Magnesium in PDB 8ix0: Cryo-Em Structure of Unprotonated Lhcii Nanodisc at High pH Value

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>>> 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 - 42;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Unprotonated Lhcii Nanodisc at High pH Value (pdb code 8ix0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 42 binding sites of Magnesium where determined in the Cryo-Em Structure of Unprotonated Lhcii Nanodisc at High pH Value, PDB code: 8ix0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 42 in the Cryo-Em Structure of Unprotonated Lhcii Nanodisc at High pH Value


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 Unprotonated Lhcii Nanodisc at High pH Value within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg601 b:29.6 occ:1.00 MG N:CHL601 0.0 29.6 1.0 NB N:CHL601 2.0 29.3 1.0 ND N:CHL601 2.0 29.5 1.0 NA N:CHL601 2.1 29.4 1.0 NC N:CHL601 2.1 28.4 1.0 O N:TYR24 2.2 30.4 1.0 C4D N:CHL601 2.9 29.3 1.0 C1B N:CHL601 3.0 29.1 1.0 C4B N:CHL601 3.1 29.4 1.0 C4A N:CHL601 3.1 28.7 1.0 C1C N:CHL601 3.1 28.9 1.0 C4C N:CHL601 3.1 28.3 1.0 C1D N:CHL601 3.1 29.2 1.0 C1A N:CHL601 3.2 29.9 1.0 C N:TYR24 3.4 30.8 1.0 CHC N:CHL601 3.4 30.1 1.0 CHB N:CHL601 3.4 28.7 1.0 CHA N:CHL601 3.5 29.2 1.0 CHD N:CHL601 3.5 28.8 1.0 CA N:TYR24 3.9 31.8 1.0 CD2 N:TYR24 4.1 29.7 1.0 CB N:TYR24 4.1 31.2 1.0 C3D N:CHL601 4.3 29.2 1.0 C2B N:CHL601 4.3 29.4 1.0 C3B N:CHL601 4.3 29.2 1.0 C2C N:CHL601 4.3 28.8 1.0 C2D N:CHL601 4.3 29.3 1.0 C3C N:CHL601 4.4 28.6 1.0 C3A N:CHL601 4.4 29.1 1.0 C2A N:CHL601 4.5 30.1 1.0 CG N:TYR24 4.5 30.3 1.0 N N:LEU25 4.5 29.4 1.0 C8 N:LHG618 4.7 29.8 1.0 CA N:LEU25 4.8 28.7 1.0 CBD N:CHL601 4.9 28.7 1.0 CD1 N:LEU25 5.0 30.9 1.0

Magnesium binding site 2 out of 42 in the Cryo-Em Structure of Unprotonated Lhcii Nanodisc at High pH Value


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 Unprotonated Lhcii Nanodisc at High pH Value within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg602 b:29.8 occ:1.00 MG N:CLA602 0.0 29.8 1.0 NB N:CLA602 2.0 30.3 1.0 ND N:CLA602 2.0 28.5 1.0 OE1 N:GLU65 2.0 30.9 1.0 NC N:CLA602 2.1 30.0 1.0 NA N:CLA602 2.1 28.0 1.0 C4D N:CLA602 2.9 29.0 1.0 C1B N:CLA602 3.0 29.2 1.0 C4B N:CLA602 3.1 29.8 1.0 C4A N:CLA602 3.1 28.4 1.0 CD N:GLU65 3.1 31.4 1.0 C1C N:CLA602 3.1 29.9 1.0 C1A N:CLA602 3.2 27.7 1.0 C4C N:CLA602 3.2 29.7 1.0 C1D N:CLA602 3.2 29.0 1.0 NH1 N:ARG185 3.2 32.5 1.0 CHC N:CLA602 3.4 29.8 1.0 CHB N:CLA602 3.4 29.5 1.0 CHA N:CLA602 3.5 28.9 1.0 CHD N:CLA602 3.6 29.7 1.0 OE2 N:GLU65 3.6 32.5 1.0 C38 N:LUT616 3.7 33.9 1.0 C3D N:CLA602 4.3 29.8 1.0 C2B N:CLA602 4.3 29.1 1.0 CG N:GLU65 4.3 31.5 1.0 C3B N:CLA602 4.3 29.1 1.0 CZ N:ARG185 4.3 32.5 1.0 C2C N:CLA602 4.3 29.8 1.0 C2D N:CLA602 4.4 29.1 1.0 C3C N:CLA602 4.4 29.6 1.0 C3A N:CLA602 4.4 28.3 1.0 C2A N:CLA602 4.5 28.2 1.0 NH2 N:ARG185 4.8 32.2 1.0 CB N:GLU65 4.9 31.1 1.0 O2A N:CLA602 4.9 28.7 1.0 CBD N:CLA602 4.9 30.2 1.0

