Calcium in PDB 5vgt: X-Ray Structure of Bacteriophage SF6 Tail Adaptor Protein GP7

The structure of X-Ray Structure of Bacteriophage SF6 Tail Adaptor Protein GP7, PDB code: 5vgt was solved by L.Tang, L.Liang, H.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 1.78
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.297, 101.297, 76.465, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.4

The structure of X-Ray Structure of Bacteriophage SF6 Tail Adaptor Protein GP7 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the X-Ray Structure of Bacteriophage SF6 Tail Adaptor Protein GP7 (pdb code 5vgt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the X-Ray Structure of Bacteriophage SF6 Tail Adaptor Protein GP7, PDB code: 5vgt:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the X-Ray Structure of Bacteriophage SF6 Tail Adaptor Protein GP7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Bacteriophage SF6 Tail Adaptor Protein GP7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:47.1 occ:1.00 O A:HOH410 2.4 48.8 1.0 O A:GLY73 2.4 26.5 1.0 O A:HOH369 2.5 42.7 1.0 O A:HOH413 2.5 47.5 1.0 O A:GLY56 2.6 24.6 1.0 C A:GLY73 3.5 28.8 1.0 C A:GLY56 3.5 29.3 1.0 CA A:GLY56 3.9 30.1 1.0 CA A:GLY73 4.0 24.9 1.0 O A:HOH391 4.5 38.8 1.0 O A:HOH437 4.5 49.3 1.0 N A:LEU74 4.6 23.0 1.0 N A:TYR57 4.7 22.5 1.0 O A:HOH433 4.8 92.5 1.0 O A:HOH445 4.8 98.7 1.0 CA A:LEU74 5.0 23.5 1.0

Calcium binding site 2 out of 4 in the X-Ray Structure of Bacteriophage SF6 Tail Adaptor Protein GP7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Bacteriophage SF6 Tail Adaptor Protein GP7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:34.4 occ:1.00 O A:THR3 2.4 34.4 1.0 O A:HOH385 2.4 35.9 1.0 O A:HOH370 2.5 35.9 1.0 OG1 A:THR3 2.5 33.5 1.0 O A:HOH405 2.5 40.4 1.0 O A:HOH374 2.5 40.6 1.0 C A:THR3 3.3 33.5 1.0 CB A:THR3 3.6 35.8 1.0 CA A:THR3 3.8 34.8 1.0 N A:THR3 4.0 41.0 1.0 N A:VAL4 4.4 30.0 1.0 O A:VAL4 4.6 30.8 1.0 O A:HOH407 4.6 46.2 1.0 O A:HOH364 4.6 28.6 1.0 CA A:VAL4 4.8 26.5 1.0 CG2 A:THR3 4.9 36.7 1.0 C A:VAL4 5.0 27.9 1.0

Calcium binding site 3 out of 4 in the X-Ray Structure of Bacteriophage SF6 Tail Adaptor Protein GP7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of Bacteriophage SF6 Tail Adaptor Protein GP7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:39.6 occ:1.00 O A:HOH313 2.4 35.9 1.0 O A:HOH411 2.4 29.5 1.0 O B:HOH312 2.4 40.3 1.0 O A:HOH439 2.4 40.4 1.0 O B:HOH337 2.5 30.3 1.0 O A:HOH412 2.5 42.7 1.0 O A:GLY62 2.7 31.4 1.0 C A:GLY62 3.8 31.0 1.0 O B:HOH347 4.1 29.8 1.0 O B:HOH314 4.3 27.4 1.0 N A:GLY62 4.3 30.3 1.0 O B:GLY62 4.3 25.3 1.0 O B:HOH332 4.4 30.6 1.0 CA A:GLY62 4.5 29.6 1.0 O A:GLU64 4.6 33.3 1.0 O B:HOH354 4.6 40.7 1.0 O B:GLU64 4.6 27.5 1.0 C A:THR61 4.6 30.1 1.0 O B:ALA60 4.8 23.1 1.0 N A:ASP63 4.9 33.3 1.0 O A:ALA60 4.9 23.4 1.0

Calcium binding site 4 out of 4 in the X-Ray Structure of Bacteriophage SF6 Tail Adaptor Protein GP7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of Bacteriophage SF6 Tail Adaptor Protein GP7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:69.1 occ:1.00 OE1 B:GLU47 2.4 45.9 1.0 OD1 B:ASP43 2.8 56.0 1.0 OD2 B:ASP43 2.9 59.6 1.0 O B:HOH372 3.0 69.8 1.0 O B:HOH358 3.0 67.8 1.0 O A:HOH355 3.1 68.7 1.0 CG B:ASP43 3.2 54.4 1.0 CD B:GLU47 3.5 46.1 1.0 CG B:GLU47 3.9 43.3 1.0 O B:HOH304 4.2 48.1 1.0 NH1 B:ARG89 4.2 47.1 1.0 OE2 B:GLU47 4.6 46.4 1.0 CB B:ASP43 4.7 36.0 1.0 O B:ASP43 4.9 33.5 1.0 OD2 A:ASP63 5.0 56.1 1.0

L.Liang, H.Zhao, B.An, L.Tang. High-Resolution Structure of Podovirus Tail Adaptor Suggests Repositioning of An Octad Motif That Mediates the Sequential Tail Assembly. Proc. Natl. Acad. Sci. V. 115 313 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29279385
DOI: 10.1073/PNAS.1706846115