Sodium in PDB 2omd: Crystal Structure of Molybdopterin Converting Factor Subunit 2 (AQ_2181) From Aquifex Aeolicus VF5

The structure of Crystal Structure of Molybdopterin Converting Factor Subunit 2 (AQ_2181) From Aquifex Aeolicus VF5, PDB code: 2omd 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. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.89 / 2.00
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	119.995, 119.995, 125.804, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 21.5

The structure of Crystal Structure of Molybdopterin Converting Factor Subunit 2 (AQ_2181) From Aquifex Aeolicus VF5 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Molybdopterin Converting Factor Subunit 2 (AQ_2181) From Aquifex Aeolicus VF5 (pdb code 2omd). 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 Molybdopterin Converting Factor Subunit 2 (AQ_2181) From Aquifex Aeolicus VF5, PDB code: 2omd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Molybdopterin Converting Factor Subunit 2 (AQ_2181) From Aquifex Aeolicus VF5


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 Molybdopterin Converting Factor Subunit 2 (AQ_2181) From Aquifex Aeolicus VF5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:14.2 occ:1.00 O A:HOH823 3.0 51.8 1.0 O A:HOH810 3.1 28.2 1.0 N A:ALA18 3.2 18.0 1.0 NE1 A:TRP15 3.4 19.1 1.0 CA A:GLY17 3.7 19.3 1.0 CG A:PRO97 3.7 23.9 1.0 CB A:PRO97 3.8 21.4 1.0 CB A:ALA18 3.9 16.4 1.0 C A:GLY17 4.0 18.4 1.0 OE1 A:GLU19 4.1 33.2 1.0 CA A:ALA18 4.2 18.9 1.0 CD2 A:LEU38 4.2 19.2 1.0 CE2 A:TRP15 4.2 21.0 1.0 CD1 A:TRP15 4.4 19.7 1.0 CD A:PRO97 4.4 23.3 1.0 CZ2 A:TRP15 4.4 19.3 1.0 CD1 A:LEU100 4.5 19.1 1.0 CD1 A:LEU38 4.5 20.3 1.0 O A:HOH869 4.6 50.0 1.0 N A:GLY17 4.9 19.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Molybdopterin Converting Factor Subunit 2 (AQ_2181) From Aquifex Aeolicus VF5


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 Molybdopterin Converting Factor Subunit 2 (AQ_2181) From Aquifex Aeolicus VF5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na702 b:17.6 occ:1.00 O B:HOH837 3.0 50.5 1.0 N B:ALA18 3.2 18.6 1.0 O B:HOH754 3.2 26.5 1.0 NE1 B:TRP15 3.3 22.9 1.0 CA B:GLY17 3.7 21.1 1.0 CG B:PRO97 3.9 20.6 1.0 CB B:PRO97 3.9 20.4 1.0 CB B:ALA18 3.9 18.1 1.0 C B:GLY17 3.9 20.6 1.0 OE1 B:GLU19 4.0 36.5 1.0 CD2 B:LEU38 4.1 18.2 1.0 CE2 B:TRP15 4.1 21.0 1.0 CA B:ALA18 4.1 18.8 1.0 O B:HOH755 4.2 43.0 1.0 CD1 B:TRP15 4.3 20.4 1.0 CZ2 B:TRP15 4.3 22.5 1.0 CD1 B:LEU38 4.4 16.4 1.0 O B:HOH848 4.5 60.4 1.0 CD B:PRO97 4.6 21.8 1.0 CD1 B:LEU100 4.6 17.3 1.0 CG B:LEU38 4.9 17.1 1.0 N B:GLY17 4.9 18.9 1.0 CD B:GLU19 4.9 38.1 1.0

J.Jeyakanthan, S.P.Kanaujia, C.Vasuki Ranjani, K.Sekar, Y.Agari, A.Ebihara, S.Kuramitsu, A.Shinkai, Y.Shiro, S.Yokoyama. Crystal Structure of Molybdopterin Converting Factor Subunit 2 (AQ_2181) From Aquifex Aeolicus VF5 To Be Published.