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Cobalt 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:

Manganese (Mn) 1 atom
Iron (Fe) 3 atoms
Sodium (Na) 2 atoms

Cobalt Binding Sites:

The binding sites of Cobalt 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 Cobalt atom.
In total 6 binding sites of Cobalt 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 Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in 6h08

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Cobalt binding site 1 out of 6 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 Cobalt with other atoms in the Co 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:Co302

b:46.5
occ:1.00
 O A:HOH585 1.8 49.2 1.0
NE2 A:HIS60 2.0 47.6 1.0
NE2 A:HIS0 2.1 62.3 1.0
O A:HOH524 2.1 44.0 1.0
NE2 A:HIS2 2.3 40.9 1.0
CE1 A:HIS0 2.9 67.5 1.0
CE1 A:HIS2 3.0 47.4 1.0
CD2 A:HIS60 3.0 38.9 1.0
CE1 A:HIS60 3.0 48.6 1.0
CD2 A:HIS0 3.2 81.4 1.0
CD2 A:HIS2 3.4 36.0 1.0
ND1 A:HIS0 4.0 67.0 1.0
O A:HOH608 4.0 53.3 1.0
ND1 A:HIS60 4.1 45.8 1.0
CG A:HIS60 4.1 46.4 1.0
ND1 A:HIS2 4.2 43.4 1.0
CG A:HIS0 4.2 80.6 1.0
CG A:HIS2 4.4 36.8 1.0

Cobalt binding site 2 out of 6 in 6h08

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Cobalt binding site 2 out of 6 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 Cobalt with other atoms in the Co 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:Co303

b:31.1
occ:0.50
 ND1 B:HIS-1 2.2 51.6 1.0
O B:HOH588 2.2 45.3 1.0
N B:HIS-1 2.2 70.6 1.0
O B:HOH589 2.3 29.5 1.0
CB B:HIS-2 2.8 98.2 1.0
CD2 B:HIS-2 2.9 76.2 1.0
C B:HIS-2 2.9 82.8 1.0
CG B:HIS-1 2.9 66.9 1.0
CG B:HIS-2 3.0 96.5 1.0
CA B:HIS-2 3.0 81.9 1.0
CB B:HIS-1 3.1 63.2 1.0
CA B:HIS-1 3.1 66.2 1.0
N B:HIS-2 3.2 85.6 1.0
CE1 B:HIS-1 3.3 64.4 1.0
O B:HIS-1 3.6 50.5 1.0
C B:HIS-1 3.7 64.2 1.0
NE2 B:HIS-2 4.0 69.6 1.0
O B:HIS-2 4.1 67.6 1.0
CD2 B:HIS-1 4.2 58.9 1.0
ND1 B:HIS-2 4.2 0.4 1.0
NE2 B:HIS-1 4.3 55.7 1.0
CE1 B:HIS-2 4.7 95.5 1.0
N B:HIS0 5.0 60.0 1.0

Cobalt binding site 3 out of 6 in 6h08

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Cobalt binding site 3 out of 6 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 Cobalt with other atoms in the Co binding site number 3 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:Co304

b:44.1
occ:1.00
 O B:HOH550 2.0 45.6 1.0
NE2 B:HIS0 2.1 56.0 1.0
O B:HOH561 2.2 45.9 1.0
NE2 B:HIS2 2.3 46.4 1.0
NE2 B:HIS60 2.3 38.2 1.0
O B:HOH534 2.3 42.5 1.0
CE1 B:HIS2 3.0 54.3 1.0
CE1 B:HIS0 3.0 59.9 1.0
CD2 B:HIS0 3.1 51.0 1.0
CD2 B:HIS60 3.1 37.0 1.0
CE1 B:HIS60 3.3 49.4 1.0
CD2 B:HIS2 3.4 44.4 1.0
ND1 B:HIS0 4.1 58.9 1.0
ND1 B:HIS2 4.2 50.4 1.0
CG B:HIS0 4.2 53.8 1.0
CG B:HIS60 4.3 45.9 1.0
ND1 B:HIS60 4.4 39.0 1.0
CG B:HIS2 4.4 44.4 1.0
OD2 B:ASP61 4.8 38.1 1.0
CB B:ASP61 4.9 35.4 1.0

