Iron in PDB 2wjm: Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose)
Protein crystallography data
The structure of Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose), PDB code: 2wjm
was solved by
A.B.Woehri,
W.Y.Wahlgren,
E.Malmerberg,
L.C.Johansson,
R.Neutze,
G.Katona,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
176.78 /
1.95
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.450,
138.498,
177.770,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.3 /
20.1
|
Other elements in 2wjm:
The structure of Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose) also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose)
(pdb code 2wjm). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose), PDB code: 2wjm:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 2wjm
Go back to
Iron Binding Sites List in 2wjm
Iron binding site 1 out
of 5 in the Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:29.4
occ:1.00
|
FE
|
C:HEC401
|
0.0
|
29.4
|
1.0
|
NE2
|
C:HIS91
|
2.0
|
28.8
|
1.0
|
NB
|
C:HEC401
|
2.0
|
31.6
|
1.0
|
NC
|
C:HEC401
|
2.0
|
29.2
|
1.0
|
NA
|
C:HEC401
|
2.1
|
30.4
|
1.0
|
ND
|
C:HEC401
|
2.1
|
30.5
|
1.0
|
SD
|
C:MET74
|
2.3
|
29.8
|
1.0
|
CE1
|
C:HIS91
|
3.0
|
29.0
|
1.0
|
CD2
|
C:HIS91
|
3.0
|
29.0
|
1.0
|
C4C
|
C:HEC401
|
3.0
|
30.4
|
1.0
|
C1B
|
C:HEC401
|
3.1
|
29.4
|
1.0
|
C4D
|
C:HEC401
|
3.1
|
30.9
|
1.0
|
C1D
|
C:HEC401
|
3.1
|
28.6
|
1.0
|
C4B
|
C:HEC401
|
3.1
|
32.2
|
1.0
|
C4A
|
C:HEC401
|
3.1
|
29.0
|
1.0
|
C1A
|
C:HEC401
|
3.1
|
29.2
|
1.0
|
C1C
|
C:HEC401
|
3.1
|
30.9
|
1.0
|
CHD
|
C:HEC401
|
3.4
|
29.8
|
1.0
|
CG
|
C:MET74
|
3.4
|
29.9
|
1.0
|
CE
|
C:MET74
|
3.4
|
29.9
|
1.0
|
CHB
|
C:HEC401
|
3.4
|
30.6
|
1.0
|
CHA
|
C:HEC401
|
3.4
|
29.8
|
1.0
|
CHC
|
C:HEC401
|
3.5
|
31.4
|
1.0
|
ND1
|
C:HIS91
|
4.1
|
27.1
|
1.0
|
CG
|
C:HIS91
|
4.2
|
28.0
|
1.0
|
CB
|
C:MET74
|
4.3
|
29.7
|
1.0
|
C3C
|
C:HEC401
|
4.3
|
29.7
|
1.0
|
C3D
|
C:HEC401
|
4.3
|
30.2
|
1.0
|
C2B
|
C:HEC401
|
4.3
|
32.6
|
1.0
|
C2D
|
C:HEC401
|
4.3
|
27.9
|
1.0
|
C3B
|
C:HEC401
|
4.3
|
31.6
|
1.0
|
C2C
|
C:HEC401
