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Magnesium in PDB 3lw5: Improved Model of Plant Photosystem I

Protein crystallography data

The structure of Improved Model of Plant Photosystem I, PDB code: 3lw5 was solved by N.Nelson, H.Toporik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 120.655, 189.086, 129.388, 90.00, 91.24, 90.00
R / Rfree (%) 34.9 / 38.3

Other elements in 3lw5:

The structure of Improved Model of Plant Photosystem I also contains other interesting chemical elements:

Iron (Fe) 12 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 174 in 3lw5

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Magnesium binding site 1 out of 174 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1101

b:18.8
occ:1.00
MG A:CLA1101 0.0 18.8 1.0
NA A:CLA1101 2.0 18.6 1.0
ND A:CLA1101 2.0 18.7 1.0
NB A:CLA1101 2.0 18.5 1.0
NC A:CLA1101 2.1 18.4 1.0
CE1 A:HIS58 2.7 17.7 1.0
C4D A:CLA1101 3.0 18.8 1.0
C1A A:CLA1101 3.0 18.6 1.0
C4A A:CLA1101 3.0 18.3 1.0
C1B A:CLA1101 3.1 18.5 1.0
C4B A:CLA1101 3.1 18.2 1.0
C1C A:CLA1101 3.1 18.3 1.0
C4C A:CLA1101 3.1 18.5 1.0
C1D A:CLA1101 3.2 18.8 1.0
CHB A:CLA1101 3.4 18.4 1.0
CHA A:CLA1101 3.4 18.6 1.0
ND1 A:HIS58 3.4 18.6 1.0
CHC A:CLA1101 3.6 18.6 1.0
CHD A:CLA1101 3.7 19.0 1.0
NE2 A:HIS58 3.8 17.9 1.0
C3D A:CLA1101 4.2 19.0 1.0
C3B A:CLA1101 4.2 18.1 1.0
C2C A:CLA1101 4.3 18.1 1.0
C3C A:CLA1101 4.3 18.2 1.0
C2B A:CLA1101 4.3 18.2 1.0
C2D A:CLA1101 4.3 18.7 1.0
C3A A:CLA1101 4.3 18.3 1.0
C2A A:CLA1101 4.3 18.3 1.0
CG A:HIS58 4.7 19.1 1.0
CBD A:CLA1101 4.9 18.6 1.0
CD2 A:HIS58 4.9 18.6 1.0

Magnesium binding site 2 out of 174 in 3lw5

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Magnesium binding site 2 out of 174 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:20.5
occ:1.00
MG A:CLA1102 0.0 20.5 1.0
NA A:CLA1102 2.0 19.6 1.0
NB A:CLA1102 2.0 19.7 1.0
ND A:CLA1102 2.1 20.2 1.0
NC A:CLA1102 2.1 20.0 1.0
C4D A:CLA1102 3.0 20.1 1.0
C4A A:CLA1102 3.0 19.3 1.0
C1A A:CLA1102 3.0 19.5 1.0
C1B A:CLA1102 3.0 19.5 1.0
C4B A:CLA1102 3.1 19.6 1.0
C1C A:CLA1102 3.1 19.9 1.0
C4C A:CLA1102 3.1 20.1 1.0
C1D A:CLA1102 3.2 19.8 1.0
CHB A:CLA1102 3.4 19.5 1.0
CHA A:CLA1102 3.4 19.8 1.0
CHC A:CLA1102 3.6 19.9 1.0
CHD A:CLA1102 3.7 19.8 1.0
CBB A:CLA1101 4.0 17.2 1.0
C3D A:CLA1102 4.2 19.9 1.0
C3B A:CLA1102 4.2 19.5 1.0
C2C A:CLA1102 4.3 19.9 1.0
C2B A:CLA1102 4.3 19.5 1.0
C3C A:CLA1102 4.3 20.1 1.0
C2D A:CLA1102 4.3 19.7 1.0
C3A A:CLA1102 4.3 19.4 1.0
C2A A:CLA1102 4.3 19.1 1.0
C7 A:CLA1109 4.4 16.3 1.0
CBD A:CLA1102 4.9 19.5 1.0
CAB A:CLA1101 4.9 17.8 1.0
NE2 A:HIS62 4.9 21.5 1.0

