Magnesium in PDB 8ypd: Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
28;
Binding sites:
The binding sites of Magnesium atom in the Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum
(pdb code 8ypd). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 28 binding sites of Magnesium where determined in the
Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum, PDB code: 8ypd:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 28 in 8ypd
Go back to
Magnesium Binding Sites List in 8ypd
Magnesium binding site 1 out
of 28 in the Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
b:Mg101
b:5.8
occ:1.00
|
MG
|
b:BCL101
|
0.0
|
5.8
|
1.0
|
|
NB
|
b:BCL101
|
2.0
|
5.8
|
1.0
|
|
ND
|
b:BCL101
|
2.0
|
5.8
|
1.0
|
|
NC
|
b:BCL101
|
2.1
|
5.8
|
1.0
|
|
NA
|
b:BCL101
|
2.1
|
5.8
|
1.0
|
|
NE2
|
b:HIS37
|
2.2
|
4.6
|
1.0
|
|
C4D
|
b:BCL101
|
2.9
|
5.8
|
1.0
|
|
CE1
|
b:HIS37
|
3.0
|
4.6
|
1.0
|
|
C4B
|
b:BCL101
|
3.0
|
5.8
|
1.0
|
|
C1C
|
b:BCL101
|
3.0
|
5.8
|
1.0
|
|
C4A
|
b:BCL101
|
3.0
|
5.8
|
1.0
|
|
C1B
|
b:BCL101
|
3.0
|
5.8
|
1.0
|
|
C1A
|
b:BCL101
|
3.0
|
5.8
|
1.0
|
|
C4C
|
b:BCL101
|
3.1
|
5.8
|
1.0
|
|
C1D
|
b:BCL101
|
3.1
|
5.8
|
1.0
|
|
CD2
|
b:HIS37
|
3.3
|
4.6
|
1.0
|
|
CHC
|
b:BCL101
|
3.4
|
5.8
|
1.0
|
|
CHB
|
b:BCL101
|
3.4
|
5.8
|
1.0
|
|
CHA
|
b:BCL101
|
3.4
|
5.8
|
1.0
|
|
CHD
|
b:BCL101
|
3.6
|
5.8
|
1.0
|
|
CBB
|
a:BCL102
|
4.1
|
6.7
|
1.0
|
|
C3D
|
b:BCL101
|
4.1
|
5.8
|
1.0
|
|
ND1
|
b:HIS37
|
4.2
|
4.6
|
1.0
|
|
C2D
|
b:BCL101
|
4.3
|
5.8
|
1.0
|
|
C3B
|
b:BCL101
|
4.3
|
5.8
|
1.0
|
|
CG
|
b:HIS37
|
4.3
|
4.6
|
1.0
|
|
C2C
|
b:BCL101
|
4.4
|
5.8
|
1.0
|
|
C3C
|
b:BCL101
|
4.4
|
5.8
|
1.0
|
|
C2B
|
b:BCL101
|
4.4
|
5.8
|
1.0
|
|
C2A
|
b:BCL101
|
4.4
|
5.8
|
1.0
|
|
C3A
|
b:BCL101
|
4.4
|
5.8
|
1.0
|
|
CMB
|
a:BCL102
|
4.4
|
6.7
|
1.0
|
|
C2B
|
a:BCL102
|
4.6
|
6.7
|
1.0
|
|
CAB
|
a:BCL102
|
4.8
|
6.7
|
1.0
|
|
CBD
|
b:BCL101
|
4.8
|
5.8
|
1.0
|
|
CD1
|
F:ILE28
|
4.8
|
4.5
|
1.0
|
|
C10
|
b:BCL101
|
4.9
|
5.8
|
1.0
|
|
CG2
|
F:ILE28
|
4.9
|
4.5
|
1.0
|
|
C3B
|
a:BCL102
|
5.0
|
6.7
|
1.0
|
|
Magnesium binding site 2 out