|
4.3
|
29.6
|
1.0
|
C2A
|
C:HEC401
|
4.3
|
29.2
|
1.0
|
C3A
|
C:HEC401
|
4.3
|
29.4
|
1.0
|
|
Iron binding site 2 out
of 5 in 2wjm
Go back to
Iron Binding Sites List in 2wjm
Iron binding site 2 out
of 5 in the Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe402
b:27.2
occ:1.00
|
FE
|
C:HEC402
|
0.0
|
27.2
|
1.0
|
NA
|
C:HEC402
|
2.0
|
25.7
|
1.0
|
NC
|
C:HEC402
|
2.0
|
26.6
|
1.0
|
ND
|
C:HEC402
|
2.1
|
28.4
|
1.0
|
NE2
|
C:HIS136
|
2.1
|
31.0
|
1.0
|
NB
|
C:HEC402
|
2.1
|
26.2
|
1.0
|
SD
|
C:MET110
|
2.4
|
29.5
|
1.0
|
CE1
|
C:HIS136
|
3.0
|
28.3
|
1.0
|
C4A
|
C:HEC402
|
3.0
|
26.1
|
1.0
|
C4C
|
C:HEC402
|
3.0
|
27.8
|
1.0
|
C1A
|
C:HEC402
|
3.0
|
28.2
|
1.0
|
C1D
|
C:HEC402
|
3.1
|
26.8
|
1.0
|
C1C
|
C:HEC402
|
3.1
|
27.6
|
1.0
|
C1B
|
C:HEC402
|
3.1
|
24.4
|
1.0
|
C4D
|
C:HEC402
|
3.1
|
26.2
|
1.0
|
CD2
|
C:HIS136
|
3.1
|
30.1
|
1.0
|
C4B
|
C:HEC402
|
3.2
|
27.8
|
1.0
|
CHD
|
C:HEC402
|
3.4
|
26.2
|
1.0
|
CHB
|
C:HEC402
|
3.4
|
26.7
|
1.0
|
CG
|
C:MET110
|
3.4
|
30.3
|
1.0
|
CHA
|
C:HEC402
|
3.4
|
27.2
|
1.0
|
CE
|
C:MET110
|
3.5
|
27.7
|
1.0
|
CHC
|
C:HEC402
|
3.5
|
25.9
|
1.0
|
ND1
|
C:HIS136
|
4.2
|
29.0
|
1.0
|
CB
|
C:MET110
|
4.2
|
30.0
|
1.0
|
C3A
|
C:HEC402
|
4.2
|
26.1
|
1.0
|
C3C
|
C:HEC402
|
4.2
|
26.0
|
1.0
|
CG
|
C:HIS136
|
4.2
|
29.0
|
1.0
|
C2A
|
C:HEC402
|
4.3
|
26.8
|
1.0
|
C2C
|
C:HEC402
|
4.3
|
25.9
|
1.0
|
C2D
|
C:HEC402
|
4.3
|
26.1
|
1.0
|
C3D
|
C:HEC402
|
4.3
|
26.6
|
1.0
|
C2B
|
C:HEC402
|
4.3
|
27.6
|
1.0
|
C3B
|
C:HEC402
|
4.4
|
26.9
|
1.0
|
CG
|
C:PRO142
|
5.0
|
30.0
|
1.0
|
|
Iron binding site 3 out
of 5 in 2wjm
Go back to
Iron Binding Sites List in 2wjm
Iron binding site 3 out
of 5 in the Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe403
b:24.6
occ:1.00
|
FE
|
C:HEC403
|
0.0
|
24.6
|
1.0
|
NC
|
C:HEC403
|
2.0
|
23.7
|
1.0
|
NB
|
C:HEC403
|
2.1
|
23.4
|
1.0
|
NA
|
C:HEC403
|
2.1
|
24.4
|
1.0
|
NE2
|
C:HIS248
|
2.1
|
31.9
|
1.0
|
ND
|
C:HEC403
|
2.1
|
22.5
|
1.0
|
SD
|
C:MET233
|
2.3
|
31.4
|
1.0
|
C4C
|
C:HEC403
|
3.0
|
23.9
|
1.0
|
C4B
|
C:HEC403
|
3.1
|
24.2
|
1.0
|
C1C
|
