Magnesium in PDB 8vtm: Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Bromophenylalanine
Protein crystallography data
The structure of Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Bromophenylalanine, PDB code: 8vtm
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)
|
39.99 /
3.51
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
141.79,
141.79,
187.71,
90,
90,
120
|
R / Rfree (%)
|
22 /
26.1
|
Other elements in 8vtm:
The structure of Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Bromophenylalanine 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-Bromophenylalanine
(pdb code 8vtm). 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-Bromophenylalanine, PDB code: 8vtm:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8vtm
Go back to
Magnesium Binding Sites List in 8vtm
Magnesium binding site 1 out
of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Bromophenylalanine
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-Bromophenylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg301
b:52.8
occ:1.00
|
MG
|
L:BCL301
|
0.0
|
52.8
|
1.0
|
NE2
|
L:HIS153
|
1.9
|
62.2
|
1.0
|
ND
|
L:BCL301
|
2.0
|
55.5
|
1.0
|
NB
|
L:BCL301
|
2.1
|
58.4
|
1.0
|
NC
|
L:BCL301
|
2.1
|
52.6
|
1.0
|
NA
|
L:BCL301
|
2.2
|
56.4
|
1.0
|
CD2
|
L:HIS153
|
2.9
|
61.4
|
1.0
|
CE1
|
L:HIS153
|
2.9
|
60.5
|
1.0
|
C4D
|
L:BCL301
|
3.0
|
58.7
|
1.0
|
C1B
|
L:BCL301
|
3.1
|
56.6
|
1.0
|
C4B
|
L:BCL301
|
3.1
|
57.8
|
1.0
|
C1C
|
L:BCL301
|
3.1
|
56.7
|
1.0
|
C1D
|
L:BCL301
|
3.1
|
52.7
|
1.0
|
C4A
|
L:BCL301
|
3.1
|
58.8
|
1.0
|
C4C
|
L:BCL301
|
3.2
|
50.0
|
1.0
|
C1A
|
L:BCL301
|
3.2
|
60.5
|
1.0
|
CHB
|
L:BCL301
|
3.4
|
59.6
|
1.0
|
CHC
|
L:BCL301
|
3.4
|
59.8
|
1.0
|
CHA
|
L:BCL301
|
3.5
|
59.6
|
1.0
|
CHD
|
L:BCL301
|
3.5
|
50.5
|
1.0
|
ND1
|
L:HIS153
|
4.0
|
61.3
|
1.0
|
CG
|
L:HIS153
|
4.0
|
61.2
|
1.0
|
C3D
|
L:BCL301
|
4.2
|
56.6
|
1.0
|
C2D
|
L:BCL301
|
4.3
|
55.5
|
1.0
|
C2B
|
L:BCL301
|
4.3
|
53.3
|
1.0
|
C3B
|
L:BCL301
|
4.3
|
53.6
|
1.0
|
C2C
|
L:BCL301
|
4.4
|
52.0
|
1.0
|
C3A
|
L:BCL301
|
4.4
|
56.7
|
1.0
|
C3C
|
L:BCL301
|
4.5
|
51.6
|
1.0
|
C2A
|
L:BCL301
|
4.5
|
59.0
|
1.0
|
CD1
|
L:LEU154
|
4.8
|
56.5
|
1.0
|
CBD
|
L:BCL301
|
5.0
|
57.1
|
1.0
|
OBB
|
M:BPH408
|
5.0
|
59.2
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8vtm
Go back to
Magnesium Binding Sites List in 8vtm
Magnesium binding site 2 out
