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

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

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

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

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of A C-Terminal Domain of the Bacteriophage P2 Tail Spike Protein, Gpv, PDB code: 3aqj:
Jump to Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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 C:Ca135 b:9.3 occ:1.00 OD1 C:ASP125 2.2 9.0 1.0 OD1 B:ASP125 2.3 10.2 1.0 OD1 A:ASP125 2.3 8.6 1.0 OG A:SER126 2.4 11.4 1.0 OG B:SER126 2.4 11.5 1.0 OG C:SER126 2.4 11.0 1.0 CB A:SER126 3.4 11.4 1.0 CG C:ASP125 3.4 8.0 1.0 CB B:SER126 3.5 11.4 1.0 CB C:SER126 3.5 9.1 1.0 CG A:ASP125 3.5 8.8 1.0 CG B:ASP125 3.5 10.0 1.0 N A:SER126 3.8 9.3 1.0 N C:SER126 3.8 8.0 1.0 N B:SER126 3.8 11.0 1.0 CL A:CL136 3.9 8.7 1.0 C A:ASP125 4.1 10.1 1.0 C B:ASP125 4.1 11.9 1.0 OD2 B:ASP125 4.2 10.3 1.0 OD2 C:ASP125 4.2 8.3 1.0 CA A:SER126 4.2 11.3 1.0 OD2 A:ASP125 4.2 8.4 1.0 CA B:SER126 4.2 12.2 1.0 CA C:SER126 4.3 8.5 1.0 C C:ASP125 4.3 7.5 1.0 N A:ASP125 4.3 8.0 1.0 N B:ASP125 4.4 9.7 1.0 N C:ASP125 4.4 6.9 1.0 O B:HOH291 4.5 24.9 1.0 O A:HOH248 4.5 31.1 1.0 CA B:ASP125 4.5 10.7 1.0 CA A:ASP125 4.5 9.3 1.0 CA C:ASP125 4.6 7.5 1.0 CB C:ASP125 4.6 9.3 1.0 CB A:ASP125 4.6 8.9 1.0 CB B:ASP125 4.6 10.3 1.0 O A:ASP125 4.7 12.7 1.0 O B:ASP125 4.8 12.9 1.0 O C:HOH379 4.8 22.1 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca136 b:8.9 occ:1.00 OD1 R:ASP125 2.2 9.1 1.0 OD1 P:ASP125 2.3 8.2 1.0 OD1 Q:ASP125 2.3 7.4 1.0 OG R:SER126 2.4 11.3 1.0 OG P:SER126 2.4 9.6 1.0 OG Q:SER126 2.5 11.0 1.0 CB R:SER126 3.4 12.4 1.0 CB Q:SER126 3.4 10.0 1.0 CG P:ASP125 3.5 8.1 1.0 CB P:SER126 3.5 10.1 1.0 CG R:ASP125 3.5 7.7 1.0 CG Q:ASP125 3.5 7.7 1.0 N Q:SER126 3.8 9.2 1.0 N P:SER126 3.8 9.0 1.0 N R:SER126 3.8 10.7 1.0 CL P:CL137 3.9 8.2 1.0 C R:ASP125 4.0 11.0 1.0 OD2 P:ASP125 4.1 9.2 1.0 OD2 Q:ASP125 4.2 8.1 1.0 C Q:ASP125 4.2 10.1 1.0 OD2 R:ASP125 4.2 7.5 1.0 CA R:SER126 4.2 11.2 1.0 CA P:SER126 4.2 8.8 1.0 CA Q:SER126 4.2 10.6 1.0 C P:ASP125 4.3 9.2 1.0 N R:ASP125 4.3 8.6 1.0 N Q:ASP125 4.4 8.3 1.0 N P:ASP125 4.4 7.0 1.0 CA R:ASP125 4.5 9.1 1.0 O Q:HOH536 4.5 32.5 1.0 CA Q:ASP125 4.5 9.9 1.0 CB R:ASP125 4.5 9.6 1.0 CB P:ASP125 4.6 8.7 1.0 O R:HOH707 4.6 28.7 1.0 CA P:ASP125 4.6 7.9 1.0 CB Q:ASP125 4.6 8.7 1.0 O P:HOH472 4.6 21.3 1.0 O R:ASP125 4.6 14.5 1.0 O R:HOH165 4.7 27.3 1.0 O Q:ASP125 4.9 12.0 1.0

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