C:HEC403
|
3.1
|
25.4
|
1.0
|
CD2
|
C:HIS248
|
3.1
|
30.7
|
1.0
|
C1D
|
C:HEC403
|
3.1
|
24.4
|
1.0
|
C1B
|
C:HEC403
|
3.1
|
23.8
|
1.0
|
C1A
|
C:HEC403
|
3.1
|
26.1
|
1.0
|
C4A
|
C:HEC403
|
3.1
|
23.2
|
1.0
|
CE1
|
C:HIS248
|
3.1
|
33.1
|
1.0
|
C4D
|
C:HEC403
|
3.1
|
25.7
|
1.0
|
CHD
|
C:HEC403
|
3.4
|
23.1
|
1.0
|
CG
|
C:MET233
|
3.4
|
31.8
|
1.0
|
CE
|
C:MET233
|
3.4
|
31.8
|
1.0
|
CHC
|
C:HEC403
|
3.4
|
22.0
|
1.0
|
CHB
|
C:HEC403
|
3.4
|
23.7
|
1.0
|
CHA
|
C:HEC403
|
3.5
|
24.7
|
1.0
|
ND1
|
C:HIS248
|
4.2
|
31.3
|
1.0
|
CG
|
C:HIS248
|
4.2
|
30.8
|
1.0
|
C3C
|
C:HEC403
|
4.3
|
23.6
|
1.0
|
C3B
|
C:HEC403
|
4.3
|
24.8
|
1.0
|
C2B
|
C:HEC403
|
4.3
|
22.3
|
1.0
|
C2C
|
C:HEC403
|
4.3
|
23.9
|
1.0
|
CB
|
C:MET233
|
4.3
|
29.9
|
1.0
|
C2A
|
C:HEC403
|
4.3
|
25.2
|
1.0
|
C2D
|
C:HEC403
|
4.3
|
23.5
|
1.0
|
C3A
|
C:HEC403
|
4.3
|
25.4
|
1.0
|
C3D
|
C:HEC403
|
4.4
|
23.4
|
1.0
|
|
Iron binding site 4 out
of 5 in 2wjm
Go back to
Iron Binding Sites List in 2wjm
Iron binding site 4 out
of 5 in the Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe404
b:25.4
occ:1.00
|
FE
|
C:HEC404
|
0.0
|
25.4
|
1.0
|
NC
|
C:HEC404
|
2.0
|
23.7
|
1.0
|
NA
|
C:HEC404
|
2.0
|
24.9
|
1.0
|
ND
|
C:HEC404
|
2.1
|
24.1
|
1.0
|
NB
|
C:HEC404
|
2.1
|
24.2
|
1.0
|
NE2
|
C:HIS124
|
2.1
|
31.5
|
1.0
|
NE2
|
C:HIS309
|
2.1
|
31.3
|
1.0
|
CE1
|
C:HIS124
|
3.0
|
31.0
|
1.0
|
C4C
|
C:HEC404
|
3.0
|
23.0
|
1.0
|
C1A
|
C:HEC404
|
3.0
|
24.9
|
1.0
|
C1C
|
C:HEC404
|
3.0
|
23.1
|
1.0
|
C4A
|
C:HEC404
|
3.0
|
23.6
|
1.0
|
C1D
|
C:HEC404
|
3.1
|
24.0
|
1.0
|
C4D
|
C:HEC404
|
3.1
|
24.7
|
1.0
|
CD2
|
C:HIS309
|
3.1
|
30.4
|
1.0
|
C4B
|
C:HEC404
|
3.1
|
24.0
|
1.0
|
CE1
|
C:HIS309
|
3.1
|
30.5
|
1.0
|
C1B
|
C:HEC404
|
3.1
|
21.6
|
1.0
|
CD2
|
C:HIS124
|
3.2
|
31.3
|
1.0
|
CHD
|
C:HEC404
|
3.4
|
23.0
|
1.0
|
CHA
|
C:HEC404
|
3.4
|
23.2
|
1.0
|
CHC
|
C:HEC404
|
3.4
|
24.1
|
1.0
|
CHB
|
C:HEC404
|
3.5
|
24.3
|
1.0
|
ND1
|
C:HIS124
|
4.1
|
28.7
|
1.0
|
ND1
|
C:HIS309
|
4.2
|
30.9
|
1.0
|
C2C
|
C:HEC404
|
4.2
|
24.6
|
1.0
|
C2A
|
C:HEC404
|
4.2
|
24.8
|
1.0
|
C3A
|