of 28 in 8ypd
Go back to
Magnesium Binding Sites List in 8ypd
Magnesium binding site 2 out
of 28 in the Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg101
b:6.3
occ:1.00
|
MG
|
F:BCL101
|
0.0
|
6.3
|
1.0
|
|
NB
|
F:BCL101
|
2.0
|
6.3
|
1.0
|
|
ND
|
F:BCL101
|
2.0
|
6.3
|
1.0
|
|
NC
|
F:BCL101
|
2.1
|
6.3
|
1.0
|
|
NA
|
F:BCL101
|
2.1
|
6.3
|
1.0
|
|
NE2
|
F:HIS29
|
2.2
|
4.9
|
1.0
|
|
C4D
|
F:BCL101
|
2.9
|
6.3
|
1.0
|
|
CE1
|
F:HIS29
|
3.0
|
4.9
|
1.0
|
|
C1C
|
F:BCL101
|
3.0
|
6.3
|
1.0
|
|
C4B
|
F:BCL101
|
3.0
|
6.3
|
1.0
|
|
C1B
|
F:BCL101
|
3.0
|
6.3
|
1.0
|
|
C1A
|
F:BCL101
|
3.0
|
6.3
|
1.0
|
|
C4A
|
F:BCL101
|
3.0
|
6.3
|
1.0
|
|
C4C
|
F:BCL101
|
3.1
|
6.3
|
1.0
|
|
C1D
|
F:BCL101
|
3.2
|
6.3
|
1.0
|
|
CD2
|
F:HIS29
|
3.3
|
4.9
|
1.0
|
|
CHC
|
F:BCL101
|
3.3
|
6.3
|
1.0
|
|
CHA
|
F:BCL101
|
3.4
|
6.3
|
1.0
|
|
CHB
|
F:BCL101
|
3.4
|
6.3
|
1.0
|
|
CHD
|
F:BCL101
|
3.6
|
6.3
|
1.0
|
|
CBB
|
A:BCL101
|
4.1
|
5.5
|
1.0
|
|
C3D
|
F:BCL101
|
4.1
|
6.3
|
1.0
|
|
ND1
|
F:HIS29
|
4.2
|
4.9
|
1.0
|
|
C2B
|
F:BCL101
|
4.3
|
6.3
|
1.0
|
|
C3B
|
F:BCL101
|
4.3
|
6.3
|
1.0
|
|
C2D
|
F:BCL101
|
4.3
|
6.3
|
1.0
|
|
C2C
|
F:BCL101
|
4.4
|
6.3
|
1.0
|
|
CG
|
F:HIS29
|
4.4
|
4.9
|
1.0
|
|
C2A
|
F:BCL101
|
4.4
|
6.3
|
1.0
|
|
C3C
|
F:BCL101
|
4.4
|
6.3
|
1.0
|
|
C3A
|
F:BCL101
|
4.4
|
6.3
|
1.0
|
|
CMD
|
b:BCL101
|
4.4
|
5.8
|
1.0
|
|
CBD
|
F:BCL101
|
4.8
|
6.3
|
1.0
|
|
C2B
|
A:BCL101
|
4.9
|
5.5
|
1.0
|
|
CMB
|
A:BCL101
|
4.9
|
5.5
|
1.0
|
|
Magnesium binding site 3 out
of 28 in 8ypd
Go back to
Magnesium Binding Sites List in 8ypd
Magnesium binding site 3 out
of 28 in the Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg101
b:5.5
occ:1.00
|
MG
|
A:BCL101
|
0.0
|
5.5
|
1.0
|
|
NB
|
A:BCL101
|
2.0
|
5.5
|
1.0
|
|
ND
|
A:BCL101
|
2.0
|
5.5
|
1.0
|
|
NC
|
A:BCL101
|
2.1
|
5.5
|
1.0
|
|
NA
|
A:BCL101
|
2.1
|
5.5
|
1.0
|
|
NE2
|
A:HIS37
|
2.2
|
4.8
|
1.0
|
|
C4D
|
A:BCL101
|
2.9
|
5.5
|
1.0
|
|
C4B
|
A:BCL101
|
3.0
|
5.5
|
1.0
|
|
C1C
|
A:BCL101
|
3.0
|
5.5
|
1.0
|
|
C1A
|
A:BCL101
|
3.0
|
5.5
|
1.0
|
|
C4A
|
A:BCL101
|
3.0
