Calcium in PDB 3vto: The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike

The structure of The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike, PDB code: 3vto was solved by K.Harada, E.Yamashita, A.Nakagawa, S.Takeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.52 / 1.44
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.403, 152.399, 53.062, 90.00, 91.01, 90.00
R / Rfree (%)	16.2 / 19.5

The structure of The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike (pdb code 3vto). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike, PDB code: 3vto:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:13.6 occ:1.00 OD1 C:ASP188 2.2 14.1 1.0 OD1 A:ASP188 2.2 14.4 1.0 OD1 B:ASP188 2.3 14.0 1.0 OG B:SER189 2.4 12.6 1.0 OG A:SER189 2.4 15.1 1.0 OG C:SER189 2.5 12.3 1.0 CB B:SER189 3.3 12.9 1.0 CG C:ASP188 3.4 14.4 1.0 CG A:ASP188 3.5 14.8 1.0 CB C:SER189 3.5 13.0 1.0 CB A:SER189 3.5 15.2 1.0 CG B:ASP188 3.5 14.1 1.0 N C:SER189 3.7 12.4 1.0 N A:SER189 3.8 14.4 1.0 CL C:CL301 3.8 15.5 1.0 N B:SER189 3.9 12.8 1.0 OD2 A:ASP188 4.1 15.7 1.0 OD2 C:ASP188 4.1 14.4 1.0 OD2 B:ASP188 4.1 16.8 1.0 CA B:SER189 4.2 12.9 1.0 CA A:SER189 4.2 16.0 1.0 CA C:SER189 4.2 12.9 1.0 C A:ASP188 4.3 15.4 1.0 C B:ASP188 4.3 14.2 1.0 C C:ASP188 4.4 13.5 1.0 N C:ASP188 4.4 13.8 1.0 N A:ASP188 4.4 15.3 1.0 N B:ASP188 4.4 14.8 1.0 O B:HOH362 4.5 17.5 1.0 CA A:ASP188 4.6 15.2 1.0 CB A:ASP188 4.6 15.8 1.0 CA C:ASP188 4.6 13.8 1.0 CB C:ASP188 4.6 14.7 1.0 CA B:ASP188 4.6 14.6 1.0 CB B:ASP188 4.7 15.3 1.0 O A:ASP188 5.0 16.9 1.0 O B:ASP188 5.0 15.6 1.0

Calcium binding site 2 out of 2 in the The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike within 5.0Å range: probe atom residue distance (Å) B Occ Q:Ca301 b:14.3 occ:1.00 OD1 Q:ASP188 2.2 14.5 1.0 OD1 R:ASP188 2.2 14.3 1.0 OD1 P:ASP188 2.3 14.5 1.0 OG P:SER189 2.4 14.7 1.0 OG R:SER189 2.4 14.6 1.0 OG Q:SER189 2.5 13.2 1.0 CB R:SER189 3.4 15.0 1.0 CB P:SER189 3.4 15.7 1.0 CG Q:ASP188 3.4 15.0 1.0 CG R:ASP188 3.5 13.8 1.0 CB Q:SER189 3.5 12.5 1.0 CG P:ASP188 3.5 16.6 1.0 N Q:SER189 3.7 11.9 1.0 N R:SER189 3.8 14.4 1.0 CL P:CL302 3.8 15.7 1.0 N P:SER189 3.9 15.6 1.0 OD2 Q:ASP188 4.1 16.2 1.0 OD2 P:ASP188 4.1 15.2 1.0 OD2 R:ASP188 4.1 16.2 1.0 CA R:SER189 4.2 16.1 1.0 C R:ASP188 4.2 15.2 1.0 CA Q:SER189 4.2 12.6 1.0 CA P:SER189 4.3 15.5 1.0 C P:ASP188 4.3 15.0 1.0 N Q:ASP188 4.3 13.2 1.0 C Q:ASP188 4.4 12.7 1.0 N R:ASP188 4.4 14.4 1.0 N P:ASP188 4.4 14.8 1.0 CA R:ASP188 4.6 14.8 1.0 CB Q:ASP188 4.6 15.2 1.0 CB R:ASP188 4.6 14.3 1.0 CA Q:ASP188 4.6 13.1 1.0 CA P:ASP188 4.7 15.2 1.0 CB P:ASP188 4.7 15.6 1.0 O R:ASP188 4.9 16.9 1.0 O P:ASP188 5.0 17.0 1.0

K.Harada, E.Yamashita, A.Nakagawa, T.Miyafusa, K.Tsumoto, T.Ueno, Y.Toyama, S.Takeda. Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike and Functions of Bound Calcium Ion Biochim.Biophys.Acta V.1834 284 2013.
ISSN: ISSN 0006-3002
PubMed: 22922659
DOI: 10.1016/J.BBAPAP.2012.08.015