Magnesium in PDB 4in5: (M)L214G Mutant of the Rhodobacter Sphaeroides Reaction Center
Protein crystallography data
The structure of (M)L214G Mutant of the Rhodobacter Sphaeroides Reaction Center, PDB code: 4in5
was solved by
R.G.Saer,
A.Hardjasa,
M.E.Murphy,
J.T.Beatty,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
55.62 /
2.20
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
139.109,
139.109,
184.692,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.1 /
20.6
|
Other elements in 4in5:
The structure of (M)L214G Mutant of the Rhodobacter Sphaeroides Reaction Center also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the (M)L214G Mutant of the Rhodobacter Sphaeroides Reaction Center
(pdb code 4in5). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
(M)L214G Mutant of the Rhodobacter Sphaeroides Reaction Center, PDB code: 4in5:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 4in5
Go back to
Magnesium Binding Sites List in 4in5
Magnesium binding site 1 out
of 4 in the (M)L214G Mutant of the Rhodobacter Sphaeroides Reaction Center
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of (M)L214G Mutant of the Rhodobacter Sphaeroides Reaction Center within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg305
b:32.2
occ:1.00
|
MG
|
L:BCL305
|
0.0
|
32.2
|
1.0
|
ND
|
L:BCL305
|
2.0
|
35.4
|
1.0
|
NC
|
L:BCL305
|
2.0
|
35.6
|
1.0
|
NB
|
L:BCL305
|
2.0
|
36.2
|
1.0
|
NA
|
L:BCL305
|
2.1
|
35.0
|
1.0
|
NE2
|
L:HIS173
|
2.3
|
33.9
|
1.0
|
C4D
|
L:BCL305
|
2.9
|
36.2
|
1.0
|
C1C
|
L:BCL305
|
3.0
|
34.0
|
1.0
|
C4C
|
L:BCL305
|
3.0
|
33.8
|
1.0
|
C4B
|
L:BCL305
|
3.0
|
35.8
|
1.0
|
C1B
|
L:BCL305
|
3.1
|
35.1
|
1.0
|
C1A
|
L:BCL305
|
3.1
|
33.9
|
1.0
|
C4A
|
L:BCL305
|
3.1
|
34.6
|
1.0
|
C1D
|
L:BCL305
|
3.1
|
36.6
|
1.0
|
CE1
|
L:HIS173
|
3.2
|
29.7
|
1.0
|
CHC
|
L:BCL305
|
3.4
|
34.9
|
1.0
|
CD2
|
L:HIS173
|
3.4
|
32.1
|
1.0
|
CHB
|
L:BCL305
|
3.4
|
31.9
|
1.0
|
CHA
|
L:BCL305
|
3.4
|
33.1
|
1.0
|
OBB
|
M:BCL403
|
3.5
|
41.1
|
1.0
|
CHD
|
L:BCL305
|
3.5
|
30.2
|
1.0
|
CAB
|
M:BCL403
|
3.6
|
34.2
|
1.0
|
CBB
|
M:BCL403
|
3.9
|
29.0
|
1.0
|
C3D
|
L:BCL305
|
4.2
|
35.2
|
1.0
|
C2D
|
L:BCL305
|
4.4
|
40.3
|
1.0
|
C3B
|
L:BCL305
|
4.4
|
31.7
|
1.0
|
C3B
|
M:BCL403
|
4.4
|
31.4
|
1.0
|
C2B
|
L:BCL305
|
4.4
|
37.9
|
1.0
|
C3C
|
L:BCL305
|
4.4
|
36.4
|
1.0
|
ND1
|
L:HIS173
|
4.4
|
31.3
|
1.0
|
C2C
|
L:BCL305
|
4.4
|
32.7
|
1.0
|
C3A
|
L:BCL305
|
4.4
|
36.8
|
1.0
|
C2A
|
L:BCL305
|
4.4
|
34.8
|
1.0
|
CG
|
L:HIS173
|
4.5
|
30.0
|
1.0
|
CD2
|
L:PHE167
|
4.7
|
36.7
|
1.0
|
CBD
|
L:BCL305
|
4.9
|
32.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 4in5
Go back to
Magnesium Binding Sites List in 4in5