Magnesium binding site 3 out of 42 in the Cryo-Em Structure of Unprotonated Lhcii Nanodisc at High pH Value


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 Unprotonated Lhcii Nanodisc at High pH Value within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg603 b:32.4 occ:1.00 MG N:CLA603 0.0 32.4 1.0 NE2 N:HIS68 1.9 31.1 1.0 NB N:CLA603 2.0 33.5 1.0 ND N:CLA603 2.0 32.5 1.0 NC N:CLA603 2.1 33.3 1.0 NA N:CLA603 2.1 32.6 1.0 CE1 N:HIS68 2.7 31.5 1.0 C4D N:CLA603 2.9 32.6 1.0 CD2 N:HIS68 3.0 31.1 1.0 C1B N:CLA603 3.0 33.5 1.0 C4A N:CLA603 3.1 32.8 1.0 C4B N:CLA603 3.1 33.1 1.0 C1C N:CLA603 3.1 32.7 1.0 C4C N:CLA603 3.2 33.4 1.0 C1D N:CLA603 3.2 32.8 1.0 C1A N:CLA603 3.2 32.2 1.0 CHB N:CLA603 3.4 33.2 1.0 CHC N:CLA603 3.5 32.5 1.0 CHA N:CLA603 3.5 32.3 1.0 CHD N:CLA603 3.6 33.0 1.0 ND1 N:HIS68 3.9 30.8 1.0 CG N:HIS68 4.1 30.1 1.0 C3D N:CLA603 4.3 32.7 1.0 C2B N:CLA603 4.3 32.7 1.0 C3B N:CLA603 4.3 32.4 1.0 C2C N:CLA603 4.4 32.4 1.0 C2D N:CLA603 4.4 32.9 1.0 C3C N:CLA603 4.4 33.2 1.0 C3A N:CLA603 4.4 32.8 1.0 C2A N:CLA603 4.5 32.3 1.0 CBD N:CLA603 4.9 32.7 1.0 C9 N:CHL609 5.0 33.3 1.0

Magnesium binding site 4 out of 42 in the Cryo-Em Structure of Unprotonated Lhcii Nanodisc at High pH Value


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 Unprotonated Lhcii Nanodisc at High pH Value within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg604 b:21.3 occ:1.00 MG N:CLA604 0.0 21.3 1.0 NB N:CLA604 2.0 24.4 1.0 ND N:CLA604 2.0 22.2 1.0 NC N:CLA604 2.1 23.5 1.0 NA N:CLA604 2.1 23.4 1.0 C4D N:CLA604 2.9 23.7 1.0 C1B N:CLA604 3.0 24.6 1.0 C4B N:CLA604 3.1 25.1 1.0 C4A N:CLA604 3.1 23.6 1.0 C1C N:CLA604 3.1 23.9 1.0 C4C N:CLA604 3.2 24.7 1.0 C1A N:CLA604 3.2 24.3 1.0 C1D N:CLA604 3.2 23.3 1.0 CHB N:CLA604 3.4 24.0 1.0 CHC N:CLA604 3.4 24.4 1.0 CHA N:CLA604 3.5 24.2 1.0 CHD N:CLA604 3.6 24.6 1.0 C3D N:CLA604 4.3 24.6 1.0 C2B N:CLA604 4.3 25.5 1.0 C24 N:NEX617 4.3 25.2 1.0 C3B N:CLA604 4.3 25.3 1.0 C2C N:CLA604 4.3 24.2 1.0 C2D N:CLA604 4.4 24.0 1.0 C3C N:CLA604 4.4 25.0 1.0 C3A N:CLA604 4.4 24.9 1.0 C2A N:CLA604 4.5 24.6 1.0 O23 N:NEX617 4.5 26.3 1.0 O N:GLY78 4.8 27.3 1.0 CBA N:CLA604 4.9 25.5 1.0 CBD N:CLA604 4.9 23.9 1.0 CA N:GLY78 5.0 28.7 1.0

Magnesium binding site 5 out of 42 in the Cryo-Em Structure of Unprotonated Lhcii Nanodisc at High pH Value


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 Unprotonated Lhcii Nanodisc at High pH Value within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg605 b:20.3 occ:1.00 MG N:CHL605 0.0 20.3 1.0 NB N:CHL605 2.0 18.9 1.0 ND N:CHL605 2.0 19.7 1.0 NC N:CHL605 2.1 21.1 1.0 NA N:CHL605 2.1 17.5 1.0 C4D N:CHL605 3.0 18.2 1.0 C1B N:CHL605 3.0 19.1 1.0 C4A N:CHL605 3.1 19.0 1.0 C4B N:CHL605 3.1 17.5 1.0 C1C N:CHL605 3.1 20.0 1.0 C4C N:CHL605 3.1 20.1 1.0 C1D N:CHL605 3.2 19.5 1.0 C1A N:CHL605 3.2 17.0 1.0 CHC N:CHL605 3.4 17.9 1.0 CHB N:CHL605 3.4 19.7 1.0 CHA N:CHL605 3.5 17.2 1.0 CHD N:CHL605 3.5 19.2 1.0 O N:HIS120 3.8 20.2 1.0 N N:HIS120 4.0 23.7 1.0 C3D N:CHL605 4.3 18.9 1.0 CB N:HIS120 4.3 19.2 1.0 C2B N:CHL605 4.3 18.4 1.0 C3B N:CHL605 4.3 18.4 1.0 C2C N:CHL605 4.3 20.6 1.0 C3C N:CHL605 4.4 19.3 1.0 C3A N:CHL605 4.4 17.8 1.0 C2D N:CHL605 4.4 19.1 1.0 C N:HIS120 4.4 20.8 1.0 C2A N:CHL605 4.5 18.5 1.0 CA N:HIS120 4.5 21.7 1.0 CG2 N:VAL119 4.5 20.2 1.0 CBD N:CHL605 5.0 17.9 1.0 CMA N:CHL605 5.0 20.2 1.0 C N:VAL119 5.0 22.5 1.0

Magnesium binding site 6 out of 42 in the Cryo-Em Structure of Unprotonated Lhcii Nanodisc at High pH Value


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 Unprotonated Lhcii Nanodisc at High pH Value within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg606 b:23.6 occ:1.00 MG N:CHL606 0.0 23.6 1.0 NB N:CHL606 2.0 22.8 1.0 ND N:CHL606 2.0 20.3 1.0 OE1 N:GLN131 2.1 27.6 1.0 NC N:CHL606 2.1 21.5 1.0 NA N:CHL606 2.1 21.6 1.0 C4D N:CHL606 2.9 20.2 1.0 C1B N:CHL606 3.0 21.8 1.0 C4A N:CHL606 3.1 20.7 1.0 C4B N:CHL606 3.1 21.6 1.0 C1C N:CHL606 3.1 22.0 1.0 C4C N:CHL606 3.2 21.9 1.0 C1D N:CHL606 3.2 21.6 1.0 C1A N:CHL606 3.2 20.4 1.0 CD N:GLN131 3.2 26.6 1.0 CHC N:CHL606 3.4 21.9 1.0 CHB N:CHL606 3.4 20.7 1.0 CHA N:CHL606 3.5 19.4 1.0 CHD N:CHL606 3.5 21.8 1.0 NE2 N:GLN131 3.8 26.5 1.0 C3D N:CHL606 4.3 21.6 1.0 C2B N:CHL606 4.3 21.9 1.0 C3B N:CHL606 4.3 21.3 1.0 C2C N:CHL606 4.4 22.7 1.0 C2D N:CHL606 4.4 22.5 1.0 C3C N:CHL606 4.4 23.1 1.0 C3A N:CHL606 4.4 22.0 1.0 CG N:GLN131 4.4 26.0 1.0 C2A N:CHL606 4.5 22.0 1.0 CB N:GLN131 4.9 25.5 1.0 CG2 N:ILE127 4.9 23.9 1.0 CBD N:CHL606 5.0 20.0 1.0

Magnesium binding site 7 out of 42 in the Cryo-Em Structure of Unprotonated Lhcii Nanodisc at High pH Value


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 Unprotonated Lhcii Nanodisc at High pH Value within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg607 b:28.5 occ:1.00 MG N:CHL607 0.0 28.5 1.0 NB N:CHL607 2.0 28.0 1.0 ND N:CHL607 2.0 29.2 1.0 NC N:CHL607 2.1 27.4 1.0 NA N:CHL607 2.1 27.5 1.0 C4D N:CHL607 2.9 28.7 1.0 C1B N:CHL607 3.0 29.1 1.0 C4A N:CHL607 3.1 28.8 1.0 C4B N:CHL607 3.1 28.9 1.0 C1C N:CHL607 3.1 27.0 1.0 C4C N:CHL607 3.1 27.6 1.0 C1D N:CHL607 3.2 29.1 1.0 C1A N:CHL607 3.2 27.3 1.0 CHB N:CHL607 3.4 29.6 1.0 CHC N:CHL607 3.4 28.6 1.0 CHA N:CHL607 3.5 28.0 1.0 CHD N:CHL607 3.5 28.9 1.0 OMC N:CHL606 3.5 24.0 1.0 C3D N:CHL607 4.3 28.8 1.0 C2B N:CHL607 4.3 29.4 1.0 C3B N:CHL607 4.3 29.6 1.0 C2C N:CHL607 4.3 26.9 1.0 C2D N:CHL607 4.4 28.9 1.0 CMC N:CHL606 4.4 23.3 1.0 C3C N:CHL607 4.4 27.2 1.0 C3A N:CHL607 4.4 29.1 1.0 C2A N:CHL607 4.5 28.0 1.0 CBD N:CHL607 4.9 28.4 1.0 C16 N:LUT616 5.0 32.2 1.0

Magnesium binding site 8 out of 42 in the Cryo-Em Structure of Unprotonated Lhcii Nanodisc at High pH Value


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 Unprotonated Lhcii Nanodisc at High pH Value within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg608 b:28.7 occ:1.00 MG N:CHL608 0.0 28.7 1.0 NB N:CHL608 2.0 23.8 1.0 ND N:CHL608 2.0 26.2 1.0 NC N:CHL608 2.1 26.1 1.0 NA N:CHL608 2.1 25.9 1.0 CZ N:PHE161 2.1 25.8 1.0 CE1 N:PHE161 2.9 24.0 1.0 C4D N:CHL608 3.0 26.2 1.0 C1B N:CHL608 3.0 23.2 1.0 C4A N:CHL608 3.1 25.7 1.0 C4B N:CHL608 3.1 23.9 1.0 C1C N:CHL608 3.1 26.2 1.0 CE2 N:PHE161 3.1 25.0 1.0 C4C N:CHL608 3.1 25.3 1.0 C1D N:CHL608 3.2 25.6 1.0 C1A N:CHL608 3.2 25.2 1.0 CHB N:CHL608 3.4 25.2 1.0 CHC N:CHL608 3.4 25.7 1.0 CHA N:CHL608 3.5 25.6 1.0 CHD N:CHL608 3.5 25.1 1.0 CD1 N:PHE161 4.2 21.8 1.0 C3D N:CHL608 4.3 26.1 1.0 C2B N:CHL608 4.3 23.2 1.0 C3B N:CHL608 4.3 23.5 1.0 C2C N:CHL608 4.3 25.3 1.0 O1A N:CHL608 4.4 26.6 1.0 CD2 N:PHE161 4.4 22.5 1.0 C2D N:CHL608 4.4 26.2 1.0 C3C N:CHL608 4.4 25.2 1.0 C3A N:CHL608 4.4 26.1 1.0 C2A N:CHL608 4.5 24.8 1.0 CG N:ARG142 4.7 25.3 1.0 CG N:PHE161 4.8 21.7 1.0 CBD N:CHL608 5.0 24.8 1.0 CGA N:CHL608 5.0 24.3 1.0

Magnesium binding site 9 out of 42 in the Cryo-Em Structure of Unprotonated Lhcii Nanodisc at High pH Value


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 Unprotonated Lhcii Nanodisc at High pH Value within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg609 b:32.3 occ:1.00 MG N:CHL609 0.0 32.3 1.0 NB N:CHL609 2.0 32.5 1.0 ND N:CHL609 2.0 32.6 1.0 NC N:CHL609 2.1 32.6 1.0 NA N:CHL609 2.1 32.0 1.0 OE2 N:GLU139 2.2 25.5 1.0 C4D N:CHL609 2.9 31.5 1.0 C1B N:CHL609 3.0 32.1 1.0 C4A N:CHL609 3.0 32.9 1.0 C4B N:CHL609 3.1 32.2 1.0 C1C N:CHL609 3.1 31.5 1.0 C4C N:CHL609 3.1 32.7 1.0 C1D N:CHL609 3.1 32.7 1.0 C1A N:CHL609 3.1 32.4 1.0 CD N:GLU139 3.2 26.3 1.0 CHB N:CHL609 3.4 32.4 1.0 CHC N:CHL609 3.4 31.9 1.0 CHD N:CHL609 3.5 33.3 1.0 CHA N:CHL609 3.5 32.0 1.0 OE1 N:GLU139 3.8 26.9 1.0 CG N:GLU139 4.1 26.2 1.0 C3D N:CHL609 4.3 31.9 1.0 C2B N:CHL609 4.3 32.3 1.0 C3B N:CHL609 4.3 32.6 1.0 C2C N:CHL609 4.3 31.8 1.0 C2D N:CHL609 4.3 31.9 1.0 C3C N:CHL609 4.4 31.3 1.0 C3A N:CHL609 4.4 33.4 1.0 C2A N:CHL609 4.4 32.9 1.0 CBA N:CHL609 4.6 32.7 1.0 CBD N:CHL609 4.9 32.4 1.0 CMD N:CLA603 5.0 32.8 1.0

Magnesium binding site 10 out of 42 in the Cryo-Em Structure of Unprotonated Lhcii Nanodisc at High pH Value


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 Unprotonated Lhcii Nanodisc at High pH Value within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg610 b:6.4 occ:1.00 MG N:CLA610 0.0 6.4 1.0 ND N:CLA610 2.0 7.0 1.0 NB N:CLA610 2.0 6.6 1.0 NA N:CLA610 2.1 5.8 1.0 NC N:CLA610 2.1 6.7 1.0 OE2 N:GLU180 2.5 26.7 1.0 C4D N:CLA610 2.9 5.3 1.0 C1B N:CLA610 3.0 5.5 1.0 C4A N:CLA610 3.0 5.2 1.0 C4B N:CLA610 3.1 5.7 1.0 C1C N:CLA610 3.1 5.9 1.0 C4C N:CLA610 3.1 6.0 1.0 C1A N:CLA610 3.2 6.3 1.0 C1D N:CLA610 3.2 5.1 1.0 CD N:GLU180 3.3 27.4 1.0 CHB N:CLA610 3.4 6.4 1.0 CHC N:CLA610 3.4 5.8 1.0 CHA N:CLA610 3.5 5.9 1.0 OE1 N:GLU180 3.5 28.6 1.0 CHD N:CLA610 3.5 5.4 1.0 NH2 N:ARG70 3.7 27.9 1.0 C3D N:CLA610 4.3 5.8 1.0 C2B N:CLA610 4.3 6.5 1.0 C3B N:CLA610 4.3 6.9 1.0 C2C N:CLA610 4.3 5.7 1.0 C2D N:CLA610 4.4 5.6 1.0 C3A N:CLA610 4.4 6.4 1.0 C3C N:CLA610 4.4 6.1 1.0 C2A N:CLA610 4.5 6.6 1.0 C38 N:LUT615 4.6 22.9 1.0 CZ N:ARG70 4.6 27.5 1.0 CG N:GLU180 4.6 27.2 1.0 NE N:ARG70 4.9 27.5 1.0 CBD N:CLA610 4.9 5.2 1.0 CMA N:CLA610 5.0 5.6 1.0

M.X.Ruan, H.Li, Y.Zhang, R.Q.Zhao, J.Zhang, Y.J.Wang, J.L.Gao, Z.Wang, Y.M.Wang, D.P.Sun, W.Ding, Y.X.Weng. Cryo-Em Structures of Lhcii in Photo-Active and Photo-Protecting States Reveal Allosteric Regulation of Light-Harvesting and Excess Energy-Dissipation To Be Published.