of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Bromophenylalanine
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-Bromophenylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg302
b:54.5
occ:1.00
|
MG
|
L:BCL302
|
0.0
|
54.5
|
1.0
|
NE2
|
L:HIS173
|
1.9
|
52.5
|
1.0
|
ND
|
L:BCL302
|
2.0
|
53.7
|
1.0
|
NB
|
L:BCL302
|
2.1
|
51.3
|
1.0
|
NC
|
L:BCL302
|
2.1
|
59.1
|
1.0
|
NA
|
L:BCL302
|
2.2
|
53.9
|
1.0
|
CE1
|
L:HIS173
|
2.3
|
53.3
|
1.0
|
C4D
|
L:BCL302
|
3.0
|
59.2
|
1.0
|
C4B
|
L:BCL302
|
3.1
|
54.8
|
1.0
|
C1B
|
L:BCL302
|
3.1
|
53.8
|
1.0
|
C1C
|
L:BCL302
|
3.1
|
57.8
|
1.0
|
C4A
|
L:BCL302
|
3.1
|
55.4
|
1.0
|
C1D
|
L:BCL302
|
3.2
|
50.5
|
1.0
|
C4C
|
L:BCL302
|
3.2
|
57.3
|
1.0
|
C1A
|
L:BCL302
|
3.2
|
55.4
|
1.0
|
CD2
|
L:HIS173
|
3.2
|
51.7
|
1.0
|
CHC
|
L:BCL302
|
3.4
|
56.6
|
1.0
|
CHB
|
L:BCL302
|
3.4
|
54.9
|
1.0
|
CHA
|
L:BCL302
|
3.5
|
60.4
|
1.0
|
CHD
|
L:BCL302
|
3.5
|
54.3
|
1.0
|
CBB
|
M:BCL401
|
3.5
|
60.6
|
1.0
|
ND1
|
L:HIS173
|
3.6
|
53.9
|
1.0
|
CAB
|
M:BCL401
|
3.9
|
60.7
|
1.0
|
CG
|
L:HIS173
|
4.0
|
51.6
|
1.0
|
OBB
|
M:BCL401
|
4.1
|
61.2
|
1.0
|
C3D
|
L:BCL302
|
4.2
|
58.5
|
1.0
|
C2B
|
L:BCL302
|
4.3
|
55.2
|
1.0
|
C2D
|
L:BCL302
|
4.3
|
53.6
|
1.0
|
C3B
|
L:BCL302
|
4.3
|
55.8
|
1.0
|
C3A
|
L:BCL302
|
4.4
|
52.5
|
1.0
|
C2C
|
L:BCL302
|
4.5
|
55.6
|
1.0
|
C3C
|
L:BCL302
|
4.5
|
56.1
|
1.0
|
C2A
|
L:BCL302
|
4.5
|
54.4
|
1.0
|
CD2
|
L:PHE167
|
4.7
|
54.4
|
1.0
|
CMA
|
L:BCL302
|
4.8
|
47.6
|
1.0
|
C3B
|
M:BCL401
|
4.8
|
57.6
|
1.0
|
CBD
|
L:BCL302
|
4.9
|
62.6
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8vtm
Go back to
Magnesium Binding Sites List in 8vtm
Magnesium binding site 3 out
of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Bromophenylalanine
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-Bromophenylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg401
b:52.8
occ:1.00
|
MG
|
M:BCL401
|
0.0
|
52.8
|
1.0
|
NE2
|
M:HIS202
|
1.9
|
58.1
|
1.0
|
ND
|
M:BCL401
|
2.0
|
54.2
|
1.0
|
NB
|
M:BCL401
|
2.1
|
56.5
|
1.0
|
NC
|
M:BCL401
|
2.1
|
52.0
|
1.0
|
NA
|
M:BCL401
|
2.2
|
52.8
|
1.0
|
CE1
|
M:HIS202
|
2.7
|
55.5
|
1.0
|
C4D
|
M:BCL401
|
3.0
|
56.0
|
1.0
|
CD2
|
M:HIS202
|
3.1
|
56.5
|
1.0
|
C4B
|
M:BCL401
|
3.1
|
54.3
|
1.0
|
C1B
|
M:BCL401
|
3.1
|
59.0
|
1.0
|
C1C
|
M:BCL401
|
3.1
|
53.8
|
1.0
|
C1D
|
M:BCL401
|
3.2
|
51.9
|
1.0
|
C4A
|
M:BCL401
