Sodium in PDB 3ipo: Crystal Structure of Ynje

All present enzymatic activity of Crystal Structure of Ynje:
2.8.1.1;

The structure of Crystal Structure of Ynje, PDB code: 3ipo was solved by P.Haenzelmann, J.Kuper, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.00 / 2.40
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	160.949, 160.949, 173.992, 90.00, 90.00, 120.00
R / Rfree (%)	15.9 / 21.1

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

Sodium binding site 1 out of 2 in the Crystal Structure of Ynje


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 Ynje within 5.0Å range: probe atom residue distance (Å) B Occ A:Na436 b:36.0 occ:1.00 O A:ASP410 2.3 29.4 1.0 O A:THR387 2.4 31.9 1.0 OD1 A:ASN204 2.4 31.6 1.0 OD1 A:ASP410 2.5 27.6 1.0 O A:HOH594 2.5 29.7 1.0 O A:TRP203 2.6 30.1 1.0 C A:ASP410 3.0 29.1 1.0 C A:THR387 3.3 32.9 1.0 CG A:ASP410 3.4 30.9 1.0 C A:TRP203 3.4 31.6 1.0 CG A:ASN204 3.6 31.2 1.0 CA A:ASN204 3.7 31.0 1.0 CA A:THR387 3.8 33.5 1.0 N A:GLY411 3.8 29.6 1.0 N A:ASN204 3.8 30.6 1.0 NH2 A:ARG238 3.9 30.7 1.0 CA A:ASP410 3.9 28.9 1.0 CA A:GLY411 3.9 28.1 1.0 O A:LEU202 4.0 36.2 1.0 CB A:ASP410 4.1 29.7 1.0 CB A:THR387 4.1 34.0 1.0 O A:HOH544 4.2 41.2 1.0 CB A:ASN204 4.3 31.4 1.0 OD2 A:ASP410 4.3 31.8 1.0 C A:GLY411 4.3 29.0 1.0 N A:GLY388 4.3 33.0 1.0 O A:GLY411 4.4 29.3 1.0 NH1 A:ARG238 4.5 31.2 1.0 CZ A:ARG238 4.6 33.7 1.0 CA A:TRP203 4.6 32.8 1.0 CA A:GLY388 4.6 31.5 1.0 ND2 A:ASN204 4.6 29.8 1.0 CB A:TRP203 4.8 33.3 1.0 O A:HOH531 4.8 30.1 1.0 C A:LEU202 4.8 35.2 1.0 OG1 A:THR387 4.9 36.6 1.0 C A:ASN204 5.0 30.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Ynje


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 Ynje within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1 b:37.6 occ:1.00 O B:ASP410 2.3 31.1 1.0 O B:THR387 2.3 31.6 1.0 O B:HOH598 2.4 31.6 1.0 OD1 B:ASP410 2.4 31.5 1.0 O B:TRP203 2.4 34.6 1.0 OD1 B:ASN204 2.5 36.4 1.0 C B:ASP410 3.2 30.9 1.0 C B:THR387 3.2 31.4 1.0 C B:TRP203 3.3 34.3 1.0 CG B:ASP410 3.4 30.8 1.0 NH2 B:ARG238 3.6 29.4 1.0 CA B:ASN204 3.6 33.0 1.0 CG B:ASN204 3.7 33.5 1.0 CA B:THR387 3.7 31.1 1.0 N B:ASN204 3.8 33.4 1.0 O B:LEU202 3.9 36.1 1.0 CA B:ASP410 4.0 30.5 1.0 N B:GLY411 4.1 30.6 1.0 CB B:THR387 4.1 31.6 1.0 OD2 B:ASP410 4.1 29.8 1.0 CA B:GLY411 4.1 29.8 1.0 CB B:ASP410 4.2 30.2 1.0 CB B:ASN204 4.3 33.3 1.0 O B:HOH696 4.3 37.2 1.0 N B:GLY388 4.3 30.5 1.0 CZ B:ARG238 4.4 31.2 1.0 CA B:TRP203 4.5 34.7 1.0 C B:GLY411 4.5 30.1 1.0 NH1 B:ARG238 4.6 23.9 1.0 O B:GLY411 4.6 30.2 1.0 CA B:GLY388 4.7 30.3 1.0 CB B:TRP203 4.7 34.9 1.0 ND2 B:ASN204 4.8 32.9 1.0 C B:ASN204 4.8 32.5 1.0 C B:LEU202 4.8 36.4 1.0 OG1 B:THR387 4.9 33.7 1.0

P.Hanzelmann, J.U.Dahl, J.Kuper, A.Urban, U.Muller-Theissen, S.Leimkuhler, H.Schindelin. Crystal Structure of Ynje From Escherichia Coli, A Sulfurtransferase with Three Rhodanese Domains. Protein Sci. V. 18 2480 2009.
ISSN: ISSN 0961-8368
PubMed: 19798741
DOI: 10.1002/PRO.260