Calcium in PDB 4zvf: Crystal Structure of Ggdef Domain of the E. Coli Dosc - Form II (Gtp- Alpha-S-Bound)

All present enzymatic activity of Crystal Structure of Ggdef Domain of the E. Coli Dosc - Form II (Gtp- Alpha-S-Bound):
2.7.7.65;

The structure of Crystal Structure of Ggdef Domain of the E. Coli Dosc - Form II (Gtp- Alpha-S-Bound), PDB code: 4zvf was solved by M.Tarnawski, T.R.M.Barends, I.Schlichting, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.81 / 1.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.500, 52.530, 50.930, 90.00, 106.08, 90.00
R / Rfree (%)	13.8 / 16.5

The binding sites of Calcium atom in the Crystal Structure of Ggdef Domain of the E. Coli Dosc - Form II (Gtp- Alpha-S-Bound) (pdb code 4zvf). 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 Ggdef Domain of the E. Coli Dosc - Form II (Gtp- Alpha-S-Bound), PDB code: 4zvf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Ggdef Domain of the E. Coli Dosc - Form II (Gtp- Alpha-S-Bound)


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 Ggdef Domain of the E. Coli Dosc - Form II (Gtp- Alpha-S-Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:12.4 occ:1.00 OD1 A:ASP333 2.3 13.6 1.0 OD2 A:ASP376 2.3 14.6 1.0 O1B A:GAV501 2.3 14.4 1.0 O A:VAL334 2.3 12.8 1.0 O2G A:GAV501 2.4 12.9 1.0 O A:HOH627 2.5 17.7 1.0 CG A:ASP376 3.3 13.3 1.0 CG A:ASP333 3.3 15.0 1.0 PB A:GAV501 3.4 14.1 1.0 PG A:GAV501 3.5 13.2 1.0 C A:VAL334 3.5 11.6 1.0 OD1 A:ASP376 3.6 15.7 1.0 O3A A:GAV501 3.8 15.4 1.0 OD2 A:ASP333 3.8 19.7 1.0 O3B A:GAV501 3.8 13.9 1.0 NZ A:LYS446 3.9 13.3 1.0 O1G A:GAV501 3.9 12.2 1.0 O A:HOH618 3.9 27.9 1.0 N A:VAL334 4.0 10.9 1.0 CA A:VAL334 4.2 11.4 1.0 CA A:CA503 4.4 18.2 0.7 C A:ASP333 4.4 11.4 1.0 CB A:PHE337 4.4 13.6 1.0 N A:ASP335 4.6 11.5 1.0 CB A:ASP333 4.6 13.0 1.0 CB A:ASP376 4.6 13.8 1.0 N A:PHE337 4.6 12.7 1.0 N A:LYS336 4.7 12.6 1.0 CB A:VAL334 4.7 12.0 1.0 CE A:LYS446 4.7 13.5 1.0 CA A:ASP335 4.8 12.1 1.0 O2B A:GAV501 4.8 15.4 1.0 C5' A:GAV501 4.8 19.2 1.0 O3G A:GAV501 4.8 15.9 1.0 O A:ASP333 4.8 12.3 1.0 PA A:GAV501 4.9 19.7 1.0 O A:ASP376 4.9 13.3 1.0 CA A:ASP333 4.9 11.8 1.0 C A:ASP335 4.9 12.2 1.0 OE2 A:GLU377 5.0 24.0 0.6

Calcium binding site 2 out of 2 in the Crystal Structure of Ggdef Domain of the E. Coli Dosc - Form II (Gtp- Alpha-S-Bound)


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 Ggdef Domain of the E. Coli Dosc - Form II (Gtp- Alpha-S-Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:18.2 occ:0.69 OE2 A:GLU377 2.2 24.0 0.6 OD2 A:ASP333 2.3 19.7 1.0 O A:HOH736 2.3 39.5 1.0 OE2 A:GLU377 2.4 26.1 0.4 O A:HOH618 2.4 27.9 1.0 O A:HOH732 2.4 41.9 1.0 O A:HOH627 2.6 17.7 1.0 O A:HOH726 3.0 50.4 1.0 CD A:GLU377 3.4 24.8 0.6 CD A:GLU377 3.4 25.1 0.4 CG A:ASP333 3.5 15.0 1.0 CG A:GLU377 3.9 19.2 0.4 CG A:GLU377 3.9 20.3 0.6 OD1 A:ASP333 3.9 13.6 1.0 O A:HOH610 4.1 23.0 1.0 O2G A:GAV501 4.3 12.9 1.0 CA A:CA502 4.4 12.4 1.0 OE1 A:GLU377 4.4 27.9 0.4 OE1 A:GLU377 4.4 25.6 0.6 OD1 A:ASP376 4.4 15.7 1.0 O A:HOH696 4.5 46.1 1.0 S1A A:GAV501 4.5 20.9 1.0 O A:HOH763 4.6 49.4 1.0 CB A:ASP333 4.7 13.0 1.0 O A:HOH611 4.7 39.2 1.0

M.Tarnawski, T.R.Barends, I.Schlichting. Structural Analysis of An Oxygen-Regulated Diguanylate Cyclase. Acta Crystallogr.,Sect.D V. 71 2158 2015.
ISSN: ESSN 1399-0047
PubMed: 26527135
DOI: 10.1107/S139900471501545X