Calcium in PDB 3q4w: The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Substrate

The structure of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Substrate, PDB code: 3q4w was solved by R.C.Hughes, E.J.Meehan, L.Coates, J.D.Ng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.88 / 1.44
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	100.046, 100.046, 98.711, 90.00, 90.00, 120.00
R / Rfree (%)	10.9 / 13.9

The structure of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Substrate also contains other interesting chemical elements:

Bromine	(Br)	1 atom
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Substrate (pdb code 3q4w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Substrate, PDB code: 3q4w:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca224 b:9.9 occ:1.00 OD2 A:ASP98 2.2 10.6 1.0 O6 A:POP227 2.2 9.9 1.0 OD2 A:ASP103 2.3 10.4 1.0 O A:HOH302 2.3 13.3 1.0 O2 A:POP227 2.4 9.4 1.0 O A:HOH205 2.5 10.7 1.0 CG A:ASP98 3.3 10.9 1.0 P1 A:POP227 3.4 9.9 1.0 CG A:ASP103 3.5 10.3 1.0 P2 A:POP227 3.5 9.4 1.0 O A:POP227 3.7 9.4 1.0 O1 A:POP227 3.7 10.3 1.0 CA A:CA225 3.8 9.8 1.0 CB A:ASP98 3.9 11.4 1.0 OD2 A:ASP66 4.0 12.3 1.0 NZ A:LYS141 4.0 13.4 0.6 CA A:CA284 4.1 18.6 0.5 NZ A:LYS141 4.2 10.6 0.5 OH A:TYR140 4.2 9.6 1.0 NZ A:LYS105 4.2 10.0 1.0 O5 A:POP227 4.3 9.7 1.0 OD1 A:ASP98 4.3 11.4 1.0 CB A:ASP103 4.3 10.8 1.0 OD1 A:ASP103 4.4 9.9 1.0 CA A:CA284 4.5 32.5 0.5 O A:HOH307 4.6 16.8 1.0 O A:HOH451 4.6 31.1 0.6 O4 A:POP227 4.7 11.4 1.0 OD1 A:ASP71 4.7 10.2 1.0 O3 A:POP227 4.8 12.6 1.0 CE A:LYS141 4.9 14.5 0.6

Calcium binding site 2 out of 4 in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca225 b:9.8 occ:1.00 O A:HOH189 2.4 10.8 1.0 OD1 A:ASP71 2.4 10.2 1.0 OD2 A:ASP66 2.4 12.3 1.0 O2 A:POP227 2.4 9.4 1.0 OD1 A:ASP103 2.5 9.9 1.0 O A:HOH228 2.5 12.2 1.0 OD2 A:ASP71 2.7 10.7 1.0 OD2 A:ASP103 2.7 10.4 1.0 CG A:ASP71 2.9 10.8 1.0 CG A:ASP103 2.9 10.3 1.0 CG A:ASP66 3.4 14.3 1.0 P1 A:POP227 3.6 9.9 1.0 OD1 A:ASP66 3.7 15.2 1.0 NA A:NA283 3.8 13.9 0.4 CA A:CA224 3.8 9.9 1.0 O3 A:POP227 3.8 12.6 1.0 O A:HOH185 3.9 10.7 1.0 O A:HOH302 4.0 13.3 1.0 O1 A:POP227 4.2 10.3 1.0 NZ A:LYS105 4.3 10.0 1.0 CB A:ASP71 4.3 9.9 1.0 O A:HOH292 4.5 12.4 0.8 CB A:ASP103 4.5 10.8 1.0 O A:PRO69 4.6 11.8 1.0 CA A:CA284 4.6 32.5 0.5 CA A:CA284 4.6 18.6 0.5 CB A:ASP68 4.6 20.7 1.0 CB A:ASP66 4.6 16.4 1.0 OH A:TYR56 4.7 11.9 1.0 O A:HOH205 4.8 10.7 1.0 OD2 A:ASP68 4.8 27.6 1.0 O A:POP227 4.9 9.4 1.0

Calcium binding site 3 out of 4 in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca284 b:32.5 occ:0.51 CA A:CA284 0.0 32.5 0.5 CA A:CA284 0.6 18.6 0.5 O A:HOH280 2.4 35.4 1.0 O A:HOH448 2.4 36.6 1.0 O A:HOH450 2.5 31.3 0.6 OD2 A:ASP68 2.5 27.6 1.0 O A:HOH451 2.7 31.1 0.6 O A:HOH281 3.2 26.7 1.0 O A:HOH228 3.5 12.2 1.0 O A:HOH302 3.5 13.3 1.0 OD2 A:ASP66 3.6 12.3 1.0 CG A:ASP68 3.7 24.8 1.0 O2 A:POP227 3.7 9.4 1.0 O A:POP227 4.1 9.4 1.0 O6 A:POP227 4.3 9.9 1.0 O A:HOH187 4.4 43.1 1.0 O4 A:POP227 4.4 11.4 1.0 P1 A:POP227 4.4 9.9 1.0 CG A:ASP66 4.4 14.3 1.0 CB A:ASP68 4.4 20.7 1.0 CA A:CA224 4.5 9.9 1.0 P2 A:POP227 4.6 9.4 1.0 OD1 A:ASP68 4.6 26.0 1.0 O3 A:POP227 4.6 12.6 1.0 CA A:CA225 4.6 9.8 1.0 O A:HOH433 4.7 38.9 1.0 O A:ASP66 4.7 18.3 1.0 CB A:ASP66 4.9 16.4 1.0

Calcium binding site 4 out of 4 in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca284 b:18.6 occ:0.49 CA A:CA284 0.0 18.6 0.5 CA A:CA284 0.6 32.5 0.5 O A:HOH451 2.3 31.1 0.6 O A:HOH450 2.7 31.3 0.6 O A:HOH280 2.7 35.4 1.0 O A:HOH448 2.8 36.6 1.0 O A:HOH281 2.9 26.7 1.0 OD2 A:ASP68 3.1 27.6 1.0 O A:HOH302 3.3 13.3 1.0 O2 A:POP227 3.5 9.4 1.0 O A:POP227 3.6 9.4 1.0 O A:HOH228 3.7 12.2 1.0 O6 A:POP227 3.7 9.9 1.0 OD2 A:ASP66 3.8 12.3 1.0 O4 A:POP227 3.8 11.4 1.0 P2 A:POP227 4.0 9.4 1.0 P1 A:POP227 4.1 9.9 1.0 CA A:CA224 4.1 9.9 1.0 CG A:ASP68 4.3 24.8 1.0 O3 A:POP227 4.4 12.6 1.0 CA A:CA225 4.6 9.8 1.0 CG A:ASP66 4.7 14.3 1.0 O A:HOH345 4.8 23.1 0.8 O A:HOH267 4.9 39.8 0.9 O A:HOH187 4.9 43.1 1.0 OE2 A:GLU32 4.9 13.2 0.5 O A:HOH433 4.9 38.9 1.0 CB A:ASP68 5.0 20.7 1.0

R.C.Hughes, L.Coates, M.P.Blakeley, S.J.Tomanicek, P.Langan, A.Y.Kovalevsky, J.M.Garcia-Ruiz, J.D.Ng. Inorganic Pyrophosphatase Crystals From Thermococcus Thioreducens For X-Ray and Neutron Diffraction. Acta Crystallogr.,Sect.F V. 68 1482 2012.
ISSN: ESSN 1744-3091
PubMed: 23192028
DOI: 10.1107/S1744309112032447