Sodium in the structure of Crystal Structure of Molybdopterin Converting Factor Subunit 2 (AQ_2181) From Aquifex Aeolicus VF5 (pdb 2omd)

The binding sites of Sodium atom in the structure of Crystal Structure of Molybdopterin Converting Factor Subunit 2 (AQ_2181) From Aquifex Aeolicus VF5 (pdb code 2omd). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2omd structure was solved by J.JEYAKANTHAN, S.P.KANAUJIA, C.VASUKI RANJANI, K.SEKAR, Y.AGARI, A.EBIHARA, S.KURAMITSU, A.SHINKAI, Y.SHIRO, S.YOKOYAMA, RIKEN STRUCTURALGENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 38.9-2.0 Space group P6122 a (A) 119.995 b (A) 119.995 c (A) 125.804 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19 Rfree (%) 21.5 Sodium Binding Sites: Sodium binding site 1 out of 2 in 2omd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2omd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Trp15, A: Gly17, A: Ala18, A: Glu19, A: Leu38, A: Pro97, A: Leu100, A: Hoh810, A: Hoh823, A: Hoh869, conact list: Atom Atom Distance (A) Na CD1 A:Trp15 4.35 Na CZ2 A:Trp15 4.38 Na CE2 A:Trp15 4.20 Na NE1 A:Trp15 3.36 Na N A:Gly17 4.94 Na C A:Gly17 3.96 Na CA A:Gly17 3.68 Na N A:Ala18 3.21 Na CB A:Ala18 3.94 Na CA A:Ala18 4.19 Na OE1 A:Glu19 4.11 Na CD1 A:Leu38 4.52 Na CD2 A:Leu38 4.20 Na CB A:Pro97 3.76 Na CD A:Pro97 4.36 Na CG A:Pro97 3.71 Na CD1 A:Leu100 4.47 Na O A:Hoh810 3.12 Na O A:Hoh823 2.95 Na O A:Hoh869 4.57 interactive model: Sodium binding site 2 out of 2 in 2omd Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2omd. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Trp15, B: Gly17, B: Ala18, B: Glu19, B: Leu38, B: Pro97, B: Leu100, B: Hoh754, B: Hoh755, B: Hoh837, B: Hoh848, conact list: Atom Atom Distance (A) Na CD1 B:Trp15 4.28 Na CZ2 B:Trp15 4.31 Na CE2 B:Trp15 4.13 Na NE1 B:Trp15 3.29 Na N B:Gly17 4.94 Na C B:Gly17 3.93 Na CA B:Gly17 3.68 Na N B:Ala18 3.16 Na CB B:Ala18 3.88 Na CA B:Ala18 4.13 Na OE1 B:Glu19 3.97 Na CD B:Glu19 4.95 Na CD1 B:Leu38 4.37 Na CD2 B:Leu38 4.10 Na CG B:Leu38 4.91 Na CB B:Pro97 3.87 Na CD B:Pro97 4.58 Na CG B:Pro97 3.85 Na CD1 B:Leu100 4.60 Na O B:Hoh754 3.20 Na O B:Hoh755 4.23 Na O B:Hoh837 3.00 Na O B:Hoh848 4.50 interactive model: