Iron in PDB 2c1v: Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form
Enzymatic activity of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form
All present enzymatic activity of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form:
1.11.1.5;
Protein crystallography data
The structure of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form, PDB code: 2c1v
was solved by
A.Echalier,
V.Fulop,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.22 /
1.2
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
101.370,
141.200,
51.580,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.3 /
18.8
|
Other elements in 2c1v:
The structure of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form
(pdb code 2c1v). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form, PDB code: 2c1v:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 2c1v
Go back to
Iron Binding Sites List in 2c1v
Iron binding site 1 out
of 4 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:9.6
occ:1.00
|
FE
|
A:HEC401
|
0.0
|
9.6
|
1.0
|
NC
|
A:HEC401
|
2.0
|
9.7
|
1.0
|
NA
|
A:HEC401
|
2.0
|
9.8
|
1.0
|
ND
|
A:HEC401
|
2.0
|
10.2
|
1.0
|
NB
|
A:HEC401
|
2.0
|
9.8
|
1.0
|
NE2
|
A:HIS69
|
2.0
|
10.3
|
1.0
|
O
|
A:HOH2498
|
2.1
|
17.3
|
1.0
|
C1D
|
A:HEC401
|
3.0
|
10.1
|
1.0
|
C4A
|
A:HEC401
|
3.0
|
9.8
|
1.0
|
CE1
|
A:HIS69
|
3.0
|
10.5
|
1.0
|
C4C
|
A:HEC401
|
3.0
|
9.8
|
1.0
|
CD2
|
A:HIS69
|
3.0
|
10.1
|
1.0
|
C1B
|
A:HEC401
|
3.0
|
9.6
|
1.0
|
C4D
|
A:HEC401
|
3.0
|
9.5
|
1.0
|
C1A
|
A:HEC401
|
3.0
|
8.9
|
1.0
|
C4B
|
A:HEC401
|
3.0
|
9.6
|
1.0
|
C1C
|
A:HEC401
|
3.0
|
10.0
|
1.0
|
CHD
|
A:HEC401
|
3.4
|
10.6
|
1.0
|
CHB
|
A:HEC401
|
3.4
|
10.1
|
1.0
|
CHA
|
A:HEC401
|
3.4
|
9.2
|
1.0
|
CHC
|
A:HEC401
|
3.4
|
10.0
|
1.0
|
NE2
|
A:GLN118
|
4.0
|
11.4
|
1.0
|
ND1
|
A:HIS69
|
4.1
|
10.4
|
1.0
|
CG
|
A:HIS69
|
4.2
|
10.5
|
1.0
|
C2D
|
A:HEC401
|
4.2
|
9.7
|
1.0
|
C3A
|
A:HEC401
|
4.2
|
9.9
|
1.0
|
C3C
|
A:HEC401
|
4.2
|
10.1
|
1.0
|
C2B
|
A:HEC401
|
4.2
|
9.7
|
1.0
|
C2A
|
A:HEC401
|
4.2
|
9.9
|
1.0
|
O
|
A:HOH2255
|
4.2
|
21.2
|
1.0
|
C3D
|
A:HEC401
|
4.2
|
10.6
|
1.0
|
C2C
|
A:HEC401
|
4.3
|
10.0
|
1.0
|
C3B
|
A:HEC401
|
4.3
|
9.4
|
1.0
|
OE1
|
A:GLU128
|
4.6
|
21.9
|
1.0
|
CG
|
A:PRO122
|
4.7
|
14.3
|
1.0
|
CB
|
A:PRO122
|
4.7
|
