Sodium in PDB 2wqk: Crystal Structure of Sure Protein From Aquifex Aeolicus

All present enzymatic activity of Crystal Structure of Sure Protein From Aquifex Aeolicus:
3.1.3.5;

The structure of Crystal Structure of Sure Protein From Aquifex Aeolicus, PDB code: 2wqk was solved by S.V.Antonyuk, M.J.Ellis, R.W.Strange, S.S.Hasnain, Y.Bessho, S.Kuramitsu, S.Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.47 / 1.50
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	65.006, 65.006, 239.194, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / 19.1

The binding sites of Sodium atom in the Crystal Structure of Sure Protein From Aquifex Aeolicus (pdb code 2wqk). 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 Sure Protein From Aquifex Aeolicus, PDB code: 2wqk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Sure Protein From Aquifex Aeolicus


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 Sure Protein From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na254 b:16.7 occ:1.00 OD1 A:ASN94 2.3 13.8 1.0 OD1 A:ASP10 2.3 18.6 1.0 OG A:SER40 2.4 21.4 1.0 O2 A:SO4252 2.4 18.0 1.0 O A:HOH2161 2.4 26.4 1.0 O1 A:SO4252 2.7 19.0 1.0 S A:SO4252 3.1 15.8 1.0 CG A:ASN94 3.2 13.2 1.0 CG A:ASP10 3.3 16.4 1.0 CB A:SER40 3.5 21.2 1.0 ND2 A:ASN94 3.5 14.6 1.0 OD2 A:ASP10 3.6 18.0 1.0 O A:HOH2058 3.9 31.8 1.0 O3 A:SO4252 3.9 12.9 1.0 O4 A:SO4252 4.3 16.7 1.0 O A:HOH2314 4.3 53.6 1.0 CB A:ASP9 4.3 15.1 1.0 O A:HOH2176 4.3 16.1 1.0 OD2 A:ASP9 4.3 19.9 1.0 CA A:SER40 4.4 20.9 1.0 OG1 A:THR108 4.5 12.1 1.0 OD1 A:ASN38 4.5 19.8 1.0 O A:GLU95 4.6 21.8 1.0 CB A:ASP10 4.6 15.2 1.0 CB A:ASN94 4.7 12.6 1.0 N A:ASP10 4.7 14.0 1.0 N A:GLU95 4.7 15.4 1.0 C A:ASP9 4.7 14.4 1.0 CG A:ASP9 4.8 17.2 1.0 CA A:ASP10 4.9 14.9 1.0 O A:ASP9 4.9 15.8 1.0 N A:SER40 4.9 19.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Sure Protein From Aquifex Aeolicus


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 Sure Protein From Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na255 b:16.9 occ:1.00 OD1 B:ASN94 2.3 14.1 1.0 OD1 B:ASP10 2.4 19.2 1.0 OG B:SER40 2.4 22.0 1.0 O3 B:SO4252 2.4 18.8 1.0 O B:HOH2129 2.4 26.0 1.0 O2 B:SO4252 2.7 19.4 1.0 S B:SO4252 3.1 16.2 1.0 CG B:ASN94 3.2 12.8 1.0 CG B:ASP10 3.3 16.5 1.0 CB B:SER40 3.5 21.0 1.0 ND2 B:ASN94 3.5 14.4 1.0 OD2 B:ASP10 3.7 17.8 1.0 O B:HOH2132 3.9 36.1 1.0 O1 B:SO4252 4.0 13.5 1.0 OD2 B:ASP9 4.3 19.4 1.0 O4 B:SO4252 4.3 17.4 1.0 CB B:ASP9 4.3 14.8 1.0 O B:HOH2291 4.3 55.1 1.0 O B:HOH2145 4.3 16.9 1.0 CA B:SER40 4.3 20.6 1.0 OD1 B:ASN38 4.5 21.0 1.0 OG1 B:THR108 4.5 12.6 1.0 CB B:ASP10 4.6 14.6 1.0 O B:GLU95 4.7 22.0 1.0 N B:GLU95 4.7 15.3 1.0 CB B:ASN94 4.7 12.3 1.0 N B:ASP10 4.7 14.6 1.0 C B:ASP9 4.7 14.5 1.0 CG B:ASP9 4.8 16.8 1.0 CA B:ASP10 4.8 14.8 1.0 O B:ASP9 4.9 16.5 1.0 N B:SER40 4.9 18.8 1.0 ND2 B:ASN38 5.0 23.4 1.0

S.V.Antonyuk, M.J.Ellis, R.W.Strange, Y.Bessho, S.Kuramitsu, A.Shinkai, S.Yokoyama, S.S.Hasnain. Structure of Sure Protein From Aquifex Aeolicus VF5 at 1.5 A Resolution. Acta Crystallogr.,Sect.F V. 65 1204 2009.
ISSN: ESSN 1744-3091
PubMed: 20054112
DOI: 10.1107/S1744309109043814