Iron in PDB 4cas: Serial Femtosecond Crystallography Structure of A Photosynthetic Reaction Center
Protein crystallography data
The structure of Serial Femtosecond Crystallography Structure of A Photosynthetic Reaction Center, PDB code: 4cas
was solved by
L.C.Johansson,
D.Arnlund,
G.Katona,
T.A.White,
A.Barty,
D.P.Deponte,
R.L.Shoeman,
C.Wickstrand,
A.Sharma,
G.J.Williams,
A.Aquila,
M.J.Bogan,
C.Caleman,
J.Davidsson,
R.B.Doak,
M.Frank,
R.Fromme,
L.Galli,
I.Grotjohann,
M.S.Hunter,
S.Kassemeyer,
R.A.Kirian,
C.Kupitz,
M.Liang,
L.Lomb,
E.Malmerberg,
A.V.Martin,
M.Messerschmidt,
K.Nass,
L.Redecke,
M.M.Seibert,
J.Sjohamn,
J.Steinbrener,
F.Stellato,
D.Wang,
W.Y.Wahlgren,
U.Weierstall,
S.Westenhoff,
N.A.Zatsepin,
S.Boutet,
J.C.H.Spence,
I.Schlichting,
H.N.Chapman,
P.Fromme,
R.Neutze,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.64 /
3.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.900,
84.800,
384.300,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
29.461 /
32.903
|
Other elements in 4cas:
The structure of Serial Femtosecond Crystallography Structure of A Photosynthetic Reaction Center also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Serial Femtosecond Crystallography Structure of A Photosynthetic Reaction Center
(pdb code 4cas). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
Serial Femtosecond Crystallography Structure of A Photosynthetic Reaction Center, PDB code: 4cas:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 4cas
Go back to
Iron Binding Sites List in 4cas
Iron binding site 1 out
of 5 in the Serial Femtosecond Crystallography Structure of A Photosynthetic Reaction Center
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Serial Femtosecond Crystallography Structure of A Photosynthetic Reaction Center within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1333
b:30.7
occ:1.00
|
FE
|
A:HEM1333
|
0.0
|
30.7
|
1.0
|
ND
|
A:HEM1333
|
1.9
|
33.5
|
1.0
|
NA
|
A:HEM1333
|
2.0
|
31.1
|
1.0
|
NC
|
A:HEM1333
|
2.1
|
30.5
|
1.0
|
NB
|
A:HEM1333
|
2.1
|
30.8
|
1.0
|
SD
|
A:MET74
|
2.3
|
50.5
|
1.0
|
NE2
|
A:HIS91
|
2.3
|
48.4
|
1.0
|
C4D
|
A:HEM1333
|
2.9
|
32.9
|
1.0
|
C1D
|
A:HEM1333
|
2.9
|
34.3
|
1.0
|
C1A
|
A:HEM1333
|
3.0
|
31.5
|
1.0
|
C4C
|
A:HEM1333
|
3.1
|
32.8
|
1.0
|
C4A
|
A:HEM1333
|
3.1
|
30.5
|
1.0
|
C4B
|
A:HEM1333
|
3.1
|
30.0
|
1.0
|
C1C
|
A:HEM1333
|
3.1
|
30.6
|
1.0
|
C1B
|
A:HEM1333
|
3.1
|
28.3
|
1.0
|
CD2
|
A:HIS91
|
3.2
|
48.0
|
1.0
|
CE1
|
A:HIS91
|
3.3
|
47.6
|
1.0
|
CE
|
A:MET74
|
3.4
|
49.9
|
1.0
|
CHA
|
A:HEM1333
|
3.4
|
32.7
|
1.0
|
CHD
|
A:HEM1333
|
3.4
|
34.5
|
1.0
|
CHC
|
A:HEM1333
|
