Calcium in PDB 2vma: The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae

The structure of The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae, PDB code: 2vma was solved by J.Abendroth, K.V.Korotkov, D.D.Mitchell, A.Kreger, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.32 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.816, 54.368, 88.587, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.5

The structure of The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae also contains other interesting chemical elements:

Iodine

(I)

15 atoms

The binding sites of Calcium atom in the The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae (pdb code 2vma). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae, PDB code: 2vma:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1178 b:24.4 occ:1.00 OE2 B:GLU97 2.3 23.2 1.0 OE2 A:GLU151 2.3 15.4 1.0 O A:HOH2088 2.4 34.4 1.0 OD2 A:ASP155 2.5 13.3 1.0 O A:HOH2084 2.5 22.5 1.0 O B:HOH2024 2.5 28.3 1.0 OD1 A:ASP155 2.6 14.4 1.0 CG A:ASP155 2.9 16.1 1.0 CD B:GLU97 3.3 26.5 1.0 CD A:GLU151 3.4 17.4 1.0 CG B:GLU97 3.5 24.7 1.0 CG A:GLU151 3.9 15.4 1.0 O B:HOH2028 4.2 43.0 1.0 O B:HOH2029 4.2 37.2 1.0 O A:HOH2091 4.3 35.6 1.0 O B:HOH2025 4.3 23.6 1.0 CB A:ASP155 4.4 16.2 1.0 OE1 A:GLU151 4.4 19.3 1.0 OE1 B:GLU97 4.4 26.5 1.0 NH1 A:ARG73 4.6 17.9 1.0 NH2 A:ARG73 4.6 16.9 1.0 O B:GLN95 4.7 21.0 1.0 O A:GLU151 4.7 14.8 1.0 O A:HOH2089 4.8 33.8 1.0 O A:HOH2086 4.8 38.3 1.0 O B:HOH2030 4.8 29.7 1.0 CB B:GLU97 5.0 23.7 1.0

Calcium binding site 2 out of 3 in the The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1178 b:21.5 occ:1.00 OE2 B:GLU151 2.3 13.0 1.0 O A:HOH2036 2.4 20.8 1.0 O B:HOH2074 2.4 18.4 1.0 OE2 A:GLU97 2.4 19.7 1.0 OD1 B:ASP155 2.4 14.7 1.0 O B:HOH2078 2.5 29.6 1.0 OD2 B:ASP155 2.6 18.1 1.0 CG B:ASP155 2.9 15.9 1.0 CD A:GLU97 3.3 22.2 1.0 CD B:GLU151 3.4 16.3 1.0 CG A:GLU97 3.6 20.8 1.0 CG B:GLU151 3.8 15.1 1.0 O B:HOH2083 4.3 26.8 1.0 OE1 B:GLU151 4.4 16.4 1.0 O A:HOH2037 4.4 21.4 1.0 CB B:ASP155 4.4 15.9 1.0 NH1 B:ARG73 4.4 17.2 1.0 OE1 A:GLU97 4.4 22.9 1.0 O A:HOH2043 4.5 41.4 1.0 NH2 B:ARG73 4.6 15.5 1.0 O A:GLN95 4.7 19.4 1.0 O B:HOH2080 4.9 29.4 1.0 O B:GLU151 4.9 17.0 1.0 CZ B:ARG73 4.9 13.8 1.0 O A:HOH2041 5.0 19.5 1.0 CB A:GLU97 5.0 20.1 1.0

Calcium binding site 3 out of 3 in the The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1179 b:37.2 occ:1.00 OG B:SER135 3.7 23.6 1.0 OE2 B:GLU131 3.8 29.4 1.0 CA B:LEU132 3.9 19.2 1.0 CG B:GLU131 4.0 23.9 1.0 N B:LEU132 4.1 19.3 1.0 C B:GLU131 4.3 19.5 1.0 CB B:SER135 4.3 20.1 1.0 CB B:LEU132 4.3 19.1 1.0 O B:GLU131 4.3 19.2 1.0 CD B:GLU131 4.4 28.1 1.0 CD1 B:LEU132 4.4 19.2 1.0 CB B:GLU131 4.6 21.2 1.0 CG B:LEU132 5.0 18.9 1.0

J.Abendroth, D.D.Mitchell, K.V.Korotkov, T.L.Johnson, A.Kreger, M.Sandkvist, W.G.Hol. The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae. J.Struct.Biol. V. 166 303 2009.
ISSN: ISSN 1047-8477
PubMed: 19324092
DOI: 10.1016/J.JSB.2009.03.009