Sodium in PDB 1ems: Crystal Structure of the C. Elegans Nitfhit Protein

The structure of Crystal Structure of the C. Elegans Nitfhit Protein, PDB code: 1ems was solved by H.C.Pace, S.C.Hodawadekar, A.Draganescu, J.Huang, P.Bieganowski, Y.Pekarsky, C.M.Croce, C.Brenner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.750, 100.440, 158.650, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.1

The structure of Crystal Structure of the C. Elegans Nitfhit Protein also contains other interesting chemical elements:

Mercury

(Hg)

5 atoms

The binding sites of Sodium atom in the Crystal Structure of the C. Elegans Nitfhit Protein (pdb code 1ems). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the C. Elegans Nitfhit Protein, PDB code: 1ems:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the C. Elegans Nitfhit Protein


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 the C. Elegans Nitfhit Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na456 b:16.4 occ:1.00 OH A:TYR218 2.5 9.7 1.0 OG B:SER252 2.7 11.0 1.0 O A:HOH531 2.7 3.6 1.0 CE2 A:TYR218 3.2 10.1 1.0 CZ A:TYR218 3.2 11.2 1.0 CB B:SER252 3.9 14.9 1.0 O A:GLU261 3.9 21.3 1.0 CB A:ASP242 4.0 13.2 1.0 CD2 A:TYR266 4.4 8.6 1.0 O B:HOH495 4.4 2.2 1.0 CG1 A:VAL248 4.4 14.8 1.0 O B:HOH480 4.4 17.2 1.0 N A:ASP263 4.5 16.6 1.0 CD2 A:TYR218 4.5 10.8 1.0 CE1 A:TYR218 4.6 10.9 1.0 CA A:ILE262 4.6 19.9 1.0 OD2 A:ASP242 4.6 13.5 1.0 CE2 A:TYR266 4.8 10.8 1.0 CG A:ASP242 4.9 14.2 1.0 C A:ILE262 5.0 18.2 1.0 C A:GLU261 5.0 21.2 1.0 CA B:SER252 5.0 17.1 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the C. Elegans Nitfhit Protein


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 the C. Elegans Nitfhit Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na457 b:19.7 occ:1.00 O A:HOH561 2.8 6.2 1.0 OG A:SER167 2.9 18.8 1.0 OG A:SER178 3.1 8.8 1.0 OD1 A:ASN181 3.2 13.0 1.0 CA A:SER178 3.6 13.0 1.0 CD2 A:LEU189 3.7 2.6 1.0 CZ A:PHE191 3.8 14.1 1.0 CB A:SER178 3.9 13.3 1.0 N A:SER178 3.9 14.0 1.0 CB A:SER167 4.0 15.4 1.0 O A:LEU177 4.1 17.6 1.0 CG A:ASN181 4.1 13.8 1.0 C A:LEU177 4.1 16.4 1.0 CE2 A:PHE191 4.1 13.6 1.0 CD2 A:LEU177 4.2 18.5 1.0 CB A:ASN181 4.4 10.7 1.0 CD1 A:LEU177 4.4 17.1 1.0 O A:LEU166 4.5 15.7 1.0 CG A:LEU189 4.5 6.4 1.0 CD1 A:LEU189 4.5 2.9 1.0 CB A:LEU189 4.6 9.2 1.0 O A:HOH509 4.6 5.5 1.0 CB A:LEU177 4.7 14.1 1.0 CG A:LEU177 4.7 17.3 1.0 CE1 A:PHE191 4.7 14.0 1.0 C A:LEU166 4.8 16.3 1.0 C A:SER178 4.8 12.2 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the C. Elegans Nitfhit Protein


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 the C. Elegans Nitfhit Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na459 b:11.3 occ:1.00 SG A:CYS377 2.5 34.5 1.0 CB A:CYS377 3.4 25.8 1.0 CD2 A:HIS394 3.4 19.0 1.0 NE2 A:GLN379 3.6 32.2 1.0 CD A:GLN379 3.8 29.3 1.0 CG A:HIS394 3.9 19.9 1.0 NE2 A:HIS394 3.9 17.9 1.0 CG A:GLN379 4.1 26.0 1.0 OE1 A:GLN379 4.4 28.9 1.0 CB A:HIS394 4.4 18.7 1.0 CE1 A:HIS394 4.6 16.8 1.0 ND1 A:HIS394 4.6 20.0 1.0 CA A:CYS377 4.7 22.2 1.0 C A:CYS377 4.8 22.3 1.0 O A:CYS377 4.9 23.3 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the C. Elegans Nitfhit Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the C. Elegans Nitfhit Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na458 b:20.4 occ:1.00 OE2 B:GLU76 2.4 78.4 1.0 SG B:CYS75 2.6 65.7 1.0 CG B:MET71 2.8 62.3 1.0 CB B:CYS75 3.3 65.3 1.0 CB B:TYR77 3.5 52.8 1.0 CD B:GLU76 3.6 77.5 1.0 CB B:MET71 3.7 61.0 1.0 SD B:MET71 3.8 62.5 1.0 N B:TYR77 3.9 56.4 1.0 OE1 B:GLU76 4.2 80.4 1.0 CA B:TYR77 4.4 52.1 1.0 CA B:MET71 4.4 60.4 1.0 N B:GLU76 4.5 63.2 1.0 CG B:TYR77 4.6 52.6 1.0 CA B:CYS75 4.7 65.1 1.0 CG B:GLU76 4.8 73.2 1.0 C B:CYS75 4.9 64.1 1.0

H.C.Pace, S.C.Hodawadekar, A.Draganescu, J.Huang, P.Bieganowski, Y.Pekarsky, C.M.Croce, C.Brenner. Crystal Structure of the Worm Nitfhit Rosetta Stone Protein Reveals A Nit Tetramer Binding Two Fhit Dimers. Curr.Biol. V. 10 907 2000.
ISSN: ISSN 0960-9822
PubMed: 10959838
DOI: 10.1016/S0960-9822(00)00621-7