Magnesium binding site 2 out
of 4 in the (M)L214G Mutant of the Rhodobacter Sphaeroides Reaction Center
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of (M)L214G Mutant of the Rhodobacter Sphaeroides Reaction Center within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg401
b:31.9
occ:1.00
|
MG
|
M:BCL401
|
0.0
|
31.9
|
1.0
|
NC
|
M:BCL401
|
2.0
|
29.1
|
1.0
|
NA
|
M:BCL401
|
2.0
|
27.8
|
1.0
|
ND
|
M:BCL401
|
2.0
|
27.4
|
1.0
|
NB
|
M:BCL401
|
2.0
|
30.4
|
1.0
|
NE2
|
L:HIS153
|
2.4
|
38.8
|
1.0
|
C4D
|
M:BCL401
|
2.9
|
24.3
|
1.0
|
C4A
|
M:BCL401
|
2.9
|
27.5
|
1.0
|
C1A
|
M:BCL401
|
2.9
|
27.2
|
1.0
|
C4C
|
M:BCL401
|
3.0
|
30.1
|
1.0
|
C1C
|
M:BCL401
|
3.0
|
30.6
|
1.0
|
C1B
|
M:BCL401
|
3.0
|
26.6
|
1.0
|
C4B
|
M:BCL401
|
3.0
|
27.9
|
1.0
|
C1D
|
M:BCL401
|
3.1
|
27.9
|
1.0
|
CD2
|
L:HIS153
|
3.2
|
34.1
|
1.0
|
CHB
|
M:BCL401
|
3.3
|
29.5
|
1.0
|
CHA
|
M:BCL401
|
3.3
|
27.6
|
1.0
|
CHC
|
M:BCL401
|
3.4
|
29.8
|
1.0
|
CE1
|
L:HIS153
|
3.4
|
41.3
|
1.0
|
CHD
|
M:BCL401
|
3.5
|
27.2
|
1.0
|
OBB
|
L:BPH303
|
4.1
|
49.1
|
1.0
|
C3D
|
M:BCL401
|
4.2
|
25.4
|
1.0
|
C3A
|
M:BCL401
|
4.2
|
29.5
|
1.0
|
C2A
|
M:BCL401
|
4.3
|
30.1
|
1.0
|
C2C
|
M:BCL401
|
4.3
|
32.5
|
1.0
|
C3C
|
M:BCL401
|
4.3
|
33.7
|
1.0
|
C3B
|
M:BCL401
|
4.3
|
30.2
|
1.0
|
C2B
|
M:BCL401
|
4.3
|
29.0
|
1.0
|
C2D
|
M:BCL401
|
4.3
|
30.1
|
1.0
|
CG
|
L:HIS153
|
4.5
|
36.9
|
1.0
|
ND1
|
L:HIS153
|
4.5
|
35.1
|
1.0
|
CE2
|
M:TYR210
|
4.5
|
38.8
|
1.0
|
CBA
|
M:BCL401
|
4.6
|
39.5
|
1.0
|
CBC
|
M:BCL401
|
4.8
|
32.4
|
1.0
|
CBD
|
M:BCL401
|
4.8
|
33.9
|
1.0
|
C20
|
L:BPH303
|
4.9
|
42.5
|
1.0
|
CD1
|
L:LEU154
|
4.9
|
41.6
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 4in5
Go back to
Magnesium Binding Sites List in 4in5
Magnesium binding site 3 out
of 4 in the (M)L214G Mutant of the Rhodobacter Sphaeroides Reaction Center
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of (M)L214G Mutant of the Rhodobacter Sphaeroides Reaction Center within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg402
b:32.0
occ:1.00
|
MG
|
M:BCL402
|
0.0
|
32.0
|
1.0
|
ND
|
M:BCL402
|
2.0
|
32.2
|
1.0
|
NA
|
M:BCL402
|
2.0
|
34.9
|
1.0
|
NC
|
M:BCL402
|
2.0
|
33.8
|
1.0
|
NB
|
M:BCL402
|
2.0
|
33.9
|
1.0
|
NE2
|
M:HIS182
|
2.4
|
38.5
|
1.0
|
C4D
|
M:BCL402
|
2.9
|
31.2
|
1.0
|
C4A
|
M:BCL402
|
2.9
|
33.7
|
1.0
|
C4C
|
M:BCL402
|
3.0
|
32.8
|
1.0
|
C1B
|
M:BCL402
|
3.0
|
32.2
|
1.0
|
C1A
|
M:BCL402
|
3.0
|
34.6
|
1.0
|
C1D
|
M:BCL402
|
3.1
|
31.4
|
1.0
|
C1C
|
M:BCL402
|
3.1
|
32.9
|
1.0
|
C4B
|
M:BCL402
|
3.1
|
33.4
|
1.0
|
CD2
|
M:HIS182
|
3.3
|
35.6
|
1.0
|
CHB
|
M:BCL402
|
3.3
|
32.5
|
1.0
|
CHA
|
M:BCL402
|
3.4
|
31.4
|
1.0
|
CHD
|
M:BCL402
|
3.4
|
30.5
|
1.0
|
CE1
|
