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Magnesium in PDB 1kzu: Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050

Protein crystallography data

The structure of Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050, PDB code: 1kzu was solved by R.J.Cogdell, A.A.Freer, N.W.Isaacs, A.M.Hawthornthwaite-Lawless, G.Mcdermott, M.Z.Papiz, S.M.Prince, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 2.50
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 120.300, 120.300, 296.200, 90.00, 90.00, 120.00
R / Rfree (%) 22.7 / 25.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050 (pdb code 1kzu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050, PDB code: 1kzu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 1kzu

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Magnesium binding site 1 out of 9 in the Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg55

b:12.4
occ:1.00
 MG A:BCL55 0.0 12.4 1.0
ND A:BCL55 2.0 5.4 1.0
NB A:BCL55 2.0 3.7 1.0
NC A:BCL55 2.1 10.7 1.0
NA A:BCL55 2.1 10.8 1.0
NE2 A:HIS31 2.4 11.7 1.0
C4D A:BCL55 3.0 7.4 1.0
C1B A:BCL55 3.0 7.7 1.0
C4A A:BCL55 3.1 5.3 1.0
C1D A:BCL55 3.1 10.8 1.0
C4B A:BCL55 3.1 8.7 1.0
C1C A:BCL55 3.1 11.1 1.0
C4C A:BCL55 3.1 14.8 1.0
CE1 A:HIS31 3.1 9.7 1.0
C1A A:BCL55 3.2 7.0 1.0
CHA A:BCL55 3.3 9.5 1.0
CHB A:BCL55 3.4 7.6 1.0
CHC A:BCL55 3.4 8.1 1.0
CHD A:BCL55 3.4 13.1 1.0
CD2 A:HIS31 3.5 9.4 1.0
CM3 A:RG154 3.9 39.9 1.0
C3D A:BCL55 4.2 10.7 1.0
C2B A:BCL55 4.3 6.3 1.0
C2D A:BCL55 4.3 9.0 1.0
C3B A:BCL55 4.3 5.8 1.0
ND1 A:HIS31 4.4 7.7 1.0
C3A A:BCL55 4.4 8.1 1.0
C3C A:BCL55 4.4 15.4 1.0
C2C A:BCL55 4.4 13.8 1.0
C2A A:BCL55 4.4 10.4 1.0
C5 A:RG154 4.5 31.5 1.0
CG A:HIS31 4.6 8.7 1.0
CMD B:BCL43 4.6 13.1 1.0
C3 A:RG154 4.7 28.2 1.0
CBD A:BCL55 4.8 12.3 1.0

Magnesium binding site 2 out of 9 in 1kzu

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Magnesium binding site 2 out of 9 in the Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg56

b:20.8
occ:1.00
 MG A:BCL56 0.0 20.8 1.0
ND A:BCL56 2.0 17.6 1.0
NC A:BCL56 2.0 22.0 1.0
NB A:BCL56 2.0 19.0 1.0
NA A:BCL56 2.1 18.3 1.0
O1 A:FME1 2.5 34.6 1.0
C4D A:BCL56 3.0 18.6 1.0
C1C A:BCL56 3.1 23.3 1.0
C4C A:BCL56 3.1 24.3 1.0
C1D A:BCL56 3.1 17.4 1.0
C4B A:BCL56 3.1 16.8 1.0
C4A A:BCL56 3.1 17.9 1.0
C1B A:BCL56 3.1 19.3 1.0
C1A A:BCL56 3.2 19.4 1.0
CHA A:BCL56 3.3 19.5 1.0
CHC A:BCL56 3.4 18.4 1.0
CHB A:BCL56 3.4 20.8 1.0
CHD A:BCL56 3.4 19.5 1.0
CN A:FME1 3.6 22.0 1.0
N A:FME1 3.8 31.7 1.0
O A:HOH57 4.1 22.6 1.0
C3D A:BCL56 4.2 17.7 1.0
C2D A:BCL56 4.3 14.6 1.0
C2B A:BCL56 4.3 18.1 1.0
C3C A:BCL56 4.3 27.1 1.0
C3B A:BCL56 4.4 18.4 1.0
C2C A:BCL56 4.4 26.3 1.0
C13 B:BCL43 4.4 31.9 1.0
C3A A:BCL56 4.4 18.9 1.0
C15 B:BCL43 4.4 26.5 1.0
C2A A:BCL56 4.4 20.5 1.0
C12 B:BCL43 4.8 30.6 1.0
CBD A:BCL56 4.9 19.9 1.0
CG A:GLN3 4.9 17.0 1.0
CD1 B:ILE16 5.0 22.9 1.0

