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

Protein crystallography data

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

Other elements in 5vgt:

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

Magnesium (Mg) 1 atom

Calcium Binding Sites:

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 5vgt

Go back to Calcium Binding Sites List in 5vgt
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 5vgt

Go back to Calcium Binding Sites List in 5vgt
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 5vgt

Go back to Calcium Binding Sites List in 5vgt
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 5vgt

Go back to Calcium Binding Sites List in 5vgt
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

Reference:

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
Page generated: Sat Dec 12 05:47:30 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy