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Magnesium in PDB 2wsc: Improved Model of Plant Photosystem I

Protein crystallography data

The structure of Improved Model of Plant Photosystem I, PDB code: 2wsc was solved by A.Amunts, H.Toporik, A.Borovikov, N.Nelson, 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 (%) 36.3 / 36.6

Other elements in 2wsc:

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

Iron (Fe) 12 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 160; Page 17, Binding sites: 161 - 170; Page 18, Binding sites: 171 - 173;

Binding sites:

The binding sites of Magnesium atom in the Improved Model of Plant Photosystem I (pdb code 2wsc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 173 binding sites of Magnesium where determined in the Improved Model of Plant Photosystem I, PDB code: 2wsc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 173 in 2wsc

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Magnesium binding site 1 out of 173 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
1:Mg1187

b:20.0
occ:1.00
 MG 1:CLA1187 0.0 20.0 1.0
NA 1:CLA1187 2.0 20.0 1.0
NB 1:CLA1187 2.0 20.0 1.0
ND 1:CLA1187 2.0 20.0 1.0
NC 1:CLA1187 2.1 20.0 1.0
C4A 1:CLA1187 2.9 20.0 1.0
C4D 1:CLA1187 2.9 20.0 1.0
C1A 1:CLA1187 3.0 20.0 1.0
C1B 1:CLA1187 3.0 20.0 1.0
C4B 1:CLA1187 3.0 20.0 1.0
C1C 1:CLA1187 3.1 20.0 1.0
C4C 1:CLA1187 3.1 20.0 1.0
C1D 1:CLA1187 3.1 20.0 1.0
CHB 1:CLA1187 3.3 20.0 1.0
CHA 1:CLA1187 3.4 20.0 1.0
CHC 1:CLA1187 3.6 20.0 1.0
CHD 1:CLA1187 3.6 20.0 1.0
C3D 1:CLA1187 4.1 20.0 1.0
C3B 1:CLA1187 4.2 20.0 1.0
C2D 1:CLA1187 4.2 20.0 1.0
C2B 1:CLA1187 4.2 20.0 1.0
C3A 1:CLA1187 4.2 20.0 1.0
C3C 1:CLA1187 4.2 20.0 1.0
C2C 1:CLA1187 4.2 20.0 1.0
C2A 1:CLA1187 4.3 20.0 1.0
OE2 1:GLU142 4.6 44.8 1.0
CBD 1:CLA1187 4.9 20.0 1.0

Magnesium binding site 2 out of 173 in 2wsc

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Magnesium binding site 2 out of 173 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
1:Mg1188

b:20.0
occ:1.00
 MG 1:CLA1188 0.0 20.0 1.0
NA 1:CLA1188 2.0 20.0 1.0
ND 1:CLA1188 2.0 20.0 1.0
NB 1:CLA1188 2.0 20.0 1.0
NC 1:CLA1188 2.1 20.0 1.0
C4D 1:CLA1188 2.9 20.0 1.0
C4A 1:CLA1188 3.0 20.0 1.0
C1A 1:CLA1188 3.0 20.0 1.0
C1B 1:CLA1188 3.0 20.0 1.0
C4B 1:CLA1188 3.1 20.0 1.0
ND2 1:ASN150 3.1 32.9 1.0
C1C 1:CLA1188 3.1 20.0 1.0
C4C 1:CLA1188 3.1 20.0 1.0
C1D 1:CLA1188 3.1 20.0 1.0
CHB 1:CLA1188 3.3 20.0 1.0
CHA 1:CLA1188 3.4 20.0 1.0
CHC 1:CLA1188 3.6 20.0 1.0
CHD 1:CLA1188 3.7 20.0 1.0
CG 1:ASN150 4.1 32.4 1.0
C3D 1:CLA1188 4.1 20.0 1.0
C2B 1:CLA1188 4.2 20.0 1.0
C3B 1:CLA1188 4.3 20.0 1.0
C2D 1:CLA1188 4.3 20.0 1.0
C2C 1:CLA1188 4.3 20.0 1.0
C2A 1:CLA1188 4.3 20.0 1.0
C3C 1:CLA1188 4.3 20.0 1.0
C3A 1:CLA1188 4.3 20.0 1.0
OD1 1:ASN150 4.4 32.3 1.0
CBD 1:CLA1188 4.9 20.0 1.0

