Magnesium in PDB 7mh5: Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Iodotyrosine
Protein crystallography data
The structure of Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Iodotyrosine, PDB code: 7mh5
was solved by
I.Mathews,
J.Weaver,
S.G.Boxer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.95 /
2.85
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
141.414,
141.414,
186.502,
90,
90,
120
|
R / Rfree (%)
|
18 /
20.5
|
Other elements in 7mh5:
The structure of Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Iodotyrosine 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; Y(M210)3-Iodotyrosine
(pdb code 7mh5). 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; Y(M210)3-Iodotyrosine, PDB code: 7mh5:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7mh5
Go back to
Magnesium Binding Sites List in 7mh5
Magnesium binding site 1 out
of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Iodotyrosine
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; Y(M210)3-Iodotyrosine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg303
b:56.1
occ:1.00
|
MG
|
L:BCL303
|
0.0
|
56.1
|
1.0
|
NC
|
L:BCL303
|
2.0
|
58.0
|
1.0
|
NA
|
L:BCL303
|
2.0
|
57.6
|
1.0
|
ND
|
L:BCL303
|
2.0
|
58.9
|
1.0
|
NB
|
L:BCL303
|
2.1
|
53.8
|
1.0
|
NE2
|
L:HIS173
|
2.3
|
56.7
|
1.0
|
C4D
|
L:BCL303
|
2.9
|
60.5
|
1.0
|
C1C
|
L:BCL303
|
3.0
|
58.8
|
1.0
|
C4A
|
L:BCL303
|
3.0
|
54.4
|
1.0
|
C1A
|
L:BCL303
|
3.0
|
59.3
|
1.0
|
C4C
|
L:BCL303
|
3.0
|
57.0
|
1.0
|
C4B
|
L:BCL303
|
3.1
|
52.9
|
1.0
|
C1B
|
L:BCL303
|
3.1
|
51.1
|
1.0
|
C1D
|
L:BCL303
|
3.2
|
58.7
|
1.0
|
CD2
|
L:HIS173
|
3.3
|
57.7
|
1.0
|
CE1
|
L:HIS173
|
3.3
|
57.4
|
1.0
|
CHC
|
L:BCL303
|
3.4
|
57.1
|
1.0
|
CHB
|
L:BCL303
|
3.4
|
50.3
|
1.0
|
CHA
|
L:BCL303
|
3.4
|
58.7
|
1.0
|
CHD
|
L:BCL303
|
3.5
|
55.9
|
1.0
|
OBB
|
M:BCL403
|
3.6
|
75.9
|
1.0
|
CAB
|
M:BCL403
|
3.8
|
66.3
|
1.0
|
CBB
|
M:BCL403
|
3.8
|
66.4
|
1.0
|
C3D
|
L:BCL303
|
4.2
|
60.9
|
1.0
|
C3A
|
L:BCL303
|
4.3
|
56.8
|
1.0
|
C3C
|
L:BCL303
|
4.3
|
57.2
|
1.0
|
C2A
|
L:BCL303
|
4.3
|
58.7
|
1.0
|
C2C
|
L:BCL303
|
4.3
|
55.6
|
1.0
|
C3B
|
L:BCL303
|
4.4
|
51.0
|
1.0
|
C2D
|
L:BCL303
|
4.4
|
62.9
|
1.0
|
ND1
|
L:HIS173
|
4.4
|
58.0
|
1.0
|
C2B
|
L:BCL303
|
4.4
|
51.7
|
1.0
|
CG
|
L:HIS173
|
4.4
|
57.4
|
1.0
|
CD2
|
L:PHE167
|
4.6
|
57.8
|
1.0
|
C3B
|
M:BCL403
|
4.6
|
60.5
|
1.0
|
CBD
|
L:BCL303
|
4.9
|
59.3
|
1.0
|
CMA
|
L:BCL303
|
5.0
|
57.9
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7mh5
Go back to
