Magnesium in PDB 8vtk: Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine
Protein crystallography data
The structure of Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine, PDB code: 8vtk
was solved by
K.Tran,
I.Mathews,
S.G.Boxer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.76 /
3.07
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
140.95,
140.95,
186.72,
90,
90,
120
|
R / Rfree (%)
|
17.7 /
21.3
|
Other elements in 8vtk:
The structure of Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine 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)2-Chlorophenylalanine
(pdb code 8vtk). 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)2-Chlorophenylalanine, PDB code: 8vtk:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8vtk
Go back to
Magnesium Binding Sites List in 8vtk
Magnesium binding site 1 out
of 4 in the Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine
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)2-Chlorophenylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg303
b:46.0
occ:1.00
|
MG
|
L:BCL303
|
0.0
|
46.0
|
1.0
|
NE2
|
L:HIS153
|
1.9
|
57.5
|
1.0
|
ND
|
L:BCL303
|
2.0
|
43.8
|
1.0
|
NB
|
L:BCL303
|
2.1
|
49.7
|
1.0
|
NC
|
L:BCL303
|
2.2
|
49.5
|
1.0
|
NA
|
L:BCL303
|
2.2
|
48.9
|
1.0
|
CE1
|
L:HIS153
|
2.9
|
54.7
|
1.0
|
CD2
|
L:HIS153
|
3.0
|
52.1
|
1.0
|
C4D
|
L:BCL303
|
3.0
|
46.4
|
1.0
|
C1B
|
L:BCL303
|
3.1
|
49.2
|
1.0
|
C4B
|
L:BCL303
|
3.1
|
49.4
|
1.0
|
C1D
|
L:BCL303
|
3.1
|
49.8
|
1.0
|
C1C
|
L:BCL303
|
3.1
|
50.8
|
1.0
|
C4A
|
L:BCL303
|
3.2
|
47.6
|
1.0
|
C4C
|
L:BCL303
|
3.2
|
45.3
|
1.0
|
C1A
|
L:BCL303
|
3.2
|
51.4
|
1.0
|
CHB
|
L:BCL303
|
3.4
|
49.5
|
1.0
|
CHC
|
L:BCL303
|
3.4
|
49.0
|
1.0
|
CHD
|
L:BCL303
|
3.5
|
49.8
|
1.0
|
CHA
|
L:BCL303
|
3.5
|
51.0
|
1.0
|
ND1
|
L:HIS153
|
4.0
|
56.8
|
1.0
|
CG
|
L:HIS153
|
4.1
|
58.8
|
1.0
|
C3D
|
L:BCL303
|
4.2
|
46.3
|
1.0
|
C2D
|
L:BCL303
|
4.3
|
45.3
|
1.0
|
C2B
|
L:BCL303
|
4.3
|
44.8
|
1.0
|
C3B
|
L:BCL303
|
4.4
|
51.0
|
1.0
|
C3A
|
L:BCL303
|
4.4
|
42.8
|
1.0
|
C2C
|
L:BCL303
|
4.4
|
47.6
|
1.0
|
C3C
|
L:BCL303
|
4.5
|
47.5
|
1.0
|
C2A
|
L:BCL303
|
4.5
|
48.2
|
1.0
|
OBB
|
L:BPH304
|
4.6
|
53.4
|
1.0
|
CD1
|
L:LEU154
|
4.7
|
51.8
|
1.0
|
CMA
|
L:BCL303
|
4.9
|
44.6
|
1.0
|
CL
|
M:2L5210
|
4.9
|
53.5
|
1.0
|
CBD
|
L:BCL303
|
5.0
|
48.0
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8vtk
Go back to
Magnesium Binding Sites List in 8vtk
Magnesium binding site 2 out
