Magnesium in PDB 2uww: X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 6.5 in the Neutral State
Protein crystallography data
The structure of X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 6.5 in the Neutral State, PDB code: 2uww
was solved by
J.Koepke,
R.Diehm,
G.Fritzsch,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
119.52 /
2.05
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
138.690,
138.690,
184.613,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20.5 /
23.3
|
Other elements in 2uww:
The structure of X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 6.5 in the Neutral State also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 6.5 in the Neutral State
(pdb code 2uww). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 6.5 in the Neutral State, PDB code: 2uww:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 2uww
Go back to
Magnesium Binding Sites List in 2uww
Magnesium binding site 1 out
of 4 in the X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 6.5 in the Neutral State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 6.5 in the Neutral State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg1282
b:26.2
occ:1.00
|
MG
|
L:BCL1282
|
0.0
|
26.2
|
1.0
|
ND
|
L:BCL1282
|
2.0
|
24.7
|
1.0
|
NC
|
L:BCL1282
|
2.0
|
26.2
|
1.0
|
NB
|
L:BCL1282
|
2.1
|
25.4
|
1.0
|
NE2
|
L:HIS153
|
2.1
|
27.6
|
1.0
|
NA
|
L:BCL1282
|
2.1
|
24.7
|
1.0
|
C4D
|
L:BCL1282
|
2.9
|
22.8
|
1.0
|
C1C
|
L:BCL1282
|
3.0
|
25.9
|
1.0
|
CD2
|
L:HIS153
|
3.0
|
26.9
|
1.0
|
C4A
|
L:BCL1282
|
3.1
|
24.8
|
1.0
|
C1D
|
L:BCL1282
|
3.1
|
25.0
|
1.0
|
C4C
|
L:BCL1282
|
3.1
|
25.2
|
1.0
|
C4B
|
L:BCL1282
|
3.1
|
25.7
|
1.0
|
CE1
|
L:HIS153
|
3.1
|
30.1
|
1.0
|
C1A
|
L:BCL1282
|
3.1
|
23.9
|
1.0
|
C1B
|
L:BCL1282
|
3.1
|
24.1
|
1.0
|
CHA
|
L:BCL1282
|
3.4
|
24.0
|
1.0
|
CHC
|
L:BCL1282
|
3.4
|
25.1
|
1.0
|
CHB
|
L:BCL1282
|
3.5
|
23.3
|
1.0
|
CHD
|
L:BCL1282
|
3.5
|
25.3
|
1.0
|
C3D
|
L:BCL1282
|
4.1
|
23.3
|
1.0
|
C2D
|
L:BCL1282
|
4.2
|
24.5
|
1.0
|
ND1
|
L:HIS153
|
4.2
|
29.5
|
1.0
|
CG
|
L:HIS153
|
4.2
|
29.0
|
1.0
|
C3B
|
L:BCL1282
|
4.3
|
26.4
|
1.0
|
C2B
|
L:BCL1282
|
4.3
|
25.1
|
1.0
|
OBB
|
L:BPH1288
|
4.3
|
34.0
|
1.0
|
C2C
|
L:BCL1282
|
4.3
|
25.3
|
1.0
|
C3A
|
L:BCL1282
|
4.4
|
26.1
|
1.0
|
C3C
|
L:BCL1282
|
4.4
|
26.5
|
1.0
|
C2A
|
L:BCL1282
|
4.4
|
25.4
|
1.0
|
CE2
|
M:TYR210
|
4.6
|
28.0
|
1.0
|
CBC
|
L:BCL1282
|
4.8
|
25.6
|
1.0
|
CBA
|
L:BCL1282
|
4.8
|
26.7
|
1.0
|
CD1
|
L:LEU154
|
4.8
|
32.3
|
1.0
|
C20
|
L:BPH1288
|
4.9
|
29.5
|
1.0
|
CBD
|
L:BCL1282
|
4.9
|
26.0
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 2uww
Go back to
Magnesium Binding Sites List in 2uww