Magnesium binding site 3 out of 173 in 2wsc

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Magnesium binding site 3 out of 173 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
1:Mg1189

b:20.0
occ:1.00
 MG 1:CLA1189 0.0 20.0 1.0
NA 1:CLA1189 2.0 20.0 1.0
NB 1:CLA1189 2.0 20.0 1.0
ND 1:CLA1189 2.1 20.0 1.0
NC 1:CLA1189 2.1 20.0 1.0
C4D 1:CLA1189 3.0 20.0 1.0
C4A 1:CLA1189 3.0 20.0 1.0
C1A 1:CLA1189 3.0 20.0 1.0
C1B 1:CLA1189 3.1 20.0 1.0
C4B 1:CLA1189 3.1 20.0 1.0
C1C 1:CLA1189 3.1 20.0 1.0
C4C 1:CLA1189 3.1 20.0 1.0
C1D 1:CLA1189 3.2 20.0 1.0
CHB 1:CLA1189 3.4 20.0 1.0
CHA 1:CLA1189 3.5 20.0 1.0
CHC 1:CLA1189 3.6 20.0 1.0
CHD 1:CLA1189 3.7 20.0 1.0
C3D 1:CLA1189 4.2 20.0 1.0
C3B 1:CLA1189 4.3 20.0 1.0
C2B 1:CLA1189 4.3 20.0 1.0
C2D 1:CLA1189 4.3 20.0 1.0
C2C 1:CLA1189 4.3 20.0 1.0
C3C 1:CLA1189 4.3 20.0 1.0
C3A 1:CLA1189 4.4 20.0 1.0
C2A 1:CLA1189 4.4 20.0 1.0
CD1 1:PHE161 4.4 42.8 1.0
CBD 1:CLA1189 4.9 20.0 1.0
CAB 1:CLA1189 5.0 20.0 1.0

Magnesium binding site 4 out of 173 in 2wsc

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Magnesium binding site 4 out of 173 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
1:Mg1190

b:20.0
occ:1.00
 MG 1:CLA1190 0.0 20.0 1.0
NA 1:CLA1190 2.0 20.0 1.0
ND 1:CLA1190 2.0 20.0 1.0
NB 1:CLA1190 2.0 20.0 1.0
NC 1:CLA1190 2.1 20.0 1.0
C4D 1:CLA1190 2.9 20.0 1.0
C1A 1:CLA1190 2.9 20.0 1.0
C4A 1:CLA1190 3.0 20.0 1.0
C1B 1:CLA1190 3.0 20.0 1.0
C4B 1:CLA1190 3.1 20.0 1.0
C1C 1:CLA1190 3.1 20.0 1.0
C4C 1:CLA1190 3.1 20.0 1.0
C1D 1:CLA1190 3.2 20.0 1.0
CHA 1:CLA1190 3.4 20.0 1.0
CHB 1:CLA1190 3.4 20.0 1.0
CHC 1:CLA1190 3.6 20.0 1.0
CHD 1:CLA1190 3.7 20.0 1.0
C3D 1:CLA1190 4.1 20.0 1.0
O2A 1:CLA1190 4.1 20.0 1.0
C3B 1:CLA1190 4.3 20.0 1.0
C2B 1:CLA1190 4.3 20.0 1.0
C2C 1:CLA1190 4.3 20.0 1.0
C2D 1:CLA1190 4.3 20.0 1.0
C2A 1:CLA1190 4.3 20.0 1.0
C3C 1:CLA1190 4.3 20.0 1.0
C3A 1:CLA1190 4.3 20.0 1.0
CGA 1:CLA1190 4.4 20.0 1.0
CBA 1:CLA1190 4.7 20.0 1.0
C1 1:CLA1190 4.8 20.0 1.0
CBD 1:CLA1190 4.8 20.0 1.0
CAB 1:CLA1190 4.9 20.0 1.0
O1A 1:CLA1190 4.9 20.0 1.0