|
5.5
|
1.0
|
|
C1B
|
A:BCL101
|
3.0
|
5.5
|
1.0
|
|
C4C
|
A:BCL101
|
3.1
|
5.5
|
1.0
|
|
CD2
|
A:HIS37
|
3.1
|
4.8
|
1.0
|
|
C1D
|
A:BCL101
|
3.1
|
5.5
|
1.0
|
|
CE1
|
A:HIS37
|
3.2
|
4.8
|
1.0
|
|
CHC
|
A:BCL101
|
3.4
|
5.5
|
1.0
|
|
CHB
|
A:BCL101
|
3.4
|
5.5
|
1.0
|
|
CHA
|
A:BCL101
|
3.4
|
5.5
|
1.0
|
|
CHD
|
A:BCL101
|
3.6
|
5.5
|
1.0
|
|
CMB
|
F:BCL101
|
4.1
|
6.3
|
1.0
|
|
C3D
|
A:BCL101
|
4.1
|
5.5
|
1.0
|
|
CBB
|
F:BCL101
|
4.2
|
6.3
|
1.0
|
|
CG
|
A:HIS37
|
4.3
|
4.8
|
1.0
|
|
ND1
|
A:HIS37
|
4.3
|
4.8
|
1.0
|
|
C2D
|
A:BCL101
|
4.3
|
5.5
|
1.0
|
|
C3B
|
A:BCL101
|
4.3
|
5.5
|
1.0
|
|
C3C
|
A:BCL101
|
4.4
|
5.5
|
1.0
|
|
C2C
|
A:BCL101
|
4.4
|
5.5
|
1.0
|
|
C2B
|
A:BCL101
|
4.4
|
5.5
|
1.0
|
|
C2A
|
A:BCL101
|
4.4
|
5.5
|
1.0
|
|
C3A
|
A:BCL101
|
4.4
|
5.5
|
1.0
|
|
CAB
|
F:BCL101
|
4.8
|
6.3
|
1.0
|
|
C2B
|
F:BCL101
|
4.8
|
6.3
|
1.0
|
|
CBD
|
A:BCL101
|
4.8
|
5.5
|
1.0
|
|
CD1
|
B:ILE28
|
4.9
|
4.7
|
1.0
|
|
C3B
|
F:BCL101
|
4.9
|
6.3
|
1.0
|
|
C10
|
A:BCL101
|
4.9
|
5.5
|
1.0
|
|
CG2
|
B:ILE28
|
5.0
|
4.7
|
1.0
|
|
Magnesium binding site 4 out
of 28 in 8ypd
Go back to
Magnesium Binding Sites List in 8ypd
Magnesium binding site 4 out
of 28 in the Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg101
b:6.5
occ:1.00
|
MG
|
B:BCL101
|
0.0
|
6.5
|
1.0
|
|
NB
|
B:BCL101
|
2.0
|
6.5
|
1.0
|
|
ND
|
B:BCL101
|
2.0
|
6.5
|
1.0
|
|
NC
|
B:BCL101
|
2.1
|
6.5
|
1.0
|
|
NA
|
B:BCL101
|
2.1
|
6.5
|
1.0
|
|
NE2
|
B:HIS29
|
2.2
|
4.9
|
1.0
|
|
C4D
|
B:BCL101
|
2.9
|
6.5
|
1.0
|
|
C1C
|
B:BCL101
|
3.0
|
6.5
|
1.0
|
|
C4B
|
B:BCL101
|
3.0
|
6.5
|
1.0
|
|
C1A
|
B:BCL101
|
3.0
|
6.5
|
1.0
|
|
C1B
|
B:BCL101
|
3.0
|
6.5
|
1.0
|
|
C4A
|
B:BCL101
|
3.0
|
6.5
|
1.0
|
|
C4C
|
B:BCL101
|
3.1
|
6.5
|
1.0
|
|
CE1
|
B:HIS29
|
3.1
|
4.9
|
1.0
|
|
C1D
|
B:BCL101
|
3.2
|
6.5
|
1.0
|
|
CD2
|
B:HIS29
|
3.2
|
4.9
|
1.0
|
|
CHC
|
B:BCL101
|
3.3
|
6.5
|
1.0
|
|
CHA
|
B:BCL101
|
3.4
|
6.5
|
1.0
|
|
CHB
|
B:BCL101
|
3.4
|
6.5
|
1.0
|
|
CHD
|
B:BCL101
|
3.6
|
6.5
|
1.0
|
|
C3D
|
B:BCL101
|
4.2
|
6.5
|
1.0
|
|
ND1
|
B:HIS29
|
4.2
|
4.9
|
1.0
|
|
C3B
|