3.4
|
30.7
|
1.0
|
CHB
|
A:HEM1333
|
3.5
|
28.9
|
1.0
|
CG
|
A:MET74
|
3.8
|
50.2
|
1.0
|
C2D
|
A:HEM1333
|
4.2
|
33.7
|
1.0
|
C3D
|
A:HEM1333
|
4.2
|
32.5
|
1.0
|
C2A
|
A:HEM1333
|
4.2
|
32.0
|
1.0
|
C3A
|
A:HEM1333
|
4.2
|
32.2
|
1.0
|
C2C
|
A:HEM1333
|
4.3
|
33.0
|
1.0
|
C3C
|
A:HEM1333
|
4.3
|
33.1
|
1.0
|
C2B
|
A:HEM1333
|
4.3
|
26.3
|
1.0
|
CG
|
A:HIS91
|
4.3
|
48.3
|
1.0
|
ND1
|
A:HIS91
|
4.3
|
48.1
|
1.0
|
C3B
|
A:HEM1333
|
4.4
|
26.7
|
1.0
|
CB
|
A:MET74
|
4.5
|
49.7
|
1.0
|
|
Iron binding site 2 out
of 5 in 4cas
Go back to
Iron Binding Sites List in 4cas
Iron binding site 2 out
of 5 in the Serial Femtosecond Crystallography Structure of A Photosynthetic Reaction Center
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Serial Femtosecond Crystallography Structure of A Photosynthetic Reaction Center within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1334
b:23.2
occ:1.00
|
FE
|
A:HEM1334
|
0.0
|
23.2
|
1.0
|
ND
|
A:HEM1334
|
1.9
|
24.3
|
1.0
|
NA
|
A:HEM1334
|
2.0
|
24.8
|
1.0
|
NB
|
A:HEM1334
|
2.1
|
25.3
|
1.0
|
NC
|
A:HEM1334
|
2.1
|
25.2
|
1.0
|
SD
|
A:MET110
|
2.2
|
32.9
|
1.0
|
NE2
|
A:HIS136
|
2.2
|
34.6
|
1.0
|
C1D
|
A:HEM1334
|
2.9
|
24.7
|
1.0
|
C4D
|
A:HEM1334
|
2.9
|
25.1
|
1.0
|
C1A
|
A:HEM1334
|
3.0
|
25.7
|
1.0
|
C4B
|
A:HEM1334
|
3.0
|
25.2
|
1.0
|
C4A
|
A:HEM1334
|
3.1
|
24.1
|
1.0
|
CE1
|
A:HIS136
|
3.1
|
34.9
|
1.0
|
C4C
|
A:HEM1334
|
3.1
|
26.4
|
1.0
|
C1B
|
A:HEM1334
|
3.1
|
25.7
|
1.0
|
C1C
|
A:HEM1334
|
3.1
|
24.6
|
1.0
|
CD2
|
A:HIS136
|
3.2
|
33.9
|
1.0
|
CE
|
A:MET110
|
3.3
|
33.3
|
1.0
|
CHD
|
A:HEM1334
|
3.4
|
25.7
|
1.0
|
CHA
|
A:HEM1334
|
3.4
|
26.0
|
1.0
|
CHC
|
A:HEM1334
|
3.5
|
25.3
|
1.0
|
CHB
|
A:HEM1334
|
3.5
|
24.4
|
1.0
|
CG
|
A:MET110
|
3.5
|
32.8
|
1.0
|
C2D
|
A:HEM1334
|
4.2
|
26.8
|
1.0
|
C3D
|
A:HEM1334
|
4.2
|
25.9
|
1.0
|
ND1
|
A:HIS136
|
4.2
|
34.8
|
1.0
|
C3A
|
A:HEM1334
|
4.2
|
24.8
|
1.0
|
C2A
|
A:HEM1334
|
4.2
|
25.7
|
1.0
|
CB
|
A:MET110
|
4.3
|
32.4
|
1.0
|
C2B
|
A:HEM1334
|
4.3
|
26.1
|
1.0
|
C3C
|
A:HEM1334
|
4.3
|
26.2
|
1.0
|
C2C
|
A:HEM1334
|
4.3
|
24.4
|
1.0
|
C3B
|
A:HEM1334
|
4.3
|
25.5
|
1.0
|
CG
|
A:HIS136
|
4.3
|
34.5
|
1.0
|
CE
|
A:MET113
|
5.0
|
28.6
|
1.0
|
CG
|
A:PRO142
|
5.0
|
39.5
|
1.0
|
|
Iron binding site 3 out
of 5 in 4cas
Go back to
Iron Binding Sites List in 4cas
Iron binding site 3 out
of 5 in the Serial Femtosecond Crystallography Structure of A Photosynthetic Reaction Center
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Serial Femtosecond Crystallography Structure of A Photosynthetic Reaction Center within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1335
