Iron in PDB 1eys: Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum
Protein crystallography data
The structure of Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum, PDB code: 1eys
was solved by
T.Nogi,
I.Fathir,
M.Kobayashi,
T.Nozawa,
K.Miki,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
10.00 /
2.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
133.299,
196.596,
84.163,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.1 /
28.7
|
Other elements in 1eys:
The structure of Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum
(pdb code 1eys). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum, PDB code: 1eys:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 1eys
Go back to
Iron Binding Sites List in 1eys
Iron binding site 1 out
of 5 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum
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 Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe609
b:31.2
occ:1.00
|
FE
|
C:HEM609
|
0.0
|
31.2
|
1.0
|
NC
|
C:HEM609
|
1.9
|
28.5
|
1.0
|
NB
|
C:HEM609
|
2.0
|
28.3
|
1.0
|
ND
|
C:HEM609
|
2.0
|
26.2
|
1.0
|
SD
|
C:MET72
|
2.1
|
33.9
|
1.0
|
NA
|
C:HEM609
|
2.2
|
31.6
|
1.0
|
NE2
|
C:HIS89
|
2.4
|
31.0
|
1.0
|
C4C
|
C:HEM609
|
2.9
|
27.9
|
1.0
|
C1D
|
C:HEM609
|
2.9
|
27.2
|
1.0
|
C1C
|
C:HEM609
|
3.0
|
25.6
|
1.0
|
C4B
|
C:HEM609
|
3.0
|
25.1
|
1.0
|
C1B
|
C:HEM609
|
3.1
|
33.3
|
1.0
|
C4D
|
C:HEM609
|
3.1
|
29.7
|
1.0
|
C1A
|
C:HEM609
|
3.2
|
36.1
|
1.0
|
C4A
|
C:HEM609
|
3.2
|
33.6
|
1.0
|
CHD
|
C:HEM609
|
3.2
|
26.7
|
1.0
|
CHC
|
C:HEM609
|
3.3
|
24.7
|
1.0
|
CE
|
C:MET72
|
3.3
|
23.6
|
1.0
|
CE1
|
C:HIS89
|
3.4
|
30.1
|
1.0
|
CD2
|
C:HIS89
|
3.4
|
31.1
|
1.0
|
CHA
|
C:HEM609
|
3.5
|
34.0
|
1.0
|
CHB
|
C:HEM609
|
3.5
|
34.0
|
1.0
|
CG
|
C:MET72
|
3.6
|
26.3
|
1.0
|
C3C
|
C:HEM609
|
4.1
|
27.0
|
1.0
|
C2C
|
C:HEM609
|
4.1
|
25.8
|
1.0
|
C2D
|
C:HEM609
|
4.2
|
25.5
|
1.0
|
C3B
|
C:HEM609
|
4.2
|
28.6
|
1.0
|
C2B
|
C:HEM609
|
4.3
|
30.6
|
1.0
|
C3D
|
C:HEM609
|
4.3
|
23.5
|
1.0
|
CB
|
C:MET72
|
4.3
|
29.0
|
1.0
|
C2A
|
C:HEM609
|
4.4
|
32.9
|
1.0
|
C3A
|
C:HEM609
|
4.4
|
32.2
|
1.0
|
ND1
|
