Sodium in PDB 1m4y: Crystal Structure of Hslv From Thermotoga Maritima

The structure of Crystal Structure of Hslv From Thermotoga Maritima, PDB code: 1m4y was solved by H.K.Song, R.Ramachandran, M.B.Bochtler, C.Hartmann, M.K.Azim, R.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	77.533, 93.748, 146.167, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.9

The binding sites of Sodium atom in the Crystal Structure of Hslv From Thermotoga Maritima (pdb code 1m4y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Hslv From Thermotoga Maritima, PDB code: 1m4y:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Hslv From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Hslv From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Na252 b:20.7 occ:1.00 O A:THR162 2.2 19.9 1.0 O A:GLY156 2.2 24.4 1.0 O A:CYS159 2.3 20.5 1.0 O A:HOH294 2.4 30.4 1.0 O A:HOH257 2.5 21.0 1.0 O A:HOH273 2.8 38.6 1.0 C A:GLY156 3.3 24.9 1.0 C A:THR162 3.4 19.4 1.0 C A:CYS159 3.5 20.6 1.0 CA A:GLY156 3.9 22.7 1.0 CA A:ILE160 4.0 19.2 1.0 N A:THR162 4.1 21.4 1.0 N A:ILE160 4.2 18.6 1.0 CA A:ASN163 4.2 17.7 1.0 N A:ASN163 4.3 19.0 1.0 C A:ILE160 4.3 19.2 1.0 CA A:THR162 4.3 19.8 1.0 N A:GLU157 4.5 24.0 1.0 OE1 A:GLN19 4.5 23.1 1.0 N A:CYS159 4.6 20.6 1.0 CA A:CYS159 4.6 21.7 1.0 O A:ILE160 4.6 19.6 1.0 N A:TYR161 4.8 19.7 1.0 C A:GLU157 4.8 23.7 1.0 CA A:GLU157 4.8 24.1 1.0 CB A:THR162 4.8 20.5 1.0 O A:GLU157 4.9 22.3 1.0 O A:ALA155 5.0 20.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Hslv From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Hslv From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ B:Na251 b:22.0 occ:1.00 O B:GLY156 2.2 23.2 1.0 O B:THR162 2.2 21.1 1.0 O B:CYS159 2.4 22.0 1.0 O B:HOH290 2.4 37.1 1.0 O B:HOH271 2.5 26.3 1.0 O B:HOH253 2.5 35.5 1.0 C B:GLY156 3.3 22.7 1.0 C B:THR162 3.5 21.4 1.0 C B:CYS159 3.5 21.9 1.0 CA B:GLY156 3.8 22.2 1.0 CA B:ILE160 4.1 21.6 1.0 CA B:ASN163 4.2 23.9 1.0 N B:THR162 4.3 22.4 1.0 N B:ILE160 4.3 20.8 1.0 N B:ASN163 4.3 22.8 1.0 C B:ILE160 4.4 23.4 1.0 CA B:THR162 4.4 22.2 1.0 N B:GLU157 4.5 24.1 1.0 OE1 B:GLN19 4.6 19.5 1.0 N B:CYS159 4.6 23.7 1.0 CA B:CYS159 4.6 22.1 1.0 O B:ILE160 4.6 21.8 1.0 C B:GLU157 4.8 24.4 1.0 O B:GLU157 4.8 25.7 1.0 O B:ALA155 4.8 20.4 1.0 CA B:GLU157 4.9 24.9 1.0 N B:TYR161 4.9 23.5 1.0 CB B:THR162 4.9 21.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Hslv From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Hslv From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ C:Na250 b:25.2 occ:1.00 O C:CYS159 2.2 27.4 1.0 O C:GLY156 2.2 28.5 1.0 O C:THR162 2.3 25.8 1.0 O C:HOH301 2.4 29.7 1.0 O C:HOH288 2.5 28.9 1.0 O C:HOH268 2.8 41.5 1.0 C C:CYS159 3.4 27.4 1.0 C C:GLY156 3.4 29.0 1.0 C C:THR162 3.5 23.4 1.0 CA C:ILE160 4.0 27.1 1.0 CA C:GLY156 4.1 27.4 1.0 N C:ILE160 4.1 27.0 1.0 N C:THR162 4.1 26.0 1.0 C C:ILE160 4.2 27.9 1.0 CA C:THR162 4.4 23.5 1.0 CA C:ASN163 4.4 24.4 1.0 N C:ASN163 4.4 23.3 1.0 N C:GLU157 4.4 29.2 1.0 CA C:CYS159 4.5 27.8 1.0 N C:CYS159 4.5 27.8 1.0 O C:ILE160 4.5 28.4 1.0 OE1 C:GLN19 4.5 28.4 1.0 C C:GLU157 4.6 30.0 1.0 O C:GLU157 4.6 29.2 1.0 CA C:GLU157 4.7 30.7 1.0 N C:TYR161 4.7 27.0 1.0 CB C:THR162 4.9 22.7 1.0 O C:ALA155 4.9 24.4 1.0

H.K.Song, M.Bochtler, M.K.Azim, C.Hartmann, R.Huber, R.Ramachandran. Isolation and Characterization of the Prokaryotic Proteasome Homolog Hslvu (Clpqy) From Thermotoga Maritima and the Crystal Structure of Hslv. Biophys.Chem. V. 100 437 2003.
ISSN: ISSN 0301-4622
PubMed: 12646382
DOI: 10.1016/S0301-4622(02)00297-1