b:26.1
occ:1.00
|
FE
|
A:HEM1335
|
0.0
|
26.1
|
1.0
|
ND
|
A:HEM1335
|
1.9
|
26.5
|
1.0
|
NA
|
A:HEM1335
|
2.0
|
25.3
|
1.0
|
NB
|
A:HEM1335
|
2.1
|
24.3
|
1.0
|
NC
|
A:HEM1335
|
2.1
|
24.2
|
1.0
|
NE2
|
A:HIS248
|
2.1
|
29.0
|
1.0
|
SD
|
A:MET233
|
2.5
|
31.8
|
1.0
|
C4D
|
A:HEM1335
|
2.9
|
26.3
|
1.0
|
C1D
|
A:HEM1335
|
2.9
|
26.3
|
1.0
|
C1A
|
A:HEM1335
|
3.0
|
25.9
|
1.0
|
C4B
|
A:HEM1335
|
3.0
|
24.2
|
1.0
|
CD2
|
A:HIS248
|
3.0
|
27.8
|
1.0
|
C4A
|
A:HEM1335
|
3.0
|
24.3
|
1.0
|
C1B
|
A:HEM1335
|
3.0
|
24.1
|
1.0
|
C4C
|
A:HEM1335
|
3.1
|
24.3
|
1.0
|
C1C
|
A:HEM1335
|
3.1
|
23.6
|
1.0
|
CE1
|
A:HIS248
|
3.2
|
28.4
|
1.0
|
CHA
|
A:HEM1335
|
3.4
|
25.7
|
1.0
|
CG
|
A:MET233
|
3.4
|
32.7
|
1.0
|
CHD
|
A:HEM1335
|
3.4
|
25.2
|
1.0
|
CHB
|
A:HEM1335
|
3.4
|
24.1
|
1.0
|
CHC
|
A:HEM1335
|
3.4
|
23.8
|
1.0
|
CE
|
A:MET233
|
3.5
|
32.8
|
1.0
|
C3D
|
A:HEM1335
|
4.2
|
26.4
|
1.0
|
C2A
|
A:HEM1335
|
4.2
|
26.5
|
1.0
|
CG
|
A:HIS248
|
4.2
|
27.4
|
1.0
|
C2D
|
A:HEM1335
|
4.2
|
26.5
|
1.0
|
C3A
|
A:HEM1335
|
4.2
|
25.1
|
1.0
|
ND1
|
A:HIS248
|
4.2
|
28.1
|
1.0
|
C2B
|
A:HEM1335
|
4.3
|
24.8
|
1.0
|
CB
|
A:MET233
|
4.3
|
32.7
|
1.0
|
C3B
|
A:HEM1335
|
4.3
|
25.7
|
1.0
|
C2C
|
A:HEM1335
|
4.3
|
22.6
|
1.0
|
C3C
|
A:HEM1335
|
4.3
|
23.2
|
1.0
|
|
Iron binding site 4 out
of 5 in 4cas
Go back to
Iron Binding Sites List in 4cas
Iron binding site 4 out
of 5 in the Serial Femtosecond Crystallography Structure of A Photosynthetic Reaction Center
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Serial Femtosecond Crystallography Structure of A Photosynthetic Reaction Center within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1336
b:32.6
occ:1.00
|
FE
|
A:HEM1336
|
0.0
|
32.6
|
1.0
|
NE2
|
A:HIS309
|
1.9
|
40.1
|
1.0
|
ND
|
A:HEM1336
|
1.9
|
38.1
|
1.0
|
NA
|
A:HEM1336
|
2.0
|
36.5
|
1.0
|
NB
|
A:HEM1336
|
2.1
|
35.7
|
1.0
|
NC
|
A:HEM1336
|
2.1
|
36.6
|
1.0
|
NE2
|
A:HIS124
|
2.3
|
35.0
|
1.0
|
CE1
|
A:HIS309
|
2.8
|
41.4
|
1.0
|
C1D
|
A:HEM1336
|
2.9
|
38.8
|
1.0
|
C4D
|
A:HEM1336
|
2.9
|
40.9
|
1.0
|
CD2
|
A:HIS309
|
3.0
|
39.3
|
1.0
|
C4A
|
A:HEM1336
|
3.0
|
38.2
|
1.0
|
C1A
|
A:HEM1336
|
3.0
|
37.9
|
1.0
|
C1B
|
A:HEM1336
|
3.1
|
37.5
|
1.0
|
C4B
|
A:HEM1336
|
3.1
|
36.5
|
1.0
|
C4C
|
A:HEM1336
|
3.1
|
36.4
|
1.0
|
C1C
|
A:HEM1336
|
3.1
|
37.2
|
1.0
|
CE1
|
A:HIS124
|
3.2
|
33.1
|
1.0
|
CD2
|
A:HIS124
|
3.3
|
34.0
|
1.0
|
CHA
|
A:HEM1336
|
3.4
|
40.0
|
1.0
|
CHD
|
A:HEM1336
|
3.4
|
37.2
|
1.0
|
CHB
|
A:HEM1336
|
3.4
|
38.1
|
1.0
|
CHC
|
A:HEM1336
|
3.5
|
37.5
|
1.0
|
ND1
|
A:HIS309
|
3.9
|
42.1
|
1.0
|
CG
|
A:HIS309
|
4.0
|
39.7
|
1.0
|
C2D
|
