Iron in PDB 1i8p: Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris
Protein crystallography data
The structure of Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris, PDB code: 1i8p
was solved by
G.Garau,
S.Geremia,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.95
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
50.119,
71.706,
67.357,
90.00,
93.67,
90.00
|
R / Rfree (%)
|
16.1 /
23.7
|
Iron Binding Sites:
The binding sites of Iron atom in the Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris
(pdb code 1i8p). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris, PDB code: 1i8p:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1i8p
Go back to
Iron Binding Sites List in 1i8p
Iron binding site 1 out
of 4 in the Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe115
b:9.8
occ:1.00
|
FE
|
A:HEC115
|
0.0
|
9.8
|
1.0
|
ND
|
A:HEC115
|
1.9
|
13.4
|
1.0
|
NE2
|
A:HIS17
|
2.0
|
7.0
|
1.0
|
NC
|
A:HEC115
|
2.0
|
8.8
|
1.0
|
NA
|
A:HEC115
|
2.0
|
10.2
|
1.0
|
NB
|
A:HEC115
|
2.1
|
9.9
|
1.0
|
SD
|
A:MET93
|
2.4
|
10.8
|
1.0
|
CE1
|
A:HIS17
|
2.9
|
10.1
|
1.0
|
C1D
|
A:HEC115
|
3.0
|
12.8
|
1.0
|
CD2
|
A:HIS17
|
3.0
|
3.8
|
1.0
|
C4D
|
A:HEC115
|
3.0
|
12.6
|
1.0
|
C4C
|
A:HEC115
|
3.0
|
6.3
|
1.0
|
C1A
|
A:HEC115
|
3.1
|
10.8
|
1.0
|
C4B
|
A:HEC115
|
3.1
|
6.1
|
1.0
|
C1B
|
A:HEC115
|
3.1
|
9.3
|
1.0
|
C1C
|
A:HEC115
|
3.1
|
11.8
|
1.0
|
C4A
|
A:HEC115
|
3.1
|
8.0
|
1.0
|
CHD
|
A:HEC115
|
3.4
|
9.9
|
1.0
|
CHA
|
A:HEC115
|
3.4
|
11.6
|
1.0
|
CE
|
A:MET93
|
3.4
|
2.7
|
1.0
|
CG
|
A:MET93
|
3.5
|
13.7
|
1.0
|
CHC
|
A:HEC115
|
3.5
|
3.7
|
1.0
|
CHB
|
A:HEC115
|
3.5
|
5.6
|
1.0
|
ND1
|
A:HIS17
|
4.1
|
9.8
|
1.0
|
CG
|
A:HIS17
|
4.1
|
12.2
|
1.0
|
C2D
|
A:HEC115
|
4.2
|
11.7
|
1.0
|
C3D
|
A:HEC115
|
4.2
|
12.6
|
1.0
|
CB
|
A:MET93
|
4.3
|
12.6
|
1.0
|
C2B
|
A:HEC115
|
4.3
|
7.4
|
1.0
|
C3C
|
A:HEC115
|
4.3
|
9.1
|
1.0
|
C2A
|
A:HEC115
|
4.3
|
7.8
|
1.0
|
C3B
|
A:HEC115
|
4.3
|
6.3
|
1.0
|
C2C
|
A:HEC115
|
4.3
|
13.9
|
1.0
|
C3A
|
A:HEC115
|
4.3
|
6.4
|
1.0
|
OH
|
A:TYR66
|
5.0
|
12.4
|
1.0
|
|
Iron binding site 2 out
of 4 in 1i8p
Go back to
Iron Binding Sites List in 1i8p
Iron binding site 2 out
of 4 in the Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe115
b:9.2
occ:1.00
|
FE
|
B:HEC115
|
0.0
|
9.2
|
1.0
|
