Iron 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:
Iron Binding Sites:
The binding sites of Iron 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 Iron atom.
In total 3 binding sites of Iron 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 Iron binding site number:
1;
2;
3;
Iron binding site 1 out
of 3 in 6h08
Go back to
Iron Binding Sites List in 6h08
Iron binding site 1 out
of 3 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 Iron with other atoms in the Fe 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:Fe301
b:22.9
occ:1.00
|
FE
|
A:HEM301
|
0.0
|
22.9
|
1.0
|
ND
|
A:HEM301
|
1.9
|
24.6
|
1.0
|
NA
|
A:HEM301
|
2.0
|
24.3
|
1.0
|
NB
|
A:HEM301
|
2.1
|
24.3
|
1.0
|
NC
|
A:HEM301
|
2.1
|
23.8
|
1.0
|
NE2
|
A:MHS175
|
2.1
|
24.9
|
1.0
|
O
|
A:HOH459
|
2.4
|
44.7
|
1.0
|
C4D
|
A:HEM301
|
2.9
|
23.7
|
1.0
|
C1D
|
A:HEM301
|
2.9
|
21.6
|
1.0
|
C1A
|
A:HEM301
|
3.0
|
23.7
|
1.0
|
C4A
|
A:HEM301
|
3.0
|
26.0
|
1.0
|
C4B
|
A:HEM301
|
3.0
|
25.8
|
1.0
|
C1B
|
A:HEM301
|
3.1
|
23.6
|
1.0
|
CE1
|
A:MHS175
|
3.1
|
23.9
|
1.0
|
C4C
|
A:HEM301
|
3.1
|
21.8
|
1.0
|
C1C
|
A:HEM301
|
3.1
|
22.6
|
1.0
|
CD2
|
A:MHS175
|
3.1
|
25.9
|
1.0
|
CHA
|
A:HEM301
|
3.4
|
22.2
|
1.0
|
CHD
|
A:HEM301
|
3.4
|
22.7
|
1.0
|
CHC
|
A:HEM301
|
3.4
|
22.5
|
1.0
|
CHB
|
A:HEM301
|
3.4
|
25.4
|
1.0
|
NE1
|
A:TRP51
|
4.0
|
21.6
|
1.0
|
NE
|
A:ARG48
|
4.1
|
18.6
|
0.5
|
O
|
A:HOH537
|
4.1
|
34.9
|
1.0
|
C2D
|
A:HEM301
|
4.2
|
20.9
|
1.0
|
C2A
|
A:HEM301
|
4.2
|
23.6
|
1.0
|
ND1
|
A:MHS175
|
4.2
|
25.1
|
1.0
|
C3D
|
A:HEM301
|
4.2
|
21.2
|
1.0
|
C3A
|
A:HEM301
|
4.2
|
25.8
|
1.0
|
C2C
|
A:HEM301
|
4.3
|
21.9
|
1.0
|
CG
|
A:MHS175
|
4.3
|
23.8
|
1.0
|
C2B
|
A:HEM301
|
4.3
|
24.2
|
1.0
|
C3C
|
A:HEM301
|
4.3
|
22.1
|
1.0
|
C3B
|
A:HEM301
|
4.3
|
23.4
|
1.0
|
CD1
|
A:TRP51
|
4.6
|
23.5
|
1.0
|
NH1
|
A:ARG48
|
4.6
|
12.8
|
0.5
|
CZ
|
A:ARG48
|
4.9
|
16.9
|
0.5
|
CH2
|
A:TRP191
|
4.9
|
23.6
|
1.0
|
CD
|
A:ARG48
|
4.9
|
19.7
|
0.5
|
|
Iron binding site 2 out
of 3 in 6h08
Go back to
Iron Binding Sites List in 6h08
Iron binding site 2 out
of 3 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 Iron with other atoms in the Fe 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:Fe302
b:24.0
occ:1.00
|
FE
|
B:HEM302
|
0.0
|
24.0
|
1.0
|
ND
|
B:HEM302
|
1.9
|
23.4
|
1.0
|
NA
|
B:HEM302
|
2.0
|
23.0
|
1.0
|
NC
|
B:HEM302
|
2.1
|
22.8
|
1.0
|
NB
|
B:HEM302
|
2.1
|
23.8
|
1.0
|
NE2
|
B:MHS175
|
2.2
|
25.6
|
1.0
|
O
|
B:HOH470
|
2.3
|
46.3
|
1.0
|
C4D
|
B:HEM302
|
2.9
|
24.3
|
1.0
|
C1D
|
B:HEM302
|
2.9
|
21.3
|
1.0
|
C1A
|
B:HEM302
|
3.0
|
27.1
|
1.0
|
C4A
|
B:HEM302
|
3.0
|
24.1
|
1.0
|
C4B
|
B:HEM302
|
3.0
|
23.4
|
1.0
|
C4C
|
B:HEM302
|
3.1
|