of 4 in the Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine
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)2-Chlorophenylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg306
b:47.3
occ:1.00
|
MG
|
L:BCL306
|
0.0
|
47.3
|
1.0
|
NE2
|
L:HIS173
|
1.9
|
54.5
|
1.0
|
ND
|
L:BCL306
|
2.0
|
47.0
|
1.0
|
NB
|
L:BCL306
|
2.1
|
47.9
|
1.0
|
NC
|
L:BCL306
|
2.1
|
49.6
|
1.0
|
NA
|
L:BCL306
|
2.2
|
49.8
|
1.0
|
CE1
|
L:HIS173
|
2.7
|
48.3
|
1.0
|
C4D
|
L:BCL306
|
3.0
|
54.5
|
1.0
|
CD2
|
L:HIS173
|
3.1
|
47.5
|
1.0
|
C1B
|
L:BCL306
|
3.1
|
49.8
|
1.0
|
C4B
|
L:BCL306
|
3.1
|
49.4
|
1.0
|
C4A
|
L:BCL306
|
3.1
|
49.4
|
1.0
|
C1C
|
L:BCL306
|
3.1
|
50.1
|
1.0
|
C1D
|
L:BCL306
|
3.1
|
48.2
|
1.0
|
C4C
|
L:BCL306
|
3.2
|
51.5
|
1.0
|
C1A
|
L:BCL306
|
3.2
|
49.7
|
1.0
|
CHB
|
L:BCL306
|
3.4
|
47.4
|
1.0
|
CHC
|
L:BCL306
|
3.4
|
48.4
|
1.0
|
CHD
|
L:BCL306
|
3.5
|
50.6
|
1.0
|
CHA
|
L:BCL306
|
3.5
|
54.5
|
1.0
|
CBB
|
M:BCL401
|
3.7
|
51.8
|
1.0
|
ND1
|
L:HIS173
|
3.9
|
48.8
|
1.0
|
CAB
|
M:BCL401
|
3.9
|
58.3
|
1.0
|
OBB
|
M:BCL401
|
4.0
|
61.7
|
1.0
|
CG
|
L:HIS173
|
4.1
|
47.8
|
1.0
|
C3D
|
L:BCL306
|
4.2
|
50.8
|
1.0
|
C2D
|
L:BCL306
|
4.3
|
48.2
|
1.0
|
C2B
|
L:BCL306
|
4.3
|
52.9
|
1.0
|
C3B
|
L:BCL306
|
4.3
|
49.9
|
1.0
|
C3A
|
L:BCL306
|
4.4
|
46.0
|
1.0
|
C2C
|
L:BCL306
|
4.5
|
45.7
|
1.0
|
C3C
|
L:BCL306
|
4.5
|
50.2
|
1.0
|
C2A
|
L:BCL306
|
4.5
|
51.0
|
1.0
|
CD2
|
L:PHE167
|
4.6
|
48.9
|
1.0
|
C3B
|
M:BCL401
|
4.7
|
52.6
|
1.0
|
CMA
|
L:BCL306
|
4.8
|
43.0
|
1.0
|
CBD
|
L:BCL306
|
5.0
|
55.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8vtk
Go back to
Magnesium Binding Sites List in 8vtk
Magnesium binding site 3 out
of 4 in the Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine
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)2-Chlorophenylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg401
b:49.9
occ:1.00
|
MG
|
M:BCL401
|
0.0
|
49.9
|
1.0
|
NE2
|
M:HIS202
|
1.9
|
51.9
|
1.0
|
ND
|
M:BCL401
|
2.1
|
51.7
|
1.0
|
NB
|
M:BCL401
|
2.1
|
50.3
|
1.0
|
NC
|
M:BCL401
|
2.1
|
47.9
|
1.0
|
NA
|
M:BCL401
|
2.2
|
43.9
|
1.0
|
CE1
|
M:HIS202
|
2.8
|
47.1
|
1.0
|
C4D
|
M:BCL401
|
3.0
|
50.7
|
1.0
|
CD2
|
M:HIS202
|
3.0
|
48.2
|
1.0
|
C4B
|
M:BCL401
|
3.1
|
48.8
|
1.0
|
C1B
|
M:BCL401
|
3.1
|
48.8
|
1.0
|
C4A
|
M:BCL401
|
3.1
|
46.7
|
1.0
|
C1C
|
M:BCL401
|
3.1
|
54.7
|
1.0
|
C1D
|
M:BCL401
|
3.2
|
46.0
|
1.0
|
C4C
|
M:BCL401
|
3.2
|
47.8
|
1.0
|
C1A
|
M:BCL401
|
3.2
|
48.1
|