Magnesium binding site 5 out of 173 in 2wsc

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Magnesium binding site 5 out of 173 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
1:Mg1191

b:20.0
occ:1.00
 MG 1:CLA1191 0.0 20.0 1.0
NA 1:CLA1191 2.0 20.0 1.0
ND 1:CLA1191 2.0 20.0 1.0
NB 1:CLA1191 2.1 20.0 1.0
NC 1:CLA1191 2.1 20.0 1.0
C4D 1:CLA1191 3.0 20.0 1.0
C1A 1:CLA1191 3.0 20.0 1.0
C4A 1:CLA1191 3.0 20.0 1.0
C1B 1:CLA1191 3.1 20.0 1.0
C4B 1:CLA1191 3.1 20.0 1.0
C1C 1:CLA1191 3.1 20.0 1.0
C4C 1:CLA1191 3.1 20.0 1.0
C1D 1:CLA1191 3.2 20.0 1.0
CHA 1:CLA1191 3.4 20.0 1.0
CHB 1:CLA1191 3.4 20.0 1.0
CHC 1:CLA1191 3.6 20.0 1.0
O 1:ALA53 3.7 62.0 1.0
CHD 1:CLA1191 3.7 20.0 1.0
CA 1:GLY56 4.1 59.6 1.0
C3D 1:CLA1191 4.2 20.0 1.0
C3B 1:CLA1191 4.3 20.0 1.0
C2B 1:CLA1191 4.3 20.0 1.0
C2C 1:CLA1191 4.3 20.0 1.0
C2D 1:CLA1191 4.3 20.0 1.0
C3C 1:CLA1191 4.3 20.0 1.0
C2A 1:CLA1191 4.3 20.0 1.0
C3A 1:CLA1191 4.3 20.0 1.0
N 1:GLY56 4.5 60.0 1.0
C 1:ALA53 4.7 62.0 1.0
CBD 1:CLA1191 4.9 20.0 1.0

Magnesium binding site 6 out of 173 in 2wsc

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Magnesium binding site 6 out of 173 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
1:Mg1192

b:20.0
occ:1.00
 MG 1:CLA1192 0.0 20.0 1.0
NA 1:CLA1192 2.0 20.0 1.0
ND 1:CLA1192 2.0 20.0 1.0
NB 1:CLA1192 2.0 20.0 1.0
NC 1:CLA1192 2.1 20.0 1.0
C4D 1:CLA1192 2.9 20.0 1.0
C1A 1:CLA1192 3.0 20.0 1.0
C4A 1:CLA1192 3.0 20.0 1.0
C1B 1:CLA1192 3.1 20.0 1.0
C4B 1:CLA1192 3.1 20.0 1.0
C1C 1:CLA1192 3.1 20.0 1.0
C4C 1:CLA1192 3.1 20.0 1.0
C1D 1:CLA1192 3.1 20.0 1.0
CHB 1:CLA1192 3.4 20.0 1.0
CHA 1:CLA1192 3.4 20.0 1.0
CHC 1:CLA1192 3.6 20.0 1.0
CHD 1:CLA1192 3.7 20.0 1.0
C3D 1:CLA1192 4.1 20.0 1.0
C3B 1:CLA1192 4.3 20.0 1.0
C2C 1:CLA1192 4.3 20.0 1.0
C2D 1:CLA1192 4.3 20.0 1.0
C2B 1:CLA1192 4.3 20.0 1.0
C3C 1:CLA1192 4.3 20.0 1.0
C2A 1:CLA1192 4.3 20.0 1.0
C3A 1:CLA1192 4.4 20.0 1.0
C7 1:CLA1192 4.4 20.0 1.0
C8 1:CLA1192 4.7 20.0 1.0
CBD 1:CLA1192 4.8 20.0 1.0
O2D 1:CLA1192 4.9 20.0 1.0

