Sodium in PDB 1ye8: Crystal Structure of THEP1 From the Hyperthermophile Aquifex Aeolicus

The structure of Crystal Structure of THEP1 From the Hyperthermophile Aquifex Aeolicus, PDB code: 1ye8 was solved by M.Rossbach, O.Daumke, C.Klinger, A.Wittinghofer, M.Kaufmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.21 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.870, 64.240, 39.620, 90.00, 105.23, 90.00
R / Rfree (%)	17.2 / 20.7

The structure of Crystal Structure of THEP1 From the Hyperthermophile Aquifex Aeolicus also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of THEP1 From the Hyperthermophile Aquifex Aeolicus (pdb code 1ye8). 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 THEP1 From the Hyperthermophile Aquifex Aeolicus, PDB code: 1ye8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of THEP1 From the Hyperthermophile 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 THEP1 From the Hyperthermophile Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1003 b:33.9 occ:1.00 O3 A:PO41001 2.0 23.5 1.0 NZ A:LYS13 2.3 21.1 1.0 O A:GLU8 2.5 14.6 1.0 O A:HOH1247 3.0 35.6 1.0 O4 A:PO41001 3.0 26.5 1.0 P A:PO41001 3.0 24.6 1.0 C A:GLU8 3.3 14.7 1.0 N A:GLY10 3.4 15.9 1.0 CE A:LYS13 3.4 18.3 1.0 CA A:PRO9 3.4 16.2 1.0 CG A:LYS13 3.6 12.7 1.0 C A:PRO9 3.7 15.7 1.0 N A:PRO9 3.7 15.6 1.0 O1 A:PO41001 3.8 18.0 1.0 N A:VAL11 3.8 15.0 1.0 CD A:LYS13 3.8 14.8 1.0 O A:GLY7 3.9 12.9 1.0 CG1 A:VAL11 3.9 13.2 1.0 CB A:LYS13 4.2 12.6 1.0 O2 A:PO41001 4.2 25.4 1.0 O A:HOH1246 4.2 22.8 1.0 O A:HOH1161 4.2 38.6 1.0 O A:HOH1252 4.2 17.6 0.5 C A:GLY7 4.3 12.4 1.0 N A:LYS13 4.4 12.8 1.0 CA A:GLY10 4.4 16.4 1.0 N A:GLY12 4.5 13.9 1.0 C A:GLY10 4.6 15.4 1.0 CA A:GLU8 4.6 14.0 1.0 N A:GLU8 4.6 12.8 1.0 CB A:VAL11 4.7 13.9 1.0 CA A:VAL11 4.7 14.2 1.0 O A:PRO9 4.7 16.4 1.0 CB A:PRO9 4.8 16.6 1.0 O A:HOH1067 4.9 16.0 1.0 CA A:LYS13 4.9 12.5 1.0 O A:HOH1028 5.0 18.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of THEP1 From the Hyperthermophile 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 THEP1 From the Hyperthermophile Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1004 b:29.5 occ:1.00 O A:HOH1250 1.8 19.4 1.0 O2 A:PO41001 2.0 25.4 1.0 O A:HOH1227 2.5 19.9 1.0 P A:PO41001 3.0 24.6 1.0 O1 A:PO41001 3.2 18.0 1.0 O4 A:PO41001 3.6 26.5 1.0 O A:HOH1082 3.9 21.9 1.0 CA A:GLY12 4.1 14.0 1.0 CB A:THR14 4.2 13.1 1.0 O3 A:PO41001 4.2 23.5 1.0 OG1 A:THR15 4.3 17.9 1.0 MG A:MG1002 4.3 21.1 1.0 O A:HOH1251 4.3 35.2 1.0 N A:GLY12 4.4 13.9 1.0 N A:THR14 4.5 12.6 1.0 C A:GLY12 4.6 13.4 1.0 N A:THR15 4.6 14.2 1.0 OG1 A:THR14 4.6 13.2 1.0 N A:LYS13 4.7 12.8 1.0 O A:HOH1252 4.7 17.6 0.5 O A:HOH1252 4.8 26.4 0.5 CA A:THR14 4.9 12.8 1.0 OE1 A:GLU35 5.0 22.8 1.0 O A:GLY10 5.0 16.4 1.0 CA A:GLY10 5.0 16.4 1.0

M.Rossbach, O.Daumke, C.Klinger, A.Wittinghofer, M.Kaufmann. Crystal Structure of THEP1 From the Hyperthermophile Aquifex Aeolicus: A Variation of the Reca Fold Bmc Struct.Biol. V. 5 7 2005.
ISSN: ESSN 1472-6807
PubMed: 15777481
DOI: 10.1186/1472-6807-5-7