Sodium in PDB 1htw: Complex of HI0065 with Adp and Magnesium

The structure of Complex of HI0065 with Adp and Magnesium, PDB code: 1htw was solved by A.Teplyakov, G.L.Gilliland, Structure 2 Function Project (S2F), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.350, 71.340, 95.700, 90.00, 109.45, 90.00
R / Rfree (%)	19.9 / 23.5

The structure of Complex of HI0065 with Adp and Magnesium also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Sodium atom in the Complex of HI0065 with Adp and Magnesium (pdb code 1htw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Complex of HI0065 with Adp and Magnesium, PDB code: 1htw:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Complex of HI0065 with Adp and Magnesium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex of HI0065 with Adp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na563 b:28.1 occ:1.00 OG A:SER115 2.7 23.4 1.0 O A:ILE112 2.8 19.2 1.0 O A:LEU38 2.8 17.1 1.0 N A:SER115 2.9 20.5 1.0 OD1 A:ASN39 3.0 22.3 1.0 CB A:SER115 3.2 20.3 1.0 N A:TRP114 3.3 18.9 1.0 N A:LEU38 3.4 17.0 1.0 O A:HOH654 3.5 39.2 1.0 O A:HOH581 3.5 24.2 1.0 C A:LEU38 3.6 17.3 1.0 CA A:SER115 3.7 21.2 1.0 C A:ILE112 3.7 22.5 1.0 C A:GLU113 3.7 19.9 1.0 CA A:GLU113 3.8 18.7 1.0 C A:TRP114 3.9 23.3 1.0 C A:TYR37 3.9 17.9 1.0 CB A:TYR37 3.9 16.2 1.0 CA A:TRP114 4.0 21.4 1.0 CA A:TYR37 4.0 17.5 1.0 CG A:ASN39 4.1 21.3 1.0 CA A:LEU38 4.1 15.9 1.0 N A:GLU113 4.2 19.8 1.0 OE1 A:GLU116 4.3 30.4 1.0 N A:ASN39 4.4 16.4 1.0 O A:GLU113 4.5 20.6 1.0 CG A:TYR37 4.5 20.2 1.0 CG2 A:ILE112 4.5 21.3 1.0 CA A:ASN39 4.6 19.6 1.0 CB A:ILE112 4.8 15.6 1.0 O A:TYR37 4.8 19.7 1.0 O A:HOH604 4.8 29.8 1.0 C A:SER115 4.9 26.6 1.0 ND2 A:ASN39 4.9 24.1 1.0 CA A:ILE112 4.9 17.2 1.0 CB A:LEU38 4.9 12.8 1.0 CD2 A:TYR37 4.9 21.3 1.0 CB A:ASN39 5.0 20.8 1.0 N A:GLU116 5.0 25.4 1.0

Sodium binding site 2 out of 3 in the Complex of HI0065 with Adp and Magnesium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Complex of HI0065 with Adp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Na663 b:39.5 occ:1.00 OG B:SER115 2.5 30.9 1.0 N B:SER115 2.8 27.7 1.0 O B:ILE112 2.8 25.0 1.0 O B:LEU38 2.9 23.7 1.0 OD1 B:ASN39 2.9 27.6 1.0 CB B:SER115 3.0 35.3 1.0 N B:TRP114 3.4 25.2 1.0 CA B:SER115 3.5 26.3 1.0 N B:LEU38 3.5 19.3 1.0 C B:LEU38 3.6 25.9 1.0 CB B:TYR37 3.8 25.9 1.0 C B:ILE112 3.8 24.0 1.0 O B:HOH694 3.8 35.5 1.0 C B:GLU113 3.8 29.8 1.0 C B:TRP114 3.8 34.3 1.0 C B:TYR37 3.9 23.0 1.0 CA B:TRP114 3.9 32.1 1.0 CA B:TYR37 4.0 23.2 1.0 CA B:GLU113 4.0 26.2 1.0 CG B:ASN39 4.0 26.9 1.0 CA B:LEU38 4.2 19.6 1.0 N B:ASN39 4.3 20.4 1.0 N B:GLU113 4.3 22.9 1.0 CG B:TYR37 4.4 28.7 1.0 CG2 B:ILE112 4.5 30.7 1.0 CA B:ASN39 4.6 21.6 1.0 O B:GLU113 4.6 26.3 1.0 CB B:ILE112 4.7 24.5 1.0 C B:SER115 4.7 37.0 1.0 O B:TYR37 4.8 24.2 1.0 CD2 B:TYR37 4.8 33.7 1.0 ND2 B:ASN39 4.8 27.9 1.0 CA B:ILE112 4.9 22.8 1.0 N B:GLU116 4.9 38.6 1.0 CB B:ASN39 4.9 18.4 1.0 O B:TRP114 5.0 34.4 1.0 CD1 B:TYR37 5.0 29.6 1.0 CB B:LEU38 5.0 22.2 1.0

Sodium binding site 3 out of 3 in the Complex of HI0065 with Adp and Magnesium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Complex of HI0065 with Adp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ C:Na763 b:32.8 occ:1.00 O C:ILE112 2.7 20.6 1.0 OG C:SER115 2.8 32.6 1.0 O C:LEU38 2.9 22.2 1.0 N C:SER115 2.9 25.3 1.0 OD1 C:ASN39 2.9 24.8 1.0 CB C:SER115 3.0 27.6 1.0 N C:TRP114 3.3 28.8 1.0 N C:LEU38 3.5 18.2 1.0 CA C:SER115 3.5 32.2 1.0 C C:LEU38 3.6 15.8 1.0 O C:HOH768 3.6 23.9 1.0 C C:GLU113 3.7 27.2 1.0 C C:ILE112 3.7 13.2 1.0 CA C:GLU113 3.8 22.8 1.0 C C:TRP114 3.9 30.8 1.0 CB C:TYR37 3.9 19.2 1.0 C C:TYR37 3.9 12.3 1.0 CA C:TRP114 4.0 28.9 1.0 CA C:TYR37 4.0 19.7 1.0 CG C:ASN39 4.0 16.5 1.0 O C:HOH821 4.1 39.1 1.0 N C:GLU113 4.2 18.8 1.0 CA C:LEU38 4.3 16.5 1.0 N C:ASN39 4.3 21.4 1.0 CG2 C:ILE112 4.4 24.2 1.0 CG C:TYR37 4.4 23.5 1.0 O C:GLU113 4.4 24.5 1.0 CB C:ILE112 4.4 24.7 1.0 CA C:ASN39 4.4 24.2 1.0 C C:SER115 4.8 34.4 1.0 CA C:ILE112 4.8 17.6 1.0 O C:TYR37 4.9 18.5 1.0 ND2 C:ASN39 4.9 20.0 1.0 CD2 C:TYR37 4.9 24.9 1.0 CB C:ASN39 4.9 19.6 1.0 CB C:LEU38 5.0 14.7 1.0 N C:GLU116 5.0 40.3 1.0 O C:HOH807 5.0 36.2 1.0 CD1 C:TYR37 5.0 23.1 1.0

A.Teplyakov, G.Obmolova, M.Tordova, N.Thanki, N.Bonander, E.Eisenstein, A.J.Howard, G.L.Gilliland. Crystal Structure of the Yjee Protein From Haemophilus Influenzae: A Putative Atpase Involved in Cell Wall Synthesis Proteins V. 48 220 2002.
ISSN: ISSN 0887-3585
PubMed: 12112691
DOI: 10.1002/PROT.10114