B:BCL101
|
4.3
|
6.5
|
1.0
|
|
C2D
|
B:BCL101
|
4.3
|
6.5
|
1.0
|
|
C2B
|
B:BCL101
|
4.3
|
6.5
|
1.0
|
|
CG
|
B:HIS29
|
4.3
|
4.9
|
1.0
|
|
CBB
|
C:BCL101
|
4.3
|
5.9
|
1.0
|
|
C2C
|
B:BCL101
|
4.4
|
6.5
|
1.0
|
|
C2A
|
B:BCL101
|
4.4
|
6.5
|
1.0
|
|
C3C
|
B:BCL101
|
4.4
|
6.5
|
1.0
|
|
CMD
|
A:BCL101
|
4.4
|
5.5
|
1.0
|
|
C3A
|
B:BCL101
|
4.4
|
6.5
|
1.0
|
|
CMB
|
C:BCL101
|
4.8
|
5.9
|
1.0
|
|
CBD
|
B:BCL101
|
4.8
|
6.5
|
1.0
|
|
C2B
|
C:BCL101
|
4.9
|
5.9
|
1.0
|
|
Magnesium binding site 5 out
of 28 in 8ypd
Go back to
Magnesium Binding Sites List in 8ypd
Magnesium binding site 5 out
of 28 in the Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg101
b:5.9
occ:1.00
|
MG
|
C:BCL101
|
0.0
|
5.9
|
1.0
|
|
NB
|
C:BCL101
|
2.0
|
5.9
|
1.0
|
|
ND
|
C:BCL101
|
2.0
|
5.9
|
1.0
|
|
NC
|
C:BCL101
|
2.1
|
5.9
|
1.0
|
|
NA
|
C:BCL101
|
2.1
|
5.9
|
1.0
|
|
NE2
|
C:HIS37
|
2.2
|
4.9
|
1.0
|
|
C4D
|
C:BCL101
|
2.9
|
5.9
|
1.0
|
|
CE1
|
C:HIS37
|
2.9
|
4.9
|
1.0
|
|
C1C
|
C:BCL101
|
3.0
|
5.9
|
1.0
|
|
C4B
|
C:BCL101
|
3.0
|
5.9
|
1.0
|
|
C1B
|
C:BCL101
|
3.0
|
5.9
|
1.0
|
|
C4A
|
C:BCL101
|
3.0
|
5.9
|
1.0
|
|
C1A
|
C:BCL101
|
3.0
|
5.9
|
1.0
|
|
C4C
|
C:BCL101
|
3.1
|
5.9
|
1.0
|
|
C1D
|
C:BCL101
|
3.1
|
5.9
|
1.0
|
|
CHC
|
C:BCL101
|
3.3
|
5.9
|
1.0
|
|
CHB
|
C:BCL101
|
3.4
|
5.9
|
1.0
|
|
CD2
|
C:HIS37
|
3.4
|
4.9
|
1.0
|
|
CHA
|
C:BCL101
|
3.4
|
5.9
|
1.0
|
|
CHD
|
C:BCL101
|
3.6
|
5.9
|
1.0
|
|
CMB
|
B:BCL101
|
3.9
|
6.5
|
1.0
|
|
ND1
|
C:HIS37
|
4.1
|
4.9
|
1.0
|
|
C3D
|
C:BCL101
|
4.2
|
5.9
|
1.0
|
|
C2D
|
C:BCL101
|
4.3
|
5.9
|
1.0
|
|
C2C
|
C:BCL101
|
4.3
|
5.9
|
1.0
|
|
C3B
|
C:BCL101
|
4.3
|
5.9
|
1.0
|
|
C2B
|
C:BCL101
|
4.4
|
5.9
|
1.0
|
|
C3A
|
C:BCL101
|
4.4
|
5.9
|
1.0
|
|
CG
|
C:HIS37
|
4.4
|
4.9
|
1.0
|
|
C2A
|
C:BCL101
|
4.4
|
5.9
|
1.0
|
|
C3C
|
C:BCL101
|
4.4
|
5.9
|
1.0
|
|
CBB
|
B:BCL101
|
4.6
|
6.5
|
1.0
|
|
CAB
|
B:BCL101
|
4.7
|
6.5
|
1.0
|
|
CD1
|
D:ILE28
|
4.7
|
4.6
|
1.0
|
|
C2B
|
B:BCL101
|
4.7
|
6.5
|
1.0
|
|
CBD
|
C:BCL101
|
4.8
|
5.9
|
1.0
|
|
CG2
|
D:ILE28
|
4.8
|
4.6
|
1.0
|
|
C3B
|
B:BCL101
|
4.9
|
6.5
|
1.0
|