Magnesium binding site 3 out of 9 in 1kzu

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Magnesium binding site 3 out of 9 in the Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg43

b:16.1
occ:1.00
 MG B:BCL43 0.0 16.1 1.0
ND B:BCL43 2.0 9.5 1.0
NB B:BCL43 2.0 9.0 1.0
NC B:BCL43 2.1 12.5 1.0
NA B:BCL43 2.1 12.5 1.0
NE2 B:HIS30 2.4 20.2 1.0
C4D B:BCL43 3.0 13.9 1.0
C1B B:BCL43 3.1 13.3 1.0
C4B B:BCL43 3.1 11.5 1.0
C4A B:BCL43 3.1 10.7 1.0
C1C B:BCL43 3.1 13.0 1.0
C1D B:BCL43 3.1 13.9 1.0
C4C B:BCL43 3.1 15.6 1.0
C1A B:BCL43 3.2 12.4 1.0
CE1 B:HIS30 3.3 23.3 1.0
CHA B:BCL43 3.3 11.9 1.0
CD2 B:HIS30 3.4 17.2 1.0
CHB B:BCL43 3.4 12.3 1.0
CHC B:BCL43 3.4 11.7 1.0
CHD B:BCL43 3.5 15.3 1.0
CMB D:BCL55 4.3 5.3 1.0
C3D B:BCL43 4.3 13.5 1.0
C2B B:BCL43 4.3 13.8 1.0
C3B B:BCL43 4.3 10.7 1.0
C2D B:BCL43 4.3 11.5 1.0
C3C B:BCL43 4.4 13.3 1.0
C3A B:BCL43 4.4 8.9 1.0
C2C B:BCL43 4.4 12.8 1.0
C2A B:BCL43 4.4 15.2 1.0
CBB D:BCL55 4.4 5.5 1.0
ND1 B:HIS30 4.5 20.7 1.0
CG B:HIS30 4.5 16.2 1.0
CBD B:BCL43 4.9 12.0 1.0

Magnesium binding site 4 out of 9 in 1kzu

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Magnesium binding site 4 out of 9 in the Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg55

b:12.4
occ:1.00
 MG D:BCL55 0.0 12.4 1.0
ND D:BCL55 2.0 5.4 1.0
NB D:BCL55 2.0 3.7 1.0
NC D:BCL55 2.1 10.7 1.0
NA D:BCL55 2.1 10.8 1.0
NE2 D:HIS31 2.4 11.7 1.0
C4D D:BCL55 3.0 7.4 1.0
C1B D:BCL55 3.0 7.7 1.0
C4A D:BCL55 3.1 5.3 1.0
C1D D:BCL55 3.1 10.8 1.0
C4B D:BCL55 3.1 8.7 1.0
C1C D:BCL55 3.1 11.1 1.0
C4C D:BCL55 3.1 14.8 1.0
CE1 D:HIS31 3.1 9.7 1.0
C1A D:BCL55 3.2 7.0 1.0
CHA D:BCL55 3.3 9.5 1.0
CHB D:BCL55 3.4 7.6 1.0
CHC D:BCL55 3.4 8.1 1.0
CHD D:BCL55 3.4 13.1 1.0
CD2 D:HIS31 3.5 9.4 1.0
CM3 D:RG154 3.9 39.9 1.0
C3D D:BCL55 4.2 10.7 1.0
C2B D:BCL55 4.3 6.3 1.0
C2D D:BCL55 4.3 9.0 1.0
C3B D:BCL55 4.3 5.8 1.0
ND1 D:HIS31 4.4 7.7 1.0
C3A D:BCL55 4.4 8.1 1.0
C3C D:BCL55 4.4 15.4 1.0
C2C D:BCL55 4.4 13.8 1.0
C2A D:BCL55 4.4 10.4 1.0
C5 D:RG154 4.5 31.5 1.0
CG D:HIS31 4.6 8.7 1.0
CMD E:BCL43 4.6 13.1 1.0
C3 D:RG154 4.7 28.2 1.0
CBD D:BCL55 4.8 12.3 1.0

