Atomistry » Cobalt » PDB 6ega-6kfl » 6h08
Atomistry »
  Cobalt »
    PDB 6ega-6kfl »
      6h08 »

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

Go back to Cobalt Binding Sites List in 6h08
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

Go back to Cobalt Binding Sites List in 6h08
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

Go back to Cobalt Binding Sites List in 6h08
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

Go back to Cobalt Binding Sites List in 6h08
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

Go back to Cobalt Binding Sites List in 6h08
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

Go back to Cobalt Binding Sites List in 6h08
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: Tue Jul 30 18:37:24 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy