Iron in PDB 1prc: Crystallographic Refinement at 2.3 Angstroms Resolution and Refined Model of the Photosynthetic Reaction Center From Rhodopseudomonas Viridis
Protein crystallography data
The structure of Crystallographic Refinement at 2.3 Angstroms Resolution and Refined Model of the Photosynthetic Reaction Center From Rhodopseudomonas Viridis, PDB code: 1prc
was solved by
J.Deisenhofer,
O.Epp,
K.Miki,
R.Huber,
H.Michel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.99 /
2.30
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
223.500,
223.500,
113.600,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Other elements in 1prc:
The structure of Crystallographic Refinement at 2.3 Angstroms Resolution and Refined Model of the Photosynthetic Reaction Center From Rhodopseudomonas Viridis also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystallographic Refinement at 2.3 Angstroms Resolution and Refined Model of the Photosynthetic Reaction Center From Rhodopseudomonas Viridis
(pdb code 1prc). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
Crystallographic Refinement at 2.3 Angstroms Resolution and Refined Model of the Photosynthetic Reaction Center From Rhodopseudomonas Viridis, PDB code: 1prc:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 1prc
Go back to
Iron Binding Sites List in 1prc
Iron binding site 1 out
of 5 in the Crystallographic Refinement at 2.3 Angstroms Resolution and Refined Model of the Photosynthetic Reaction Center From Rhodopseudomonas Viridis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystallographic Refinement at 2.3 Angstroms Resolution and Refined Model of the Photosynthetic Reaction Center From Rhodopseudomonas Viridis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe609
b:22.8
occ:1.00
|
FE
|
C:HEM609
|
0.0
|
22.8
|
1.0
|
NE2
|
C:HIS91
|
1.9
|
23.9
|
1.0
|
NB
|
C:HEM609
|
2.0
|
22.1
|
1.0
|
NA
|
C:HEM609
|
2.0
|
20.4
|
1.0
|
NC
|
C:HEM609
|
2.0
|
26.1
|
1.0
|
ND
|
C:HEM609
|
2.1
|
23.0
|
1.0
|
SD
|
C:MET74
|
2.3
|
24.3
|
1.0
|
CE1
|
C:HIS91
|
2.8
|
33.5
|
1.0
|
CD2
|
C:HIS91
|
2.9
|
25.8
|
1.0
|
C1B
|
C:HEM609
|
2.9
|
27.7
|
1.0
|
C4A
|
C:HEM609
|
2.9
|
27.5
|
1.0
|
C4C
|
C:HEM609
|
3.0
|
15.7
|
1.0
|
C1D
|
C:HEM609
|
3.0
|
26.0
|
1.0
|
C1A
|
C:HEM609
|
3.0
|
18.5
|
1.0
|
C1C
|
C:HEM609
|
3.0
|
32.3
|
1.0
|
C4B
|
C:HEM609
|
3.1
|
24.4
|
1.0
|
C4D
|
C:HEM609
|
3.1
|
21.7
|
1.0
|
CHB
|
C:HEM609
|
3.3
|
15.4
|
1.0
|
CHD
|
C:HEM609
|
3.3
|
24.8
|
1.0
|
CHA
|
C:HEM609
|
3.4
|
21.9
|
1.0
|
CHC
|
C:HEM609
|
3.5
|
33.6
|
1.0
|
CE
|