Magnesium binding site 3 out of 174 in 3lw5

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Magnesium binding site 3 out of 174 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:14.1
occ:1.00
MG A:CLA1103 0.0 14.1 1.0
NA A:CLA1103 2.0 14.5 1.0
ND A:CLA1103 2.0 14.4 1.0
NB A:CLA1103 2.1 14.1 1.0
NC A:CLA1103 2.1 14.6 1.0
NE2 A:HIS82 2.6 17.0 1.0
C4D A:CLA1103 3.0 14.5 1.0
C1A A:CLA1103 3.0 14.7 1.0
CMB A:CLA1128 3.0 17.1 1.0
C4A A:CLA1103 3.0 14.5 1.0
C1B A:CLA1103 3.1 14.1 1.0
C1C A:CLA1103 3.1 14.5 1.0
C4B A:CLA1103 3.1 14.0 1.0
C4C A:CLA1103 3.1 14.9 1.0
C1D A:CLA1103 3.2 14.2 1.0
CHB A:CLA1103 3.4 14.1 1.0
CD2 A:HIS82 3.4 17.2 1.0
CHA A:CLA1103 3.4 14.7 1.0
CE1 A:HIS82 3.4 16.9 1.0
CHC A:CLA1103 3.6 14.1 1.0
CHD A:CLA1103 3.7 14.4 1.0
C3D A:CLA1103 4.2 14.3 1.0
C3B A:CLA1103 4.2 13.9 1.0
C2C A:CLA1103 4.3 14.9 1.0
C3C A:CLA1103 4.3 15.3 1.0
C2B A:CLA1103 4.3 14.0 1.0
C2D A:CLA1103 4.3 14.3 1.0
C2A A:CLA1103 4.3 14.9 1.0
C3A A:CLA1103 4.3 14.8 1.0
C2B A:CLA1128 4.4 16.7 1.0
ND1 A:HIS82 4.4 17.0 1.0
CG A:HIS82 4.4 17.7 1.0
CBB A:CLA1128 4.6 16.3 1.0
CAB A:CLA1128 4.8 16.6 1.0
CBD A:CLA1103 4.9 14.8 1.0

Magnesium binding site 4 out of 174 in 3lw5

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Magnesium binding site 4 out of 174 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1104

b:15.8
occ:1.00
MG A:CLA1104 0.0 15.8 1.0
NA A:CLA1104 2.0 15.4 1.0
NB A:CLA1104 2.0 15.2 1.0
ND A:CLA1104 2.0 15.7 1.0
NC A:CLA1104 2.1 15.1 1.0
C4D A:CLA1104 3.0 15.5 1.0
C1A A:CLA1104 3.0 15.6 1.0
C4A A:CLA1104 3.0 15.2 1.0
C1B A:CLA1104 3.1 15.3 1.0
C1C A:CLA1104 3.1 14.9 1.0
C4B A:CLA1104 3.1 15.1 1.0
C4C A:CLA1104 3.1 15.2 1.0
C1D A:CLA1104 3.2 15.2 1.0
NE2 A:GLN85 3.3 15.6 1.0
CHB A:CLA1104 3.4 15.2 1.0
CHA A:CLA1104 3.4 15.6 1.0
OE1 A:GLN85 3.4 15.1 1.0
CD A:GLN85 3.5 15.9 1.0
CHC A:CLA1104 3.6 15.0 1.0
CHD A:CLA1104 3.7 15.0 1.0
C3D A:CLA1104 4.2 15.5 1.0
C3B A:CLA1104 4.2 15.1 1.0
C2C A:CLA1104 4.3 15.1 1.0
C3C A:CLA1104 4.3 15.3 1.0
C2B A:CLA1104 4.3 15.5 1.0
C2A A:CLA1104 4.3 15.8 1.0
C3A A:CLA1104 4.3 15.5 1.0
C2D A:CLA1104 4.3 15.1 1.0
CG A:GLN85 4.5 17.2 1.0
CBD A:CLA1104 4.9 15.9 1.0
CMA A:CLA1103 5.0 14.8 1.0