C:HIS89
|
4.5
|
29.5
|
1.0
|
CG
|
C:HIS89
|
4.6
|
29.7
|
1.0
|
|
Iron binding site 2 out
of 5 in 1eys
Go back to
Iron Binding Sites List in 1eys
Iron binding site 2 out
of 5 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum
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 Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe610
b:25.8
occ:1.00
|
FE
|
C:HEM610
|
0.0
|
25.8
|
1.0
|
SD
|
C:MET108
|
1.9
|
31.2
|
1.0
|
NA
|
C:HEM610
|
2.0
|
27.9
|
1.0
|
ND
|
C:HEM610
|
2.0
|
22.7
|
1.0
|
NB
|
C:HEM610
|
2.0
|
20.0
|
1.0
|
NC
|
C:HEM610
|
2.1
|
24.9
|
1.0
|
NE2
|
C:HIS134
|
2.5
|
23.3
|
1.0
|
C1A
|
C:HEM610
|
2.9
|
23.5
|
1.0
|
C4D
|
C:HEM610
|
2.9
|
24.6
|
1.0
|
C4A
|
C:HEM610
|
3.0
|
22.2
|
1.0
|
C1B
|
C:HEM610
|
3.0
|
26.8
|
1.0
|
C1D
|
C:HEM610
|
3.1
|
25.8
|
1.0
|
C4C
|
C:HEM610
|
3.1
|
23.3
|
1.0
|
C4B
|
C:HEM610
|
3.2
|
27.7
|
1.0
|
CE1
|
C:HIS134
|
3.2
|
28.2
|
1.0
|
CG
|
C:MET108
|
3.2
|
30.1
|
1.0
|
CHA
|
C:HEM610
|
3.2
|
25.9
|
1.0
|
C1C
|
C:HEM610
|
3.2
|
21.0
|
1.0
|
CE
|
C:MET108
|
3.3
|
24.9
|
1.0
|
CHB
|
C:HEM610
|
3.3
|
25.1
|
1.0
|
CHD
|
C:HEM610
|
3.5
|
25.6
|
1.0
|
CD2
|
C:HIS134
|
3.6
|
24.0
|
1.0
|
CHC
|
C:HEM610
|
3.6
|
25.4
|
1.0
|
CB
|
C:MET108
|
4.0
|
30.3
|
1.0
|
C2A
|
C:HEM610
|
4.1
|
22.8
|
1.0
|
C3A
|
C:HEM610
|
4.2
|
24.8
|
1.0
|
C3D
|
C:HEM610
|
4.2
|
27.5
|
1.0
|
C2D
|
C:HEM610
|
4.2
|
25.3
|
1.0
|
C2B
|
C:HEM610
|
4.3
|
26.6
|
1.0
|
C3B
|
C:HEM610
|
4.3
|
23.4
|
1.0
|
C3C
|
C:HEM610
|
4.4
|
22.0
|
1.0
|
ND1
|
C:HIS134
|
4.4
|
28.0
|
1.0
|
C2C
|
C:HEM610
|
4.4
|
22.9
|
1.0
|
CG
|
C:HIS134
|
4.6
|
27.9
|
1.0
|
|
Iron binding site 3 out
of 5 in 1eys
Go back to
Iron Binding Sites List in 1eys
Iron binding site 3 out
of 5 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum
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 Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe611
b:22.5
occ:1.00
|
FE
|
C:HEM611
|
0.0
|
22.5
|
1.0
|
ND
|
C:HEM611
|
2.0
|
19.7
|
1.0
|
NC
|
C:HEM611
|
2.0
|
18.7
|
1.0
|
NA
|
C:HEM611
|
2.0
|
12.0
|
1.0
|
NB
|
C:HEM611
|
2.0
|
19.4
|
1.0
|
SD
|
C:MET214
|
2.1
|
25.8
|
1.0
|
NE2
|
C:HIS229
|
2.4