M:HIS182
|
3.4
|
36.4
|
1.0
|
CHC
|
M:BCL402
|
3.5
|
34.1
|
1.0
|
C3D
|
M:BCL402
|
4.1
|
29.3
|
1.0
|
C3A
|
M:BCL402
|
4.3
|
34.7
|
1.0
|
C2B
|
M:BCL402
|
4.3
|
33.9
|
1.0
|
C2D
|
M:BCL402
|
4.3
|
31.7
|
1.0
|
C2A
|
M:BCL402
|
4.3
|
36.5
|
1.0
|
C3B
|
M:BCL402
|
4.3
|
32.6
|
1.0
|
C3C
|
M:BCL402
|
4.3
|
32.5
|
1.0
|
C2C
|
M:BCL402
|
4.4
|
35.3
|
1.0
|
OBB
|
L:BPH313
|
4.4
|
45.1
|
1.0
|
CG
|
M:HIS182
|
4.5
|
35.7
|
1.0
|
ND1
|
M:HIS182
|
4.5
|
37.2
|
1.0
|
CE2
|
L:PHE181
|
4.7
|
37.2
|
1.0
|
CBA
|
M:BCL402
|
4.8
|
39.7
|
1.0
|
CBD
|
M:BCL402
|
4.9
|
33.9
|
1.0
|
CMA
|
M:BCL402
|
4.9
|
37.4
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 4in5
Go back to
Magnesium Binding Sites List in 4in5
Magnesium binding site 4 out
of 4 in the (M)L214G Mutant of the Rhodobacter Sphaeroides Reaction Center
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of (M)L214G Mutant of the Rhodobacter Sphaeroides Reaction Center within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg403
b:30.9
occ:1.00
|
MG
|
M:BCL403
|
0.0
|
30.9
|
1.0
|
NB
|
M:BCL403
|
2.0
|
31.7
|
1.0
|
ND
|
M:BCL403
|
2.0
|
31.3
|
1.0
|
NC
|
M:BCL403
|
2.0
|
32.3
|
1.0
|
NA
|
M:BCL403
|
2.1
|
35.2
|
1.0
|
NE2
|
M:HIS202
|
2.4
|
33.3
|
1.0
|
C4D
|
M:BCL403
|
3.0
|
33.6
|
1.0
|
C4C
|
M:BCL403
|
3.0
|
31.3
|
1.0
|
C1C
|
M:BCL403
|
3.0
|
29.7
|
1.0
|
C1B
|
M:BCL403
|
3.0
|
31.6
|
1.0
|
C4B
|
M:BCL403
|
3.0
|
31.1
|
1.0
|
C4A
|
M:BCL403
|
3.0
|
30.9
|
1.0
|
C1A
|
M:BCL403
|
3.1
|
30.8
|
1.0
|
C1D
|
M:BCL403
|
3.1
|
35.5
|
1.0
|
CE1
|
M:HIS202
|
3.3
|
28.3
|
1.0
|
CHC
|
M:BCL403
|
3.4
|
30.6
|
1.0
|
CHB
|
M:BCL403
|
3.4
|
31.6
|
1.0
|
CD2
|
M:HIS202
|
3.4
|
31.3
|
1.0
|
CHD
|
M:BCL403
|
3.4
|
31.5
|
1.0
|
CBB
|
L:BCL305
|
3.5
|
36.4
|
1.0
|
CHA
|
M:BCL403
|
3.5
|
29.6
|
1.0
|
CAB
|
L:BCL305
|
3.6
|
34.6
|
1.0
|
OBB
|
L:BCL305
|
3.8
|
35.1
|
1.0
|
C3D
|
M:BCL403
|
4.2
|
31.2
|
1.0
|
C3B
|
M:BCL403
|
4.3
|
31.4
|
1.0
|
C2B
|
M:BCL403
|
4.3
|
28.8
|
1.0
|
C3B
|
L:BCL305
|
4.3
|
31.7
|
1.0
|
C2C
|
M:BCL403
|
4.3
|
31.9
|
1.0
|
C3C
|
M:BCL403
|
4.4
|
31.6
|
1.0
|
C2D
|
M:BCL403
|
4.4
|
31.1
|
1.0
|
C3A
|
M:BCL403
|
4.4
|
31.7
|
1.0
|
ND1
|
M:HIS202
|
4.5
|
29.4
|
1.0
|
C2A
|
M:BCL403
|
4.5
|
33.9
|
1.0
|
CG
|
M:HIS202
|
4.5
|
30.2
|
1.0
|
CBD
|
M:BCL403
|
5.0
|
32.3
|
1.0
|
CMC
|
M:BCL403
|
5.0
|
30.8
|
1.0
|
|
Reference:
R.G.Saer,
A.Hardjasa,
F.I.Rosell,
A.G.Mauk,
M.E.Murphy,
J.T.Beatty.
Role of Rhodobacter Sphaeroides Photosynthetic Reaction Center Residue M214 in the Composition, Absorbance Properties, and Conformations of Ha and Ba Cofactors. Biochemistry V. 52 2206 2013.
ISSN: ISSN 0006-2960
PubMed: 23480277
DOI: 10.1021/BI400207M
Page generated: Fri Aug 16 16:47:17 2024
|