Magnesium binding site 5 out of 174 in 3lw5

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Magnesium binding site 5 out of 174 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1105

b:22.7
occ:1.00
MG A:CLA1105 0.0 22.7 1.0
NA A:CLA1105 2.0 22.7 1.0
ND A:CLA1105 2.0 23.2 1.0
NB A:CLA1105 2.0 22.5 1.0
NC A:CLA1105 2.1 23.1 1.0
NE2 A:HIS99 2.7 22.9 1.0
C4D A:CLA1105 3.0 23.2 1.0
C1A A:CLA1105 3.0 22.9 1.0
C4A A:CLA1105 3.0 22.6 1.0
C1B A:CLA1105 3.0 22.8 1.0
C4B A:CLA1105 3.1 22.5 1.0
C1C A:CLA1105 3.1 22.9 1.0
C4C A:CLA1105 3.1 23.1 1.0
C1D A:CLA1105 3.1 23.3 1.0
CHB A:CLA1105 3.4 22.7 1.0
CHA A:CLA1105 3.4 23.1 1.0
CE1 A:HIS99 3.4 22.8 1.0
CHC A:CLA1105 3.6 22.7 1.0
CHD A:CLA1105 3.7 23.4 1.0
CD2 A:HIS99 3.7 23.0 1.0
C3D A:CLA1105 4.2 23.4 1.0
C3B A:CLA1105 4.3 23.0 1.0
C2B A:CLA1105 4.3 23.0 1.0
C2D A:CLA1105 4.3 23.4 1.0
C2C A:CLA1105 4.3 22.7 1.0
C2A A:CLA1105 4.3 23.2 1.0
C3C A:CLA1105 4.3 22.6 1.0
C3A A:CLA1105 4.3 22.7 1.0
O1A A:CLA1105 4.6 23.5 1.0
ND1 A:HIS99 4.6 22.7 1.0
CG A:HIS99 4.7 22.7 1.0
CBD A:CLA1105 4.9 23.2 1.0

Magnesium binding site 6 out of 174 in 3lw5

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Magnesium binding site 6 out of 174 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1106

b:13.6
occ:1.00
MG A:CLA1106 0.0 13.6 1.0
NA A:CLA1106 2.0 13.2 1.0
ND A:CLA1106 2.0 13.0 1.0
NB A:CLA1106 2.0 13.5 1.0
NC A:CLA1106 2.1 13.4 1.0
C4D A:CLA1106 2.9 13.1 1.0
C1A A:CLA1106 3.0 13.0 1.0
C4A A:CLA1106 3.0 13.2 1.0
C1B A:CLA1106 3.1 13.3 1.0
C1C A:CLA1106 3.1 13.3 1.0
C4B A:CLA1106 3.1 13.4 1.0
C4C A:CLA1106 3.1 13.2 1.0
C1D A:CLA1106 3.1 13.1 1.0
C4 A:CLA1126 3.2 13.2 1.0
OE1 A:GLN121 3.2 18.7 1.0
CHB A:CLA1106 3.4 13.4 1.0
CHA A:CLA1106 3.4 13.0 1.0
CHC A:CLA1106 3.6 13.5 1.0
CHD A:CLA1106 3.6 13.2 1.0
C3 A:CLA1126 3.9 12.8 1.0
C6 A:CLA1126 4.1 12.4 1.0
CD A:GLN121 4.1 18.9 1.0
O1A A:CLA1106 4.1 12.8 1.0
C3D A:CLA1106 4.1 13.2 1.0
NE2 A:GLN121 4.2 19.1 1.0
C3B A:CLA1106 4.2 13.0 1.0
C5 A:CLA1126 4.3 12.5 1.0
C3C A:CLA1106 4.3 13.1 1.0
C2B A:CLA1106 4.3 13.0 1.0
C2C A:CLA1106 4.3 13.2 1.0
C2D A:CLA1106 4.3 13.1 1.0
C2A A:CLA1106 4.3 13.1 1.0
C3A A:CLA1106 4.3 13.2 1.0
C2 A:CLA1126 4.8 12.8 1.0
CBD A:CLA1106 4.9 12.8 1.0
CAA A:CLA1106 5.0 12.8 1.0