|
CMA
|
C:BCL101
|
5.0
|
5.9
|
1.0
|
|
Magnesium binding site 6 out
of 28 in 8ypd
Go back to
Magnesium Binding Sites List in 8ypd
Magnesium binding site 6 out
of 28 in the Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg101
b:6.6
occ:1.00
|
MG
|
D:BCL101
|
0.0
|
6.6
|
1.0
|
|
NB
|
D:BCL101
|
2.0
|
6.6
|
1.0
|
|
ND
|
D:BCL101
|
2.0
|
6.6
|
1.0
|
|
NC
|
D:BCL101
|
2.1
|
6.6
|
1.0
|
|
NA
|
D:BCL101
|
2.1
|
6.6
|
1.0
|
|
NE2
|
D:HIS29
|
2.2
|
5.1
|
1.0
|
|
C4D
|
D:BCL101
|
2.9
|
6.6
|
1.0
|
|
C4B
|
D:BCL101
|
3.0
|
6.6
|
1.0
|
|
C1C
|
D:BCL101
|
3.0
|
6.6
|
1.0
|
|
C1A
|
D:BCL101
|
3.0
|
6.6
|
1.0
|
|
C1B
|
D:BCL101
|
3.0
|
6.6
|
1.0
|
|
CE1
|
D:HIS29
|
3.0
|
5.1
|
1.0
|
|
C4A
|
D:BCL101
|
3.0
|
6.6
|
1.0
|
|
C4C
|
D:BCL101
|
3.1
|
6.6
|
1.0
|
|
C1D
|
D:BCL101
|
3.2
|
6.6
|
1.0
|
|
CD2
|
D:HIS29
|
3.3
|
5.1
|
1.0
|
|
CHC
|
D:BCL101
|
3.3
|
6.6
|
1.0
|
|
CHA
|
D:BCL101
|
3.4
|
6.6
|
1.0
|
|
CHB
|
D:BCL101
|
3.4
|
6.6
|
1.0
|
|
CHD
|
D:BCL101
|
3.6
|
6.6
|
1.0
|
|
C3D
|
D:BCL101
|
4.1
|
6.6
|
1.0
|
|
ND1
|
D:HIS29
|
4.2
|
5.1
|
1.0
|
|
C3B
|
D:BCL101
|
4.3
|
6.6
|
1.0
|
|
CMD
|
C:BCL101
|
4.3
|
5.9
|
1.0
|
|
C2D
|
D:BCL101
|
4.3
|
6.6
|
1.0
|
|
C2B
|
D:BCL101
|
4.3
|
6.6
|
1.0
|
|
CBB
|
E:BCL101
|
4.3
|
5.5
|
1.0
|
|
CG
|
D:HIS29
|
4.4
|
5.1
|
1.0
|
|
C2C
|
D:BCL101
|
4.4
|
6.6
|
1.0
|
|
C2A
|
D:BCL101
|
4.4
|
6.6
|
1.0
|
|
C3C
|
D:BCL101
|
4.4
|
6.6
|
1.0
|
|
C3A
|
D:BCL101
|
4.4
|
6.6
|
1.0
|
|
CBD
|
D:BCL101
|
4.8
|
6.6
|
1.0
|
|
CMB
|
E:BCL101
|
4.9
|
5.5
|
1.0
|
|
C2B
|
E:BCL101
|
5.0
|
5.5
|
1.0
|
|
OBD
|
C:BCL101
|
5.0
|
5.9
|
1.0
|
|
Magnesium binding site 7 out
of 28 in 8ypd
Go back to
Magnesium Binding Sites List in 8ypd
Magnesium binding site 7 out
of 28 in the Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg101
b:5.5
occ:1.00
|
MG
|
E:BCL101
|
0.0
|
5.5
|
1.0
|
|
NB
|
E:BCL101
|
2.0
|
5.5
|
1.0
|
|
ND
|
E:BCL101
|
2.0
|
5.5
|
1.0
|
|
NC
|
E:BCL101
|
2.1
|
5.5
|
1.0
|
|
NA
|
E:BCL101
|
2.1
|
5.5
|
1.0
|
|
NE2
|
E:HIS37
|
2.2
|
5.0
|
1.0
|
|
C4D
|
E:BCL101
|
2.9
|
5.5
|
1.0
|
|
CE1
|
E:HIS37
|
2.9
|
5.0
|
1.0
|
|
C1C
