Sodium in PDB 2pmh: Crystal Structure of THR132ALA of ST1022 From Sulfolobus Tokodaii

The structure of Crystal Structure of THR132ALA of ST1022 From Sulfolobus Tokodaii, PDB code: 2pmh was solved by T.S.Kumarevel, P.Karthe, N.Nakano, A.Shinkai, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 1.90
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	103.697, 103.697, 74.939, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 24.4

The structure of Crystal Structure of THR132ALA of ST1022 From Sulfolobus Tokodaii also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of THR132ALA of ST1022 From Sulfolobus Tokodaii (pdb code 2pmh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of THR132ALA of ST1022 From Sulfolobus Tokodaii, PDB code: 2pmh:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of THR132ALA of ST1022 From Sulfolobus Tokodaii


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 THR132ALA of ST1022 From Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1002 b:66.6 occ:1.00 O A:HOH1051 4.1 52.7 1.0 CG1 A:ILE140 4.2 39.0 1.0 CD1 A:ILE140 4.3 40.4 1.0 CG1 A:ILE64 4.4 33.3 1.0 O A:VAL137 4.6 32.0 1.0 O A:VAL138 4.8 33.9 1.0 N A:ILE140 4.8 35.5 1.0 C A:VAL138 4.8 35.5 1.0 N A:LYS139 4.9 35.0 1.0 O A:ASP62 5.0 42.9 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of THR132ALA of ST1022 From Sulfolobus Tokodaii


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 THR132ALA of ST1022 From Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1003 b:53.3 occ:0.50 O A:HOH1027 4.0 49.9 1.0 OG A:SER68 4.0 38.1 1.0 OD2 A:ASP100 4.3 54.4 1.0 CD1 A:ILE104 4.3 35.2 1.0 OE1 A:GLN135 4.7 51.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of THR132ALA of ST1022 From Sulfolobus Tokodaii


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 THR132ALA of ST1022 From Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1004 b:60.8 occ:1.00 CG A:PHE96 4.1 36.2 1.0 CZ A:PHE103 4.3 32.9 1.0 CB A:PHE96 4.3 36.0 1.0 CD1 A:PHE96 4.3 38.6 1.0 CG2 A:VAL79 4.3 45.5 1.0 CD2 A:PHE96 4.4 39.5 1.0 CE1 A:PHE103 4.5 36.1 1.0 O A:HOH1031 4.5 51.5 1.0 CA A:VAL79 4.7 42.6 1.0 N A:VAL79 4.7 41.6 1.0 CB A:HIS78 4.8 38.0 1.0 C A:HIS78 4.8 40.4 1.0 O A:HIS78 4.8 38.8 1.0 CE1 A:PHE96 4.9 40.2 1.0 CE2 A:PHE96 5.0 41.0 1.0

T.S.Kumarevel, N.Nakano, K.Ponnuraj, S.C.B.Gopinath, K.Sakamoto, A.Shinkai, P.K.R.Kumar, S.Yokoyama. Crystal Structure of Glutamine Receptor Protein From Sulfolobus Tokodaii Strain 7 in Complex with Its Effector L-Glutamine: Implications of Effector Binding in Molecular Association and Dna Binding Nucleic Acids Res. V. 36 4808 2008.
ISSN: ISSN 0305-1048
PubMed: 18653535
DOI: 10.1093/NAR/GKN456