Magnesium binding site 7 out of 174 in 3lw5

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Magnesium binding site 7 out of 174 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1107

b:16.6
occ:1.00
MG A:CLA1107 0.0 16.6 1.0
NE2 A:GLN129 1.4 15.3 1.0
NA A:CLA1107 2.0 17.0 1.0
ND A:CLA1107 2.0 16.7 1.0
NB A:CLA1107 2.1 16.8 1.0
NC A:CLA1107 2.1 16.3 1.0
CD A:GLN129 2.7 15.7 1.0
C4D A:CLA1107 2.9 16.7 1.0
C1A A:CLA1107 3.0 17.2 1.0
C4A A:CLA1107 3.0 17.0 1.0
C1C A:CLA1107 3.0 16.2 1.0
C4B A:CLA1107 3.1 16.6 1.0
C1B A:CLA1107 3.1 16.8 1.0
C4C A:CLA1107 3.1 16.3 1.0
C1D A:CLA1107 3.2 16.7 1.0
CHA A:CLA1107 3.3 16.9 1.0
CHB A:CLA1107 3.4 17.1 1.0
OE1 A:GLN129 3.6 15.3 1.0
CHC A:CLA1107 3.6 16.0 1.0
CG A:GLN129 3.6 16.0 1.0
CHD A:CLA1107 3.7 16.5 1.0
C16 A:CLA1126 4.0 15.2 1.0
C3D A:CLA1107 4.2 16.5 1.0
C2C A:CLA1107 4.2 16.3 1.0
C3B A:CLA1107 4.2 17.0 1.0
C2D A:CLA1107 4.3 16.5 1.0
C3C A:CLA1107 4.3 16.2 1.0
C2B A:CLA1107 4.3 16.8 1.0
C2A A:CLA1107 4.3 17.4 1.0
C3A A:CLA1107 4.3 17.0 1.0
C15 A:CLA1126 4.5 15.3 1.0
CBB A:CLA1106 4.8 13.1 1.0
CBD A:CLA1107 4.8 16.6 1.0
CB A:GLN129 4.8 15.9 1.0
C17 A:CLA1126 4.9 14.7 1.0
CAB A:CLA1107 4.9 17.2 1.0
CBA A:CLA1107 4.9 19.9 1.0

Magnesium binding site 8 out of 174 in 3lw5

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Magnesium binding site 8 out of 174 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1108

b:23.0
occ:1.00
MG A:CLA1108 0.0 23.0 1.0
NA A:CLA1108 2.0 23.4 1.0
ND A:CLA1108 2.0 23.2 1.0
NB A:CLA1108 2.0 22.4 1.0
NC A:CLA1108 2.1 21.9 1.0
C4D A:CLA1108 3.0 23.5 1.0
C1A A:CLA1108 3.0 23.4 1.0
C4A A:CLA1108 3.0 23.3 1.0
C1B A:CLA1108 3.0 22.5 1.0
C1C A:CLA1108 3.1 21.8 1.0
C4B A:CLA1108 3.1 22.4 1.0
C4C A:CLA1108 3.1 21.6 1.0
C1D A:CLA1108 3.2 22.9 1.0
CHB A:CLA1108 3.4 22.9 1.0
CHA A:CLA1108 3.4 23.4 1.0
CHC A:CLA1108 3.6 21.8 1.0
CHD A:CLA1108 3.7 22.3 1.0
C3D A:CLA1108 4.2 23.6 1.0
C3B A:CLA1108 4.2 22.7 1.0
C2C A:CLA1108 4.3 21.4 1.0
C2B A:CLA1108 4.3 22.8 1.0
C3C A:CLA1108 4.3 21.0 1.0
C2D A:CLA1108 4.3 23.4 1.0
C2A A:CLA1108 4.3 23.4 1.0
C3A A:CLA1108 4.3 23.6 1.0
CBD A:CLA1108 4.9 23.6 1.0

Magnesium binding site 9 out of 174 in 3lw5

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Magnesium binding site 9 out of 174 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1109

