Sodium in PDB 1m65: Ycdx Protein

The structure of Ycdx Protein, PDB code: 1m65 was solved by A.Teplyakov, G.Obmolova, P.P.Khil, R.D.Camerini-Otero, 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)	10.00 / 1.57
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.230, 77.230, 79.990, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 20.8

The structure of Ycdx Protein also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Ycdx Protein (pdb code 1m65). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ycdx Protein, PDB code: 1m65:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Ycdx Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ycdx Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:15.7 occ:1.00 O A:HOH562 2.0 26.4 1.0 OD1 A:ASP192 2.1 20.3 1.0 NE2 A:HIS9 2.2 15.1 1.0 OE1 A:GLU73 2.3 17.3 1.0 NE2 A:HIS7 2.4 20.4 1.0 CG A:ASP192 3.0 22.6 1.0 CE1 A:HIS9 3.0 16.1 1.0 CE1 A:HIS7 3.2 18.4 1.0 CD2 A:HIS9 3.3 14.9 1.0 OD2 A:ASP192 3.3 26.1 1.0 CD A:GLU73 3.3 21.2 1.0 CD2 A:HIS7 3.4 22.7 1.0 NA A:NA302 3.4 17.9 1.0 OE2 A:GLU73 3.8 20.6 1.0 CE1 A:HIS40 3.8 22.9 1.0 CE1 A:HIS194 4.0 18.8 1.0 ND1 A:HIS9 4.2 13.6 1.0 NE2 A:HIS40 4.3 13.1 1.0 ND1 A:HIS7 4.3 17.8 1.0 CB A:ASP192 4.3 18.9 1.0 CG A:HIS9 4.3 13.8 1.0 O A:HOH572 4.3 27.8 1.0 CG A:HIS7 4.4 16.4 1.0 ZN A:ZN300 4.5 20.0 1.0 NE2 A:HIS194 4.5 16.9 1.0 CG A:GLU73 4.5 14.7 1.0 CA A:ASP192 4.7 16.3 1.0 ND1 A:HIS40 4.7 16.3 1.0 CB A:GLU73 4.8 13.4 1.0

Sodium binding site 2 out of 3 in the Ycdx Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ycdx Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:17.9 occ:1.00 O A:HOH562 1.7 26.4 1.0 NE2 A:HIS101 2.2 27.7 1.0 OE2 A:GLU73 2.3 20.6 1.0 NE2 A:HIS131 2.4 34.4 1.0 CE1 A:HIS101 2.8 22.5 1.0 CD A:GLU73 3.0 21.2 1.0 OE1 A:GLU73 3.0 17.3 1.0 CD2 A:HIS131 3.3 28.2 1.0 CE1 A:HIS131 3.4 39.0 1.0 NA A:NA301 3.4 15.7 1.0 CD2 A:HIS101 3.4 23.1 1.0 CE1 A:HIS40 4.0 22.9 1.0 ND1 A:HIS101 4.0 22.2 1.0 O A:HOH572 4.3 27.8 1.0 OD2 A:ASP192 4.3 26.1 1.0 CG A:HIS101 4.4 17.0 1.0 CG A:GLU73 4.4 14.7 1.0 CG A:HIS131 4.4 23.8 1.0 OG A:SER130 4.5 19.2 1.0 ND1 A:HIS131 4.5 38.0 1.0 CE1 A:HIS7 4.6 18.4 1.0 ND1 A:HIS40 4.6 16.3 1.0 NE2 A:HIS7 4.7 20.4 1.0 OD1 A:ASP192 4.8 20.3 1.0 CB A:SER130 5.0 17.7 1.0 CG A:ASP192 5.0 22.6 1.0

Sodium binding site 3 out of 3 in the Ycdx Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ycdx Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:32.6 occ:1.00 O A:HOH641 2.3 35.2 1.0 O A:LEU93 2.4 17.5 1.0 O A:HOH599 2.5 30.1 1.0 O A:PHE90 2.5 20.2 1.0 O A:HOH533 2.6 21.8 1.0 O A:HOH592 2.7 29.4 1.0 C A:LEU93 3.6 16.0 1.0 C A:PHE90 3.6 19.9 1.0 O A:HOH530 3.9 21.1 1.0 O A:HOH770 4.1 46.8 1.0 N A:LEU93 4.3 13.6 1.0 O A:HOH673 4.4 38.2 1.0 CA A:PHE90 4.4 19.1 1.0 CA A:LEU93 4.4 15.0 1.0 O A:HOH525 4.4 19.6 1.0 N A:ASP94 4.6 13.5 1.0 N A:ASP91 4.6 18.8 1.0 C A:ASP91 4.6 18.2 1.0 CA A:ASP91 4.6 19.5 1.0 O A:ASP91 4.7 20.8 1.0 CB A:PHE90 4.7 21.8 1.0 CA A:ASP94 4.7 14.6 1.0 CB A:LEU93 4.8 13.3 1.0 O A:HOH796 5.0 49.6 1.0

A.Teplyakov, G.Obmolova, P.P.Khil, A.J.Howard, R.D.Camerini-Otero, G.L.Gilliland. Crystal Structure of the Escherichia Coli Ycdx Protein Reveals A Trinuclear Zinc Active Site Proteins: V. 51 315 2003STRUCT.,Funct.,Genet..
ISSN: ISSN 0887-3585
PubMed: 12661000
DOI: 10.1002/PROT.10352