Magnesium in PDB 7mha: Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant
Protein crystallography data
The structure of Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant, PDB code: 7mha
was solved by
S.G.Boxer,
I.I.Mathews,
J.B.Weaver,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.19 /
2.79
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
142.193,
142.193,
187.673,
90,
90,
120
|
R / Rfree (%)
|
15.6 /
17.8
|
Other elements in 7mha:
The structure of Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant
(pdb code 7mha). 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 R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant, PDB code: 7mha:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7mha
Go back to
Magnesium Binding Sites List in 7mha
Magnesium binding site 1 out
of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant
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 R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg301
b:36.6
occ:1.00
|
MG
|
L:BCL301
|
0.0
|
36.6
|
1.0
|
NA
|
L:BCL301
|
2.0
|
37.2
|
1.0
|
NC
|
L:BCL301
|
2.0
|
35.8
|
1.0
|
ND
|
L:BCL301
|
2.0
|
34.5
|
1.0
|
NB
|
L:BCL301
|
2.0
|
34.6
|
1.0
|
NE2
|
L:HIS153
|
2.5
|
50.8
|
1.0
|
C4D
|
L:BCL301
|
2.9
|
35.2
|
1.0
|
C1A
|
L:BCL301
|
3.0
|
37.9
|
1.0
|
C4A
|
L:BCL301
|
3.0
|
36.9
|
1.0
|
C1C
|
L:BCL301
|
3.0
|
37.8
|
1.0
|
C4C
|
L:BCL301
|
3.0
|
37.1
|
1.0
|
C1B
|
L:BCL301
|
3.0
|
35.0
|
1.0
|
C4B
|
L:BCL301
|
3.1
|
35.3
|
1.0
|
C1D
|
L:BCL301
|
3.1
|
35.5
|
1.0
|
CD2
|
L:HIS153
|
3.3
|
52.4
|
1.0
|
CHB
|
L:BCL301
|
3.4
|
35.2
|
1.0
|
CHA
|
L:BCL301
|
3.4
|
37.0
|
1.0
|
CHC
|
L:BCL301
|
3.4
|
36.7
|
1.0
|
CHD
|
L:BCL301
|
3.5
|
35.5
|
1.0
|
CE1
|
L:HIS153
|
3.6
|
51.9
|
1.0
|
C3D
|
L:BCL301
|
4.1
|
35.1
|
1.0
|
C3A
|
L:BCL301
|
4.3
|
38.5
|
1.0
|
C2A
|
L:BCL301
|
4.3
|
39.5
|
1.0
|
C3C
|
L:BCL301
|
4.3
|
40.3
|
1.0
|
C2C
|
L:BCL301
|
4.3
|
39.7
|
1.0
|
C2B
|
L:BCL301
|
4.4
|
34.8
|
1.0
|
C3B
|
L:BCL301
|
4.4
|
35.5
|
1.0
|
C2D
|
L:BCL301
|
4.4
|
34.8
|
1.0
|
OBB
|
L:BPH302
|
4.5
|
51.7
|
1.0
|
CG
|
L:HIS153
|
4.6
|
52.8
|
1.0
|
ND1
|
L:HIS153
|
4.6
|
52.0
|
1.0
|
CE2
|
M:TYR210
|
4.7
|
44.0
|
1.0
|
CBC
|
L:BCL301
|
4.7
|
43.1
|
1.0
|
CBA
|
L:BCL301
|
4.9
|
47.8
|
1.0
|
CBD
|
L:BCL301
|
4.9
|
40.8
|
1.0
|
CD1
|
L:LEU154
|
5.0
|
53.5
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7mha
Go back to
Magnesium Binding Sites List in 7mha
Magnesium binding site 2 out
of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant
