Sodium in PDB 3hlt: The Crystal Structure of Human Haloacid Dehalogenase-Like Hydrolase Domain Containing 2 (HDHD2)

The structure of The Crystal Structure of Human Haloacid Dehalogenase-Like Hydrolase Domain Containing 2 (HDHD2), PDB code: 3hlt was solved by E.Ugochukwu, N.Shafqat, W.W.Yue, R.Cocking, J.E.Bray, J.R.C.Muniz, T.Krojer, F.Von Delft, C.Bountra, C.H.Arrowsmith, J.Weigelt, A.Edwards, U.Oppermann, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.36 / 2.30
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	68.940, 77.680, 103.990, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 26.6

The structure of The Crystal Structure of Human Haloacid Dehalogenase-Like Hydrolase Domain Containing 2 (HDHD2) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the The Crystal Structure of Human Haloacid Dehalogenase-Like Hydrolase Domain Containing 2 (HDHD2) (pdb code 3hlt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Crystal Structure of Human Haloacid Dehalogenase-Like Hydrolase Domain Containing 2 (HDHD2), PDB code: 3hlt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Crystal Structure of Human Haloacid Dehalogenase-Like Hydrolase Domain Containing 2 (HDHD2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Human Haloacid Dehalogenase-Like Hydrolase Domain Containing 2 (HDHD2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na269 b:43.9 occ:1.00 O A:HOH307 2.0 21.4 1.0 OD2 A:ASP13 2.0 29.5 1.0 O A:HOH314 2.3 34.2 1.0 OD1 A:ASP204 2.3 28.5 1.0 O A:SER15 2.4 22.6 1.0 CG A:ASP13 2.8 27.0 1.0 OD1 A:ASP13 3.1 24.7 1.0 CG A:ASP204 3.5 23.8 1.0 C A:SER15 3.6 22.2 1.0 OD2 A:ASP209 3.7 28.5 1.0 OD2 A:ASP204 3.9 24.1 1.0 O A:HOH288 4.0 18.2 1.0 CB A:ASP13 4.1 23.6 1.0 NZ A:LYS179 4.5 24.8 1.0 N A:ASP204 4.5 19.5 1.0 N A:GLY16 4.5 21.9 1.0 CA A:SER15 4.6 21.7 1.0 CA A:GLY16 4.6 22.7 1.0 N A:SER15 4.6 21.5 1.0 CG A:ASP209 4.6 28.9 1.0 OD1 A:ASP209 4.7 29.3 1.0 CB A:ASP204 4.8 20.4 1.0 CB A:SER15 4.8 21.4 1.0 CB A:ASP205 4.9 24.8 1.0 OG1 A:THR17 4.9 26.7 1.0 N A:ASP205 5.0 22.9 1.0

Sodium binding site 2 out of 2 in the The Crystal Structure of Human Haloacid Dehalogenase-Like Hydrolase Domain Containing 2 (HDHD2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Human Haloacid Dehalogenase-Like Hydrolase Domain Containing 2 (HDHD2) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na269 b:59.9 occ:1.00 OD2 C:ASP13 2.1 25.4 1.0 O C:SER15 2.3 25.8 1.0 OD1 C:ASP204 2.4 29.6 1.0 CG C:ASP13 3.3 25.7 1.0 C C:SER15 3.5 25.9 1.0 CG C:ASP204 3.6 30.0 1.0 OD1 C:ASP13 4.0 27.8 1.0 OG1 C:THR17 4.0 25.3 1.0 OD2 C:ASP204 4.1 30.1 1.0 OD2 C:ASP209 4.1 27.9 1.0 CB C:ASP13 4.3 24.4 1.0 CA C:GLY16 4.3 26.4 1.0 N C:GLY16 4.4 26.2 1.0 C C:GLY16 4.5 26.4 1.0 N C:SER15 4.6 25.0 1.0 CA C:SER15 4.6 25.6 1.0 N C:ASP204 4.6 29.7 1.0 N C:THR17 4.7 26.2 1.0 CB C:ASP204 4.8 29.8 1.0 N C:ASP205 4.9 30.1 1.0 O C:GLY16 5.0 26.6 1.0 CG C:ASP209 5.0 27.8 1.0 C C:LEU14 5.0 24.7 1.0

E.Ugochukwu, N.Shafqat, W.W.Yue, R.Cocking, J.E.Bray, J.R.C.Muniz, T.Krojer, F.Von Delft, C.Bountra, C.H.Arrowsmith, J.Weigelt, A.Edwards, U.Oppermann, Structural Genomics Consortium (Sgc). The Crystal Structure of Human Haloacid Dehalogenase-Like Hydrolase Domain Containing 2 (HDHD2) To Be Published.