Sodium in PDB 3ipp: Crystal Structure of Sulfur-Free Ynje

All present enzymatic activity of Crystal Structure of Sulfur-Free Ynje:
2.8.1.1;

The structure of Crystal Structure of Sulfur-Free Ynje, PDB code: 3ipp 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)	46.41 / 2.40
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	160.250, 160.250, 170.821, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 21.4

The binding sites of Sodium atom in the Crystal Structure of Sulfur-Free Ynje (pdb code 3ipp). 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 Sulfur-Free Ynje, PDB code: 3ipp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Sulfur-Free 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 Sulfur-Free Ynje within 5.0Å range: probe atom residue distance (Å) B Occ A:Na438 b:37.9 occ:1.00 O A:HOH594 2.3 25.5 1.0 O A:ASP410 2.3 23.5 1.0 O A:THR387 2.4 30.4 1.0 O A:TRP203 2.5 30.1 1.0 OD1 A:ASP410 2.5 27.0 1.0 OD1 A:ASN204 2.5 27.8 1.0 C A:ASP410 3.1 23.0 1.0 C A:TRP203 3.3 30.9 1.0 C A:THR387 3.3 29.9 1.0 CG A:ASP410 3.5 24.2 1.0 CG A:ASN204 3.7 29.7 1.0 CA A:ASN204 3.7 28.9 1.0 CA A:THR387 3.7 30.8 1.0 N A:ASN204 3.7 29.3 1.0 O A:LEU202 3.8 35.3 1.0 CB A:THR387 3.9 32.3 1.0 N A:GLY411 3.9 22.8 1.0 NH2 A:ARG238 3.9 26.8 1.0 CA A:ASP410 3.9 22.8 1.0 CA A:GLY411 4.1 21.7 1.0 CB A:ASP410 4.2 22.8 1.0 CB A:ASN204 4.3 28.6 1.0 OD2 A:ASP410 4.3 25.4 1.0 CA A:TRP203 4.4 32.3 1.0 C A:GLY411 4.5 21.8 1.0 N A:GLY388 4.5 29.3 1.0 NH1 A:ARG238 4.5 24.7 1.0 CZ A:ARG238 4.6 29.6 1.0 O A:GLY411 4.6 21.3 1.0 CB A:TRP203 4.6 32.7 1.0 C A:LEU202 4.7 34.7 1.0 ND2 A:ASN204 4.7 30.9 1.0 OG1 A:THR387 4.8 33.3 1.0 O A:HOH487 4.8 24.8 1.0 CG2 A:THR387 4.8 31.8 1.0 CA A:GLY388 4.8 27.5 1.0 C A:ASN204 4.9 27.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Sulfur-Free 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 Sulfur-Free Ynje within 5.0Å range: probe atom residue distance (Å) B Occ B:Na436 b:37.7 occ:1.00 O B:ASP410 2.2 23.3 1.0 O B:THR387 2.3 30.5 1.0 O B:HOH444 2.4 33.2 1.0 OD1 B:ASN204 2.5 32.5 1.0 OD1 B:ASP410 2.6 27.9 1.0 O B:TRP203 2.6 32.9 1.0 C B:ASP410 3.1 24.4 1.0 C B:THR387 3.2 30.4 1.0 C B:TRP203 3.4 34.6 1.0 CG B:ASP410 3.4 26.0 1.0 CA B:THR387 3.6 30.5 1.0 NH2 B:ARG238 3.6 25.6 1.0 CG B:ASN204 3.7 34.0 1.0 CA B:ASN204 3.7 32.5 1.0 CB B:THR387 3.8 30.7 1.0 N B:ASN204 3.8 33.4 1.0 O B:LEU202 3.9 37.9 1.0 CA B:ASP410 3.9 24.5 1.0 N B:GLY411 4.0 24.1 1.0 CA B:GLY411 4.1 23.0 1.0 CB B:ASP410 4.1 24.5 1.0 OD2 B:ASP410 4.2 27.9 1.0 O B:HOH665 4.3 35.2 1.0 CB B:ASN204 4.3 32.7 1.0 N B:GLY388 4.4 30.7 1.0 C B:GLY411 4.4 23.5 1.0 O B:GLY411 4.4 24.5 1.0 CZ B:ARG238 4.5 26.7 1.0 CA B:TRP203 4.6 35.4 1.0 OG1 B:THR387 4.6 29.2 1.0 NH1 B:ARG238 4.6 25.0 1.0 CA B:GLY388 4.7 29.7 1.0 CB B:TRP203 4.8 36.0 1.0 ND2 B:ASN204 4.8 33.6 1.0 O B:HOH511 4.8 30.8 1.0 C B:LEU202 4.8 38.3 1.0 CG2 B:THR387 4.9 32.1 1.0 C B:ASN204 4.9 31.5 1.0 N B:THR387 5.0 30.3 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