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Sodium in PDB 6h08: The Crystal Structure of Engineered Cytochrome C Peroxidase From Saccharomyces Cerevisiae with A HIS175ME-His Proximal Ligand Substitution

Enzymatic activity of The Crystal Structure of Engineered Cytochrome C Peroxidase From Saccharomyces Cerevisiae with A HIS175ME-His Proximal Ligand Substitution

All present enzymatic activity of The Crystal Structure of Engineered Cytochrome C Peroxidase From Saccharomyces Cerevisiae with A HIS175ME-His Proximal Ligand Substitution:
1.11.1.5;

Protein crystallography data

The structure of The Crystal Structure of Engineered Cytochrome C Peroxidase From Saccharomyces Cerevisiae with A HIS175ME-His Proximal Ligand Substitution, PDB code: 6h08 was solved by M.Ortmayer, C.Levy, A.P.Green, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.86 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.920, 106.770, 163.720, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.5

Other elements in 6h08:

The structure of The Crystal Structure of Engineered Cytochrome C Peroxidase From Saccharomyces Cerevisiae with A HIS175ME-His Proximal Ligand Substitution also contains other interesting chemical elements:

Cobalt (Co) 6 atoms
Manganese (Mn) 1 atom
Iron (Fe) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of Engineered Cytochrome C Peroxidase From Saccharomyces Cerevisiae with A HIS175ME-His Proximal Ligand Substitution (pdb code 6h08). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Crystal Structure of Engineered Cytochrome C Peroxidase From Saccharomyces Cerevisiae with A HIS175ME-His Proximal Ligand Substitution, PDB code: 6h08:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6h08

Go back to Sodium Binding Sites List in 6h08
Sodium binding site 1 out of 2 in the The Crystal Structure of Engineered Cytochrome C Peroxidase From Saccharomyces Cerevisiae with A HIS175ME-His Proximal Ligand Substitution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Engineered Cytochrome C Peroxidase From Saccharomyces Cerevisiae with A HIS175ME-His Proximal Ligand Substitution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:17.6
occ:1.00
 OD2 A:ASP34 2.0 27.6 1.0
O A:HOH407 2.1 24.8 1.0
O A:HOH533 2.6 34.5 1.0
CG A:ASP34 3.0 29.9 1.0
OD1 A:ASP34 3.3 31.6 1.0
O A:HOH530 4.0 42.3 1.0
CB A:ASP34 4.3 35.0 1.0
O A:ARG31 4.4 36.3 1.0

Sodium binding site 2 out of 2 in 6h08

Go back to Sodium Binding Sites List in 6h08
Sodium binding site 2 out of 2 in the The Crystal Structure of Engineered Cytochrome C Peroxidase From Saccharomyces Cerevisiae with A HIS175ME-His Proximal Ligand Substitution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Engineered Cytochrome C Peroxidase From Saccharomyces Cerevisiae with A HIS175ME-His Proximal Ligand Substitution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:34.6
occ:1.00
 O B:HOH503 2.2 36.9 1.0
NE2 B:HIS3 2.3 46.7 1.0
NE2 B:HIS1 3.0 41.8 1.0
CD2 B:HIS3 3.1 43.0 1.0
CE1 B:HIS3 3.3 58.3 1.0
CD2 B:HIS1 3.9 52.7 1.0
CE1 B:HIS1 4.0 47.9 1.0
CG B:HIS3 4.3 52.4 1.0
ND1 B:HIS3 4.4 52.7 1.0
O B:HOH522 4.6 30.3 1.0

Reference:

M.Ortmayer, K.Fisher, J.Basran, E.M.Wolde-Michael, D.J.Heyes, C.Levy, S.Lovelock, E.L.Raven, S.Hay, S.E.J.Rigby, A.P.Green. Rewiring the Push-Pull Catalytic Machinery of A Haem Enzyme Using An Expanded Genetic Code To Be Published.
Page generated: Tue Oct 8 09:09:33 2024

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