Iron in PDB 6prc: Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex)
Protein crystallography data
The structure of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex), PDB code: 6prc
was solved by
C.R.D.Lancaster,
H.Michel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
10.00 /
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 (%)
|
18.4 /
22.5
|
Other elements in 6prc:
The structure of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex) also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex)
(pdb code 6prc). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex), PDB code: 6prc:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 6prc
Go back to
Iron Binding Sites List in 6prc
Iron binding site 1 out
of 5 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe337
b:32.4
occ:1.00
|
FE
|
C:HEM337
|
0.0
|
32.4
|
1.0
|
NE2
|
C:HIS91
|
1.9
|
31.3
|
1.0
|
NC
|
C:HEM337
|
2.0
|
29.9
|
1.0
|
NB
|
C:HEM337
|
2.0
|
30.4
|
1.0
|
NA
|
C:HEM337
|
2.0
|
32.1
|
1.0
|
ND
|
C:HEM337
|
2.1
|
30.8
|
1.0
|
SD
|
C:MET74
|
2.2
|
33.4
|
1.0
|
CE1
|
C:HIS91
|
2.9
|
34.2
|
1.0
|
CD2
|
C:HIS91
|
2.9
|
35.1
|
1.0
|
C4C
|
C:HEM337
|
3.0
|
30.6
|
1.0
|
C1C
|
C:HEM337
|
3.0
|
29.8
|
1.0
|
C1B
|
C:HEM337
|
3.0
|
33.5
|
1.0
|
C4B
|
C:HEM337
|
3.0
|
31.5
|
1.0
|
C4A
|
C:HEM337
|
3.1
|
35.5
|
1.0
|
C1D
|
C:HEM337
|
3.1
|
29.4
|
1.0
|
C1A
|
C:HEM337
|
3.1
|
34.9
|
1.0
|
C4D
|
C:HEM337
|
3.1
|
31.0
|
1.0
|
CHD
|
C:HEM337
|
3.4
|
27.2
|
1.0
|
CHC
|
C:HEM337
|
3.4
|
29.9
|
1.0
|
CHB
|
C:HEM337
|
3.4
|
33.0
|
1.0
|
CE
|
C:MET74
|
3.5
|
25.4
|
1.0
|
CHA
|
C:HEM337
|
3.5
|
34.3
|
1.0
|
CG
|
C:MET74
|
3.5
|
28.9
|
1.0
|
ND1
|
C:HIS91
|
4.0
|
34.2
|
1.0
|
CG
|
C:HIS91
|
4.1
|
32.0
|
1.0
|
C3C
|
C:HEM337
|
4.2
|
29.4
|
1.0
|
C2C
|
C:HEM337
|
4.2
|
28.9
|
1.0
|
C2B
|
C:HEM337
|
4.3
|
32.9
|
1.0
|
C3B
|
C:HEM337
|
4.3
|
30.0
|
1.0
|
C3A
|
C:HEM337
|
4.3
|
37.3
|
1.0
|
C2A
|
C:HEM337
|
4.3
|
38.8
|
1.0
|
CB
|
C:MET74
|
4.3
|
30.1
|
1.0
|
C2D
|
C:HEM337
|
4.3
|
32.7
|
1.0
|
C3D
|
C:HEM337
|
4.3
|
30.4
|
1.0
|
|
Iron binding site 2 out
of 5 in 6prc
Go back to
Iron Binding Sites List in 6prc
Iron binding site 2 out
of 5 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe338
b:27.5
occ:1.00
|
FE
|
C:HEM338
|
0.0
|
27.5
|
1.0
|
NE2
|
C:HIS136
|
2.0
|
23.3
|
1.0
|
NA
|
C:HEM338
|
2.0
|
27.0
|
1.0
|
NB
|
C:HEM338
|
2.0
|
26.8
|
1.0
|
ND
|
C:HEM338
|
2.0
|
29.8
|
1.0
|
NC
|
C:HEM338
|
2.1
|
28.1
|
1.0
|
SD
|
C:MET110
|
2.2
|
30.3
|
1.0
|
CE1
|
C:HIS136
|
2.9
|
25.9
|
1.0
|
C4A
|
C:HEM338
|
3.0
|
30.0
|
1.0
|
C1B
|
C:HEM338
|
3.0
|
28.2
|
1.0
|
CD2
|
C:HIS136
|
3.0
|
24.3
|
1.0
|
C1D
|
C:HEM338
|
3.1
|
32.4
|
1.0
|