C:MET74
|
3.5
|
4.9
|
1.0
|
CG
|
C:MET74
|
3.7
|
22.9
|
1.0
|
ND1
|
C:HIS91
|
4.0
|
35.9
|
1.0
|
CG
|
C:HIS91
|
4.0
|
17.7
|
1.0
|
C3C
|
C:HEM609
|
4.1
|
21.7
|
1.0
|
C2B
|
C:HEM609
|
4.1
|
26.1
|
1.0
|
C3A
|
C:HEM609
|
4.2
|
29.9
|
1.0
|
C2C
|
C:HEM609
|
4.2
|
26.8
|
1.0
|
C2A
|
C:HEM609
|
4.2
|
28.0
|
1.0
|
C3B
|
C:HEM609
|
4.2
|
20.8
|
1.0
|
C2D
|
C:HEM609
|
4.2
|
31.1
|
1.0
|
C3D
|
C:HEM609
|
4.3
|
21.5
|
1.0
|
CB
|
C:MET74
|
4.5
|
17.5
|
1.0
|
|
Iron binding site 2 out
of 5 in 1prc
Go back to
Iron Binding Sites List in 1prc
Iron binding site 2 out
of 5 in the Crystallographic Refinement at 2.3 Angstroms Resolution and Refined Model of the Photosynthetic Reaction Center From Rhodopseudomonas Viridis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystallographic Refinement at 2.3 Angstroms Resolution and Refined Model of the Photosynthetic Reaction Center From Rhodopseudomonas Viridis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe610
b:23.1
occ:1.00
|
FE
|
C:HEM610
|
0.0
|
23.1
|
1.0
|
NE2
|
C:HIS136
|
2.0
|
19.8
|
1.0
|
NC
|
C:HEM610
|
2.0
|
20.5
|
1.0
|
NA
|
C:HEM610
|
2.0
|
18.9
|
1.0
|
ND
|
C:HEM610
|
2.0
|
18.2
|
1.0
|
NB
|
C:HEM610
|
2.1
|
12.4
|
1.0
|
SD
|
C:MET110
|
2.3
|
22.0
|
1.0
|
CD2
|
C:HIS136
|
2.9
|
19.2
|
1.0
|
C4C
|
C:HEM610
|
3.0
|
25.2
|
1.0
|
CE1
|
C:HIS136
|
3.0
|
15.3
|
1.0
|
C1C
|
C:HEM610
|
3.0
|
21.4
|
1.0
|
C4A
|
C:HEM610
|
3.0
|
21.5
|
1.0
|
C1D
|
C:HEM610
|
3.0
|
22.0
|
1.0
|
C1A
|
C:HEM610
|
3.0
|
26.9
|
1.0
|
C4D
|
C:HEM610
|
3.0
|
23.6
|
1.0
|
C1B
|
C:HEM610
|
3.1
|
13.3
|
1.0
|
C4B
|
C:HEM610
|
3.1
|
21.1
|
1.0
|
CHB
|
C:HEM610
|
3.4
|
21.2
|
1.0
|
CHD
|
C:HEM610
|
3.4
|
15.1
|
1.0
|
CHC
|
C:HEM610
|
3.4
|
23.4
|
1.0
|
CHA
|
C:HEM610
|
3.5
|
26.9
|
1.0
|
CE
|
C:MET110
|
3.5
|
19.2
|
1.0
|
CG
|
C:MET110
|
3.6
|
16.8
|
1.0
|
C3C
|
C:HEM610
|
4.1
|
24.5
|
1.0
|
ND1
|
C:HIS136
|
4.1
|
22.6
|
1.0
|
CG
|
C:HIS136
|
4.1
|
19.2
|
1.0
|
C2C
|
C:HEM610
|
4.1
|
18.2
|
1.0
|
C3A
|
C:HEM610
|
4.2
|
29.8
|
1.0
|
C2A
|
C:HEM610
|
4.2
|
29.7
|
1.0
|
C2D
|
C:HEM610
|
4.2
|
18.0
|
1.0
|
C3D
|
C:HEM610
|
4.2
|
19.4
|
1.0
|
C2B
|
C:HEM610
|
4.3
|
20.2
|
1.0
|
CB
|
C:MET110
|
4.3
|
13.4
|
1.0
|
C3B
|
C:HEM610
|
4.3
|
16.7
|
1.0
|
|
Iron binding site 3 out
of 5 in 1prc
Go back to
Iron Binding Sites List in 1prc
Iron binding site 3 out
of 5 in the Crystallographic Refinement at 2.3 Angstroms Resolution and Refined Model of the Photosynthetic Reaction Center From Rhodopseudomonas Viridis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystallographic Refinement at 2.3 Angstroms Resolution and Refined Model of the Photosynthetic Reaction Center From Rhodopseudomonas Viridis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe611
