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Chlorine in PDB 3aqj: Crystal Structure of A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv

Protein crystallography data

The structure of Crystal Structure of A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv, PDB code: 3aqj was solved by S.Takeda, E.Yamashita, A.Nakagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.42 / 1.27
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.912, 64.463, 67.186, 90.00, 91.32, 90.00
R / Rfree (%) 16 / 19

Other elements in 3aqj:

The structure of Crystal Structure of A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Iron (Fe) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv (pdb code 3aqj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv, PDB code: 3aqj:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 3aqj

Go back to Chlorine Binding Sites List in 3aqj
Chlorine binding site 1 out of 2 in the Crystal Structure of A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl136

b:8.7
occ:1.00
N C:ASP125 3.3 6.9 1.0
N A:ASP125 3.3 8.0 1.0
N B:ASP125 3.3 9.7 1.0
OD1 C:ASP125 3.5 9.0 1.0
OD1 B:ASP125 3.5 10.2 1.0
OD1 A:ASP125 3.6 8.6 1.0
CA B:GLY124 3.6 9.7 1.0
CA A:GLY124 3.6 7.9 1.0
CA C:GLY124 3.7 7.9 1.0
CG C:ASP125 3.8 8.0 1.0
CA C:CA135 3.9 9.3 1.0
CG B:ASP125 3.9 10.0 1.0
C C:GLY124 4.0 7.5 1.0
C A:GLY124 4.0 10.6 1.0
CG A:ASP125 4.0 8.8 1.0
C B:GLY124 4.0 8.6 1.0
CG2 B:THR130 4.2 6.5 1.0
CB C:ASP125 4.3 9.3 1.0
CG2 A:THR130 4.3 8.4 1.0
CA C:ASP125 4.3 7.5 1.0
CG2 C:THR130 4.4 7.2 1.0
CA B:ASP125 4.4 10.7 1.0
CB A:ASP125 4.4 8.9 1.0
CA A:ASP125 4.4 9.3 1.0
CB B:ASP125 4.4 10.3 1.0
OD2 B:ASP125 4.5 10.3 1.0
OD2 C:ASP125 4.5 8.3 1.0
OD2 A:ASP125 4.6 8.4 1.0
N B:GLY124 5.0 8.1 1.0

Chlorine binding site 2 out of 2 in 3aqj

Go back to Chlorine Binding Sites List in 3aqj
Chlorine binding site 2 out of 2 in the Crystal Structure of A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cl137

b:8.2
occ:1.00
N Q:ASP125 3.3 8.3 1.0
N P:ASP125 3.3 7.0 1.0
N R:ASP125 3.3 8.6 1.0
OD1 R:ASP125 3.5 9.1 1.0
OD1 P:ASP125 3.5 8.2 1.0
OD1 Q:ASP125 3.5 7.4 1.0
CA R:GLY124 3.6 7.6 1.0
CA P:GLY124 3.6 7.1 1.0
CA Q:GLY124 3.7 8.8 1.0
CA P:CA136 3.9 8.9 1.0
CG P:ASP125 3.9 8.1 1.0
CG Q:ASP125 3.9 7.7 1.0
C R:GLY124 4.0 7.1 1.0
CG R:ASP125 4.0 7.7 1.0
C P:GLY124 4.0 7.4 1.0
C Q:GLY124 4.0 8.5 1.0
CG2 R:THR130 4.1 7.2 1.0
CB P:ASP125 4.3 8.7 1.0
CB Q:ASP125 4.3 8.7 1.0
CG2 P:THR130 4.3 7.6 1.0
CA Q:ASP125 4.3 9.9 1.0
CA P:ASP125 4.3 7.9 1.0
CG2 Q:THR130 4.4 6.8 1.0
CA R:ASP125 4.4 9.1 1.0
CB R:ASP125 4.4 9.6 1.0
OD2 R:ASP125 4.5 7.5 1.0
OD2 Q:ASP125 4.5 8.1 1.0
OD2 P:ASP125 4.5 9.2 1.0
N R:GLY124 4.9 6.6 1.0

Reference:

E.Yamashita, A.Nakagawa, J.Takahashi, K.Tsunoda, S.Yamada, S.Takeda. The Host-Binding Domain of the P2 Phage Tail Spike Reveals A Trimeric Iron-Binding Structure Acta Crystallogr.,Sect.F V. 67 837 2011.
ISSN: ESSN 1744-3091
PubMed: 21821878
DOI: 10.1107/S1744309111005999
Page generated: Sat Dec 12 09:31:48 2020

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