|
24.8
|
1.0
|
C4D
|
C:HEM611
|
3.0
|
15.0
|
1.0
|
C1D
|
C:HEM611
|
3.0
|
17.7
|
1.0
|
C4C
|
C:HEM611
|
3.0
|
22.2
|
1.0
|
C1B
|
C:HEM611
|
3.0
|
16.4
|
1.0
|
C1A
|
C:HEM611
|
3.0
|
20.0
|
1.0
|
C1C
|
C:HEM611
|
3.1
|
17.5
|
1.0
|
C4B
|
C:HEM611
|
3.1
|
15.9
|
1.0
|
CE
|
C:MET214
|
3.1
|
28.3
|
1.0
|
C4A
|
C:HEM611
|
3.1
|
16.5
|
1.0
|
CG
|
C:MET214
|
3.1
|
16.0
|
1.0
|
CD2
|
C:HIS229
|
3.4
|
28.5
|
1.0
|
CHD
|
C:HEM611
|
3.4
|
20.1
|
1.0
|
CHA
|
C:HEM611
|
3.4
|
18.8
|
1.0
|
CE1
|
C:HIS229
|
3.4
|
28.5
|
1.0
|
CHB
|
C:HEM611
|
3.4
|
17.1
|
1.0
|
CHC
|
C:HEM611
|
3.4
|
18.3
|
1.0
|
CB
|
C:MET214
|
3.9
|
18.7
|
1.0
|
C2D
|
C:HEM611
|
4.2
|
17.1
|
1.0
|
C3D
|
C:HEM611
|
4.2
|
19.7
|
1.0
|
C2B
|
C:HEM611
|
4.2
|
18.4
|
1.0
|
C3C
|
C:HEM611
|
4.2
|
18.7
|
1.0
|
C3B
|
C:HEM611
|
4.3
|
20.4
|
1.0
|
C2C
|
C:HEM611
|
4.3
|
18.0
|
1.0
|
C2A
|
C:HEM611
|
4.3
|
20.0
|
1.0
|
C3A
|
C:HEM611
|
4.3
|
16.6
|
1.0
|
ND1
|
C:HIS229
|
4.5
|
26.6
|
1.0
|
CG
|
C:HIS229
|
4.5
|
25.5
|
1.0
|
CA
|
C:MET214
|
4.9
|
17.3
|
1.0
|
|
Iron binding site 4 out
of 5 in 1eys
Go back to
Iron Binding Sites List in 1eys
Iron binding site 4 out
of 5 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum
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 Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe612
b:21.1
occ:1.00
|
FE
|
C:HEM612
|
0.0
|
21.1
|
1.0
|
NE2
|
C:HIS289
|
1.9
|
23.4
|
1.0
|
ND
|
C:HEM612
|
2.0
|
24.8
|
1.0
|
NA
|
C:HEM612
|
2.0
|
28.8
|
1.0
|
NB
|
C:HEM612
|
2.0
|
21.8
|
1.0
|
NC
|
C:HEM612
|
2.0
|
27.4
|
1.0
|
NE2
|
C:HIS122
|
2.4
|
26.3
|
1.0
|
CE1
|
C:HIS289
|
2.7
|
24.2
|
1.0
|
C1B
|
C:HEM612
|
3.0
|
25.4
|
1.0
|
C4D
|
C:HEM612
|
3.0
|
25.8
|
1.0
|
C4A
|
C:HEM612
|
3.0
|
25.7
|
1.0
|
C1A
|
C:HEM612
|
3.0
|
28.4
|
1.0
|
C1D
|
C:HEM612
|
3.0
|
26.9
|
1.0
|
C4C
|
C:HEM612
|
3.1
|
25.4
|
1.0
|
CD2
|
C:HIS289
|
3.1
|
28.5
|
1.0
|
C4B
|
C:HEM612
|
3.1
|
24.5
|
1.0
|
C1C
|
C:HEM612
|
3.1
|
24.9
|
1.0
|
CE1
|
C:HIS122
|
3.2
|
25.0
|
1.0
|
CHB
|
C:HEM612
|
3.4
|
26.2
|
1.0
|
CHA
|
C:HEM612
|
3.4
|
25.4
|
1.0
|
CHD
|
C:HEM612
|
3.4
|
26.6
|
1.0
|
CHC
|
C:HEM612
|
3.4
|
27.1
|
1.0
|