A:HEM1336
|
4.2
|
44.5
|
1.0
|
C3D
|
A:HEM1336
|
4.2
|
44.9
|
1.0
|
C3A
|
A:HEM1336
|
4.2
|
41.2
|
1.0
|
C2A
|
A:HEM1336
|
4.2
|
38.6
|
1.0
|
ND1
|
A:HIS124
|
4.3
|
32.5
|
1.0
|
C3C
|
A:HEM1336
|
4.3
|
35.6
|
1.0
|
C2B
|
A:HEM1336
|
4.3
|
37.5
|
1.0
|
C2C
|
A:HEM1336
|
4.3
|
35.3
|
1.0
|
C3B
|
A:HEM1336
|
4.3
|
35.5
|
1.0
|
CG
|
A:HIS124
|
4.4
|
33.5
|
1.0
|
CD
|
A:PRO315
|
4.8
|
32.2
|
1.0
|
CG
|
A:PRO315
|
4.9
|
32.8
|
1.0
|
|
Iron binding site 5 out
of 5 in 4cas
Go back to
Iron Binding Sites List in 4cas
Iron binding site 5 out
of 5 in the Serial Femtosecond Crystallography Structure of A Photosynthetic Reaction Center
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Serial Femtosecond Crystallography Structure of A Photosynthetic Reaction Center within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe1326
b:48.2
occ:1.00
|
NE2
|
C:HIS264
|
1.5
|
73.8
|
1.0
|
OE2
|
C:GLU232
|
2.3
|
57.3
|
1.0
|
OE1
|
C:GLU232
|
2.4
|
58.0
|
1.0
|
CE1
|
C:HIS264
|
2.4
|
73.2
|
1.0
|
NE2
|
B:HIS190
|
2.4
|
80.0
|
1.0
|
NE2
|
C:HIS217
|
2.5
|
69.8
|
1.0
|
CD
|
C:GLU232
|
2.6
|
58.2
|
1.0
|
CD2
|
C:HIS264
|
2.6
|
70.1
|
1.0
|
CE1
|
C:HIS217
|
3.1
|
69.2
|
1.0
|
NE2
|
B:HIS230
|
3.2
|
71.6
|
1.0
|
CE1
|
B:HIS190
|
3.2
|
80.0
|
1.0
|
CD2
|
B:HIS190
|
3.4
|
75.8
|
1.0
|
ND1
|
C:HIS264
|
3.5
|
72.5
|
1.0
|
CG
|
C:HIS264
|
3.7
|
70.6
|
1.0
|
CD2
|
C:HIS217
|
3.7
|
64.9
|
1.0
|
CE1
|
B:HIS230
|
3.9
|
70.4
|
1.0
|
CG1
|
B:ILE194
|
4.0
|
64.9
|
1.0
|
CG
|
C:GLU232
|
4.1
|
59.7
|
1.0
|
CD2
|
B:HIS230
|
4.2
|
67.9
|
1.0
|
ND1
|
B:HIS190
|
4.3
|
78.3
|
1.0
|
ND1
|
C:HIS217
|
4.4
|
67.3
|
1.0
|
CG
|
B:HIS190
|
4.4
|
75.8
|
1.0
|
CG
|
C:HIS217
|
4.7
|
63.5
|
1.0
|
CD1
|
B:ILE194
|
4.7
|
66.2
|
1.0
|
CB
|
C:GLU232
|
4.7
|
60.2
|
1.0
|
CB
|
B:ILE194
|
4.9
|
66.5
|
1.0
|
|
Reference:
L.C.Johansson,
D.Arnlund,
G.Katona,
T.A.White,
A.Barty,
D.P.Deponte,
R.L.Shoeman,
C.Wickstrand,
A.Sharma,
G.J.Williams,
A.Aquila,
M.J.Bogan,
C.Caleman,
J.Davidsson,
R.B.Doak,
M.Frank,
R.Fromme,
L.Galli,
I.Grotjohann,
M.S.Hunter,
S.Kassemeyer,
R.A.Kirian,
C.Kupitz,
M.Liang,
L.Lomb,
E.Malmerberg,
A.V.Martin,
M.Messerschmidt,
K.Nass,
L.Redecke,
M.M.Seibert,
J.Sjohamn,
J.Steinbrener,
F.Stellato,
D.Wang,
W.Y.Wahlgren,
U.Weierstall,
S.Westenhoff,
N.A.Zatsepin,
S.Boutet,
J.C.H.Spence,
I.Schlichting,
H.N.Chapman,
P.Fromme,
R.Neutze.
Structure of A Photosynthetic Reaction Centre Determined By Serial Femtosecond Crystallography. Nat.Commun. V. 4 2911 2013.
ISSN: ISSN 2041-1723
PubMed: 24352554
DOI: 10.1038/NCOMMS3911
Page generated: Mon Aug 5 00:23:21 2024
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