Calcium in PDB 6ifc: Crystal Structure of Vapbc From Salmonella Typhimurium

The structure of Crystal Structure of Vapbc From Salmonella Typhimurium, PDB code: 6ifc was solved by D.W.Park, B.J.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.47 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.956, 114.942, 53.998, 90.00, 114.12, 90.00
R / Rfree (%)	17.5 / 23.8

The binding sites of Calcium atom in the Crystal Structure of Vapbc From Salmonella Typhimurium (pdb code 6ifc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Vapbc From Salmonella Typhimurium, PDB code: 6ifc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Vapbc From Salmonella Typhimurium


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 Vapbc From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:78.7 occ:1.00 OD1 A:ASP98 2.6 27.7 1.0 OD2 A:ASP7 2.7 38.7 1.0 N A:THR8 3.0 21.2 1.0 NH1 B:ARG64 3.3 40.0 1.0 NH2 B:ARG64 3.3 34.1 1.0 CB A:ASP7 3.3 29.3 1.0 CG A:ASP7 3.3 35.6 1.0 CB A:THR8 3.4 21.4 1.0 CD1 A:ILE101 3.5 30.4 1.0 CZ B:ARG64 3.6 37.6 1.0 CA A:THR8 3.6 21.8 1.0 N A:ASN9 3.7 26.0 1.0 OG1 A:THR8 3.7 22.1 1.0 C A:ASP7 3.8 22.3 1.0 CG A:ASP98 3.8 30.6 1.0 CA A:ASP7 3.9 24.4 1.0 CZ A:PHE120 4.1 31.8 1.0 ND2 A:ASN9 4.2 42.0 1.0 C A:THR8 4.2 23.5 1.0 CE2 A:PHE120 4.3 31.8 1.0 OD1 A:ASP7 4.4 40.3 1.0 OD2 A:ASP98 4.5 38.1 1.0 CG A:ASN9 4.6 36.9 1.0 O A:HOH302 4.7 42.1 1.0 CG2 A:THR8 4.7 21.3 1.0 NE B:ARG64 4.7 37.4 1.0 OE1 A:GLU42 4.8 27.9 1.0 CB A:ASN9 4.8 32.5 1.0 O A:ASP7 4.8 24.8 1.0 CA A:ASN9 4.9 27.7 1.0 CA A:ASP98 4.9 25.5 1.0 CB A:ASP98 4.9 25.6 1.0 CG1 A:ILE101 4.9 27.8 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Vapbc From Salmonella Typhimurium


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 Vapbc From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:81.5 occ:1.00 OD2 C:ASP7 2.6 51.6 1.0 OD1 C:ASP98 3.0 30.4 1.0 CG C:ASP7 3.2 36.2 1.0 N C:ASN9 3.2 25.3 1.0 NH1 D:ARG64 3.4 42.4 1.0 CG C:ASN9 3.4 41.5 1.0 CB C:ASN9 3.4 33.0 1.0 N C:THR8 3.6 22.7 1.0 CB C:ASP7 3.7 29.7 1.0 ND2 C:ASN9 3.7 48.2 1.0 CG C:ASP98 3.8 33.1 1.0 OD1 C:ASN9 3.9 48.9 1.0 CZ D:ARG64 3.9 38.2 1.0 CA C:ASN9 3.9 27.7 1.0 OD2 C:ASP98 4.0 29.9 1.0 OD1 C:ASP7 4.0 34.1 1.0 NH2 D:ARG64 4.1 32.0 1.0 C C:THR8 4.2 25.1 1.0 CA C:THR8 4.2 24.0 1.0 CB C:THR8 4.2 25.8 1.0 C C:ASP7 4.2 23.1 1.0 CE2 C:PHE120 4.3 37.2 1.0 CZ C:PHE120 4.4 35.3 1.0 OD1 C:ASN116 4.5 58.2 1.0 CA C:ASP7 4.5 24.9 1.0 O C:HOH335 4.7 45.5 1.0 NE D:ARG64 4.9 40.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Vapbc From Salmonella Typhimurium