12.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 2c1v
Go back to
Iron Binding Sites List in 2c1v
Iron binding site 2 out
of 4 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:10.5
occ:1.00
|
FE
|
A:HEC402
|
0.0
|
10.5
|
1.0
|
NA
|
A:HEC402
|
2.0
|
10.3
|
1.0
|
NB
|
A:HEC402
|
2.0
|
10.5
|
1.0
|
ND
|
A:HEC402
|
2.0
|
10.0
|
1.0
|
NC
|
A:HEC402
|
2.0
|
11.3
|
1.0
|
NE2
|
A:HIS215
|
2.1
|
11.0
|
1.0
|
SD
|
A:MET289
|
2.3
|
13.4
|
1.0
|
C1A
|
A:HEC402
|
3.0
|
10.1
|
1.0
|
CE1
|
A:HIS215
|
3.0
|
10.7
|
1.0
|
C1D
|
A:HEC402
|
3.0
|
10.7
|
1.0
|
C4D
|
A:HEC402
|
3.0
|
9.6
|
1.0
|
C4B
|
A:HEC402
|
3.0
|
11.3
|
1.0
|
C1B
|
A:HEC402
|
3.0
|
11.2
|
1.0
|
C4A
|
A:HEC402
|
3.1
|
10.6
|
1.0
|
C4C
|
A:HEC402
|
3.1
|
10.8
|
1.0
|
CD2
|
A:HIS215
|
3.1
|
10.8
|
1.0
|
C1C
|
A:HEC402
|
3.1
|
10.4
|
1.0
|
CHB
|
A:HEC402
|
3.4
|
11.3
|
1.0
|
CHA
|
A:HEC402
|
3.4
|
10.5
|
1.0
|
CHC
|
A:HEC402
|
3.4
|
11.9
|
1.0
|
CHD
|
A:HEC402
|
3.4
|
11.1
|
1.0
|
CG
|
A:MET289
|
3.4
|
13.2
|
1.0
|
CE
|
A:MET289
|
3.4
|
12.7
|
1.0
|
ND1
|
A:HIS215
|
4.2
|
10.5
|
1.0
|
CG
|
A:HIS215
|
4.2
|
11.3
|
1.0
|
CB
|
A:MET289
|
4.2
|
12.7
|
1.0
|
C3B
|
A:HEC402
|
4.2
|
11.9
|
1.0
|
C3D
|
A:HEC402
|
4.3
|
11.2
|
1.0
|
C2D
|
A:HEC402
|
4.3
|
11.1
|
1.0
|
C2A
|
A:HEC402
|
4.3
|
10.2
|
1.0
|
C2B
|
A:HEC402
|
4.3
|
11.8
|
1.0
|
C3A
|
A:HEC402
|
4.3
|
11.5
|
1.0
|
C2C
|
A:HEC402
|
4.3
|
10.7
|
1.0
|
C3C
|
A:HEC402
|
4.3
|
11.5
|
1.0
|
CG
|
A:GLN293
|
5.0
|
13.2
|
1.0
|
|
Iron binding site 3 out
of 4 in 2c1v
Go back to
Iron Binding Sites List in 2c1v
Iron binding site 3 out
of 4 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:9.4
occ:1.00
|
FE
|
B:HEC401
|
0.0
|
9.4
|
1.0
|
NB
|
B:HEC401
|
2.0
|
8.8
|
1.0
|
ND
|
B:HEC401
|
2.0
|
9.9
|
1.0
|
NA
|
B:HEC401
|
2.0
|
8.9
|
1.0
|
NC
|
B:HEC401
|
2.0
|
8.4
|
1.0
|
NE2
|
B:HIS69
|
2.1
|
9.3
|
1.0
|
O
|
B:HOH2537
|
2.1
|
17.9
|
1.0
|
C1D
|
B:HEC401
|
3.0
|
10.5
|
1.0
|
C1B
|
B:HEC401
|
3.0
|
9.7
|
1.0
|
C4A
|
B:HEC401
|
3.0
|
9.5
|
1.0
|
C4C
|
B:HEC401
|
3.0
|
9.8
|
1.0
|
CE1
|
B:HIS69
|
3.0
|
10.0
|
1.0
|
C4D
|
B:HEC401
|
3.1
|
9.7
|
1.0
|
C1A
|
B:HEC401
|
3.1
|
10.0
|
1.0
|
C4B
|
B:HEC401
|
3.1
|
9.3
|
1.0
|
CD2
|
B:HIS69
|
3.1
|
9.1
|
1.0
|
C1C
|
B:HEC401
|
3.1
|
8.9
|
1.0
|
CHD
|
B:HEC401
|
3.3
|
11.1
|
1.0
|
CHB
|
B:HEC401
|
3.3
|
10.3
|
1.0
|
CHC
|
B:HEC401
|
