Calcium in PDB 7cn6: T4 Phage Spackle Protein GP61.3

The structure of T4 Phage Spackle Protein GP61.3, PDB code: 7cn6 was solved by S.Kanamaru, P.G.Leiman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.90 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	30.376, 46.921, 75.277, 90.00, 93.08, 90.00
R / Rfree (%)	17.9 / 22.8

The binding sites of Calcium atom in the T4 Phage Spackle Protein GP61.3 (pdb code 7cn6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the T4 Phage Spackle Protein GP61.3, PDB code: 7cn6:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the T4 Phage Spackle Protein GP61.3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of T4 Phage Spackle Protein GP61.3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:60.9 occ:1.00 O A:HOH291 2.4 41.5 1.0 O A:HOH211 2.5 32.6 1.0 O A:HOH213 2.5 34.9 1.0 O A:HOH313 2.6 37.2 1.0 O A:VAL94 2.6 18.0 1.0 O A:HOH324 2.9 40.6 1.0 O A:GLY96 3.5 23.1 1.0 C A:VAL94 3.7 18.0 1.0 O A:HOH201 4.1 20.9 1.0 O A:HOH242 4.2 26.2 1.0 O A:GLU93 4.3 16.9 1.0 CA A:VAL94 4.3 17.4 1.0 O A:HOH263 4.3 29.9 1.0 OH A:TYR75 4.4 14.4 1.0 C A:GLY96 4.7 23.0 1.0 O A:HOH209 4.8 37.1 1.0 N A:VAL95 4.8 18.6 1.0 OE1 A:GLN66 4.8 25.4 1.0 OXT A:GLU97 5.0 25.2 1.0

Calcium binding site 2 out of 3 in the T4 Phage Spackle Protein GP61.3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of T4 Phage Spackle Protein GP61.3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:18.8 occ:1.00 OXT B:GLU97 2.4 21.9 1.0 O B:HOH217 2.4 22.3 1.0 O B:HOH203 2.4 17.8 1.0 O B:HOH213 2.5 19.1 1.0 O B:VAL94 2.5 15.3 1.0 O B:HOH292 2.5 29.0 1.0 O B:HOH296 2.5 33.3 1.0 C B:GLU97 3.4 21.9 1.0 C B:VAL94 3.6 15.4 1.0 O B:HOH256 4.1 35.3 1.0 O B:GLU97 4.1 21.9 1.0 N B:GLU97 4.2 21.0 1.0 O B:HOH274 4.2 30.7 1.0 CA B:GLU97 4.2 21.8 1.0 OH B:TYR75 4.3 15.4 1.0 CA B:VAL94 4.3 15.0 1.0 CB B:GLU97 4.5 22.5 1.0 O B:HOH220 4.5 17.8 1.0 O B:GLU93 4.5 14.8 1.0 OE1 B:GLN66 4.6 15.6 1.0 N B:VAL95 4.7 15.8 1.0 CG1 B:VAL94 4.8 14.8 1.0 O B:HOH253 4.9 28.9 1.0 O B:HOH309 4.9 44.6 1.0 CA B:VAL95 4.9 16.4 1.0

Calcium binding site 3 out of 3 in the T4 Phage Spackle Protein GP61.3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of T4 Phage Spackle Protein GP61.3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca101 b:19.6 occ:1.00 O C:GLU97 2.4 23.7 1.0 O C:HOH218 2.4 17.6 1.0 O C:HOH246 2.4 19.5 1.0 O C:HOH217 2.5 16.5 1.0 O C:VAL94 2.5 15.8 1.0 O C:HOH240 2.5 25.5 1.0 O C:HOH310 2.9 26.1 1.0 C C:GLU97 3.5 23.6 1.0 C C:VAL94 3.6 16.0 1.0 CA C:VAL94 4.2 15.5 1.0 OXT C:GLU97 4.3 23.8 1.0 OH C:TYR75 4.3 14.8 1.0 O C:GLU93 4.4 14.8 1.0 N C:GLU97 4.4 22.4 1.0 CA C:GLU97 4.4 23.4 1.0 O C:HOH296 4.5 32.5 1.0 O C:HOH208 4.5 25.7 1.0 O C:HOH225 4.5 16.1 1.0 OE1 C:GLN66 4.6 16.7 1.0 O C:HOH267 4.6 22.4 1.0 OE2 C:GLU97 4.7 25.4 1.0 N C:VAL95 4.7 16.6 1.0 CG1 C:VAL94 4.7 15.4 1.0 O C:HOH288 4.8 31.5 1.0 CB C:GLU97 4.8 24.0 1.0 CG C:GLU97 4.9 24.6 1.0 CA C:VAL95 5.0 17.4 1.0 O C:HOH222 5.0 24.9 1.0

S.Kanamaru, K.Uchida, M.Nemoto, A.Fraser, F.Arisaka, P.G.Leiman. Structure and Function of the T4 Spackle Protein GP61.3. Viruses V. 12 2020.
ISSN: ISSN 1999-4915
PubMed: 32987925
DOI: 10.3390/V12101070