Magnesium 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:
Magnesium Binding Sites:
The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum, PDB code: 1eys:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1eys
Go back to
Magnesium Binding Sites List in 1eys
Magnesium binding site 1 out
of 4 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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
|
L:Mg602
b:18.9
occ:1.00
|
MG
|
L:BCL602
|
0.0
|
18.9
|
1.0
|
NB
|
L:BCL602
|
2.0
|
15.6
|
1.0
|
ND
|
L:BCL602
|
2.0
|
18.9
|
1.0
|
NC
|
L:BCL602
|
2.1
|
12.8
|
1.0
|
NA
|
L:BCL602
|
2.2
|
12.6
|
1.0
|
NE2
|
L:HIS181
|
2.8
|
19.7
|
1.0
|
C4D
|
L:BCL602
|
2.9
|
19.7
|
1.0
|
C1B
|
L:BCL602
|
3.0
|
21.1
|
1.0
|
C1D
|
L:BCL602
|
3.0
|
17.4
|
1.0
|
C4B
|
L:BCL602
|
3.1
|
15.6
|
1.0
|
C1C
|
L:BCL602
|
3.1
|
15.6
|
1.0
|
C4A
|
L:BCL602
|
3.1
|
15.6
|
1.0
|
C4C
|
L:BCL602
|
3.1
|
18.5
|
1.0
|
C1A
|
L:BCL602
|
3.2
|
15.1
|
1.0
|
CBB
|
M:BCL603
|
3.4
|
12.0
|
1.0
|
OBB
|
M:BCL603
|
3.4
|
19.2
|
1.0
|
CAB
|
M:BCL603
|
3.4
|
23.0
|
1.0
|
CHD
|
L:BCL602
|
3.4
|
19.7
|
1.0
|
CHC
|
L:BCL602
|
3.4
|
16.9
|
1.0
|
CHB
|
L:BCL602
|
3.4
|
16.9
|
1.0
|
CHA
|
L:BCL602
|
3.4
|
14.4
|
1.0
|
CE1
|
L:HIS181
|
3.7
|
20.0
|
1.0
|
CD2
|
L:HIS181
|
3.8
|
15.2
|
1.0
|
C3D
|
L:BCL602
|
4.2
|
20.2
|
1.0
|
C3B
|
M:BCL603
|
4.2
|
18.8
|
1.0
|
C2D
|
L:BCL602
|
4.2
|
17.3
|
1.0
|
C2B
|
L:BCL602
|
4.3
|
15.0
|
1.0
|
C3B
|
L:BCL602
|
4.3
|
19.4
|
1.0
|
C3C
|
L:BCL602
|
4.3
|
17.1
|
1.0
|
C2C
|
L:BCL602
|
4.4
|
17.3
|
1.0
|
C3A
|
L:BCL602
|
4.4
|
18.9
|
1.0
|
C2A
|
L:BCL602
|
4.4
|
17.6
|
1.0
|
ND1
|
L:HIS181
|
4.8
|
18.6
|
1.0
|
C4B
|
M:BCL603
|
4.9
|
17.6
|
1.0
|
CBD
|
L:BCL602
|
4.9
|
17.6
|
1.0
|
CG
|
L:HIS181
|
4.9
|
18.8
|
1.0
|
CHC
|
M:BCL603
|
5.0
|
21.3
|
1.0
|
CG1
|
L:VAL165
|
5.0
|
18.9
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1eys
Go back to
Magnesium Binding Sites List in 1eys
Magnesium binding site 2 out
of 4 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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
|
L:Mg604
b:26.2
occ:1.00
|
MG
|
L:BCL604
|
0.0
|
26.2
|
1.0
|
ND
|
L:BCL604
|
2.0
|
24.5
|
1.0
|
NB
|
L:BCL604
|
2.0
|
23.9
|
1.0
|
NC
|
L:BCL604
|
2.1
|
24.3