19.6
|
1.0
|
C1B
|
B:HEM302
|
3.1
|
22.3
|
1.0
|
C1C
|
B:HEM302
|
3.1
|
25.8
|
1.0
|
CE1
|
B:MHS175
|
3.1
|
25.6
|
1.0
|
CD2
|
B:MHS175
|
3.2
|
24.9
|
1.0
|
CHA
|
B:HEM302
|
3.4
|
21.0
|
1.0
|
CHD
|
B:HEM302
|
3.4
|
21.0
|
1.0
|
CHB
|
B:HEM302
|
3.4
|
26.2
|
1.0
|
CHC
|
B:HEM302
|
3.4
|
23.6
|
1.0
|
NE1
|
B:TRP51
|
4.0
|
20.8
|
1.0
|
NE
|
B:ARG48
|
4.1
|
18.8
|
0.5
|
O
|
B:HOH501
|
4.2
|
35.8
|
1.0
|
C2A
|
B:HEM302
|
4.2
|
27.3
|
1.0
|
C2D
|
B:HEM302
|
4.2
|
22.1
|
1.0
|
C3A
|
B:HEM302
|
4.2
|
28.6
|
1.0
|
C3D
|
B:HEM302
|
4.2
|
26.5
|
1.0
|
ND1
|
B:MHS175
|
4.3
|
29.9
|
1.0
|
C2C
|
B:HEM302
|
4.3
|
21.5
|
1.0
|
C3C
|
B:HEM302
|
4.3
|
20.4
|
1.0
|
C2B
|
B:HEM302
|
4.3
|
25.1
|
1.0
|
C3B
|
B:HEM302
|
4.3
|
24.9
|
1.0
|
CG
|
B:MHS175
|
4.3
|
24.8
|
1.0
|
CD1
|
B:TRP51
|
4.5
|
20.2
|
1.0
|
NH1
|
B:ARG48
|
4.6
|
16.2
|
0.5
|
CZ
|
B:ARG48
|
4.8
|
19.2
|
0.5
|
CH2
|
B:TRP191
|
4.9
|
26.7
|
1.0
|
CD
|
B:ARG48
|
4.9
|
18.8
|
0.5
|
|
Iron binding site 3 out
of 3 in 6h08
Go back to
Iron Binding Sites List in 6h08
Iron binding site 3 out
of 3 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 Iron with other atoms in the Fe 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
|
C:Fe301
b:26.9
occ:1.00
|
FE
|
C:HEM301
|
0.0
|
26.9
|
1.0
|
ND
|
C:HEM301
|
1.9
|
27.5
|
1.0
|
NA
|
C:HEM301
|
2.0
|
25.1
|
1.0
|
NC
|
C:HEM301
|
2.1
|
26.5
|
1.0
|
NE2
|
C:MHS175
|
2.1
|
25.9
|
1.0
|
NB
|
C:HEM301
|
2.1
|
28.1
|
1.0
|
O
|
C:HOH449
|
2.3
|
52.5
|
1.0
|
C1D
|
C:HEM301
|
2.9
|
26.3
|
1.0
|
C4D
|
C:HEM301
|
2.9
|
26.1
|
1.0
|
C1A
|
C:HEM301
|
3.0
|
29.0
|
1.0
|
C4B
|
C:HEM301
|
3.0
|
29.7
|
1.0
|
C4A
|
C:HEM301
|
3.0
|
26.9
|
1.0
|
CE1
|
C:MHS175
|
3.0
|
27.0
|
1.0
|
C1B
|
C:HEM301
|
3.1
|
28.5
|
1.0
|
C4C
|
C:HEM301
|
3.1
|
26.5
|
1.0
|
C1C
|
C:HEM301
|
3.1
|
30.2
|
1.0
|
CD2
|
C:MHS175
|
3.1
|
30.5
|
1.0
|
CHA
|
C:HEM301
|
3.4
|
27.0
|
1.0
|
CHD
|
C:HEM301
|
3.4
|
29.8
|
1.0
|
CHC
|
C:HEM301
|
3.4
|
27.6
|
1.0
|
CHB
|
C:HEM301
|
3.4
|
27.4
|
1.0
|
NE1
|
C:TRP51
|
4.0
|
26.3
|
1.0
|
NE
|
C:ARG48
|
4.0
|
22.1
|
0.5
|
O
|
C:HOH455
|
4.1
|
34.9
|
1.0
|
ND1
|
C:MHS175
|
4.2
|
34.5
|
1.0
|
C2D
|
C:HEM301
|
4.2
|
27.2
|
1.0
|
C3D
|
C:HEM301
|
4.2
|
27.1
|
1.0
|
C2A
|
C:HEM301
|
4.2
|
25.5
|
1.0
|
C3A
|
C:HEM301
|
4.2
|
26.4
|
1.0
|
CG
|
C:MHS175
|
4.3
|
27.8
|
1.0
|
C2C
|
C:HEM301
|
4.3
|
25.2
|
1.0
|
C3C
|
C:HEM301
|
4.3
|
28.3
|
1.0
|
C2B
|
C:HEM301
|
4.3
|
30.4
|
1.0
|
C3B
|
C:HEM301
|
4.3
|
32.5
|
1.0
|
NH2
|
C:ARG48
|
4.5
|
18.4
|
0.5
|
CD1
|
C:TRP51
|
4.6
|
26.2
|
1.0
|
CZ
|
C:ARG48
|
4.8
|
21.9
|
0.5
|
CH2
|
C:TRP191
|
4.9
|
31.6
|
1.0
|
CD
|
C:ARG48
|
4.9
|
26.1
|
0.5
|
|
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 Aug 6 20:23:53 2024
|