b:21.4
occ:1.00
|
FE
|
C:HEM611
|
0.0
|
21.4
|
1.0
|
NB
|
C:HEM611
|
1.9
|
10.2
|
1.0
|
NE2
|
C:HIS248
|
2.0
|
11.6
|
1.0
|
NA
|
C:HEM611
|
2.0
|
18.6
|
1.0
|
ND
|
C:HEM611
|
2.0
|
21.9
|
1.0
|
NC
|
C:HEM611
|
2.1
|
16.5
|
1.0
|
SD
|
C:MET233
|
2.2
|
13.6
|
1.0
|
CD2
|
C:HIS248
|
2.9
|
10.6
|
1.0
|
C1B
|
C:HEM611
|
2.9
|
22.5
|
1.0
|
C4B
|
C:HEM611
|
3.0
|
12.7
|
1.0
|
C4A
|
C:HEM611
|
3.0
|
18.4
|
1.0
|
CE1
|
C:HIS248
|
3.0
|
9.2
|
1.0
|
C1D
|
C:HEM611
|
3.0
|
20.6
|
1.0
|
C4C
|
C:HEM611
|
3.1
|
15.7
|
1.0
|
C1A
|
C:HEM611
|
3.1
|
21.0
|
1.0
|
C1C
|
C:HEM611
|
3.1
|
9.0
|
1.0
|
C4D
|
C:HEM611
|
3.1
|
20.1
|
1.0
|
CE
|
C:MET233
|
3.2
|
7.0
|
1.0
|
CHB
|
C:HEM611
|
3.3
|
11.4
|
1.0
|
CG
|
C:MET233
|
3.4
|
16.2
|
1.0
|
CHD
|
C:HEM611
|
3.4
|
15.1
|
1.0
|
CHC
|
C:HEM611
|
3.4
|
19.6
|
1.0
|
CHA
|
C:HEM611
|
3.5
|
15.6
|
1.0
|
CG
|
C:HIS248
|
4.0
|
10.4
|
1.0
|
ND1
|
C:HIS248
|
4.1
|
6.9
|
1.0
|
C3B
|
C:HEM611
|
4.1
|
6.0
|
1.0
|
CB
|
C:MET233
|
4.1
|
12.4
|
1.0
|
C2B
|
C:HEM611
|
4.1
|
13.7
|
1.0
|
C3A
|
C:HEM611
|
4.2
|
20.4
|
1.0
|
C2D
|
C:HEM611
|
4.2
|
17.4
|
1.0
|
C2A
|
C:HEM611
|
4.2
|
12.3
|
1.0
|
C3D
|
C:HEM611
|
4.3
|
13.0
|
1.0
|
C2C
|
C:HEM611
|
4.3
|
12.0
|
1.0
|
C3C
|
C:HEM611
|
4.3
|
15.5
|
1.0
|
|
Iron binding site 4 out
of 5 in 1prc
Go back to
Iron Binding Sites List in 1prc
Iron binding site 4 out
of 5 in the Crystallographic Refinement at 2.3 Angstroms Resolution and Refined Model of the Photosynthetic Reaction Center From Rhodopseudomonas Viridis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystallographic Refinement at 2.3 Angstroms Resolution and Refined Model of the Photosynthetic Reaction Center From Rhodopseudomonas Viridis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe612
b:25.2
occ:1.00
|
FE
|
C:HEM612
|
0.0
|
25.2
|
1.0
|
NE2
|
C:HIS309
|
1.9
|
9.7
|
1.0
|
NE2
|
C:HIS124
|
2.0
|
16.7
|
1.0
|
ND
|
C:HEM612
|
2.0
|
23.8
|
1.0
|
NB
|
C:HEM612
|
2.0
|
12.6
|
1.0
|
NC
|
C:HEM612
|
2.1
|
28.3
|
1.0
|
NA
|
C:HEM612
|
2.1
|
24.6
|
1.0
|
CE1
|
C:HIS309
|
2.5
|
16.9
|
1.0
|
CE1
|
C:HIS124
|
2.6
|
20.8
|
1.0
|
C4D
|
C:HEM612
|
3.0
|
21.6
|
1.0
|
C4B
|
C:HEM612
|
3.0
|
15.4
|
1.0
|
C1D
|
C:HEM612
|
3.0
|
21.0
|
1.0
|
C1C
|
C:HEM612
|
3.0
|
22.5
|
1.0
|
C1A
|
C:HEM612
|
3.0
|
31.8
|
1.0
|
C1B
|
C:HEM612
|
3.1
|
15.8
|
1.0
|
C4C
|
C:HEM612
|
3.1
|
27.8
|
1.0
|
C4A
|
C:HEM612
|
3.1
|
24.4
|
1.0
|
CD2