Magnesium binding site 2 out
of 4 in the X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 6.5 in the Neutral State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 6.5 in the Neutral State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg1290
b:26.9
occ:1.00
|
MG
|
L:BCL1290
|
0.0
|
26.9
|
1.0
|
ND
|
L:BCL1290
|
2.0
|
26.3
|
1.0
|
NB
|
L:BCL1290
|
2.1
|
25.9
|
1.0
|
NC
|
L:BCL1290
|
2.1
|
26.9
|
1.0
|
NA
|
L:BCL1290
|
2.1
|
27.2
|
1.0
|
NE2
|
L:HIS173
|
2.2
|
24.1
|
1.0
|
C4D
|
L:BCL1290
|
3.0
|
28.4
|
1.0
|
C4C
|
L:BCL1290
|
3.0
|
26.9
|
1.0
|
C4A
|
L:BCL1290
|
3.0
|
27.4
|
1.0
|
C1C
|
L:BCL1290
|
3.0
|
25.8
|
1.0
|
C1D
|
L:BCL1290
|
3.1
|
26.9
|
1.0
|
C1B
|
L:BCL1290
|
3.1
|
26.3
|
1.0
|
C4B
|
L:BCL1290
|
3.1
|
26.7
|
1.0
|
CE1
|
L:HIS173
|
3.1
|
22.5
|
1.0
|
C1A
|
L:BCL1290
|
3.2
|
26.0
|
1.0
|
CD2
|
L:HIS173
|
3.3
|
23.0
|
1.0
|
CHC
|
L:BCL1290
|
3.4
|
27.4
|
1.0
|
CHD
|
L:BCL1290
|
3.4
|
25.4
|
1.0
|
CHB
|
L:BCL1290
|
3.4
|
24.6
|
1.0
|
CHA
|
L:BCL1290
|
3.5
|
27.0
|
1.0
|
OBB
|
M:BCL1305
|
3.6
|
32.8
|
1.0
|
CAB
|
M:BCL1305
|
3.7
|
25.4
|
1.0
|
CBB
|
M:BCL1305
|
4.0
|
20.8
|
1.0
|
C3D
|
L:BCL1290
|
4.2
|
27.4
|
1.0
|
C2D
|
L:BCL1290
|
4.2
|
28.5
|
1.0
|
C2B
|
L:BCL1290
|
4.3
|
26.4
|
1.0
|
C3B
|
L:BCL1290
|
4.3
|
24.9
|
1.0
|
ND1
|
L:HIS173
|
4.3
|
23.8
|
1.0
|
C3A
|
L:BCL1290
|
4.4
|
27.7
|
1.0
|
C3C
|
L:BCL1290
|
4.4
|
25.1
|
1.0
|
C2C
|
L:BCL1290
|
4.4
|
26.9
|
1.0
|
CG
|
L:HIS173
|
4.4
|
24.9
|
1.0
|
C2A
|
L:BCL1290
|
4.5
|
27.4
|
1.0
|
C3B
|
M:BCL1305
|
4.5
|
23.9
|
1.0
|
CD1
|
L:PHE167
|
4.7
|
29.8
|
1.0
|
CBD
|
L:BCL1290
|
4.9
|
25.7
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 2uww
Go back to
Magnesium Binding Sites List in 2uww
Magnesium binding site 3 out
of 4 in the X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 6.5 in the Neutral State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 6.5 in the Neutral State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg1304
b:27.9
occ:1.00
|
MG
|
M:BCL1304
|
0.0
|
27.9
|
1.0
|
ND
|
M:BCL1304
|
2.0
|
26.1
|
1.0
|
NB
|
M:BCL1304
|
2.0
|
28.0
|
1.0
|
NE2
|
M:HIS182
|
2.0
|
29.0
|
1.0
|
NA
|
M:BCL1304
|
2.1
|
26.2
|
1.0
|
NC
|
M:BCL1304
|
2.1
|
27.4
|
1.0
|
C4D
|
M:BCL1304
|
2.9
|
24.5
|
1.0
|
CD2
|
M:HIS182
|
3.0
|
29.9
|
1.0
|
C1C
|
M:BCL1304
|
3.0
|
27.6
|
1.0
|
C4A
|
M:BCL1304
|
3.0
|
28.4
|
1.0
|
C4C
|
M:BCL1304
|
3.0
|
27.5
|
1.0
|
C1D
|
M:BCL1304
|
3.1
|
24.2
|
1.0
|
C1B
|
M:BCL1304
|
3.1
|
28.0
|
1.0
|
C4B
|
M:BCL1304
|
3.1
|
28.3
|
1.0
|
CE1
|
M:HIS182
|
3.1
|
30.4
|
1.0
|
C1A
|
M:BCL1304
|
3.1
|
26.9
|
1.0
|
CHB
|
M:BCL1304
|
3.4
|
27.1
|
1.0
|
CHD
|
M:BCL1304
|
3.4
|
25.4
|
1.0
|
CHA
|
M:BCL1304
|