|
E:BCL101
|
3.0
|
5.5
|
1.0
|
|
C4B
|
E:BCL101
|
3.0
|
5.5
|
1.0
|
|
C1A
|
E:BCL101
|
3.0
|
5.5
|
1.0
|
|
C1B
|
E:BCL101
|
3.0
|
5.5
|
1.0
|
|
C4A
|
E:BCL101
|
3.0
|
5.5
|
1.0
|
|
C4C
|
E:BCL101
|
3.1
|
5.5
|
1.0
|
|
C1D
|
E:BCL101
|
3.1
|
5.5
|
1.0
|
|
CHC
|
E:BCL101
|
3.4
|
5.5
|
1.0
|
|
CD2
|
E:HIS37
|
3.4
|
5.0
|
1.0
|
|
CHB
|
E:BCL101
|
3.4
|
5.5
|
1.0
|
|
CHA
|
E:BCL101
|
3.4
|
5.5
|
1.0
|
|
CHD
|
E:BCL101
|
3.5
|
5.5
|
1.0
|
|
C3D
|
E:BCL101
|
4.1
|
5.5
|
1.0
|
|
ND1
|
E:HIS37
|
4.1
|
5.0
|
1.0
|
|
C2D
|
E:BCL101
|
4.3
|
5.5
|
1.0
|
|
CBB
|
D:BCL101
|
4.3
|
6.6
|
1.0
|
|
CMB
|
D:BCL101
|
4.3
|
6.6
|
1.0
|
|
C2C
|
E:BCL101
|
4.3
|
5.5
|
1.0
|
|
C3B
|
E:BCL101
|
4.3
|
5.5
|
1.0
|
|
C3A
|
E:BCL101
|
4.3
|
5.5
|
1.0
|
|
C2A
|
E:BCL101
|
4.4
|
5.5
|
1.0
|
|
C2B
|
E:BCL101
|
4.4
|
5.5
|
1.0
|
|
C3C
|
E:BCL101
|
4.4
|
5.5
|
1.0
|
|
CG
|
E:HIS37
|
4.4
|
5.0
|
1.0
|
|
C2B
|
D:BCL101
|
4.5
|
6.6
|
1.0
|
|
CAB
|
D:BCL101
|
4.6
|
6.6
|
1.0
|
|
CD1
|
G:ILE28
|
4.6
|
4.7
|
1.0
|
|
CG2
|
G:ILE28
|
4.7
|
4.7
|
1.0
|
|
CBD
|
E:BCL101
|
4.8
|
5.5
|
1.0
|
|
CMA
|
E:BCL101
|
4.9
|
5.5
|
1.0
|
|
C3B
|
D:BCL101
|
4.9
|
6.6
|
1.0
|
|
C10
|
E:BCL101
|
5.0
|
5.5
|
1.0
|
|
Magnesium binding site 8 out
of 28 in 8ypd
Go back to
Magnesium Binding Sites List in 8ypd
Magnesium binding site 8 out
of 28 in the Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg101
b:6.9
occ:1.00
|
MG
|
G:BCL101
|
0.0
|
6.9
|
1.0
|
|
NB
|
G:BCL101
|
2.0
|
6.9
|
1.0
|
|
ND
|
G:BCL101
|
2.0
|
6.9
|
1.0
|
|
NC
|
G:BCL101
|
2.1
|
6.9
|
1.0
|
|
NA
|
G:BCL101
|
2.1
|
6.9
|
1.0
|
|
NE2
|
G:HIS29
|
2.2
|
5.2
|
1.0
|
|
C4D
|
G:BCL101
|
2.9
|
6.9
|
1.0
|
|
C1C
|
G:BCL101
|
3.0
|
6.9
|
1.0
|
|
C4B
|
G:BCL101
|
3.0
|
6.9
|
1.0
|
|
C1A
|
G:BCL101
|
3.0
|
6.9
|
1.0
|
|
CE1
|
G:HIS29
|
3.0
|
5.2
|
1.0
|
|
C1B
|
G:BCL101
|
3.0
|
6.9
|
1.0
|
|
C4A
|
G:BCL101
|
3.1
|
6.9
|
1.0
|
|
C4C
|
G:BCL101
|
3.1
|
6.9
|
1.0
|
|
C1D
|
G:BCL101
|
3.2
|
6.9
|
1.0
|
|
CD2
|
G:HIS29
|
3.3
|
5.2
|
1.0
|
|
CHC
|
G:BCL101
|
3.3
|
6.9
|
1.0
|
|
CHA
|
G:BCL101
|
3.4
|
6.9
|
1.0
|
|
CHB
|
G:BCL101
|
3.4
|
6.9
|