C:HEC404
|
4.2
|
21.8
|
1.0
|
C3C
|
C:HEC404
|
4.2
|
22.5
|
1.0
|
CG
|
C:HIS309
|
4.2
|
29.9
|
1.0
|
CG
|
C:HIS124
|
4.2
|
30.8
|
1.0
|
C2D
|
C:HEC404
|
4.3
|
25.0
|
1.0
|
C3D
|
C:HEC404
|
4.3
|
26.1
|
1.0
|
C3B
|
C:HEC404
|
4.3
|
20.8
|
1.0
|
C2B
|
C:HEC404
|
4.3
|
22.9
|
1.0
|
CD
|
C:PRO315
|
4.9
|
32.7
|
1.0
|
CG
|
C:PRO315
|
4.9
|
31.4
|
1.0
|
|
Iron binding site 5 out
of 5 in 2wjm
Go back to
Iron Binding Sites List in 2wjm
Iron binding site 5 out
of 5 in the Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Lipidic Sponge Phase Crystal Structure of the Photosynthetic Reaction Centre From Blastochloris Viridis (Low Dose) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Fe306
b:26.0
occ:1.00
|
NE2
|
M:HIS217
|
2.2
|
31.1
|
1.0
|
NE2
|
L:HIS190
|
2.3
|
28.9
|
1.0
|
OE2
|
M:GLU232
|
2.3
|
29.9
|
1.0
|
NE2
|
L:HIS230
|
2.3
|
32.3
|
1.0
|
NE2
|
M:HIS264
|
2.3
|
32.4
|
1.0
|
OE1
|
M:GLU232
|
2.4
|
32.0
|
1.0
|
CD
|
M:GLU232
|
2.6
|
29.9
|
1.0
|
CE1
|
M:HIS217
|
3.0
|
31.7
|
1.0
|
CE1
|
L:HIS230
|
3.2
|
31.2
|
1.0
|
CE1
|
M:HIS264
|
3.2
|
31.2
|
1.0
|
CE1
|
L:HIS190
|
3.2
|
30.8
|
1.0
|
CD2
|
M:HIS217
|
3.2
|
31.4
|
1.0
|
CD2
|
L:HIS190
|
3.3
|
31.2
|
1.0
|
CD2
|
M:HIS264
|
3.3
|
31.6
|
1.0
|
CD2
|
L:HIS230
|
3.3
|
30.4
|
1.0
|
CG
|
M:GLU232
|
4.1
|
28.6
|
1.0
|
ND1
|
M:HIS217
|
4.2
|
32.0
|
1.0
|
ND1
|
L:HIS230
|
4.3
|
30.3
|
1.0
|
ND1
|
M:HIS264
|
4.3
|
31.2
|
1.0
|
ND1
|
L:HIS190
|
4.3
|
31.1
|
1.0
|
CG
|
M:HIS217
|
4.3
|
30.5
|
1.0
|
CG
|
L:HIS190
|
4.4
|
32.1
|
1.0
|
CG
|
L:HIS230
|
4.4
|
30.8
|
1.0
|
CG
|
M:HIS264
|
4.4
|
31.6
|
1.0
|
CG1
|
M:ILE221
|
4.5
|
31.7
|
1.0
|
CG1
|
L:ILE194
|
4.6
|
30.4
|
1.0
|
O
|
M:HOH549
|
4.7
|
25.2
|
1.0
|
CB
|
M:GLU232
|
5.0
|
29.2
|
1.0
|
|
Reference:
A.B.Wohri,
W.Y.Wahlgren,
E.Malmerberg,
L.C.Johansson,
R.Neutze,
G.Katona.
Lipidic Sponge Phase Crystal Structure of A Photosynthetic Reaction Center Reveals Lipids on the Protein Surface. Biochemistry V. 48 9831 2009.
ISSN: ISSN 1520-4995
PubMed: 19743880
DOI: 10.1021/BI900545E
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