Sodium in PDB 4g1k: Crystal Structure of Triosephosphate Isomerase From Burkholderia Thailandensis

All present enzymatic activity of Crystal Structure of Triosephosphate Isomerase From Burkholderia Thailandensis:
5.3.1.1;

The structure of Crystal Structure of Triosephosphate Isomerase From Burkholderia Thailandensis, PDB code: 4g1k was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	79.510, 94.750, 170.610, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.2

The binding sites of Sodium atom in the Crystal Structure of Triosephosphate Isomerase From Burkholderia Thailandensis (pdb code 4g1k). 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 Triosephosphate Isomerase From Burkholderia Thailandensis, PDB code: 4g1k:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Triosephosphate Isomerase From Burkholderia Thailandensis


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 Triosephosphate Isomerase From Burkholderia Thailandensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:54.7 occ:1.00 O A:PHE223 2.4 30.2 1.0 O A:GLN225 2.5 31.0 1.0 O A:ILE228 2.6 27.6 1.0 O A:HOH543 2.7 38.8 1.0 C A:PHE223 3.6 31.5 1.0 C A:GLN225 3.6 32.0 1.0 C A:ILE228 3.8 25.3 1.0 C A:GLY224 4.0 34.9 1.0 N A:GLN225 4.1 32.1 1.0 O A:GLY224 4.2 34.5 1.0 CA A:GLY224 4.3 34.7 1.0 N A:ILE228 4.3 26.7 1.0 N A:GLY224 4.4 32.8 1.0 CA A:PRO226 4.4 31.2 1.0 C A:PRO226 4.4 31.6 1.0 O A:PRO226 4.5 31.5 1.0 CA A:GLN225 4.5 32.2 1.0 N A:PRO226 4.5 32.1 1.0 CA A:PHE223 4.5 31.2 1.0 CA A:ILE228 4.6 24.8 1.0 N A:ASP229 4.7 25.2 1.0 CA A:ASP229 4.8 25.0 1.0 CB A:ILE228 4.8 23.8 1.0 N A:ASP227 5.0 30.5 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Triosephosphate Isomerase From Burkholderia Thailandensis


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 Triosephosphate Isomerase From Burkholderia Thailandensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:32.2 occ:1.00 O B:PHE223 2.3 24.3 1.0 O B:HOH513 2.3 33.4 1.0 O B:ILE228 2.4 24.0 1.0 O B:GLN225 2.4 24.9 1.0 O B:HOH554 2.5 34.0 1.0 C B:PHE223 3.4 24.7 1.0 C B:ILE228 3.5 21.9 1.0 C B:GLN225 3.5 24.4 1.0 C B:GLY224 3.8 26.8 1.0 N B:GLN225 3.9 25.6 1.0 N B:ILE228 4.2 22.6 1.0 O B:GLY224 4.2 26.9 1.0 CA B:GLY224 4.2 26.6 1.0 N B:GLY224 4.2 26.6 1.0 CA B:PHE223 4.3 24.3 1.0 CA B:ILE228 4.3 21.6 1.0 CA B:GLN225 4.3 25.0 1.0 N B:PRO226 4.5 25.4 1.0 N B:ASP229 4.5 20.8 1.0 CA B:PRO226 4.5 25.6 1.0 C B:PRO226 4.5 26.4 1.0 CB B:ILE228 4.5 21.4 1.0 O B:PRO226 4.6 25.7 1.0 CA B:ASP229 4.7 19.6 1.0 CB B:PHE223 5.0 23.8 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Triosephosphate Isomerase From Burkholderia Thailandensis


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 Triosephosphate Isomerase From Burkholderia Thailandensis within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:41.8 occ:1.00 O C:HOH462 2.4 38.7 1.0 O C:PHE223 2.4 32.7 1.0 O C:ILE228 2.5 27.2 1.0 O C:GLN225 2.6 30.5 1.0 C C:PHE223 3.6 33.7 1.0 C C:ILE228 3.7 26.2 1.0 O C:HOH474 3.7 47.7 1.0 C C:GLN225 3.7 31.6 1.0 C C:GLY224 4.1 32.8 1.0 N C:GLN225 4.2 32.3 1.0 O C:GLY224 4.4 32.7 1.0 N C:ILE228 4.4 27.0 1.0 CA C:GLY224 4.4 34.0 1.0 N C:GLY224 4.4 34.9 1.0 CA C:PHE223 4.5 32.1 1.0 CA C:ILE228 4.5 25.8 1.0 CA C:PRO226 4.6 31.4 1.0 N C:ASP229 4.6 25.8 1.0 C C:PRO226 4.6 29.8 1.0 CA C:GLN225 4.6 32.5 1.0 O C:PRO226 4.6 28.0 1.0 N C:PRO226 4.6 31.5 1.0 CA C:ASP229 4.7 25.0 1.0 CB C:ILE228 4.8 25.6 1.0 OD2 C:ASP229 5.0 26.8 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Triosephosphate Isomerase From Burkholderia Thailandensis


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 Triosephosphate Isomerase From Burkholderia Thailandensis within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:49.3 occ:1.00 O D:HOH475 2.4 38.9 1.0 O D:HOH506 2.4 44.8 1.0 O D:ILE228 2.5 32.9 1.0 O D:GLN225 2.5 36.5 1.0 O D:PHE223 2.6 39.1 1.0 C D:ILE228 3.6 30.3 1.0 C D:GLN225 3.6 38.2 1.0 C D:PHE223 3.7 40.8 1.0 C D:GLY224 4.2 42.2 1.0 N D:ILE228 4.2 30.2 1.0 N D:GLN225 4.2 41.3 1.0 C D:PRO226 4.4 35.7 1.0 O D:PRO226 4.4 33.6 1.0 O D:GLY224 4.4 43.2 1.0 CA D:PRO226 4.4 38.9 1.0 CA D:ILE228 4.4 29.4 1.0 N D:PRO226 4.5 38.4 1.0 N D:ASP229 4.5 28.4 1.0 CA D:GLN225 4.5 39.7 1.0 CA D:GLY224 4.6 42.6 1.0 N D:GLY224 4.6 42.3 1.0 CA D:ASP229 4.6 27.3 1.0 CA D:PHE223 4.7 40.9 1.0 CB D:ILE228 4.7 29.4 1.0 OD2 D:ASP229 4.8 27.4 1.0 N D:ASP227 4.9 34.1 1.0

L.Baugh, L.A.Gallagher, R.Patrapuvich, M.C.Clifton, A.S.Gardberg, T.E.Edwards, B.Armour, D.W.Begley, S.H.Dieterich, D.M.Dranow, J.Abendroth, J.W.Fairman, D.Fox, B.L.Staker, I.Phan, A.Gillespie, R.Choi, S.Nakazawa-Hewitt, M.T.Nguyen, A.Napuli, L.Barrett, G.W.Buchko, R.Stacy, P.J.Myler, L.J.Stewart, C.Manoil, W.C.Van Voorhis. Combining Functional and Structural Genomics to Sample the Essential Burkholderia Structome. Plos One V. 8 53851 2013.
ISSN: ESSN 1932-6203
PubMed: 23382856
DOI: 10.1371/JOURNAL.PONE.0053851