Magnesium Binding Sites List in 7mh5
Magnesium binding site 2 out
of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Iodotyrosine
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; Y(M210)3-Iodotyrosine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg401
b:53.4
occ:1.00
|
MG
|
M:BCL401
|
0.0
|
53.4
|
1.0
|
NA
|
M:BCL401
|
2.0
|
54.4
|
1.0
|
NC
|
M:BCL401
|
2.0
|
53.6
|
1.0
|
ND
|
M:BCL401
|
2.0
|
55.9
|
1.0
|
NB
|
M:BCL401
|
2.1
|
54.4
|
1.0
|
NE2
|
L:HIS153
|
2.5
|
71.5
|
1.0
|
I2
|
M:TYI210
|
2.9
|
62.6
|
0.2
|
C4D
|
M:BCL401
|
2.9
|
55.9
|
1.0
|
C1A
|
M:BCL401
|
3.0
|
56.8
|
1.0
|
C4A
|
M:BCL401
|
3.0
|
52.8
|
1.0
|
C1C
|
M:BCL401
|
3.0
|
57.4
|
1.0
|
C4C
|
M:BCL401
|
3.0
|
54.9
|
1.0
|
C1B
|
M:BCL401
|
3.1
|
51.2
|
1.0
|
C4B
|
M:BCL401
|
3.1
|
54.4
|
1.0
|
C1D
|
M:BCL401
|
3.2
|
56.1
|
1.0
|
CHB
|
M:BCL401
|
3.4
|
51.6
|
1.0
|
CHA
|
M:BCL401
|
3.4
|
58.0
|
1.0
|
CHC
|
M:BCL401
|
3.4
|
55.9
|
1.0
|
CE1
|
L:HIS153
|
3.4
|
73.4
|
1.0
|
CD2
|
L:HIS153
|
3.5
|
73.8
|
1.0
|
CHD
|
M:BCL401
|
3.6
|
54.8
|
1.0
|
C3D
|
M:BCL401
|
4.2
|
55.7
|
1.0
|
C3A
|
M:BCL401
|
4.3
|
54.2
|
1.0
|
C2A
|
M:BCL401
|
4.3
|
57.2
|
1.0
|
C3C
|
M:BCL401
|
4.3
|
58.0
|
1.0
|
C2C
|
M:BCL401
|
4.3
|
58.7
|
1.0
|
C2B
|
M:BCL401
|
4.4
|
49.5
|
1.0
|
C3B
|
M:BCL401
|
4.4
|
52.2
|
1.0
|
C2D
|
M:BCL401
|
4.4
|
55.5
|
1.0
|
ND1
|
L:HIS153
|
4.6
|
75.1
|
1.0
|
CG
|
L:HIS153
|
4.6
|
76.2
|
1.0
|
OBB
|
L:BPH301
|
4.7
|
62.5
|
1.0
|
CBA
|
M:BCL401
|
4.8
|
63.0
|
1.0
|
CBC
|
M:BCL401
|
4.8
|
59.9
|
1.0
|
CBD
|
M:BCL401
|
4.9
|
59.3
|
1.0
|
CE2
|
M:TYI210
|
4.9
|
60.9
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7mh5
Go back to
Magnesium Binding Sites List in 7mh5
Magnesium binding site 3 out
of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Iodotyrosine
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; Y(M210)3-Iodotyrosine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg402
b:59.6
occ:1.00
|
MG
|
M:BCL402
|
0.0
|
59.6
|
1.0
|
NA
|
M:BCL402
|
2.0
|
56.6
|
1.0
|
NC
|
M:BCL402
|
2.0
|
60.1
|
1.0
|
ND
|
M:BCL402
|
2.0
|
56.8
|
1.0
|
NB
|
M:BCL402
|
2.1
|
60.5
|
1.0
|
NE2
|
M:HIS182
|
2.4
|
68.1
|
1.0
|
C4D
|
M:BCL402
|
2.9
|
57.1
|
1.0
|
C1A
|
M:BCL402
|
3.0
|
57.0
|
1.0
|
C4A
|
M:BCL402
|
3.0
|
57.2
|
1.0
|
C4C
|
M:BCL402
|
3.0
|
59.5
|
1.0
|
C1C
|
M:BCL402
|
3.0
|
61.3
|
1.0
|
C1B
|
M:BCL402
|
3.1
|
60.5
|
1.0
|
C4B
|
M:BCL402
|
3.1
|
61.5
|
1.0
|
C1D
|
M:BCL402
|
3.2
|
57.4
|
1.0
|
CD2
|
M:HIS182
|
3.3
|
69.2
|
1.0
|
CHB
|
M:BCL402
|
3.4
|
56.2
|
1.0
|
CHA