|
C:HIS309
|
3.2
|
15.1
|
1.0
|
CD2
|
C:HIS124
|
3.2
|
26.9
|
1.0
|
CHC
|
C:HEM612
|
3.4
|
20.9
|
1.0
|
CHA
|
C:HEM612
|
3.4
|
26.5
|
1.0
|
CHD
|
C:HEM612
|
3.4
|
22.9
|
1.0
|
CHB
|
C:HEM612
|
3.5
|
10.1
|
1.0
|
ND1
|
C:HIS309
|
3.8
|
16.0
|
1.0
|
ND1
|
C:HIS124
|
3.8
|
7.7
|
1.0
|
CG
|
C:HIS309
|
4.1
|
12.4
|
1.0
|
CG
|
C:HIS124
|
4.1
|
11.5
|
1.0
|
C3D
|
C:HEM612
|
4.2
|
24.0
|
1.0
|
C2D
|
C:HEM612
|
4.2
|
28.6
|
1.0
|
C2C
|
C:HEM612
|
4.2
|
24.0
|
1.0
|
C2B
|
C:HEM612
|
4.3
|
24.6
|
1.0
|
C3B
|
C:HEM612
|
4.3
|
24.6
|
1.0
|
C2A
|
C:HEM612
|
4.3
|
21.1
|
1.0
|
C3C
|
C:HEM612
|
4.3
|
26.7
|
1.0
|
C3A
|
C:HEM612
|
4.3
|
25.1
|
1.0
|
|
Iron binding site 5 out
of 5 in 1prc
Go back to
Iron Binding Sites List in 1prc
Iron binding site 5 out
of 5 in the Crystallographic Refinement at 2.3 Angstroms Resolution and Refined Model of the Photosynthetic Reaction Center From Rhodopseudomonas Viridis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystallographic Refinement at 2.3 Angstroms Resolution and Refined Model of the Photosynthetic Reaction Center From Rhodopseudomonas Viridis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Fe607
b:19.4
occ:1.00
|
NE2
|
L:HIS190
|
2.0
|
10.9
|
1.0
|
OE2
|
M:GLU232
|
2.0
|
7.8
|
1.0
|
NE2
|
M:HIS264
|
2.0
|
3.2
|
1.0
|
NE2
|
M:HIS217
|
2.1
|
7.0
|
1.0
|
OE1
|
M:GLU232
|
2.2
|
13.5
|
1.0
|
CD
|
M:GLU232
|
2.4
|
12.2
|
1.0
|
NE2
|
L:HIS230
|
2.4
|
9.6
|
1.0
|
CE1
|
L:HIS190
|
3.0
|
13.4
|
1.0
|
CE1
|
M:HIS217
|
3.0
|
10.2
|
1.0
|
CD2
|
L:HIS190
|
3.0
|
22.5
|
1.0
|
CE1
|
M:HIS264
|
3.0
|
17.2
|
1.0
|
CD2
|
M:HIS264
|
3.1
|
10.1
|
1.0
|
CD2
|
M:HIS217
|
3.2
|
13.2
|
1.0
|
CE1
|
L:HIS230
|
3.4
|
19.1
|
1.0
|
CD2
|
L:HIS230
|
3.4
|
7.0
|
1.0
|
CG
|
M:GLU232
|
3.9
|
4.5
|
1.0
|
CG
|
L:HIS190
|
4.1
|
13.1
|
1.0
|
ND1
|
L:HIS190
|
4.2
|
5.9
|
1.0
|
ND1
|
M:HIS217
|
4.2
|
12.7
|
1.0
|
ND1
|
M:HIS264
|
4.2
|
10.6
|
1.0
|
CG
|
M:HIS264
|
4.2
|
14.9
|
1.0
|
CG
|
M:HIS217
|
4.3
|
19.6
|
1.0
|
CG1
|
L:ILE194
|
4.5
|
14.2
|
1.0
|
CG
|
L:HIS230
|
4.5
|
8.3
|
1.0
|
ND1
|
L:HIS230
|
4.5
|
9.2
|
1.0
|
O
|
M:HOH659
|
4.6
|
21.8
|
1.0
|
CG1
|
M:ILE221
|
4.7
|
3.0
|
1.0
|
CB
|
M:GLU232
|
4.8
|
3.0
|
1.0
|
CD1
|
L:ILE194
|
4.9
|
12.7
|
1.0
|
|
Reference:
J.Deisenhofer,
O.Epp,
I.Sinning,
H.Michel.
Crystallographic Refinement at 2.3 A Resolution and Refined Model of the Photosynthetic Reaction Centre From Rhodopseudomonas Viridis. J.Mol.Biol. V. 246 429 1995.
ISSN: ISSN 0022-2836
PubMed: 7877166
DOI: 10.1006/JMBI.1994.0097
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