Magnesium binding site 5 out of 9 in 1kzu

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Magnesium binding site 5 out of 9 in the Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg56

b:20.8
occ:1.00
 MG D:BCL56 0.0 20.8 1.0
ND D:BCL56 2.0 17.6 1.0
NC D:BCL56 2.0 22.0 1.0
NB D:BCL56 2.0 19.0 1.0
NA D:BCL56 2.1 18.3 1.0
O1 D:FME1 2.5 34.6 1.0
C4D D:BCL56 3.0 18.6 1.0
C1C D:BCL56 3.1 23.3 1.0
C4C D:BCL56 3.1 24.3 1.0
C1D D:BCL56 3.1 17.4 1.0
C4B D:BCL56 3.1 16.8 1.0
C4A D:BCL56 3.1 17.9 1.0
C1B D:BCL56 3.1 19.3 1.0
C1A D:BCL56 3.2 19.4 1.0
CHA D:BCL56 3.3 19.5 1.0
CHC D:BCL56 3.4 18.4 1.0
CHB D:BCL56 3.4 20.8 1.0
CHD D:BCL56 3.4 19.5 1.0
CN D:FME1 3.6 22.0 1.0
N D:FME1 3.8 31.7 1.0
O D:HOH57 4.1 22.6 1.0
C3D D:BCL56 4.2 17.7 1.0
C2D D:BCL56 4.3 14.6 1.0
C2B D:BCL56 4.3 18.1 1.0
C3C D:BCL56 4.3 27.1 1.0
C3B D:BCL56 4.4 18.4 1.0
C2C D:BCL56 4.4 26.3 1.0
C13 E:BCL43 4.4 31.9 1.0
C3A D:BCL56 4.4 18.9 1.0
C15 E:BCL43 4.4 26.5 1.0
C2A D:BCL56 4.4 20.5 1.0
C12 E:BCL43 4.8 30.6 1.0
CBD D:BCL56 4.9 19.9 1.0
CG D:GLN3 4.9 17.0 1.0
CD1 E:ILE16 5.0 22.9 1.0

Magnesium binding site 6 out of 9 in 1kzu

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Magnesium binding site 6 out of 9 in the Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg43

