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

Protein crystallography data

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

Other elements in 3vto:

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
Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the The Crystal Structure of the C-Terminal Domain of Mu Phage Central Spike, PDB code: 3vto:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 3vto

Go back to Chlorine Binding Sites List in 3vto
Chlorine 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 Chlorine with other atoms in the Cl 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
C:Cl301

b:15.5
occ:1.00
N A:ASP188 3.3 15.3 1.0
N C:ASP188 3.3 13.8 1.0
N B:ASP188 3.3 14.8 1.0
CA C:GLY187 3.5 14.0 1.0
OD1 B:ASP188 3.5 14.0 1.0
CA B:GLY187 3.5 16.2 1.0
OD1 A:ASP188 3.5 14.4 1.0
OD1 C:ASP188 3.6 14.1 1.0
CA A:GLY187 3.6 14.9 1.0
CA A:CA302 3.8 13.6 1.0
CG A:ASP188 3.8 14.8 1.0
C C:GLY187 3.9 13.3 1.0
CG B:ASP188 3.9 14.1 1.0
C B:GLY187 3.9 15.3 1.0
C A:GLY187 4.0 15.1 1.0
CG C:ASP188 4.0 14.4 1.0
CG2 B:THR193 4.2 15.5 1.0
CG2 C:THR193 4.2 14.7 1.0
CG2 A:THR193 4.3 16.1 1.0
CB A:ASP188 4.3 15.8 1.0
CA A:ASP188 4.3 15.2 1.0
OD2 A:ASP188 4.4 15.7 1.0
CA B:ASP188 4.4 14.6 1.0
CA C:ASP188 4.4 13.8 1.0
CB B:ASP188 4.4 15.3 1.0
OD2 C:ASP188 4.5 14.4 1.0
CB C:ASP188 4.5 14.7 1.0
OD2 B:ASP188 4.5 16.8 1.0
N C:GLY187 4.8 14.3 1.0
N B:GLY187 4.9 14.9 1.0

Chlorine binding site 2 out of 2 in 3vto

Go back to Chlorine Binding Sites List in 3vto
Chlorine 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 Chlorine with other atoms in the Cl 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
P:Cl302

b:15.7
occ:1.00
N P:ASP188 3.2 14.8 1.0
N Q:ASP188 3.3 13.2 1.0
N R:ASP188 3.3 14.4 1.0
OD1 P:ASP188 3.4 14.5 1.0
CA Q:GLY187 3.5 13.8 1.0
OD1 R:ASP188 3.5 14.3 1.0
OD1 Q:ASP188 3.6 14.5 1.0
CA P:GLY187 3.6 15.8 1.0
CA R:GLY187 3.6 15.1 1.0
CA Q:CA301 3.8 14.3 1.0
CG P:ASP188 3.8 16.6 1.0
CG R:ASP188 3.9 13.8 1.0
C Q:GLY187 3.9 13.7 1.0
C P:GLY187 3.9 15.7 1.0
CG Q:ASP188 3.9 15.0 1.0
C R:GLY187 4.0 14.6 1.0
CG2 P:THR193 4.1 15.3 1.0
CG2 Q:THR193 4.2 15.8 1.0
CG2 R:THR193 4.2 15.0 1.0
CA P:ASP188 4.3 15.2 1.0
CB P:ASP188 4.3 15.6 1.0
CA R:ASP188 4.4 14.8 1.0
CB R:ASP188 4.4 14.3 1.0
OD2 R:ASP188 4.4 16.2 1.0
CA Q:ASP188 4.4 13.1 1.0
OD2 Q:ASP188 4.4 16.2 1.0
OD2 P:ASP188 4.5 15.2 1.0
CB Q:ASP188 4.5 15.2 1.0
N Q:GLY187 4.8 13.7 1.0
N P:GLY187 5.0 14.5 1.0

Reference:

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
Page generated: Sat Dec 12 10:18:20 2020

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