CD2
|
C:HIS122
|
3.5
|
26.8
|
1.0
|
ND1
|
C:HIS289
|
3.9
|
27.1
|
1.0
|
CG
|
C:HIS289
|
4.1
|
26.5
|
1.0
|
C2B
|
C:HEM612
|
4.2
|
24.1
|
1.0
|
C3D
|
C:HEM612
|
4.2
|
24.2
|
1.0
|
C2D
|
C:HEM612
|
4.2
|
23.6
|
1.0
|
C2A
|
C:HEM612
|
4.3
|
29.3
|
1.0
|
C3A
|
C:HEM612
|
4.3
|
27.9
|
1.0
|
C3B
|
C:HEM612
|
4.3
|
24.2
|
1.0
|
C3C
|
C:HEM612
|
4.3
|
27.1
|
1.0
|
C2C
|
C:HEM612
|
4.3
|
23.2
|
1.0
|
ND1
|
C:HIS122
|
4.4
|
24.4
|
1.0
|
CG
|
C:HIS122
|
4.6
|
24.1
|
1.0
|
CB
|
C:ALA250
|
4.9
|
28.2
|
1.0
|
CD
|
C:PRO295
|
4.9
|
32.8
|
1.0
|
|
Iron binding site 5 out
of 5 in 1eys
Go back to
Iron Binding Sites List in 1eys
Iron binding site 5 out
of 5 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Fe607
b:35.7
occ:1.00
|
NE2
|
M:HIS218
|
1.8
|
26.4
|
1.0
|
NE2
|
L:HIS198
|
1.9
|
33.2
|
1.0
|
NE2
|
M:HIS265
|
1.9
|
29.1
|
1.0
|
NE2
|
L:HIS238
|
2.0
|
25.3
|
1.0
|
OE2
|
M:GLU233
|
2.3
|
32.6
|
1.0
|
OE1
|
M:GLU233
|
2.4
|
38.2
|
1.0
|
CE1
|
M:HIS218
|
2.6
|
28.6
|
1.0
|
CD
|
M:GLU233
|
2.6
|
34.9
|
1.0
|
CE1
|
M:HIS265
|
2.7
|
30.7
|
1.0
|
CE1
|
L:HIS238
|
2.8
|
25.7
|
1.0
|
CE1
|
L:HIS198
|
2.9
|
35.7
|
1.0
|
CD2
|
L:HIS198
|
2.9
|
30.4
|
1.0
|
CD2
|
M:HIS218
|
3.0
|
26.2
|
1.0
|
CD2
|
M:HIS265
|
3.2
|
33.1
|
1.0
|
CD2
|
L:HIS238
|
3.2
|
23.9
|
1.0
|
ND1
|
M:HIS218
|
3.8
|
28.6
|
1.0
|
ND1
|
M:HIS265
|
3.9
|
26.7
|
1.0
|
ND1
|
L:HIS238
|
4.0
|
22.1
|
1.0
|
CG
|
M:HIS218
|
4.0
|
22.0
|
1.0
|
ND1
|
L:HIS198
|
4.0
|
32.1
|
1.0
|
CG
|
L:HIS198
|
4.0
|
31.5
|
1.0
|
CG
|
M:GLU233
|
4.1
|
34.0
|
1.0
|
CG
|
M:HIS265
|
4.1
|
28.7
|
1.0
|
CG
|
L:HIS238
|
4.2
|
23.7
|
1.0
|
CG1
|
M:ILE222
|
4.6
|
21.9
|
1.0
|
CG1
|
L:ILE202
|
4.7
|
33.9
|
1.0
|
O
|
M:HOH916
|
4.9
|
35.3
|
1.0
|
CB
|
M:GLU233
|
5.0
|
33.6
|
1.0
|
|
Reference:
T.Nogi,
I.Fathir,
M.Kobayashi,
T.Nozawa,
K.Miki.
Crystal Structures of Photosynthetic Reaction Center and High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum: Thermostability and Electron Transfer. Proc.Natl.Acad.Sci.Usa V. 97 13561 2000.
ISSN: ISSN 0027-8424
PubMed: 11095707
DOI: 10.1073/PNAS.240224997
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