1.0
|
CHC
|
M:BCL401
|
3.4
|
52.0
|
1.0
|
CHB
|
M:BCL401
|
3.4
|
45.2
|
1.0
|
CHA
|
M:BCL401
|
3.5
|
46.9
|
1.0
|
CHD
|
M:BCL401
|
3.5
|
49.0
|
1.0
|
CBB
|
L:BCL306
|
3.6
|
47.6
|
1.0
|
ND1
|
M:HIS202
|
4.0
|
47.5
|
1.0
|
CAB
|
L:BCL306
|
4.1
|
50.2
|
1.0
|
CG
|
M:HIS202
|
4.1
|
45.9
|
1.0
|
C3D
|
M:BCL401
|
4.2
|
49.9
|
1.0
|
C2B
|
M:BCL401
|
4.3
|
47.8
|
1.0
|
C2D
|
M:BCL401
|
4.3
|
47.5
|
1.0
|
C3B
|
M:BCL401
|
4.3
|
52.6
|
1.0
|
C2C
|
M:BCL401
|
4.4
|
46.5
|
1.0
|
OBB
|
L:BCL306
|
4.4
|
51.0
|
1.0
|
C3A
|
M:BCL401
|
4.5
|
47.2
|
1.0
|
C3C
|
M:BCL401
|
4.5
|
45.8
|
1.0
|
C2A
|
M:BCL401
|
4.5
|
46.3
|
1.0
|
C3B
|
L:BCL306
|
4.7
|
49.9
|
1.0
|
CMC
|
M:BCL401
|
4.8
|
46.8
|
1.0
|
CD1
|
M:LEU196
|
4.9
|
47.8
|
1.0
|
CD1
|
M:ILE206
|
4.9
|
49.7
|
1.0
|
CBD
|
M:BCL401
|
4.9
|
46.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8vtk
Go back to
Magnesium Binding Sites List in 8vtk
Magnesium binding site 4 out
of 4 in the Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine
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)2-Chlorophenylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg406
b:46.8
occ:1.00
|
MG
|
M:BCL406
|
0.0
|
46.8
|
1.0
|
NE2
|
M:HIS182
|
1.9
|
56.3
|
1.0
|
ND
|
M:BCL406
|
2.0
|
45.9
|
1.0
|
NB
|
M:BCL406
|
2.1
|
50.5
|
1.0
|
NC
|
M:BCL406
|
2.1
|
52.3
|
1.0
|
NA
|
M:BCL406
|
2.2
|
47.9
|
1.0
|
CE1
|
M:HIS182
|
2.9
|
50.4
|
1.0
|
CD2
|
M:HIS182
|
3.0
|
52.5
|
1.0
|
C4D
|
M:BCL406
|
3.0
|
50.6
|
1.0
|
C1B
|
M:BCL406
|
3.1
|
49.6
|
1.0
|
C4B
|
M:BCL406
|
3.1
|
49.4
|
1.0
|
C1C
|
M:BCL406
|
3.1
|
52.0
|
1.0
|
C4A
|
M:BCL406
|
3.1
|
47.1
|
1.0
|
C1D
|
M:BCL406
|
3.2
|
47.0
|
1.0
|
C4C
|
M:BCL406
|
3.2
|
53.2
|
1.0
|
C1A
|
M:BCL406
|
3.2
|
51.8
|
1.0
|
CHC
|
M:BCL406
|
3.4
|
48.7
|
1.0
|
CHB
|
M:BCL406
|
3.4
|
44.8
|
1.0
|
CHA
|
M:BCL406
|
3.5
|
54.2
|
1.0
|
CHD
|
M:BCL406
|
3.5
|
51.0
|
1.0
|
ND1
|
M:HIS182
|
4.0
|
50.9
|
1.0
|
CG
|
M:HIS182
|
4.1
|
54.3
|
1.0
|
C3D
|
M:BCL406
|
4.2
|
51.1
|
1.0
|
C2B
|
M:BCL406
|
4.3
|
49.4
|
1.0
|
C2D
|
M:BCL406
|
4.3
|
50.2
|
1.0
|
C3B
|
M:BCL406
|
4.4
|
52.9
|
1.0
|
C2C
|
M:BCL406
|
4.4
|
48.7
|
1.0
|
C3A
|
M:BCL406
|
4.5
|
44.8
|
1.0
|
C3C
|
M:BCL406
|
4.5
|
50.8
|
1.0
|
C2A
|
M:BCL406
|
4.5
|
49.5
|
1.0
|
C18
|
M:SPO404
|
4.9
|
49.7
|
1.0
|
CBD
|
M:BCL406
|
5.0
|
54.0
|
1.0
|
|
Reference:
K.Tran,
I.Mathews,
S.G.Boxer.
Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine To Be Published.
Page generated: Fri Oct 4 22:14:49 2024
|