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

Protein crystallography data

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

Other elements in 2omd:

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

Sodium Binding Sites:

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 2omd

Go back to Sodium Binding Sites List in 2omd
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 2omd

Go back to Sodium Binding Sites List in 2omd
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

Reference:

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.
Page generated: Tue Dec 15 05:52:32 2020

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