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 R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg304
b:43.4
occ:1.00
|
MG
|
L:BCL304
|
0.0
|
43.4
|
1.0
|
NA
|
L:BCL304
|
2.0
|
42.4
|
1.0
|
NC
|
L:BCL304
|
2.0
|
42.7
|
1.0
|
ND
|
L:BCL304
|
2.0
|
42.4
|
1.0
|
NB
|
L:BCL304
|
2.0
|
39.8
|
1.0
|
NE2
|
L:HIS173
|
2.3
|
42.5
|
1.0
|
C4D
|
L:BCL304
|
2.9
|
43.2
|
1.0
|
C4A
|
L:BCL304
|
3.0
|
41.1
|
1.0
|
C1A
|
L:BCL304
|
3.0
|
43.3
|
1.0
|
C1C
|
L:BCL304
|
3.0
|
43.4
|
1.0
|
C4C
|
L:BCL304
|
3.0
|
41.4
|
1.0
|
C4B
|
L:BCL304
|
3.1
|
40.5
|
1.0
|
C1B
|
L:BCL304
|
3.1
|
38.6
|
1.0
|
C1D
|
L:BCL304
|
3.2
|
41.0
|
1.0
|
CE1
|
L:HIS173
|
3.3
|
43.5
|
1.0
|
CD2
|
L:HIS173
|
3.4
|
42.8
|
1.0
|
CHC
|
L:BCL304
|
3.4
|
42.1
|
1.0
|
CHB
|
L:BCL304
|
3.4
|
38.4
|
1.0
|
CHA
|
L:BCL304
|
3.4
|
42.2
|
1.0
|
CHD
|
L:BCL304
|
3.5
|
40.8
|
1.0
|
OBB
|
M:BCL402
|
3.6
|
52.4
|
1.0
|
CAB
|
M:BCL402
|
3.7
|
47.7
|
1.0
|
CBB
|
M:BCL402
|
3.8
|
48.4
|
1.0
|
C3D
|
L:BCL304
|
4.2
|
42.2
|
1.0
|
C3A
|
L:BCL304
|
4.3
|
41.9
|
1.0
|
C3C
|
L:BCL304
|
4.4
|
41.5
|
1.0
|
C2A
|
L:BCL304
|
4.4
|
43.1
|
1.0
|
C3B
|
L:BCL304
|
4.4
|
39.3
|
1.0
|
C2C
|
L:BCL304
|
4.4
|
41.2
|
1.0
|
C2D
|
L:BCL304
|
4.4
|
43.3
|
1.0
|
C2B
|
L:BCL304
|
4.4
|
39.0
|
1.0
|
ND1
|
L:HIS173
|
4.4
|
43.7
|
1.0
|
CG
|
L:HIS173
|
4.5
|
43.8
|
1.0
|
C3B
|
M:BCL402
|
4.5
|
45.9
|
1.0
|
CD2
|
L:PHE167
|
4.8
|
49.8
|
1.0
|
CBD
|
L:BCL304
|
4.9
|
42.1
|
1.0
|
CMA
|
L:BCL304
|
5.0
|
42.0
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7mha
Go back to
Magnesium Binding Sites List in 7mha
Magnesium binding site 3 out
of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant
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 R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg401
b:47.3
occ:1.00
|
MG
|
M:BCL401
|
0.0
|
47.3
|
1.0
|
NA
|
M:BCL401
|
2.0
|
46.7
|
1.0
|
ND
|
M:BCL401
|
2.0
|
45.3
|
1.0
|
NC
|
M:BCL401
|
2.0
|
48.1
|
1.0
|
NB
|
M:BCL401
|
2.0
|
47.6
|
1.0
|
NE2
|
M:HIS182
|
2.4
|
54.3
|
1.0
|
C4D
|
M:BCL401
|
2.9
|
46.0
|
1.0
|
C1A
|
M:BCL401
|
3.0
|
45.8
|
1.0
|
C4A
|
M:BCL401
|
3.0
|
46.2
|
1.0
|
C4C
|
M:BCL401
|
3.0
|
47.1
|
1.0
|
C1B
|
M:BCL401
|
3.0
|
47.8
|
1.0
|
C1C
|
M:BCL401
|
3.0
|
46.1
|
1.0
|
C4B
|
M:BCL401
|
3.1
|
47.9
|
1.0
|
C1D
|
M:BCL401
|
3.2
|
45.4
|
1.0
|
CD2
|
M:HIS182
|
3.2
|
55.8
|
1.0
|
CHB
|
M:BCL401
|
3.4
|
45.5
|
1.0
|
CHA
|
M:BCL401
|
3.4
|
46.0
|
1.0
|
CHC
|
M:BCL401
|
3.4
|
47.6
|
1.0
|
CE1
|
M:HIS182
|
3.5