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 Vapbc From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:72.5 occ:1.00 OD2 E:ASP7 2.9 38.3 1.0 O E:HOH316 3.0 38.3 1.0 N E:ASN9 3.1 25.9 1.0 CG E:ASP7 3.2 32.2 1.0 NH1 F:ARG64 3.3 49.1 1.0 OD1 E:ASP98 3.4 33.5 1.0 N E:THR8 3.4 23.5 1.0 ND2 E:ASN9 3.6 39.2 1.0 CG E:ASN9 3.6 38.5 1.0 CB E:ASP7 3.6 29.9 1.0 CB E:ASN9 3.6 31.7 1.0 CZ F:ARG64 3.8 48.2 1.0 CB E:THR8 3.9 23.6 1.0 OD1 E:ASP7 3.9 35.5 1.0 CA E:THR8 3.9 23.1 1.0 C E:THR8 3.9 25.5 1.0 CA E:ASN9 4.0 31.1 1.0 NH2 F:ARG64 4.0 45.6 1.0 C E:ASP7 4.1 24.9 1.0 CE2 E:PHE120 4.1 33.6 1.0 OD1 E:ASN9 4.2 43.9 1.0 CG E:ASP98 4.2 33.3 1.0 OD2 E:ASP98 4.4 35.8 1.0 CZ E:PHE120 4.4 33.8 1.0 CA E:ASP7 4.4 26.9 1.0 OG1 E:THR8 4.7 24.5 1.0 NE F:ARG64 4.7 51.0 1.0 CG2 E:THR8 4.9 24.6 1.0 O E:ASP7 4.9 26.1 1.0 OG1 E:THR114 4.9 33.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Vapbc From Salmonella Typhimurium


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 Vapbc From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca201 b:93.1 occ:1.00 OD1 G:ASP98 2.8 37.0 1.0 OD2 G:ASP7 2.9 42.6 1.0 N G:THR8 2.9 24.2 1.0 NH1 H:ARG64 3.1 36.6 1.0 CG G:ASP7 3.4 32.6 1.0 CB G:THR8 3.5 23.6 1.0 N G:ASN9 3.5 29.3 1.0 NH2 H:ARG64 3.5 30.6 1.0 CB G:ASP7 3.5 30.4 1.0 CZ H:ARG64 3.5 38.0 1.0 CA G:THR8 3.6 26.0 1.0 O G:HOH318 3.8 43.5 1.0 CG G:ASP98 3.9 35.6 1.0 C G:ASP7 3.9 24.8 1.0 OG1 G:THR8 4.0 26.6 1.0 CZ G:PHE120 4.0 36.4 1.0 C G:THR8 4.0 28.7 1.0 CA G:ASP7 4.1 29.0 1.0 CE2 G:PHE120 4.1 40.8 1.0 CD1 G:ILE101 4.3 33.8 1.0 ND2 G:ASN9 4.4 47.1 1.0 OD2 G:ASP98 4.4 40.3 1.0 OD1 G:ASP7 4.4 40.9 1.0 CG G:ASN9 4.4 42.6 1.0 NE H:ARG64 4.6 36.1 1.0 CB G:ASN9 4.6 37.7 1.0 CA G:ASN9 4.7 34.1 1.0 CG2 G:THR8 4.7 24.6 1.0 OD1 G:ASN9 4.8 47.1 1.0 O G:ASP7 4.9 23.5 1.0 CB G:ASP98 5.0 27.7 1.0

D.Park, H.J.Yoon, K.Y.Lee, S.J.Park, S.H.Cheon, H.H.Lee, S.J.Lee, B.J.Lee. Crystal Structure of Proteolyzed Vapbc and Dna-Bound Vapbc From Salmonella Enterica Typhimurium LT2 and Vapc As A Putative CA2+-Dependent Ribonuclease. Faseb J. 2019.
ISSN: ESSN 1530-6860
PubMed: 31908032
DOI: 10.1096/FJ.201901989R