Magnesium binding site 7 out of 173 in 2wsc

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Magnesium binding site 7 out of 173 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
1:Mg1193

b:20.0
occ:1.00
 MG 1:CLA1193 0.0 20.0 1.0
NA 1:CLA1193 2.0 20.0 1.0
ND 1:CLA1193 2.0 20.0 1.0
NB 1:CLA1193 2.1 20.0 1.0
NC 1:CLA1193 2.1 20.0 1.0
C1A 1:CLA1193 3.0 20.0 1.0
C4D 1:CLA1193 3.0 20.0 1.0
C4A 1:CLA1193 3.0 20.0 1.0
C1C 1:CLA1193 3.1 20.0 1.0
C1B 1:CLA1193 3.1 20.0 1.0
C4B 1:CLA1193 3.1 20.0 1.0
C4C 1:CLA1193 3.1 20.0 1.0
C1D 1:CLA1193 3.2 20.0 1.0
CHA 1:CLA1193 3.4 20.0 1.0
CHB 1:CLA1193 3.4 20.0 1.0
CHC 1:CLA1193 3.6 20.0 1.0
CHD 1:CLA1193 3.7 20.0 1.0
C3D 1:CLA1193 4.2 20.0 1.0
C2A 1:CLA1193 4.2 20.0 1.0
C3B 1:CLA1193 4.3 20.0 1.0
C2C 1:CLA1193 4.3 20.0 1.0
C3C 1:CLA1193 4.3 20.0 1.0
C2B 1:CLA1193 4.3 20.0 1.0
C2D 1:CLA1193 4.3 20.0 1.0
C3A 1:CLA1193 4.4 20.0 1.0
CBA 1:CLA1193 4.8 20.0 1.0
CBD 1:CLA1193 4.9 20.0 1.0

Magnesium binding site 8 out of 173 in 2wsc

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Magnesium binding site 8 out of 173 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
1:Mg1194

b:20.0
occ:1.00
 MG 1:CLA1194 0.0 20.0 1.0
NA 1:CLA1194 2.0 20.0 1.0
ND 1:CLA1194 2.1 20.0 1.0
NC 1:CLA1194 2.1 20.0 1.0
NB 1:CLA1194 2.1 20.0 1.0
C1A 1:CLA1194 3.0 20.0 1.0
C4A 1:CLA1194 3.0 20.0 1.0
C4D 1:CLA1194 3.0 20.0 1.0
C1C 1:CLA1194 3.1 20.0 1.0
C4B 1:CLA1194 3.1 20.0 1.0
C1B 1:CLA1194 3.1 20.0 1.0
C4C 1:CLA1194 3.1 20.0 1.0
C1D 1:CLA1194 3.1 20.0 1.0
CHB 1:CLA1194 3.4 20.0 1.0
CHA 1:CLA1194 3.5 20.0 1.0
CHC 1:CLA1194 3.6 20.0 1.0
CHD 1:CLA1194 3.7 20.0 1.0
C2C 1:CLA1194 4.3 20.0 1.0
C3B 1:CLA1194 4.3 20.0 1.0
C2D 1:CLA1194 4.3 20.0 1.0
C3D 1:CLA1194 4.3 20.0 1.0
C3C 1:CLA1194 4.3 20.0 1.0
C2A 1:CLA1194 4.3 20.0 1.0
C2B 1:CLA1194 4.3 20.0 1.0
C3A 1:CLA1194 4.4 20.0 1.0