1.0
|
|
CHD
|
G:BCL101
|
3.5
|
6.9
|
1.0
|
|
C3D
|
G:BCL101
|
4.1
|
6.9
|
1.0
|
|
ND1
|
G:HIS29
|
4.2
|
5.2
|
1.0
|
|
C3B
|
G:BCL101
|
4.3
|
6.9
|
1.0
|
|
CMD
|
E:BCL101
|
4.3
|
5.5
|
1.0
|
|
C2D
|
G:BCL101
|
4.3
|
6.9
|
1.0
|
|
C2B
|
G:BCL101
|
4.3
|
6.9
|
1.0
|
|
CG
|
G:HIS29
|
4.3
|
5.2
|
1.0
|
|
C2C
|
G:BCL101
|
4.4
|
6.9
|
1.0
|
|
C2A
|
G:BCL101
|
4.4
|
6.9
|
1.0
|
|
C3C
|
G:BCL101
|
4.4
|
6.9
|
1.0
|
|
C3A
|
G:BCL101
|
4.4
|
6.9
|
1.0
|
|
CMB
|
H:BCL101
|
4.7
|
5.9
|
1.0
|
|
CBB
|
H:BCL101
|
4.7
|
5.9
|
1.0
|
|
CBD
|
G:BCL101
|
4.8
|
6.9
|
1.0
|
|
C2B
|
H:BCL101
|
4.9
|
5.9
|
1.0
|
|
Magnesium binding site 9 out
of 28 in 8ypd
Go back to
Magnesium Binding Sites List in 8ypd
Magnesium binding site 9 out
of 28 in the Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg101
b:5.9
occ:1.00
|
MG
|
H:BCL101
|
0.0
|
5.9
|
1.0
|
|
NB
|
H:BCL101
|
2.0
|
5.9
|
1.0
|
|
ND
|
H:BCL101
|
2.0
|
5.9
|
1.0
|
|
NC
|
H:BCL101
|
2.1
|
5.9
|
1.0
|
|
NA
|
H:BCL101
|
2.1
|
5.9
|
1.0
|
|
NE2
|
H:HIS37
|
2.2
|
5.0
|
1.0
|
|
C4D
|
H:BCL101
|
2.9
|
5.9
|
1.0
|
|
CE1
|
H:HIS37
|
3.0
|
5.0
|
1.0
|
|
C1C
|
H:BCL101
|
3.0
|
5.9
|
1.0
|
|
C4B
|
H:BCL101
|
3.0
|
5.9
|
1.0
|
|
C1B
|
H:BCL101
|
3.0
|
5.9
|
1.0
|
|
C1A
|
H:BCL101
|
3.0
|
5.9
|
1.0
|
|
C4A
|
H:BCL101
|
3.0
|
5.9
|
1.0
|
|
C4C
|
H:BCL101
|
3.1
|
5.9
|
1.0
|
|
C1D
|
H:BCL101
|
3.1
|
5.9
|
1.0
|
|
CHC
|
H:BCL101
|
3.3
|
5.9
|
1.0
|
|
CD2
|
H:HIS37
|
3.3
|
5.0
|
1.0
|
|
CHB
|
H:BCL101
|
3.4
|
5.9
|
1.0
|
|
CHA
|
H:BCL101
|
3.4
|
5.9
|
1.0
|
|
CHD
|
H:BCL101
|
3.6
|
5.9
|
1.0
|
|
C3D
|
H:BCL101
|
4.2
|
5.9
|
1.0
|
|
ND1
|
H:HIS37
|
4.2
|
5.0
|
1.0
|
|
CMB
|
G:BCL101
|
4.3
|
6.9
|
1.0
|
|
C2C
|
H:BCL101
|
4.3
|
5.9
|
1.0
|
|
C2D
|
H:BCL101
|
4.3
|
5.9
|
1.0
|
|
C3B
|
H:BCL101
|
4.3
|
5.9
|
1.0
|
|
C3A
|
H:BCL101
|
4.3
|
5.9
|
1.0
|
|
C2B
|
H:BCL101
|
4.3
|
5.9
|
1.0
|
|
C2A
|
H:BCL101
|
4.4
|
5.9
|
1.0
|
|
CG
|
H:HIS37
|
4.4
|
5.0
|
1.0
|
|
C3C
|
H:BCL101
|
4.4
|
5.9
|
1.0
|
|
CBB
|
G:BCL101
|
4.5
|
6.9
|
1.0
|
|
C2B
|
G:BCL101
|
4.5
|
6.9
|
1.0
|
|
CAB
|
G:BCL101
|
4.7
|
6.9
|
1.0
|
|
CD1
|
I:ILE28
|