ND
|
B:HEC115
|
2.0
|
12.1
|
1.0
|
NE2
|
B:HIS17
|
2.0
|
8.5
|
1.0
|
NC
|
B:HEC115
|
2.0
|
8.7
|
1.0
|
NA
|
B:HEC115
|
2.0
|
9.2
|
1.0
|
NB
|
B:HEC115
|
2.0
|
9.3
|
1.0
|
SD
|
B:MET93
|
2.3
|
9.4
|
1.0
|
CE1
|
B:HIS17
|
3.0
|
11.0
|
1.0
|
C1D
|
B:HEC115
|
3.0
|
12.3
|
1.0
|
C4A
|
B:HEC115
|
3.0
|
5.8
|
1.0
|
C4D
|
B:HEC115
|
3.0
|
11.2
|
1.0
|
C1A
|
B:HEC115
|
3.0
|
10.4
|
1.0
|
C4B
|
B:HEC115
|
3.0
|
6.3
|
1.0
|
C1C
|
B:HEC115
|
3.0
|
12.9
|
1.0
|
C1B
|
B:HEC115
|
3.1
|
9.2
|
1.0
|
C4C
|
B:HEC115
|
3.1
|
6.0
|
1.0
|
CD2
|
B:HIS17
|
3.1
|
3.9
|
1.0
|
CE
|
B:MET93
|
3.3
|
4.6
|
1.0
|
CHA
|
B:HEC115
|
3.4
|
11.6
|
1.0
|
CHB
|
B:HEC115
|
3.4
|
6.3
|
1.0
|
CHC
|
B:HEC115
|
3.4
|
4.3
|
1.0
|
CHD
|
B:HEC115
|
3.4
|
9.0
|
1.0
|
CG
|
B:MET93
|
3.4
|
13.3
|
1.0
|
ND1
|
B:HIS17
|
4.1
|
9.0
|
1.0
|
CG
|
B:HIS17
|
4.2
|
12.5
|
1.0
|
CB
|
B:MET93
|
4.3
|
12.3
|
1.0
|
C3D
|
B:HEC115
|
4.3
|
13.8
|
1.0
|
C2D
|
B:HEC115
|
4.3
|
12.9
|
1.0
|
C3A
|
B:HEC115
|
4.3
|
8.1
|
1.0
|
C2A
|
B:HEC115
|
4.3
|
6.7
|
1.0
|
C2B
|
B:HEC115
|
4.3
|
6.5
|
1.0
|
C2C
|
B:HEC115
|
4.3
|
13.2
|
1.0
|
C3B
|
B:HEC115
|
4.3
|
6.3
|
1.0
|
C3C
|
B:HEC115
|
4.3
|
10.5
|
1.0
|
OH
|
B:TYR66
|
5.0
|
11.4
|
1.0
|
|
Iron binding site 3 out
of 4 in 1i8p
Go back to
Iron Binding Sites List in 1i8p
Iron binding site 3 out
of 4 in the Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe115
b:9.7
occ:1.00
|
FE
|
C:HEC115
|
0.0
|
9.7
|
1.0
|
ND
|
C:HEC115
|
2.0
|
11.4
|
1.0
|
NE2
|
C:HIS17
|
2.0
|
8.7
|
1.0
|
NC
|
C:HEC115
|
2.0
|
8.9
|
1.0
|
NA
|
C:HEC115
|
2.0
|
10.0
|
1.0
|
NB
|
C:HEC115
|
2.1
|
9.5
|
1.0
|
SD
|
C:MET93
|
2.4
|
9.4
|
1.0
|
CE1
|
C:HIS17
|
3.0
|
10.3
|
1.0
|
C1D
|
C:HEC115
|
3.0
|
12.0
|
1.0
|
C4C
|
C:HEC115
|
3.0
|
6.3
|
1.0
|
C4D
|
C:HEC115
|
3.0
|
11.8
|
1.0
|
C1B
|
C:HEC115
|
3.1
|
8.5
|
1.0
|
C1A
|
C:HEC115
|
3.1
|
11.1
|
1.0
|
C1C
|
C:HEC115
|
3.1
|
11.4
|
1.0
|
CD2
|
C:HIS17
|
3.1
|
4.6
|
1.0
|
C4B
|
C:HEC115
|
3.1
|
5.9
|
1.0
|
C4A
|
C:HEC115
|
3.1
|
6.8
|
1.0
|
CG
|
C:MET93
|
3.3
|
13.1
|
1.0
|
CHD
|
C:HEC115
|
3.4
|
9.6
|
1.0
|
CHB
|
C:HEC115
|
3.4
|
5.6
|
1.0
|
CHC
|
C:HEC115
|
3.5
|
2.5
|
1.0
|
CHA
|
C:HEC115
|
3.5
|
12.1
|
1.0
|
CE
|
C:MET93
|
3.5
|
3.8
|
1.0
|
ND1
|
C:HIS17
|
4.1
|
8.7
|
1.0
|
CG
|
C:HIS17
|
4.2
|
12.8
|
1.0
|
C2D
|
C:HEC115
|
4.2
|
12.5