b:16.1
occ:1.00
 MG E:BCL43 0.0 16.1 1.0
ND E:BCL43 2.0 9.5 1.0
NB E:BCL43 2.0 9.0 1.0
NC E:BCL43 2.1 12.5 1.0
NA E:BCL43 2.1 12.5 1.0
NE2 E:HIS30 2.4 20.2 1.0
C4D E:BCL43 3.0 13.9 1.0
C1B E:BCL43 3.1 13.3 1.0
C4B E:BCL43 3.1 11.5 1.0
C4A E:BCL43 3.1 10.7 1.0
C1C E:BCL43 3.1 13.0 1.0
C1D E:BCL43 3.1 13.9 1.0
C4C E:BCL43 3.1 15.6 1.0
C1A E:BCL43 3.2 12.4 1.0
CE1 E:HIS30 3.3 23.3 1.0
CHA E:BCL43 3.3 11.9 1.0
CD2 E:HIS30 3.4 17.2 1.0
CHB E:BCL43 3.4 12.3 1.0
CHC E:BCL43 3.4 11.7 1.0
CHD E:BCL43 3.5 15.3 1.0
CMB G:BCL55 4.3 5.3 1.0
C3D E:BCL43 4.3 13.5 1.0
C2B E:BCL43 4.3 13.8 1.0
C3B E:BCL43 4.3 10.7 1.0
C2D E:BCL43 4.3 11.5 1.0
C3C E:BCL43 4.4 13.3 1.0
C3A E:BCL43 4.4 8.9 1.0
C2C E:BCL43 4.4 12.8 1.0
C2A E:BCL43 4.4 15.2 1.0
CBB G:BCL55 4.4 5.5 1.0
ND1 E:HIS30 4.5 20.7 1.0
CG E:HIS30 4.5 16.2 1.0
CBD E:BCL43 4.9 12.0 1.0

Magnesium binding site 7 out of 9 in 1kzu

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Magnesium binding site 7 out of 9 in the Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg55

b:12.4
occ:1.00
 MG G:BCL55 0.0 12.4 1.0
ND G:BCL55 2.0 5.4 1.0
NB G:BCL55 2.0 3.7 1.0
NC G:BCL55 2.1 10.7 1.0
NA G:BCL55 2.1 10.8 1.0
NE2 G:HIS31 2.4 11.7 1.0
C4D G:BCL55 3.0 7.4 1.0
C1B G:BCL55 3.0 7.7 1.0
C4A G:BCL55 3.1 5.3 1.0
C1D G:BCL55 3.1 10.8 1.0
C4B G:BCL55 3.1 8.7 1.0
C1C G:BCL55 3.1 11.1 1.0
C4C G:BCL55 3.1 14.8 1.0
CE1 G:HIS31 3.1 9.7 1.0
C1A G:BCL55 3.2 7.0 1.0
CHA G:BCL55 3.3 9.5 1.0
CHB G:BCL55 3.4 7.6 1.0
CHC G:BCL55 3.4 8.1 1.0
CHD G:BCL55 3.4 13.1 1.0
CD2 G:HIS31 3.5 9.4 1.0
CM3 G:RG154 3.9 39.9 1.0
C3D G:BCL55 4.2 10.7 1.0
C2B G:BCL55 4.3 6.3 1.0
C2D G:BCL55 4.3 9.0 1.0
C3B G:BCL55 4.3 5.8 1.0
ND1 G:HIS31 4.4 7.7 1.0
C3A G:BCL55 4.4 8.1 1.0
C3C G:BCL55 4.4 15.4 1.0
C2C G:BCL55 4.4 13.8 1.0
C2A G:BCL55 4.4 10.4 1.0
C5 G:RG154 4.5 31.5 1.0
CG G:HIS31 4.6 8.7 1.0
CMD H:BCL43 4.6 13.1 1.0
C3 G:RG154 4.7 28.2 1.0
CBD G:BCL55 4.8 12.3 1.0

Magnesium binding site 8 out of 9 in 1kzu

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Magnesium binding site 8 out of 9 in the Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg56