b:21.4
occ:1.00
MG A:CLA1109 0.0 21.4 1.0
CE1 A:HIS187 1.5 24.8 1.0
NE2 A:HIS187 1.6 24.6 1.0
NA A:CLA1109 2.0 21.8 1.0
ND A:CLA1109 2.1 21.0 1.0
NB A:CLA1109 2.1 21.4 1.0
NC A:CLA1109 2.1 20.2 1.0
ND1 A:HIS187 2.7 24.6 1.0
CD2 A:HIS187 2.8 24.4 1.0
O1A A:CLA1102 2.9 17.2 1.0
C4D A:CLA1109 2.9 21.4 1.0
C1A A:CLA1109 3.0 21.5 1.0
C4A A:CLA1109 3.0 21.9 1.0
C1C A:CLA1109 3.0 20.3 1.0
C4B A:CLA1109 3.1 21.5 1.0
CGA A:CLA1102 3.1 16.9 1.0
C1B A:CLA1109 3.1 21.8 1.0
C4C A:CLA1109 3.1 20.1 1.0
C1D A:CLA1109 3.2 20.9 1.0
CG A:HIS187 3.3 24.4 1.0
O2A A:CLA1102 3.3 16.0 1.0
CHA A:CLA1109 3.4 21.6 1.0
CHB A:CLA1109 3.4 21.7 1.0
CHC A:CLA1109 3.6 21.0 1.0
CHD A:CLA1109 3.7 20.4 1.0
CBA A:CLA1102 3.8 17.6 1.0
C3D A:CLA1109 4.2 21.4 1.0
C3B A:CLA1109 4.2 22.1 1.0
C2C A:CLA1109 4.2 20.1 1.0
C3C A:CLA1109 4.3 19.7 1.0
C2A A:CLA1109 4.3 21.5 1.0
C2D A:CLA1109 4.3 21.2 1.0
C2B A:CLA1109 4.3 22.2 1.0
C3A A:CLA1109 4.4 21.8 1.0
C1 A:CLA1102 4.5 14.7 1.0
CBA A:CLA1109 4.5 19.8 1.0
CAA A:CLA1102 4.7 18.4 1.0
CB A:HIS187 4.7 23.7 1.0
CBD A:CLA1109 4.9 21.8 1.0
CAA A:CLA1109 4.9 20.8 1.0

Magnesium binding site 10 out of 174 in 3lw5

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Magnesium binding site 10 out of 174 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1110

b:22.4
occ:1.00
MG A:CLA1110 0.0 22.4 1.0
NA A:CLA1110 2.0 22.6 1.0
ND A:CLA1110 2.0 22.2 1.0
NB A:CLA1110 2.1 22.4 1.0
NC A:CLA1110 2.1 21.7 1.0
NE2 A:HIS205 2.4 20.0 1.0
C4D A:CLA1110 2.9 22.4 1.0
C1A A:CLA1110 3.0 22.7 1.0
C4A A:CLA1110 3.0 22.5 1.0
C1C A:CLA1110 3.1 21.5 1.0
C4B A:CLA1110 3.1 22.6 1.0
C1B A:CLA1110 3.1 22.1 1.0
C4C A:CLA1110 3.1 21.8 1.0
C1D A:CLA1110 3.2 22.3 1.0
CE1 A:HIS205 3.2 20.4 1.0
CHA A:CLA1110 3.4 22.7 1.0
CHB A:CLA1110 3.4 22.3 1.0
CD2 A:HIS205 3.4 20.3 1.0
CHC A:CLA1110 3.6 22.4 1.0
CHD A:CLA1110 3.7 22.1 1.0
C3D A:CLA1110 4.1 22.6 1.0
C2C A:CLA1110 4.3 21.3 1.0
C3B A:CLA1110 4.3 22.4 1.0
C3C A:CLA1110 4.3 21.4 1.0
C2D A:CLA1110 4.3 22.5 1.0
C2A A:CLA1110 4.3 22.7 1.0
C2B A:CLA1110 4.3 22.0 1.0
C3A A:CLA1110 4.3 22.6 1.0
ND1 A:HIS205 4.4 20.9 1.0
O2A A:CLA1110 4.5 23.1 1.0
CG A:HIS205 4.5 20.7 1.0
CMC A:CLA1111 4.7 24.0 1.0
CAB A:CLA1110 4.8 22.7 1.0
CBD A:CLA1110 4.8 22.8 1.0

Reference:

A.Amunts, H.Toporik, A.Borovikova, N.Nelson. Structure Determination and Improved Model of Plant Photosystem I J.Biol.Chem. V. 285 3478 2010.
ISSN: ISSN 0021-9258
PubMed: 19923216
DOI: 10.1074/JBC.M109.072645
Page generated: Mon Dec 14 08:24:53 2020

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