|
3.2
|
51.2
|
1.0
|
C4C
|
M:BCL401
|
3.2
|
53.8
|
1.0
|
C1A
|
M:BCL401
|
3.2
|
52.7
|
1.0
|
CHC
|
M:BCL401
|
3.4
|
54.0
|
1.0
|
CHB
|
M:BCL401
|
3.4
|
53.5
|
1.0
|
CHA
|
M:BCL401
|
3.5
|
52.6
|
1.0
|
CBB
|
L:BCL302
|
3.5
|
47.8
|
1.0
|
CHD
|
M:BCL401
|
3.5
|
53.9
|
1.0
|
ND1
|
M:HIS202
|
3.9
|
52.9
|
1.0
|
CG
|
M:HIS202
|
4.1
|
53.8
|
1.0
|
C3D
|
M:BCL401
|
4.2
|
56.4
|
1.0
|
C2B
|
M:BCL401
|
4.3
|
58.4
|
1.0
|
C2D
|
M:BCL401
|
4.3
|
52.5
|
1.0
|
C3B
|
M:BCL401
|
4.3
|
57.6
|
1.0
|
CAB
|
L:BCL302
|
4.4
|
56.5
|
1.0
|
C2C
|
M:BCL401
|
4.4
|
51.4
|
1.0
|
C3A
|
M:BCL401
|
4.5
|
51.3
|
1.0
|
C3C
|
M:BCL401
|
4.5
|
49.1
|
1.0
|
C2A
|
M:BCL401
|
4.5
|
53.9
|
1.0
|
CBD
|
M:BCL401
|
4.8
|
51.8
|
1.0
|
C3B
|
L:BCL302
|
4.9
|
55.8
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8vtm
Go back to
Magnesium Binding Sites List in 8vtm
Magnesium binding site 4 out
of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Bromophenylalanine
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-Bromophenylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg409
b:59.2
occ:1.00
|
MG
|
M:BCL409
|
0.0
|
59.2
|
1.0
|
NE2
|
M:HIS182
|
1.9
|
61.6
|
1.0
|
ND
|
M:BCL409
|
2.0
|
59.2
|
1.0
|
NB
|
M:BCL409
|
2.1
|
58.3
|
1.0
|
NC
|
M:BCL409
|
2.1
|
56.4
|
1.0
|
NA
|
M:BCL409
|
2.2
|
52.9
|
1.0
|
CD2
|
M:HIS182
|
2.9
|
61.9
|
1.0
|
CE1
|
M:HIS182
|
2.9
|
56.6
|
1.0
|
C4D
|
M:BCL409
|
3.0
|
59.6
|
1.0
|
C4B
|
M:BCL409
|
3.1
|
60.0
|
1.0
|
C1B
|
M:BCL409
|
3.1
|
56.2
|
1.0
|
C1C
|
M:BCL409
|
3.1
|
56.6
|
1.0
|
C1D
|
M:BCL409
|
3.1
|
58.7
|
1.0
|
C4A
|
M:BCL409
|
3.2
|
51.7
|
1.0
|
C4C
|
M:BCL409
|
3.2
|
55.9
|
1.0
|
C1A
|
M:BCL409
|
3.2
|
55.9
|
1.0
|
CHC
|
M:BCL409
|
3.4
|
58.8
|
1.0
|
CHB
|
M:BCL409
|
3.4
|
53.1
|
1.0
|
CHA
|
M:BCL409
|
3.5
|
59.0
|
1.0
|
CHD
|
M:BCL409
|
3.5
|
57.9
|
1.0
|
ND1
|
M:HIS182
|
4.0
|
54.5
|
1.0
|
CG
|
M:HIS182
|
4.0
|
58.5
|
1.0
|
C3D
|
M:BCL409
|
4.2
|
56.1
|
1.0
|
C2B
|
M:BCL409
|
4.3
|
57.1
|
1.0
|
C2D
|
M:BCL409
|
4.3
|
54.5
|
1.0
|
C3B
|
M:BCL409
|
4.3
|
61.8
|
1.0
|
C2C
|
M:BCL409
|
4.4
|
51.9
|
1.0
|
C3A
|
M:BCL409
|
4.4
|
50.5
|
1.0
|
C3C
|
M:BCL409
|
4.5
|
53.7
|
1.0
|
C2A
|
M:BCL409
|
4.5
|
52.5
|
1.0
|
CBD
|
M:BCL409
|
4.9
|
55.2
|
1.0
|
|
Reference:
K.Tran,
I.Mathews,
S.G.Boxer.
Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Bromophenylalanine To Be Published.
Page generated: Fri Oct 4 22:14:50 2024
|