|
1.0
|
C3D
|
C:HEC115
|
4.2
|
13.1
|
1.0
|
CB
|
C:MET93
|
4.2
|
12.5
|
1.0
|
C3C
|
C:HEC115
|
4.3
|
8.9
|
1.0
|
C2B
|
C:HEC115
|
4.3
|
7.4
|
1.0
|
C2C
|
C:HEC115
|
4.3
|
13.2
|
1.0
|
C2A
|
C:HEC115
|
4.3
|
6.4
|
1.0
|
C3B
|
C:HEC115
|
4.3
|
6.6
|
1.0
|
C3A
|
C:HEC115
|
4.3
|
7.2
|
1.0
|
OH
|
C:TYR66
|
4.9
|
12.9
|
1.0
|
|
Iron binding site 4 out
of 4 in 1i8p
Go back to
Iron Binding Sites List in 1i8p
Iron binding site 4 out
of 4 in the Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure Determination of the Ferrocytochrome C2 From Rhodopseudomonas Palustris within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe115
b:9.1
occ:1.00
|
FE
|
D:HEC115
|
0.0
|
9.1
|
1.0
|
ND
|
D:HEC115
|
2.0
|
12.4
|
1.0
|
NE2
|
D:HIS17
|
2.0
|
8.6
|
1.0
|
NC
|
D:HEC115
|
2.0
|
8.5
|
1.0
|
NB
|
D:HEC115
|
2.0
|
9.7
|
1.0
|
NA
|
D:HEC115
|
2.1
|
10.4
|
1.0
|
SD
|
D:MET93
|
2.4
|
9.6
|
1.0
|
CE1
|
D:HIS17
|
2.9
|
9.2
|
1.0
|
C1D
|
D:HEC115
|
3.0
|
13.3
|
1.0
|
CD2
|
D:HIS17
|
3.0
|
5.1
|
1.0
|
C4D
|
D:HEC115
|
3.0
|
12.6
|
1.0
|
C4C
|
D:HEC115
|
3.0
|
6.8
|
1.0
|
C1C
|
D:HEC115
|
3.0
|
11.3
|
1.0
|
C1A
|
D:HEC115
|
3.1
|
11.2
|
1.0
|
C4B
|
D:HEC115
|
3.1
|
7.0
|
1.0
|
C4A
|
D:HEC115
|
3.1
|
5.8
|
1.0
|
C1B
|
D:HEC115
|
3.1
|
10.1
|
1.0
|
CHA
|
D:HEC115
|
3.4
|
11.2
|
1.0
|
CHD
|
D:HEC115
|
3.4
|
9.5
|
1.0
|
CHC
|
D:HEC115
|
3.4
|
5.2
|
1.0
|
CE
|
D:MET93
|
3.4
|
4.8
|
1.0
|
CG
|
D:MET93
|
3.4
|
13.8
|
1.0
|
CHB
|
D:HEC115
|
3.5
|
5.3
|
1.0
|
ND1
|
D:HIS17
|
4.1
|
9.8
|
1.0
|
CG
|
D:HIS17
|
4.1
|
13.5
|
1.0
|
C2D
|
D:HEC115
|
4.2
|
12.8
|
1.0
|
C3D
|
D:HEC115
|
4.3
|
13.4
|
1.0
|
C3C
|
D:HEC115
|
4.3
|
10.1
|
1.0
|
C2C
|
D:HEC115
|
4.3
|
13.8
|
1.0
|
CB
|
D:MET93
|
4.3
|
12.7
|
1.0
|
C2A
|
D:HEC115
|
4.3
|
7.8
|
1.0
|
C3B
|
D:HEC115
|
4.3
|
6.8
|
1.0
|
C3A
|
D:HEC115
|
4.3
|
7.2
|
1.0
|
C2B
|
D:HEC115
|
4.3
|
6.9
|
1.0
|
OH
|
D:TYR66
|
5.0
|
12.1
|
1.0
|
|
Reference:
S.Geremia,
G.Garau,
L.Vaccari,
R.Sgarra,
M.S.Viezzoli,
M.Calligaris,
L.Randaccio.
Cleavage of the Iron-Methionine Bond in C-Type Cytochromes: Crystal Structure of Oxidized and Reduced Cytochrome C(2) From Rhodopseudomonas Palustris and Its Ammonia Complex. Protein Sci. V. 11 6 2002.
ISSN: ISSN 0961-8368
PubMed: 11742117
DOI: 10.1110/PS.PS.13102
Page generated: Sat Aug 3 08:01:49 2024
|