C1A
|
C:HEM338
|
3.1
|
29.3
|
1.0
|
C4C
|
C:HEM338
|
3.1
|
24.7
|
1.0
|
C4D
|
C:HEM338
|
3.1
|
31.1
|
1.0
|
C4B
|
C:HEM338
|
3.1
|
29.0
|
1.0
|
C1C
|
C:HEM338
|
3.1
|
25.2
|
1.0
|
CHB
|
C:HEM338
|
3.3
|
29.2
|
1.0
|
CHD
|
C:HEM338
|
3.4
|
27.1
|
1.0
|
CHA
|
C:HEM338
|
3.5
|
32.9
|
1.0
|
CE
|
C:MET110
|
3.5
|
24.5
|
1.0
|
CHC
|
C:HEM338
|
3.5
|
28.1
|
1.0
|
CG
|
C:MET110
|
3.5
|
28.7
|
1.0
|
ND1
|
C:HIS136
|
4.1
|
23.4
|
1.0
|
CB
|
C:MET110
|
4.1
|
28.1
|
1.0
|
CG
|
C:HIS136
|
4.2
|
23.5
|
1.0
|
C3A
|
C:HEM338
|
4.2
|
30.3
|
1.0
|
C2A
|
C:HEM338
|
4.3
|
30.7
|
1.0
|
C2B
|
C:HEM338
|
4.3
|
31.1
|
1.0
|
C2D
|
C:HEM338
|
4.3
|
32.7
|
1.0
|
C3D
|
C:HEM338
|
4.3
|
32.0
|
1.0
|
C3C
|
C:HEM338
|
4.3
|
23.6
|
1.0
|
C3B
|
C:HEM338
|
4.3
|
28.6
|
1.0
|
C2C
|
C:HEM338
|
4.3
|
23.2
|
1.0
|
|
Iron binding site 3 out
of 5 in 6prc
Go back to
Iron Binding Sites List in 6prc
Iron binding site 3 out
of 5 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe339
b:18.4
occ:1.00
|
FE
|
C:HEM339
|
0.0
|
18.4
|
1.0
|
NE2
|
C:HIS248
|
1.9
|
17.2
|
1.0
|
NB
|
C:HEM339
|
2.0
|
13.2
|
1.0
|
NC
|
C:HEM339
|
2.0
|
18.4
|
1.0
|
NA
|
C:HEM339
|
2.0
|
17.0
|
1.0
|
ND
|
C:HEM339
|
2.0
|
18.7
|
1.0
|
SD
|
C:MET233
|
2.2
|
20.2
|
1.0
|
CD2
|
C:HIS248
|
2.9
|
16.0
|
1.0
|
CE1
|
C:HIS248
|
2.9
|
17.3
|
1.0
|
C4C
|
C:HEM339
|
3.0
|
21.5
|
1.0
|
C1B
|
C:HEM339
|
3.0
|
17.0
|
1.0
|
C1C
|
C:HEM339
|
3.0
|
17.2
|
1.0
|
C4B
|
C:HEM339
|
3.0
|
19.2
|
1.0
|
C4A
|
C:HEM339
|
3.0
|
15.1
|
1.0
|
C1D
|
C:HEM339
|
3.0
|
22.9
|
1.0
|
C4D
|
C:HEM339
|
3.1
|
22.2
|
1.0
|
C1A
|
C:HEM339
|
3.1
|
17.9
|
1.0
|
CHB
|
C:HEM339
|
3.4
|
16.0
|
1.0
|
CHD
|
C:HEM339
|
3.4
|
19.3
|
1.0
|
CHC
|
C:HEM339
|
3.4
|
18.2
|
1.0
|
CG
|
C:MET233
|
3.4
|
16.2
|
1.0
|
CE
|
C:MET233
|
3.5
|
13.0
|
1.0
|
CHA
|
C:HEM339
|
3.5
|
19.9
|
1.0
|
ND1
|
C:HIS248
|
4.1
|
16.4
|
1.0
|
CG
|
C:HIS248
|
4.1
|
17.4
|
1.0
|
CB
|
C:MET233
|
4.2
|
24.5
|
1.0
|
C3C
|
C:HEM339
|
4.2
|
18.3
|
1.0
|
C2C
|
C:HEM339
|
4.2
|
20.6
|
1.0
|
C2B
|
C:HEM339
|
4.3
|
15.6
|
1.0
|
C3B
|
C:HEM339
|
4.3
|
15.8
|
1.0
|
C3A
|
C:HEM339
|
4.3
|
16.5
|
1.0
|
C2D
|
C:HEM339
|
4.3
|
23.1
|
1.0
|
C2A
|
C:HEM339
|
4.3
|
15.0
|
1.0
|
C3D
|
C:HEM339
|
4.3
|
21.3
|
1.0
|
|
Iron binding site 4 out
of 5 in 6prc
Go back to
Iron Binding Sites List in 6prc
Iron binding site 4 out
of 5 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe340
b:22.8
occ:1.00
|
FE
|
C:HEM340
|
0.0
|
22.8
|
1.0
|
NE2
|
C:HIS124
|
2.0
|
24.0
|
1.0
|
NE2
|
C:HIS309
|
2.0
|
16.4
|
1.0
|
ND
|
C:HEM340
|
2.0
|
23.9
|
1.0
|
NC
|
C:HEM340
|
2.0
|
24.2
|
1.0
|
NB
|
C:HEM340
|
2.0
|
21.2
|
1.0
|
NA
|
C:HEM340
|
2.0
|
24.0
|
1.0
|
CE1
|
C:HIS124
|
2.8