|
1.0
|
NA
|
L:BCL604
|
2.1
|
22.7
|
1.0
|
NE2
|
L:HIS161
|
2.8
|
17.4
|
1.0
|
C4D
|
L:BCL604
|
3.0
|
22.7
|
1.0
|
C1D
|
L:BCL604
|
3.0
|
20.2
|
1.0
|
C1B
|
L:BCL604
|
3.1
|
26.0
|
1.0
|
C4B
|
L:BCL604
|
3.1
|
22.3
|
1.0
|
C1C
|
L:BCL604
|
3.1
|
23.6
|
1.0
|
C4A
|
L:BCL604
|
3.1
|
23.6
|
1.0
|
C4C
|
L:BCL604
|
3.1
|
22.6
|
1.0
|
C1A
|
L:BCL604
|
3.2
|
20.5
|
1.0
|
CHD
|
L:BCL604
|
3.4
|
22.1
|
1.0
|
CHC
|
L:BCL604
|
3.4
|
21.0
|
1.0
|
CHB
|
L:BCL604
|
3.4
|
23.6
|
1.0
|
CHA
|
L:BCL604
|
3.5
|
20.1
|
1.0
|
CE1
|
L:HIS161
|
3.7
|
12.3
|
1.0
|
CD2
|
L:HIS161
|
3.8
|
17.9
|
1.0
|
CBB
|
L:BPH606
|
3.8
|
16.1
|
1.0
|
C3D
|
L:BCL604
|
4.2
|
19.1
|
1.0
|
C2D
|
L:BCL604
|
4.2
|
19.0
|
1.0
|
C3B
|
L:BCL604
|
4.3
|
19.4
|
1.0
|
C2B
|
L:BCL604
|
4.3
|
27.1
|
1.0
|
C3C
|
L:BCL604
|
4.3
|
23.8
|
1.0
|
C2C
|
L:BCL604
|
4.3
|
20.5
|
1.0
|
C2A
|
L:BCL604
|
4.4
|
15.7
|
1.0
|
C3A
|
L:BCL604
|
4.4
|
19.7
|
1.0
|
CE2
|
M:TYR209
|
4.5
|
17.4
|
1.0
|
CBA
|
L:BCL604
|
4.6
|
17.2
|
1.0
|
ND1
|
L:HIS161
|
4.8
|
16.9
|
1.0
|
CG
|
L:HIS161
|
4.9
|
14.8
|
1.0
|
CBD
|
L:BCL604
|
5.0
|
19.2
|
1.0
|
C20
|
L:BPH606
|
5.0
|
15.6
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1eys
Go back to
Magnesium Binding Sites List in 1eys
Magnesium binding site 3 out
of 4 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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
|
M:Mg601
b:26.6
occ:1.00
|
MG
|
M:BCL601
|
0.0
|
26.6
|
1.0
|
ND
|
M:BCL601
|
2.0
|
21.7
|
1.0
|
NB
|
M:BCL601
|
2.0
|
23.3
|
1.0
|
NC
|
M:BCL601
|
2.1
|
16.2
|
1.0
|
NA
|
M:BCL601
|
2.1
|
21.2
|
1.0
|
NE2
|
M:HIS181
|
2.8
|
24.7
|
1.0
|
C4D
|
M:BCL601
|
3.0
|
23.8
|
1.0
|
C1D
|
M:BCL601
|
3.0
|
22.0
|
1.0
|
C1C
|
M:BCL601
|
3.1
|
19.1
|
1.0
|
C4B
|
M:BCL601
|
3.1
|
22.5
|
1.0
|
C1B
|
M:BCL601
|
3.1
|
23.6
|
1.0
|
C4C
|
M:BCL601
|
3.1
|
18.8
|
1.0
|
C4A
|
M:BCL601
|
3.1
|
24.5
|
1.0
|
C1A
|
M:BCL601
|
3.2
|
27.0
|
1.0
|
CHD
|
M:BCL601
|
3.4
|
19.6
|
1.0
|
CHC
|
M:BCL601
|
3.4
|
20.7
|
1.0
|
CHB
|
M:BCL601
|
3.4
|
20.6
|
1.0
|
CHA
|
M:BCL601
|
3.5
|
22.4
|
1.0
|
CD2
|
M:HIS181
|
3.5
|
24.0
|
1.0
|
CE1
|
M:HIS181
|
3.8
|
24.3
|
1.0
|
CBB
|
M:BPH605
|
3.9
|
26.9
|
1.0
|
C3D
|
M:BCL601
|
4.2
|
20.3
|
1.0
|
C2D
|
M:BCL601
|
4.2
|
19.8