Magnesium binding site 9 out of 173 in 2wsc

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Magnesium binding site 9 out of 173 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
1:Mg1195

b:20.0
occ:1.00
 MG 1:CLA1195 0.0 20.0 1.0
NA 1:CLA1195 2.0 20.0 1.0
NB 1:CLA1195 2.0 20.0 1.0
ND 1:CLA1195 2.0 20.0 1.0
NC 1:CLA1195 2.0 20.0 1.0
C4D 1:CLA1195 2.9 20.0 1.0
C1A 1:CLA1195 2.9 20.0 1.0
C4A 1:CLA1195 2.9 20.0 1.0
C1B 1:CLA1195 3.0 20.0 1.0
C4B 1:CLA1195 3.0 20.0 1.0
C1C 1:CLA1195 3.0 20.0 1.0
C4C 1:CLA1195 3.1 20.0 1.0
C1D 1:CLA1195 3.1 20.0 1.0
CG2 1:VAL108 3.2 62.1 1.0
CHA 1:CLA1195 3.3 20.0 1.0
CHB 1:CLA1195 3.3 20.0 1.0
CHC 1:CLA1195 3.5 20.0 1.0
CHD 1:CLA1195 3.7 20.0 1.0
C3D 1:CLA1195 4.1 20.0 1.0
C3B 1:CLA1195 4.2 20.0 1.0
C2B 1:CLA1195 4.2 20.0 1.0
C2C 1:CLA1195 4.2 20.0 1.0
C3C 1:CLA1195 4.2 20.0 1.0
C2A 1:CLA1195 4.2 20.0 1.0
C2D 1:CLA1195 4.2 20.0 1.0
C3A 1:CLA1195 4.3 20.0 1.0
CB 1:VAL108 4.4 62.1 1.0
CAB 1:CLA1195 4.7 20.0 1.0
CBD 1:CLA1195 4.8 20.0 1.0

Magnesium binding site 10 out of 173 in 2wsc

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Magnesium binding site 10 out of 173 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
1:Mg1196

b:20.0
occ:1.00
 MG 1:CLA1196 0.0 20.0 1.0
NA 1:CLA1196 2.0 20.0 1.0
ND 1:CLA1196 2.0 20.0 1.0
NB 1:CLA1196 2.1 20.0 1.0
NC 1:CLA1196 2.1 20.0 1.0
OE1 1:GLU109 2.2 61.5 1.0
C4D 1:CLA1196 3.0 20.0 1.0
C1A 1:CLA1196 3.0 20.0 1.0
C4A 1:CLA1196 3.0 20.0 1.0
C1B 1:CLA1196 3.1 20.0 1.0
C1C 1:CLA1196 3.1 20.0 1.0
C4B 1:CLA1196 3.1 20.0 1.0
C4C 1:CLA1196 3.1 20.0 1.0
CD 1:GLU109 3.2 61.7 1.0
C1D 1:CLA1196 3.2 20.0 1.0
CHB 1:CLA1196 3.4 20.0 1.0
CHA 1:CLA1196 3.4 20.0 1.0
OE2 1:GLU109 3.5 61.7 1.0
CHC 1:CLA1196 3.6 20.0 1.0
CHD 1:CLA1196 3.7 20.0 1.0
C3D 1:CLA1196 4.2 20.0 1.0
C2C 1:CLA1196 4.3 20.0 1.0
C2B 1:CLA1196 4.3 20.0 1.0
C3B 1:CLA1196 4.3 20.0 1.0
C2D 1:CLA1196 4.3 20.0 1.0
C3C 1:CLA1196 4.3 20.0 1.0
C2A 1:CLA1196 4.3 20.0 1.0
C3A 1:CLA1196 4.4 20.0 1.0
CG 1:GLU109 4.4 62.1 1.0
C3B 1:CLA1190 4.6 20.0 1.0
CAB 1:CLA1190 4.6 20.0 1.0
CBD 1:CLA1196 4.9 20.0 1.0
NH1 1:ARG112 4.9 63.9 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: Wed Aug 14 06:12:37 2024

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