3.4
|
26.1
|
1.0
|
CHC
|
M:BCL1304
|
3.4
|
26.8
|
1.0
|
C3D
|
M:BCL1304
|
4.1
|
24.9
|
1.0
|
CG
|
M:HIS182
|
4.2
|
31.1
|
1.0
|
C2D
|
M:BCL1304
|
4.2
|
24.4
|
1.0
|
ND1
|
M:HIS182
|
4.2
|
30.9
|
1.0
|
C2B
|
M:BCL1304
|
4.2
|
27.4
|
1.0
|
C3B
|
M:BCL1304
|
4.3
|
28.9
|
1.0
|
C3A
|
M:BCL1304
|
4.3
|
29.1
|
1.0
|
C2C
|
M:BCL1304
|
4.3
|
27.7
|
1.0
|
C3C
|
M:BCL1304
|
4.4
|
28.8
|
1.0
|
C2A
|
M:BCL1304
|
4.4
|
29.4
|
1.0
|
OBB
|
M:BPH1311
|
4.5
|
35.1
|
1.0
|
CE2
|
L:PHE181
|
4.9
|
28.0
|
1.0
|
CBD
|
M:BCL1304
|
4.9
|
27.0
|
1.0
|
CBA
|
M:BCL1304
|
5.0
|
33.4
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 2uww
Go back to
Magnesium Binding Sites List in 2uww
Magnesium binding site 4 out
of 4 in the X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 6.5 in the Neutral State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 6.5 in the Neutral State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg1305
b:25.4
occ:1.00
|
MG
|
M:BCL1305
|
0.0
|
25.4
|
1.0
|
ND
|
M:BCL1305
|
2.0
|
24.7
|
1.0
|
NB
|
M:BCL1305
|
2.0
|
23.2
|
1.0
|
NE2
|
M:HIS202
|
2.0
|
25.7
|
1.0
|
NC
|
M:BCL1305
|
2.1
|
25.4
|
1.0
|
NA
|
M:BCL1305
|
2.1
|
24.2
|
1.0
|
C4D
|
M:BCL1305
|
2.9
|
28.1
|
1.0
|
CE1
|
M:HIS202
|
2.9
|
23.1
|
1.0
|
C1C
|
M:BCL1305
|
3.0
|
25.5
|
1.0
|
C4C
|
M:BCL1305
|
3.1
|
26.0
|
1.0
|
C4B
|
M:BCL1305
|
3.1
|
26.6
|
1.0
|
C4A
|
M:BCL1305
|
3.1
|
23.5
|
1.0
|
C1B
|
M:BCL1305
|
3.1
|
24.2
|
1.0
|
C1A
|
M:BCL1305
|
3.1
|
23.8
|
1.0
|
C1D
|
M:BCL1305
|
3.1
|
28.4
|
1.0
|
CD2
|
M:HIS202
|
3.2
|
25.3
|
1.0
|
CHC
|
M:BCL1305
|
3.4
|
25.6
|
1.0
|
CHA
|
M:BCL1305
|
3.4
|
24.0
|
1.0
|
CHB
|
M:BCL1305
|
3.5
|
23.7
|
1.0
|
CHD
|
M:BCL1305
|
3.5
|
25.4
|
1.0
|
CBB
|
L:BCL1290
|
3.7
|
27.3
|
1.0
|
CAB
|
L:BCL1290
|
3.8
|
25.9
|
1.0
|
OBB
|
L:BCL1290
|
3.9
|
27.3
|
1.0
|
ND1
|
M:HIS202
|
4.1
|
24.5
|
1.0
|
C3D
|
M:BCL1305
|
4.1
|
26.3
|
1.0
|
CG
|
M:HIS202
|
4.2
|
24.9
|
1.0
|
C2D
|
M:BCL1305
|
4.2
|
27.1
|
1.0
|
C2B
|
M:BCL1305
|
4.3
|
23.9
|
1.0
|
C3B
|
M:BCL1305
|
4.3
|
23.9
|
1.0
|
C2C
|
M:BCL1305
|
4.4
|
26.8
|
1.0
|
C3C
|
M:BCL1305
|
4.4
|
26.0
|
1.0
|
C3A
|
M:BCL1305
|
4.4
|
25.3
|
1.0
|
C2A
|
M:BCL1305
|
4.5
|
24.0
|
1.0
|
C3B
|
L:BCL1290
|
4.5
|
24.9
|
1.0
|
CBD
|
M:BCL1305
|
4.9
|
25.5
|
1.0
|
O2D
|
M:BCL1305
|
5.0
|
28.5
|
1.0
|
CD1
|
M:ILE206
|
5.0
|
23.1
|
1.0
|
|
Reference:
J.Koepke,
E.M.Krammer,
A.R.Klingen,
P.Sebban,
G.M.Ullmann,
G.Fritzsch.
pH Modulates the Quinone Position in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Neutral and Charge Separated States. J.Mol.Biol. V. 371 396 2007.
ISSN: ISSN 0022-2836
PubMed: 17570397
DOI: 10.1016/J.JMB.2007.04.082
Page generated: Wed Aug 14 03:32:38 2024
|