|
M:BCL402
|
3.4
|
58.4
|
1.0
|
CHC
|
M:BCL402
|
3.4
|
61.1
|
1.0
|
CHD
|
M:BCL402
|
3.5
|
58.0
|
1.0
|
CE1
|
M:HIS182
|
3.5
|
69.7
|
1.0
|
C3D
|
M:BCL402
|
4.2
|
56.4
|
1.0
|
C3A
|
M:BCL402
|
4.3
|
59.0
|
1.0
|
C2A
|
M:BCL402
|
4.3
|
59.4
|
1.0
|
C3C
|
M:BCL402
|
4.3
|
58.8
|
1.0
|
C2C
|
M:BCL402
|
4.3
|
58.3
|
1.0
|
C3B
|
M:BCL402
|
4.4
|
65.4
|
1.0
|
C2D
|
M:BCL402
|
4.4
|
56.5
|
1.0
|
C2B
|
M:BCL402
|
4.4
|
63.2
|
1.0
|
CG
|
M:HIS182
|
4.5
|
68.9
|
1.0
|
ND1
|
M:HIS182
|
4.6
|
69.8
|
1.0
|
CE2
|
L:PHE181
|
4.8
|
64.2
|
1.0
|
CBD
|
M:BCL402
|
4.9
|
59.5
|
1.0
|
C18
|
M:SPO411
|
4.9
|
83.9
|
1.0
|
CBA
|
M:BCL402
|
4.9
|
66.8
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7mh5
Go back to
Magnesium Binding Sites List in 7mh5
Magnesium binding site 4 out
of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Iodotyrosine
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; Y(M210)3-Iodotyrosine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg403
b:56.9
occ:1.00
|
MG
|
M:BCL403
|
0.0
|
56.9
|
1.0
|
NA
|
M:BCL403
|
2.0
|
58.1
|
1.0
|
NC
|
M:BCL403
|
2.0
|
58.8
|
1.0
|
ND
|
M:BCL403
|
2.0
|
55.9
|
1.0
|
NB
|
M:BCL403
|
2.1
|
55.6
|
1.0
|
NE2
|
M:HIS202
|
2.4
|
53.5
|
1.0
|
C4D
|
M:BCL403
|
2.9
|
55.3
|
1.0
|
C4A
|
M:BCL403
|
3.0
|
57.2
|
1.0
|
C1A
|
M:BCL403
|
3.0
|
55.0
|
1.0
|
C1C
|
M:BCL403
|
3.0
|
58.9
|
1.0
|
C4C
|
M:BCL403
|
3.0
|
57.1
|
1.0
|
C1B
|
M:BCL403
|
3.0
|
54.8
|
1.0
|
C4B
|
M:BCL403
|
3.1
|
56.2
|
1.0
|
C1D
|
M:BCL403
|
3.2
|
57.9
|
1.0
|
CD2
|
M:HIS202
|
3.3
|
55.0
|
1.0
|
CHB
|
M:BCL403
|
3.4
|
54.8
|
1.0
|
CHA
|
M:BCL403
|
3.4
|
53.4
|
1.0
|
CHC
|
M:BCL403
|
3.4
|
56.2
|
1.0
|
CBB
|
L:BCL303
|
3.5
|
51.4
|
1.0
|
CE1
|
M:HIS202
|
3.5
|
55.1
|
1.0
|
CHD
|
M:BCL403
|
3.5
|
56.0
|
1.0
|
CAB
|
L:BCL303
|
3.7
|
50.8
|
1.0
|
OBB
|
L:BCL303
|
3.8
|
49.0
|
1.0
|
C3D
|
M:BCL403
|
4.2
|
56.3
|
1.0
|
C3A
|
M:BCL403
|
4.3
|
59.1
|
1.0
|
C2C
|
M:BCL403
|
4.3
|
60.5
|
1.0
|
C2A
|
M:BCL403
|
4.3
|
57.8
|
1.0
|
C3C
|
M:BCL403
|
4.3
|
59.8
|
1.0
|
C2B
|
M:BCL403
|
4.4
|
56.4
|
1.0
|
C2D
|
M:BCL403
|
4.4
|
56.9
|
1.0
|
C3B
|
M:BCL403
|
4.4
|
60.5
|
1.0
|
CG
|
M:HIS202
|
4.5
|
56.4
|
1.0
|
C3B
|
L:BCL303
|
4.5
|
51.0
|
1.0
|
ND1
|
M:HIS202
|
4.6
|
56.2
|
1.0
|
CBD
|
M:BCL403
|
4.8
|
56.0
|
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 Show Tyr at M210 Tunes the Initial Electron Transfer Mechanism. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 34907018
DOI: 10.1073/PNAS.2116439118
Page generated: Thu Oct 3 00:53:31 2024
|