1.0 C D:ASP25 4.7 47.7 1.0 C D:ASP21 4.8 46.6 1.0 N D:GLY26 4.9 43.6 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1002 b:93.2 occ:1.00 OD1 D:ASN98 2.4 91.9 1.0 OD1 D:ASP94 2.4 103.9 1.0 CG D:ASP94 2.6 99.2 1.0 OD2 D:ASP94 2.6 99.7 1.0 O D:TYR100 2.7 77.8 1.0 O D:ASN98 3.3 98.1 1.0 OD1 D:ASP96 3.4 77.8 1.0 C D:TYR100 3.5 85.1 1.0 CA D:ASP94 3.5 94.4 1.0 CB D:ASP94 3.5 96.9 1.0 CG D:ASN98 3.6 86.7 1.0 CA D:ILE101 3.7 75.7 1.0 N D:ILE101 3.7 81.1 1.0 N D:LYS95 4.0 88.8 1.0 C D:ASP94 4.0 92.1 1.0 CB D:ILE101 4.1 79.4 1.0 N D:ASN98 4.1 83.8 1.0 C D:ASN98 4.2 93.4 1.0 N D:GLY97 4.2 86.5 1.0 ND2 D:ASN98 4.3 86.9 1.0 CA D:ASN98 4.5 87.5 1.0 N D:ASP96 4.5 90.9 1.0 CG D:ASP96 4.6 78.8 1.0 C D:GLY97 4.6 83.0 1.0 O D:PHE93 4.6 84.9 1.0 CB D:ASN98 4.6 87.5 1.0 CG1 D:ILE101 4.7 83.5 1.0 N D:TYR100 4.7 97.8 1.0 CA D:TYR100 4.7 90.7 1.0 N D:ASP94 4.7 93.4 1.0 CA D:GLY97 4.7 87.1 1.0 O D:ASP94 4.9 92.5 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1003 b:48.1 occ:1.00 OE1 D:GLU68 2.4 37.0 1.0 O D:THR63 2.4 50.6 1.0 OG1 D:THR63 2.5 45.8 1.0 CD D:GLU68 3.4 33.4 1.0 C D:THR63 3.5 47.6 1.0 O D:VAL56 3.5 48.9 1.0 OE2 D:GLU68 3.8 37.2 1.0 CB D:THR63 3.8 49.9 1.0 OD2 D:ASP59 3.9 51.1 1.0 CA D:THR63 4.1 49.1 1.0 OD1 D:ASP59 4.4 57.1 1.0 N D:THR63 4.4 51.5 1.0 N D:ILE64 4.4 43.8 1.0 CG D:ASP59 4.4 55.7 1.0 CA D:ILE64 4.5 40.6 1.0 OD1 D:ASP57 4.6 59.1 1.0 CG1 D:VAL56 4.6 49.6 1.0 C D:VAL56 4.7 50.2 1.0 CG D:GLU68 4.7 32.7 1.0 CG2 D:THR63 4.9 50.0 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1004 b:94.6 occ:1.00 OD1 D:ASP132 2.4 99.6 1.0 OD1 D:ASP130 2.5 102.8 1.0 OD1 D:ASP134 2.5 96.8 1.0 CG D:ASP132 2.6 93.4 1.0 OD2 D:ASP132 2.6 85.4 1.0 O D:GLN136 2.6 80.6 1.0 CG D:ASP130 2.8 99.9 1.0 N D:GLY133 2.9 87.7 1.0 N D:ASP134 3.0 80.0 1.0 OD2 D:ASP130 3.3 90.5 1.0 N D:GLY135 3.4 91.1 1.0 CA D:GLY133 3.5 82.2 1.0 CB D:ASP130 3.5 107.1 1.0 CA D:ASP130 3.6 113.6 1.0 C D:GLY133 3.6 76.6 1.0 CG D:ASP134 3.6 89.0 1.0 N D:GLN136 3.6 86.4 1.0 CB D:ASP132 3.7 90.6 1.0 N D:ILE131 3.7 109.5 1.0 C D:GLN136 3.7 82.6 1.0 C D:ASP132 3.7 90.4 1.0 C D:ASP130 3.8 116.4 1.0 N D:ASP132 3.8 90.8 1.0 CA D:ASP132 3.9 90.7 1.0 CA D:ASP134 4.0 91.2 1.0 C D:ASP134 4.2 97.3 1.0 CA D:GLN136 4.3 87.3 1.0 CA D:GLY135 4.3 83.2 1.0 CB D:ASP134 4.3 91.5 1.0 C D:GLY135 4.4 82.5 1.0 OD2 D:ASP134 4.4 82.9 1.0 C D:ILE131 4.5 93.0 1.0 O D:GLY133 4.6 68.5 1.0 O D:ASP130 4.6 120.1 1.0 CA D:ILE131 4.7 97.7 1.0 O D:ASP132 4.8 89.3 1.0 N D:VAL137 4.9 73.1 1.0 N D:ASP130 5.0 122.3 1.0 CB D:GLN136 5.0 88.6 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 To Be Published.