3.4
|
9.4
|
1.0
|
CHA
|
B:HEC401
|
3.4
|
9.5
|
1.0
|
NE2
|
B:GLN118
|
4.0
|
12.5
|
1.0
|
ND1
|
B:HIS69
|
4.2
|
10.6
|
1.0
|
CG
|
B:HIS69
|
4.2
|
9.5
|
1.0
|
O
|
B:HOH2285
|
4.2
|
20.4
|
1.0
|
C3C
|
B:HEC401
|
4.2
|
9.8
|
1.0
|
C2A
|
B:HEC401
|
4.2
|
10.6
|
1.0
|
C3A
|
B:HEC401
|
4.3
|
10.1
|
1.0
|
C2B
|
B:HEC401
|
4.3
|
10.2
|
1.0
|
C2D
|
B:HEC401
|
4.3
|
10.3
|
1.0
|
C3D
|
B:HEC401
|
4.3
|
10.2
|
1.0
|
C3B
|
B:HEC401
|
4.3
|
8.9
|
1.0
|
C2C
|
B:HEC401
|
4.3
|
8.9
|
1.0
|
CG
|
B:PRO122
|
4.7
|
14.2
|
1.0
|
CB
|
B:PRO122
|
4.7
|
12.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 2c1v
Go back to
Iron Binding Sites List in 2c1v
Iron binding site 4 out
of 4 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe402
b:12.9
occ:1.00
|
FE
|
B:HEC402
|
0.0
|
12.9
|
1.0
|
NB
|
B:HEC402
|
2.0
|
12.7
|
1.0
|
ND
|
B:HEC402
|
2.0
|
12.5
|
1.0
|
NA
|
B:HEC402
|
2.0
|
12.5
|
1.0
|
NC
|
B:HEC402
|
2.0
|
13.4
|
1.0
|
NE2
|
B:HIS215
|
2.1
|
13.6
|
1.0
|
SD
|
B:MET289
|
2.3
|
15.8
|
1.0
|
C4B
|
B:HEC402
|
3.0
|
12.6
|
1.0
|
CE1
|
B:HIS215
|
3.0
|
13.1
|
1.0
|
C1D
|
B:HEC402
|
3.0
|
13.1
|
1.0
|
C4D
|
B:HEC402
|
3.0
|
11.5
|
1.0
|
C1B
|
B:HEC402
|
3.0
|
13.6
|
1.0
|
CD2
|
B:HIS215
|
3.1
|
13.5
|
1.0
|
C1C
|
B:HEC402
|
3.1
|
13.1
|
1.0
|
C4A
|
B:HEC402
|
3.1
|
13.7
|
1.0
|
C4C
|
B:HEC402
|
3.1
|
13.4
|
1.0
|
C1A
|
B:HEC402
|
3.1
|
13.3
|
1.0
|
CHC
|
B:HEC402
|
3.4
|
13.4
|
1.0
|
CHA
|
B:HEC402
|
3.4
|
12.3
|
1.0
|
CHB
|
B:HEC402
|
3.4
|
14.0
|
1.0
|
CHD
|
B:HEC402
|
3.4
|
13.7
|
1.0
|
CG
|
B:MET289
|
3.4
|
16.2
|
1.0
|
CE
|
B:MET289
|
3.5
|
15.1
|
1.0
|
ND1
|
B:HIS215
|
4.2
|
13.6
|
1.0
|
CB
|
B:MET289
|
4.2
|
14.4
|
1.0
|
CG
|
B:HIS215
|
4.2
|
13.7
|
1.0
|
C3D
|
B:HEC402
|
4.3
|
13.5
|
1.0
|
C3B
|
B:HEC402
|
4.3
|
16.2
|
1.0
|
C2D
|
B:HEC402
|
4.3
|
12.8
|
1.0
|
C3C
|
B:HEC402
|
4.3
|
14.0
|
1.0
|
C2B
|
B:HEC402
|
4.3
|
14.3
|
1.0
|
C2C
|
B:HEC402
|
4.3
|
13.3
|
1.0
|
C2A
|
B:HEC402
|
4.3
|
13.6
|
1.0
|
C3A
|
B:HEC402
|
4.3
|
15.0
|
1.0
|
CG
|
B:GLN293
|
5.0
|
15.1
|
1.0
|
|
Reference:
A.Echalier,
C.F.Goodhew,
G.W.Pettigrew,
V.Fulop.
Activation and Catalysis of the Di-Heme Cytochrome C Peroxidase From Paracoccus Pantotrophus Structure V. 14 107 2006.
ISSN: ISSN 0969-2126
PubMed: 16407070
DOI: 10.1016/J.STR.2005.09.011
Page generated: Sat Aug 3 19:54:57 2024
|