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Sodium in PDB 5v01: Crystal Structure of the Competence Damage-Inducible Protein A (Coma) From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578

Protein crystallography data

The structure of Crystal Structure of the Competence Damage-Inducible Protein A (Coma) From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578, PDB code: 5v01 was solved by D.Borek, Z.Wawrzak, S.Grimshaw, J.Sandoval, E.Evdokimova, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.22 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.452, 90.433, 44.126, 90.00, 103.75, 90.00
R / Rfree (%) 12.4 / 16.1

Other elements in 5v01:

The structure of Crystal Structure of the Competence Damage-Inducible Protein A (Coma) From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578 also contains other interesting chemical elements:

Chlorine (Cl) 10 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Competence Damage-Inducible Protein A (Coma) From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578 (pdb code 5v01). 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 the Competence Damage-Inducible Protein A (Coma) From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578, PDB code: 5v01:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5v01

Go back to Sodium Binding Sites List in 5v01
Sodium binding site 1 out of 2 in the Crystal Structure of the Competence Damage-Inducible Protein A (Coma) From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578


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 the Competence Damage-Inducible Protein A (Coma) From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:36.2
occ:1.00
O A:SER163 2.3 19.4 0.5
O A:SER163 2.3 19.0 0.5
O A:HOH379 2.4 27.3 1.0
O A:HOH397 2.8 51.3 1.0
OG A:SER163 3.2 15.9 0.5
C A:SER163 3.3 14.6 0.5
C A:SER163 3.3 14.8 0.5
O A:HOH426 3.3 34.8 1.0
CA A:SER163 3.8 13.9 0.5
CA A:SER163 3.8 14.2 0.5
N A:ALA167 3.8 13.8 1.0
CB A:LEU166 3.9 13.5 1.0
OE2 A:GLU18 3.9 31.5 1.0
CB A:ALA167 4.0 18.3 1.0
CB A:SER163 4.1 14.5 0.5
CB A:SER163 4.2 14.8 0.5
C A:LEU166 4.3 13.7 1.0
CA A:ALA167 4.3 14.8 1.0
CB A:ALA22 4.3 15.9 1.0
CG A:GLU18 4.4 19.9 1.0
N A:GLU164 4.5 12.8 1.0
CA A:LEU166 4.5 13.0 1.0
CD A:GLU18 4.6 22.0 1.0
O A:HOH357 4.6 22.4 1.0
N A:LEU166 4.8 13.3 1.0
CA A:GLU164 4.9 13.7 1.0
OG A:SER163 5.0 15.5 0.5
O A:LEU166 5.0 15.5 1.0
CD1 A:LEU166 5.0 15.5 1.0

Sodium binding site 2 out of 2 in 5v01

Go back to Sodium Binding Sites List in 5v01
Sodium binding site 2 out of 2 in the Crystal Structure of the Competence Damage-Inducible Protein A (Coma) From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578


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 the Competence Damage-Inducible Protein A (Coma) From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na210

b:16.4
occ:1.00
O B:GLN48 1.7 20.5 0.5
O B:GLN48 1.7 20.0 0.5
O B:CYS46 2.3 14.4 1.0
O B:HOH409 2.4 22.2 1.0
OG1 B:THR51 2.4 12.8 1.0
O B:HOH408 2.4 30.8 1.0
C B:GLN48 3.0 15.7 0.5
C B:GLN48 3.0 15.1 0.5
C B:CYS46 3.3 13.1 1.0
CB B:THR51 3.5 11.7 1.0
C B:ALA47 3.8 14.5 1.0
N B:GLN48 3.8 15.2 0.5
N B:GLN48 3.8 15.8 0.5
O B:ALA47 4.0 17.5 1.0
N B:ALA49 4.0 17.5 1.0
N B:THR51 4.0 12.3 1.0
CA B:GLN48 4.0 16.4 0.5
CA B:GLN48 4.0 14.9 0.5
CA B:CYS46 4.1 12.6 1.0
C B:ALA49 4.1 20.8 1.0
N B:ALA47 4.1 12.5 1.0
CA B:ALA49 4.2 20.9 1.0
CZ A:PHE62 4.2 21.2 1.0
CA B:ALA47 4.3 14.0 1.0
O B:ALA49 4.3 27.2 1.0
O B:HOH422 4.3 36.2 1.0
O B:LEU45 4.3 12.0 1.0
CA B:THR51 4.4 11.4 1.0
N B:ASP50 4.5 17.0 1.0
CG2 B:THR51 4.6 12.4 1.0
CE2 A:PHE62 4.6 18.6 1.0
O A:HOH388 4.7 34.5 1.0
O B:HOH388 4.7 17.6 1.0
CB B:GLN48 4.9 13.8 0.5
CB B:GLN48 4.9 18.2 0.5

Reference:

D.Borek, D.Borek, Z.Wawrzak, S.Grimshaw, J.Sandoval, E.Evdokimova, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). N/A N/A.
Page generated: Tue Dec 15 11:43:25 2020

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