|
55.8
|
1.0
|
CHD
|
M:BCL401
|
3.6
|
46.4
|
1.0
|
C3D
|
M:BCL401
|
4.2
|
45.4
|
1.0
|
C3A
|
M:BCL401
|
4.3
|
45.5
|
1.0
|
C2A
|
M:BCL401
|
4.3
|
47.4
|
1.0
|
C3B
|
M:BCL401
|
4.4
|
49.0
|
1.0
|
C2B
|
M:BCL401
|
4.4
|
49.5
|
1.0
|
C3C
|
M:BCL401
|
4.4
|
46.1
|
1.0
|
C2C
|
M:BCL401
|
4.4
|
44.8
|
1.0
|
C2D
|
M:BCL401
|
4.4
|
45.1
|
1.0
|
CG
|
M:HIS182
|
4.5
|
55.3
|
1.0
|
ND1
|
M:HIS182
|
4.6
|
55.5
|
1.0
|
CE2
|
L:PHE181
|
4.8
|
44.9
|
1.0
|
OBB
|
L:BPH305
|
4.8
|
62.2
|
1.0
|
CBD
|
M:BCL401
|
4.9
|
47.7
|
1.0
|
CBA
|
M:BCL401
|
5.0
|
54.6
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7mha
Go back to
Magnesium Binding Sites List in 7mha
Magnesium binding site 4 out
of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant
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 R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg402
b:44.0
occ:1.00
|
MG
|
M:BCL402
|
0.0
|
44.0
|
1.0
|
NC
|
M:BCL402
|
2.0
|
47.1
|
1.0
|
NA
|
M:BCL402
|
2.0
|
45.6
|
1.0
|
ND
|
M:BCL402
|
2.0
|
41.1
|
1.0
|
NB
|
M:BCL402
|
2.0
|
42.9
|
1.0
|
NE2
|
M:HIS202
|
2.4
|
40.8
|
1.0
|
C4D
|
M:BCL402
|
2.9
|
42.1
|
1.0
|
C4A
|
M:BCL402
|
3.0
|
43.3
|
1.0
|
C1A
|
M:BCL402
|
3.0
|
43.2
|
1.0
|
C1C
|
M:BCL402
|
3.0
|
46.8
|
1.0
|
C4C
|
M:BCL402
|
3.0
|
45.4
|
1.0
|
C1B
|
M:BCL402
|
3.0
|
42.5
|
1.0
|
C4B
|
M:BCL402
|
3.1
|
44.4
|
1.0
|
C1D
|
M:BCL402
|
3.2
|
42.2
|
1.0
|
CHB
|
M:BCL402
|
3.4
|
41.4
|
1.0
|
CHA
|
M:BCL402
|
3.4
|
41.4
|
1.0
|
CD2
|
M:HIS202
|
3.4
|
42.3
|
1.0
|
CHC
|
M:BCL402
|
3.4
|
44.6
|
1.0
|
CE1
|
M:HIS202
|
3.5
|
41.7
|
1.0
|
CBB
|
L:BCL304
|
3.5
|
44.3
|
1.0
|
CHD
|
M:BCL402
|
3.6
|
43.5
|
1.0
|
CAB
|
L:BCL304
|
3.7
|
41.5
|
1.0
|
OBB
|
L:BCL304
|
4.0
|
40.8
|
1.0
|
C3D
|
M:BCL402
|
4.2
|
41.8
|
1.0
|
C3A
|
M:BCL402
|
4.3
|
43.2
|
1.0
|
C2C
|
M:BCL402
|
4.3
|
47.4
|
1.0
|
C2A
|
M:BCL402
|
4.3
|
43.3
|
1.0
|
C3C
|
M:BCL402
|
4.3
|
45.7
|
1.0
|
C2B
|
M:BCL402
|
4.4
|
44.0
|
1.0
|
C3B
|
M:BCL402
|
4.4
|
45.9
|
1.0
|
C2D
|
M:BCL402
|
4.4
|
41.1
|
1.0
|
C3B
|
L:BCL304
|
4.5
|
39.3
|
1.0
|
CG
|
M:HIS202
|
4.6
|
43.2
|
1.0
|
ND1
|
M:HIS202
|
4.6
|
41.9
|
1.0
|
CBD
|
M:BCL402
|
4.8
|
43.4
|
1.0
|
|
Reference:
J.B.Weaver,
C.Y.Lin,
K.M.Faries,
I.I.Mathews,
S.Russi,
D.Holten,
C.Kirmaier,
S.G.Boxer.
Photosynthetic Reaction Center Variants Made Via Genetic Code Expansion Indicate Tyrosine at M210 Tunes the Mechanism For Primary Electron Transfer Thesis pH.D. Stanford 294 2022UNIVERSITY.
Page generated: Thu Oct 3 00:55:12 2024
|