|
24.0
|
1.0
|
CE1
|
C:HIS309
|
2.9
|
16.6
|
1.0
|
C1D
|
C:HEM340
|
3.0
|
24.9
|
1.0
|
C4C
|
C:HEM340
|
3.0
|
25.9
|
1.0
|
C4D
|
C:HEM340
|
3.0
|
23.7
|
1.0
|
C1B
|
C:HEM340
|
3.1
|
21.4
|
1.0
|
C1C
|
C:HEM340
|
3.1
|
24.1
|
1.0
|
CD2
|
C:HIS309
|
3.1
|
18.0
|
1.0
|
C4B
|
C:HEM340
|
3.1
|
21.6
|
1.0
|
C1A
|
C:HEM340
|
3.1
|
25.3
|
1.0
|
C4A
|
C:HEM340
|
3.1
|
24.4
|
1.0
|
CD2
|
C:HIS124
|
3.1
|
24.6
|
1.0
|
CHD
|
C:HEM340
|
3.4
|
25.4
|
1.0
|
CHA
|
C:HEM340
|
3.4
|
26.4
|
1.0
|
CHC
|
C:HEM340
|
3.4
|
26.1
|
1.0
|
CHB
|
C:HEM340
|
3.4
|
21.1
|
1.0
|
ND1
|
C:HIS124
|
4.0
|
18.0
|
1.0
|
ND1
|
C:HIS309
|
4.1
|
15.9
|
1.0
|
CG
|
C:HIS309
|
4.2
|
16.0
|
1.0
|
CG
|
C:HIS124
|
4.2
|
20.9
|
1.0
|
C2D
|
C:HEM340
|
4.2
|
24.6
|
1.0
|
C3D
|
C:HEM340
|
4.3
|
26.2
|
1.0
|
C3C
|
C:HEM340
|
4.3
|
23.5
|
1.0
|
C2C
|
C:HEM340
|
4.3
|
22.9
|
1.0
|
C2B
|
C:HEM340
|
4.3
|
22.6
|
1.0
|
C3B
|
C:HEM340
|
4.3
|
21.6
|
1.0
|
C2A
|
C:HEM340
|
4.3
|
22.9
|
1.0
|
C3A
|
C:HEM340
|
4.3
|
24.4
|
1.0
|
|
Iron binding site 5 out
of 5 in 6prc
Go back to
Iron Binding Sites List in 6prc
Iron binding site 5 out
of 5 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Fe500
b:19.0
occ:1.00
|
NE2
|
L:HIS190
|
1.8
|
21.4
|
1.0
|
OE2
|
M:GLU232
|
2.0
|
23.1
|
1.0
|
NE2
|
M:HIS217
|
2.0
|
18.2
|
1.0
|
NE2
|
M:HIS264
|
2.0
|
18.1
|
1.0
|
OE1
|
M:GLU232
|
2.3
|
22.0
|
1.0
|
NE2
|
L:HIS230
|
2.3
|
24.2
|
1.0
|
CD
|
M:GLU232
|
2.5
|
22.8
|
1.0
|
CE1
|
L:HIS190
|
2.7
|
20.1
|
1.0
|
CE1
|
M:HIS264
|
2.9
|
17.6
|
1.0
|
CE1
|
M:HIS217
|
2.9
|
17.1
|
1.0
|
CD2
|
L:HIS190
|
3.0
|
21.8
|
1.0
|
CD2
|
M:HIS217
|
3.1
|
17.5
|
1.0
|
CE1
|
L:HIS230
|
3.2
|
23.7
|
1.0
|
CD2
|
M:HIS264
|
3.2
|
15.8
|
1.0
|
CD2
|
L:HIS230
|
3.4
|
21.1
|
1.0
|
ND1
|
L:HIS190
|
3.9
|
17.4
|
1.0
|
CG
|
M:GLU232
|
4.0
|
18.5
|
1.0
|
CG
|
L:HIS190
|
4.1
|
18.7
|
1.0
|
ND1
|
M:HIS264
|
4.1
|
14.1
|
1.0
|
ND1
|
M:HIS217
|
4.1
|
15.4
|
1.0
|
CG
|
M:HIS217
|
4.2
|
17.4
|
1.0
|
CG
|
M:HIS264
|
4.3
|
16.6
|
1.0
|
ND1
|
L:HIS230
|
4.4
|
20.0
|
1.0
|
CG
|
L:HIS230
|
4.5
|
22.7
|
1.0
|
CG1
|
L:ILE194
|
4.6
|
22.1
|
1.0
|
CG1
|
M:ILE221
|
4.6
|
16.2
|
1.0
|
O
|
M:HOH1016
|
4.7
|
18.8
|
1.0
|
CB
|
M:GLU232
|
4.9
|
20.3
|
1.0
|
CD1
|
L:ILE194
|
4.9
|
23.4
|
1.0
|
|
Reference:
C.R.Lancaster,
H.Michel.
Refined Crystal Structures of Reaction Centres From Rhodopseudomonas Viridis in Complexes with the Herbicide Atrazine and Two Chiral Atrazine Derivatives Also Lead to A New Model of the Bound Carotenoid. J.Mol.Biol. V. 286 883 1999.
ISSN: ISSN 0022-2836
PubMed: 10024457
DOI: 10.1006/JMBI.1998.2532
Page generated: Wed Aug 7 06:43:02 2024
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