b:20.8
occ:1.00
 MG G:BCL56 0.0 20.8 1.0
ND G:BCL56 2.0 17.6 1.0
NC G:BCL56 2.0 22.0 1.0
NB G:BCL56 2.0 19.0 1.0
NA G:BCL56 2.1 18.3 1.0
O1 G:FME1 2.5 34.6 1.0
C4D G:BCL56 3.0 18.6 1.0
C1C G:BCL56 3.1 23.3 1.0
C4C G:BCL56 3.1 24.3 1.0
C1D G:BCL56 3.1 17.4 1.0
C4B G:BCL56 3.1 16.8 1.0
C4A G:BCL56 3.1 17.9 1.0
C1B G:BCL56 3.1 19.3 1.0
C1A G:BCL56 3.2 19.4 1.0
CHA G:BCL56 3.3 19.5 1.0
CHC G:BCL56 3.4 18.4 1.0
CHB G:BCL56 3.4 20.8 1.0
CHD G:BCL56 3.4 19.5 1.0
CN G:FME1 3.6 22.0 1.0
N G:FME1 3.8 31.7 1.0
O G:HOH57 4.1 22.6 1.0
C3D G:BCL56 4.2 17.7 1.0
C2D G:BCL56 4.3 14.6 1.0
C2B G:BCL56 4.3 18.1 1.0
C3C G:BCL56 4.3 27.1 1.0
C3B G:BCL56 4.4 18.4 1.0
C2C G:BCL56 4.4 26.3 1.0
C13 H:BCL43 4.4 31.9 1.0
C3A G:BCL56 4.4 18.9 1.0
C15 H:BCL43 4.4 26.5 1.0
C2A G:BCL56 4.4 20.5 1.0
C12 H:BCL43 4.8 30.6 1.0
CBD G:BCL56 4.9 19.9 1.0
CG G:GLN3 4.9 17.0 1.0
CD1 H:ILE16 5.0 22.9 1.0

Magnesium binding site 9 out of 9 in 1kzu

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Magnesium binding site 9 out of 9 in the Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Integral Membrane Peripheral Light Harvesting Complex From Rhodopseudomonas Acidophila Strain 10050 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg43

b:16.1
occ:1.00
 MG H:BCL43 0.0 16.1 1.0
ND H:BCL43 2.0 9.5 1.0
NB H:BCL43 2.0 9.0 1.0
NC H:BCL43 2.1 12.5 1.0
NA H:BCL43 2.1 12.5 1.0
NE2 H:HIS30 2.4 20.2 1.0
C4D H:BCL43 3.0 13.9 1.0
C1B H:BCL43 3.1 13.3 1.0
C4B H:BCL43 3.1 11.5 1.0
C4A H:BCL43 3.1 10.7 1.0
C1C H:BCL43 3.1 13.0 1.0
C1D H:BCL43 3.1 13.9 1.0
C4C H:BCL43 3.1 15.6 1.0
C1A H:BCL43 3.2 12.4 1.0
CE1 H:HIS30 3.3 23.3 1.0
CHA H:BCL43 3.3 11.9 1.0
CD2 H:HIS30 3.4 17.2 1.0
CHB H:BCL43 3.4 12.3 1.0
CHC H:BCL43 3.4 11.7 1.0
CHD H:BCL43 3.5 15.3 1.0
C3D H:BCL43 4.3 13.5 1.0
C2B H:BCL43 4.3 13.8 1.0
C3B H:BCL43 4.3 10.7 1.0
C2D H:BCL43 4.3 11.5 1.0
C3C H:BCL43 4.4 13.3 1.0
C3A H:BCL43 4.4 8.9 1.0
C2C H:BCL43 4.4 12.8 1.0
C2A H:BCL43 4.4 15.2 1.0
ND1 H:HIS30 4.5 20.7 1.0
CG H:HIS30 4.5 16.2 1.0
CBD H:BCL43 4.9 12.0 1.0

Reference:

S.M.Prince, M.Z.Papiz, A.A.Freer, G.Mcdermott, A.M.Hawthornthwaite-Lawless, R.J.Cogdell, N.W.Isaacs. Apoprotein Structure in the LH2 Complex From Rhodopseudomonas Acidophila Strain 10050: Modular Assembly and Protein Pigment Interactions. J.Mol.Biol. V. 268 412 1997.
ISSN: ISSN 0022-2836
PubMed: 9159480
DOI: 10.1006/JMBI.1997.0966
Page generated: Tue Aug 13 08:11:54 2024

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