Sodium 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
Calcium	(Ca)	4 atoms

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the The Structure of Archaeal Inorganic Pyrophosphatase in Complex with Substrate, PDB code: 3q4w:

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na283 b:13.9 occ:0.37 O A:HOH292 2.0 12.4 0.8 BR A:BR279 2.0 8.8 1.0 O A:HOH228 2.2 12.2 1.0 O3 A:POP227 2.4 12.6 1.0 O A:HOH317 2.5 13.5 0.4 OD2 A:ASP71 2.5 10.7 1.0 O A:HOH397 3.3 30.2 1.0 P1 A:POP227 3.6 9.9 1.0 CG A:ASP71 3.7 10.8 1.0 CA A:CA225 3.8 9.8 1.0 O2 A:POP227 4.0 9.4 1.0 O A:HOH433 4.1 38.9 1.0 O A:PRO69 4.2 11.8 1.0 OE1 A:GLU22 4.2 9.5 1.0 CG2 A:ILE58 4.2 13.7 1.0 OD1 A:ASP71 4.3 10.2 1.0 O A:HOH189 4.4 10.8 1.0 NZ A:LYS30 4.4 12.1 1.0 OD2 A:ASP68 4.5 27.6 1.0 O1 A:POP227 4.5 10.3 1.0 O A:HOH223 4.6 11.7 1.0 CB A:ASP68 4.6 20.7 1.0 OH A:TYR56 4.7 11.9 1.0 O A:POP227 4.7 9.4 1.0 CE2 A:TYR56 4.7 10.4 1.0 CB A:ASP71 4.8 9.9 1.0 O A:GLY57 4.8 8.3 1.0 CG A:ASP68 4.8 24.8 1.0 OE2 A:GLU22 4.9 11.2 1.0 CA A:ASP71 4.9 8.8 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