Calcium in PDB 3exm: Crystal Structure of the Phosphatase SC4828 with the Non-Hydrolyzable Nucleotide Gpcp

All present enzymatic activity of Crystal Structure of the Phosphatase SC4828 with the Non-Hydrolyzable Nucleotide Gpcp:
3.6.1.6;

The structure of Crystal Structure of the Phosphatase SC4828 with the Non-Hydrolyzable Nucleotide Gpcp, PDB code: 3exm was solved by A.U.Singer, X.Xu, H.Zheng, A.Joachimiak, A.M.Edwards, A.Savchenko, A.F.Yakunin, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.74 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.941, 79.706, 82.507, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 19.9

The structure of Crystal Structure of the Phosphatase SC4828 with the Non-Hydrolyzable Nucleotide Gpcp also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of the Phosphatase SC4828 with the Non-Hydrolyzable Nucleotide Gpcp (pdb code 3exm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Phosphatase SC4828 with the Non-Hydrolyzable Nucleotide Gpcp, PDB code: 3exm:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Phosphatase SC4828 with the Non-Hydrolyzable Nucleotide Gpcp


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 the Phosphatase SC4828 with the Non-Hydrolyzable Nucleotide Gpcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:18.1 occ:1.00 OD1 A:ASN133 2.3 18.2 1.0 OD1 A:ASP153 2.3 20.9 1.0 O1B A:GP2401 2.3 27.7 1.0 O A:HOH522 2.4 19.8 1.0 OD1 A:ASP149 2.5 22.1 1.0 O2B A:GP2401 2.6 29.4 1.0 OD2 A:ASP149 2.7 22.1 1.0 CG A:ASP149 2.9 20.4 1.0 PB A:GP2401 2.9 33.7 1.0 CG A:ASN133 3.3 17.9 1.0 CG A:ASP153 3.5 21.7 1.0 CA A:CA302 3.7 22.7 0.8 O3B A:GP2401 3.8 33.1 1.0 OH A:TYR131 3.9 29.7 1.0 ND2 A:ASN133 3.9 18.6 1.0 O A:PHE151 4.0 19.5 1.0 OD2 A:ASP153 4.3 23.9 1.0 C3A A:GP2401 4.4 34.0 1.0 CB A:ASP149 4.4 18.9 1.0 N A:PHE151 4.5 17.9 1.0 C A:PHE151 4.5 18.1 1.0 CB A:ASN133 4.5 16.9 1.0 CB A:ASP153 4.5 17.5 1.0 O A:LEU152 4.5 17.7 1.0 O A:LEU134 4.6 15.6 1.0 CA A:ASN133 4.6 15.8 1.0 CA A:PHE151 4.6 18.2 1.0 O A:HOH641 4.6 26.9 1.0 CZ A:TYR131 4.7 24.5 1.0 O A:HOH818 4.7 22.7 1.0 CE2 A:TYR131 4.7 21.9 1.0 O A:HOH512 4.8 40.7 1.0 C A:LEU152 5.0 17.7 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Phosphatase SC4828 with the Non-Hydrolyzable Nucleotide Gpcp


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 the Phosphatase SC4828 with the Non-Hydrolyzable Nucleotide Gpcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:22.7 occ:0.75 O A:PHE151 2.3 19.5 1.0 OD1 A:ASP166 2.3 25.0 1.0 OD2 A:ASP153 2.3 23.9 1.0 O3B A:GP2401 2.4 33.1 1.0 O A:HOH582 2.4 25.5 1.0 O2B A:GP2401 2.4 29.4 1.0 O A:HOH818 2.7 22.7 1.0 OD1 A:ASP153 2.9 20.9 1.0 PB A:GP2401 2.9 33.7 1.0 CG A:ASP153 2.9 21.7 1.0 CG A:ASP166 3.1 24.8 1.0 CB A:ASP166 3.2 22.9 1.0 C A:PHE151 3.4 18.1 1.0 CA A:CA301 3.7 18.1 1.0 CA A:CA303 3.8 25.7 0.8 O A:HOH664 3.9 32.4 1.0 O1B A:GP2401 4.0 27.7 1.0 CA A:PHE151 4.1 18.2 1.0 OE1 A:GLU169 4.1 32.1 1.0 OH A:TYR131 4.1 29.7 1.0 C3A A:GP2401 4.1 34.0 1.0 O A:HOH512 4.2 40.7 1.0 OD2 A:ASP166 4.3 25.4 1.0 O A:HOH829 4.4 36.3 1.0 CB A:ASP153 4.4 17.5 1.0 N A:LEU152 4.5 17.6 1.0 N A:ASP153 4.6 17.1 1.0 OD2 A:ASP149 4.6 22.1 1.0 O A:ARG165 4.6 19.7 0.3 CA A:ASP166 4.6 22.7 1.0 C A:LEU152 4.7 17.7 1.0 O A:ARG165 4.8 18.7 0.7 O A:HOH522 4.8 19.8 1.0 CA A:LEU152 4.8 17.4 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Phosphatase SC4828 with the Non-Hydrolyzable Nucleotide Gpcp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Phosphatase SC4828 with the Non-Hydrolyzable Nucleotide Gpcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:25.7 occ:0.75 O A:HOH829 2.3 36.3 1.0 OD1 A:ASP166 2.3 25.0 1.0 O A:HOH664 2.3 32.4 1.0 O A:HOH735 2.4 41.5 1.0 O A:HOH828 2.4 35.7 1.0 O3B A:GP2401 2.5 33.1 1.0 O1A A:GP2401 2.6 35.2 1.0 O A:HOH818 3.2 22.7 1.0 CG A:ASP166 3.3 24.8 1.0 OD2 A:ASP166 3.5 25.4 1.0 C3A A:GP2401 3.7 34.0 1.0 PA A:GP2401 3.7 34.2 1.0 CA A:CA302 3.8 22.7 0.8 PB A:GP2401 3.8 33.7 1.0 O A:HOH673 3.9 43.5 1.0 OE1 A:GLU169 4.3 32.1 1.0 O3' A:GP2401 4.3 36.9 1.0 OD2 A:ASP153 4.4 23.9 1.0 OH A:TYR131 4.4 29.7 1.0 NH2 A:ARG165 4.4 33.6 0.7 C5' A:GP2401 4.5 33.0 1.0 O5' A:GP2401 4.6 32.7 1.0 O2B A:GP2401 4.6 29.4 1.0 CB A:ASP166 4.6 22.9 1.0 O A:HOH582 4.7 25.5 1.0 C3' A:GP2401 4.8 34.0 1.0 O2A A:GP2401 4.9 35.6 1.0

M.Proudfoot, M.Brown, A.U.Singer, M.-C.Jobin, X.Xu, H.Zheng, C.Chang, A.M.Edwards, A.Joachimiak, A.Savchenko, A.F.Yakunin. Structure and Mechanism of A New Family of Prokaryotic Nucleoside Diphosphatases. To Be Published.