4.8
|
4.6
|
1.0
|
|
CBD
|
H:BCL101
|
4.8
|
5.9
|
1.0
|
|
CG2
|
I:ILE28
|
4.8
|
4.6
|
1.0
|
|
C3B
|
G:BCL101
|
4.9
|
6.9
|
1.0
|
|
C10
|
H:BCL101
|
4.9
|
5.9
|
1.0
|
|
CMA
|
H:BCL101
|
4.9
|
5.9
|
1.0
|
|
Magnesium binding site 10 out
of 28 in 8ypd
Go back to
Magnesium Binding Sites List in 8ypd
Magnesium binding site 10 out
of 28 in the Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg101
b:6.6
occ:1.00
|
MG
|
I:BCL101
|
0.0
|
6.6
|
1.0
|
|
NB
|
I:BCL101
|
2.0
|
6.6
|
1.0
|
|
ND
|
I:BCL101
|
2.0
|
6.6
|
1.0
|
|
NC
|
I:BCL101
|
2.1
|
6.6
|
1.0
|
|
NA
|
I:BCL101
|
2.1
|
6.6
|
1.0
|
|
NE2
|
I:HIS29
|
2.2
|
5.0
|
1.0
|
|
C4D
|
I:BCL101
|
2.9
|
6.6
|
1.0
|
|
CE1
|
I:HIS29
|
3.0
|
5.0
|
1.0
|
|
C1C
|
I:BCL101
|
3.0
|
6.6
|
1.0
|
|
C4B
|
I:BCL101
|
3.0
|
6.6
|
1.0
|
|
C1B
|
I:BCL101
|
3.0
|
6.6
|
1.0
|
|
C1A
|
I:BCL101
|
3.0
|
6.6
|
1.0
|
|
C4A
|
I:BCL101
|
3.0
|
6.6
|
1.0
|
|
C4C
|
I:BCL101
|
3.1
|
6.6
|
1.0
|
|
C1D
|
I:BCL101
|
3.2
|
6.6
|
1.0
|
|
CD2
|
I:HIS29
|
3.3
|
5.0
|
1.0
|
|
CHC
|
I:BCL101
|
3.3
|
6.6
|
1.0
|
|
CHA
|
I:BCL101
|
3.4
|
6.6
|
1.0
|
|
CHB
|
I:BCL101
|
3.4
|
6.6
|
1.0
|
|
CHD
|
I:BCL101
|
3.5
|
6.6
|
1.0
|
|
CBB
|
J:BCL101
|
4.1
|
5.9
|
1.0
|
|
C3D
|
I:BCL101
|
4.1
|
6.6
|
1.0
|
|
ND1
|
I:HIS29
|
4.2
|
5.0
|
1.0
|
|
C3B
|
I:BCL101
|
4.3
|
6.6
|
1.0
|
|
C2D
|
I:BCL101
|
4.3
|
6.6
|
1.0
|
|
C2B
|
I:BCL101
|
4.3
|
6.6
|
1.0
|
|
CMD
|
H:BCL101
|
4.4
|
5.9
|
1.0
|
|
CG
|
I:HIS29
|
4.4
|
5.0
|
1.0
|
|
C2C
|
I:BCL101
|
4.4
|
6.6
|
1.0
|
|
C2A
|
I:BCL101
|
4.4
|
6.6
|
1.0
|
|
C3C
|
I:BCL101
|
4.4
|
6.6
|
1.0
|
|
C3A
|
I:BCL101
|
4.4
|
6.6
|
1.0
|
|
CBD
|
I:BCL101
|
4.8
|
6.6
|
1.0
|
|
CMB
|
J:BCL101
|
4.8
|
5.9
|
1.0
|
|
C2B
|
J:BCL101
|
4.9
|
5.9
|
1.0
|
|
Reference:
M.J.Zou,
S.Sun,
G.L.Wang,
Y.H.Yan,
W.Ji,
Z.Y.Wang-Otomo,
M.T.Madigan,
L.J.Yu.
Probing the Dual Role of Ca 2+ in the Allochromatium Tepidum LH1-Rc Complex By Constructing and Analyzing Ca 2+ -Bound and Ca 2+ -Free LH1 Complexes. Biomolecules V. 15 2025.
ISSN: ESSN 2218-273X
PubMed: 39858518
DOI: 10.3390/BIOM15010124
Page generated: Tue Feb 25 11:01:09 2025
|
