Calcium in PDB 3gn9: Crystal Structure of the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus

The structure of Crystal Structure of the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus, PDB code: 3gn9 was solved by K.V.Korotkov, M.D.Gray, A.Kreger, S.Turley, M.Sandkvist, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.90 / 1.86
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.180, 104.510, 55.410, 90.00, 106.16, 90.00
R / Rfree (%)	17.8 / 20.4

The binding sites of Calcium atom in the Crystal Structure of the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus (pdb code 3gn9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus, PDB code: 3gn9:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus


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 the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:65.9 occ:1.00 O A:ALA125 2.2 30.2 1.0 O A:GLN118 2.2 40.9 1.0 O A:LEU113 2.3 34.2 1.0 O A:GLY120 2.4 38.5 1.0 OD1 A:ASP127 2.4 35.3 1.0 OD1 A:ASP116 2.6 33.7 1.0 CG A:ASP116 3.3 35.4 1.0 OD2 A:ASP116 3.3 36.4 1.0 C A:LEU113 3.4 33.3 1.0 C A:ALA125 3.4 29.9 1.0 C A:GLN118 3.5 41.1 1.0 CG A:ASP127 3.5 33.1 1.0 C A:GLY120 3.5 38.2 1.0 N A:GLY120 3.9 39.8 1.0 OD2 A:ASP127 4.0 36.5 1.0 N A:ASP127 4.1 29.1 1.0 C A:GLU119 4.1 40.5 1.0 C A:ALA126 4.1 29.0 1.0 CA A:LEU113 4.1 33.4 1.0 O A:HOH211 4.2 36.9 1.0 N A:GLN118 4.2 40.3 1.0 CA A:ALA125 4.3 30.8 1.0 CA A:GLY120 4.3 39.0 1.0 N A:GLU119 4.3 41.1 1.0 CB A:LEU113 4.3 33.9 1.0 CA A:GLU119 4.3 41.1 1.0 N A:GLY114 4.3 33.4 1.0 N A:ALA126 4.3 29.1 1.0 CA A:ALA126 4.4 28.9 1.0 O A:ALA126 4.4 29.0 1.0 CB A:ALA125 4.4 30.5 1.0 CA A:GLN118 4.4 41.0 1.0 N A:GLY121 4.5 37.1 1.0 CA A:GLY114 4.5 33.4 1.0 CA A:ASP127 4.5 29.7 1.0 O A:GLU119 4.6 41.0 1.0 CB A:ASP127 4.6 30.2 1.0 CA A:GLY121 4.7 36.4 1.0 CB A:ASP116 4.8 35.8 1.0 C A:GLY114 4.9 33.8 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus


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 the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:71.3 occ:1.00 O B:LEU113 2.1 36.6 1.0 O B:GLN118 2.2 45.5 1.0 OD1 B:ASP127 2.3 39.5 1.0 O B:ALA125 2.3 36.2 1.0 O B:GLY120 2.5 44.4 1.0 OD1 B:ASP116 2.5 42.5 1.0 C B:LEU113 3.2 36.5 1.0 CG B:ASP116 3.3 43.0 1.0 C B:GLN118 3.4 45.6 1.0 OD2 B:ASP116 3.4 43.4 1.0 C B:ALA125 3.5 36.5 1.0 CG B:ASP127 3.5 37.3 1.0 C B:GLY120 3.7 44.0 1.0 CA B:LEU113 3.9 36.2 1.0 N B:GLN118 4.0 45.1 1.0 N B:GLY120 4.1 44.7 1.0 CB B:LEU113 4.1 36.5 1.0 C B:GLU119 4.1 45.2 1.0 OD2 B:ASP127 4.1 40.4 1.0 N B:ASP127 4.2 35.8 1.0 N B:GLY114 4.2 37.1 1.0 C B:ALA126 4.3 36.0 1.0 CA B:GLN118 4.3 45.5 1.0 N B:GLU119 4.3 45.6 1.0 CA B:ALA125 4.4 36.9 1.0 CA B:GLY114 4.4 37.5 1.0 CA B:GLU119 4.5 45.6 1.0 CA B:GLY120 4.5 44.4 1.0 O B:GLU119 4.5 45.5 1.0 N B:ALA126 4.5 36.2 1.0 CB B:ALA125 4.5 36.9 1.0 CA B:ASP127 4.6 35.7 1.0 O B:ALA126 4.6 35.8 1.0 CA B:ALA126 4.6 36.1 1.0 N B:GLY121 4.6 43.4 1.0 CB B:ASP127 4.7 36.2 1.0 CA B:GLY121 4.8 43.0 1.0 CB B:ASP116 4.8 42.5 1.0 N B:GLY117 4.8 43.6 1.0 C B:GLY114 4.8 38.4 1.0 CD2 B:LEU113 4.9 37.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus


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 the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:60.1 occ:0.50 O C:ALA125 2.1 26.7 1.0 O C:GLN118 2.3 21.1 1.0 O C:GLY120 2.4 27.4 1.0 O C:LEU113 2.4 28.1 1.0 OD1 C:ASP127 2.5 26.8 1.0 C C:ALA125 3.3 26.4 1.0 C C:LEU113 3.4 28.8 1.0 C C:GLY120 3.5 26.8 1.0 C C:GLN118 3.5 22.3 1.0 N C:GLY120 3.7 25.6 1.0 CG C:ASP127 3.7 25.1 1.0 C C:GLU119 3.7 24.8 1.0 N C:ASP127 4.0 24.5 1.0 O C:GLU119 4.1 24.9 1.0 CA C:GLY120 4.1 26.2 1.0 C C:ALA126 4.1 25.0 1.0 CA C:GLU119 4.2 24.0 1.0 CA C:LEU113 4.2 29.2 1.0 CA C:ALA125 4.2 26.8 1.0 N C:GLU119 4.3 23.2 1.0 N C:ALA126 4.3 26.0 1.0 CB C:ALA125 4.3 26.9 1.0 OD2 C:ASP127 4.3 26.2 1.0 N C:GLY114 4.4 28.6 1.0 CA C:ALA126 4.4 25.2 1.0 CA C:GLY114 4.5 28.1 1.0 CB C:LEU113 4.5 29.5 1.0 CA C:ASP127 4.6 24.4 1.0 N C:GLY121 4.6 26.9 1.0 N C:GLN118 4.6 22.5 1.0 O C:ALA126 4.6 24.6 1.0 CA C:GLN118 4.6 22.1 1.0 CB C:ASP127 4.7 24.7 1.0 CA C:GLY121 4.9 27.2 1.0

K.V.Korotkov, M.D.Gray, A.Kreger, S.Turley, M.Sandkvist, W.G.Hol. Calcium Is Essential For the Major Pseudopilin in the Type 2 Secretion System. J.Biol.Chem. V. 284 25466 2009.
ISSN: ISSN 0021-9258
PubMed: 19640838
DOI: 10.1074/JBC.C109.037655