|
1.0
|
C3C
|
M:BCL601
|
4.3
|
18.3
|
1.0
|
C3B
|
M:BCL601
|
4.3
|
23.4
|
1.0
|
C2B
|
M:BCL601
|
4.3
|
20.9
|
1.0
|
C2C
|
M:BCL601
|
4.3
|
21.0
|
1.0
|
C3A
|
M:BCL601
|
4.4
|
30.2
|
1.0
|
C2A
|
M:BCL601
|
4.4
|
33.2
|
1.0
|
CE2
|
L:PHE189
|
4.5
|
27.8
|
1.0
|
CG
|
M:HIS181
|
4.8
|
23.8
|
1.0
|
ND1
|
M:HIS181
|
4.9
|
24.5
|
1.0
|
CBD
|
M:BCL601
|
5.0
|
20.2
|
1.0
|
CAA
|
M:BCL601
|
5.0
|
30.3
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1eys
Go back to
Magnesium Binding Sites List in 1eys
Magnesium binding site 4 out
of 4 in the Crystal Structure of Photosynthetic Reaction Center From A Thermophilic Bacterium, Thermochromatium Tepidum
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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
|
M:Mg603
b:24.2
occ:1.00
|
MG
|
M:BCL603
|
0.0
|
24.2
|
1.0
|
ND
|
M:BCL603
|
2.0
|
22.8
|
1.0
|
NB
|
M:BCL603
|
2.0
|
18.6
|
1.0
|
NC
|
M:BCL603
|
2.1
|
22.0
|
1.0
|
NA
|
M:BCL603
|
2.2
|
19.4
|
1.0
|
NE2
|
M:HIS201
|
2.7
|
15.4
|
1.0
|
C4D
|
M:BCL603
|
3.0
|
24.1
|
1.0
|
C1D
|
M:BCL603
|
3.0
|
20.9
|
1.0
|
CBB
|
L:BCL602
|
3.0
|
16.3
|
1.0
|
C1C
|
M:BCL603
|
3.1
|
21.2
|
1.0
|
C4B
|
M:BCL603
|
3.1
|
17.6
|
1.0
|
C1B
|
M:BCL603
|
3.1
|
16.6
|
1.0
|
C4C
|
M:BCL603
|
3.1
|
16.0
|
1.0
|
C4A
|
M:BCL603
|
3.1
|
17.7
|
1.0
|
C1A
|
M:BCL603
|
3.2
|
22.0
|
1.0
|
CHD
|
M:BCL603
|
3.4
|
19.5
|
1.0
|
CAB
|
L:BCL602
|
3.4
|
20.6
|
1.0
|
CHC
|
M:BCL603
|
3.4
|
21.3
|
1.0
|
CHA
|
M:BCL603
|
3.5
|
25.4
|
1.0
|
CHB
|
M:BCL603
|
3.5
|
17.1
|
1.0
|
CE1
|
M:HIS201
|
3.6
|
11.1
|
1.0
|
OBB
|
L:BCL602
|
3.7
|
27.2
|
1.0
|
CD2
|
M:HIS201
|
3.8
|
7.0
|
1.0
|
C3D
|
M:BCL603
|
4.2
|
23.2
|
1.0
|
C3B
|
L:BCL602
|
4.2
|
19.4
|
1.0
|
C2D
|
M:BCL603
|
4.2
|
24.7
|
1.0
|
C2B
|
M:BCL603
|
4.3
|
17.9
|
1.0
|
C3B
|
M:BCL603
|
4.3
|
18.8
|
1.0
|
C2C
|
M:BCL603
|
4.3
|
23.6
|
1.0
|
C3C
|
M:BCL603
|
4.3
|
17.6
|
1.0
|
C3A
|
M:BCL603
|
4.4
|
17.8
|
1.0
|
C2A
|
M:BCL603
|
4.5
|
14.9
|
1.0
|
ND1
|
M:HIS201
|
4.8
|
11.4
|
1.0
|
CG
|
M:HIS201
|
4.9
|
14.5
|
1.0
|
C4B
|
L:BCL602
|
4.9
|
15.6
|
1.0
|
C2B
|
L:BCL602
|
4.9
|
15.0
|
1.0
|
CBD
|
M:BCL603
|
4.9
|
23.6
|
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
Page generated: Tue Aug 13 03:04:35 2024
|