Cobalt binding site 4 out of 6 in 6h08

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Cobalt binding site 4 out of 6 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 Cobalt with other atoms in the Co binding site number 4 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
C:Co302

b:40.7
occ:1.00
 O B:HOH546 2.0 45.0 1.0
O B:HOH407 2.1 29.9 1.0
NE2 C:HIS1 2.2 59.8 1.0
OD2 B:ASP34 2.2 37.5 1.0
NE2 C:HIS3 2.3 40.4 1.0
O C:HOH405 2.4 52.2 1.0
O B:HOH547 2.9 60.9 1.0
CG B:ASP34 2.9 40.5 1.0
OD1 B:ASP34 3.0 32.5 1.0
CD2 C:HIS1 3.1 65.0 1.0
CD2 C:HIS3 3.1 41.4 1.0
CE1 C:HIS1 3.2 71.9 1.0
CE1 C:HIS3 3.3 58.6 1.0
O B:HOH429 4.2 45.1 1.0
O B:ARG31 4.2 39.9 1.0
CG C:HIS1 4.2 65.4 1.0
ND1 C:HIS1 4.2 63.5 1.0
O B:HOH563 4.3 60.9 1.0
CG C:HIS3 4.3 59.2 1.0
CB B:ASP34 4.4 39.4 1.0
ND1 C:HIS3 4.4 56.8 1.0
O B:GLU32 4.8 35.9 1.0

Cobalt binding site 5 out of 6 in 6h08

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Cobalt binding site 5 out of 6 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 Cobalt with other atoms in the Co binding site number 5 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
C:Co303

b:46.8
occ:1.00
 NE2 C:HIS60 2.0 38.0 1.0
O C:HOH488 2.0 49.4 1.0
O C:HOH570 2.2 30.0 1.0
NE2 C:HIS0 2.2 57.0 1.0
O C:HOH568 2.3 50.3 1.0
CE1 C:HIS2 2.5 56.1 1.0
CD2 C:HIS60 3.0 41.9 1.0
CE1 C:HIS60 3.0 51.2 1.0
CD2 C:HIS0 3.1 62.7 1.0
CE1 C:HIS0 3.3 71.1 1.0
ND1 C:HIS2 3.3 50.8 1.0
NE2 C:HIS2 3.5 63.8 1.0
CG C:HIS60 4.1 46.1 1.0
ND1 C:HIS60 4.1 47.4 1.0
CG C:HIS0 4.3 60.2 1.0
ND1 C:HIS0 4.3 59.6 1.0
CG C:HIS2 4.6 58.2 1.0
CD2 C:HIS2 4.6 63.9 1.0
O C:HOH572 4.9 51.3 1.0

Cobalt binding site 6 out of 6 in 6h08

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Cobalt binding site 6 out of 6 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 Cobalt with other atoms in the Co binding site number 6 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
C:Co304

b:40.7
occ:0.50
 N C:HIS-1 2.3 87.0 1.0
O B:HOH624 2.5 42.4 1.0
CD2 C:HIS-1 2.7 84.7 1.0
CB C:HIS-2 2.8 96.0 1.0
CD2 C:HIS-2 2.9 92.5 1.0
C C:HIS-2 3.0 89.3 1.0
CG C:HIS-1 3.0 0.2 1.0
CA C:HIS-2 3.0 76.7 1.0
CG C:HIS-2 3.0 96.7 1.0
N C:HIS-2 3.2 65.8 1.0
CA C:HIS-1 3.2 82.9 1.0
CB C:HIS-1 3.2 73.2 1.0
O C:HIS-1 3.5 81.1 1.0
C C:HIS-1 3.8 89.8 1.0
NE2 C:HIS-1 3.8 80.7 1.0
O C:HIS-2 4.1 87.0 1.0
NE2 C:HIS-2 4.1 89.5 1.0
ND1 C:HIS-1 4.1 0.7 1.0
ND1 C:HIS-2 4.3 0.5 1.0
CE1 C:HIS-1 4.5 70.7 1.0
CE1 C:HIS-2 4.8 0.6 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: Sun Jul 13 20:57:18 2025

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