Magnesium in PDB 9fvj: Xenopus Borealis Undecorated Microtubule - 15 Protofilament, 3-Start Helix

The binding sites of Magnesium atom in the Xenopus Borealis Undecorated Microtubule - 15 Protofilament, 3-Start Helix (pdb code 9fvj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Xenopus Borealis Undecorated Microtubule - 15 Protofilament, 3-Start Helix, PDB code: 9fvj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Xenopus Borealis Undecorated Microtubule - 15 Protofilament, 3-Start Helix


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Xenopus Borealis Undecorated Microtubule - 15 Protofilament, 3-Start Helix within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg502 b:44.2 occ:1.00 OE2 a:GLU70 1.9 71.1 1.0 O1G a:GTP501 2.0 39.3 1.0 OD2 a:ASP97 2.4 78.6 1.0 O1B a:GTP501 2.5 29.9 1.0 CD a:GLU70 2.8 74.6 1.0 OD1 a:ASP97 2.8 80.1 1.0 CG a:ASP97 2.9 78.4 1.0 PG a:GTP501 3.0 36.9 1.0 O2G a:GTP501 3.1 43.6 1.0 HG2 a:GLU70 3.3 68.1 1.0 OE1 a:GLU70 3.5 68.0 1.0 HZ1 A:LYS252 3.5 70.0 1.0 PB a:GTP501 3.5 25.8 1.0 O3B a:GTP501 3.6 26.6 1.0 CG a:GLU70 3.6 75.3 1.0 HB2 a:GLN11 3.9 56.9 1.0 H a:GLN11 4.2 56.9 1.0 O3A a:GTP501 4.2 28.8 1.0 HG3 a:GLU70 4.2 68.4 1.0 HG1 a:THR144 4.2 64.3 1.0 OD1 a:ASP68 4.3 72.1 1.0 O3G a:GTP501 4.3 31.5 1.0 NZ A:LYS252 4.3 74.4 1.0 CB a:ASP97 4.3 73.2 1.0 HZ3 A:LYS252 4.4 69.5 1.0 HB a:THR144 4.4 63.6 1.0 HB2 a:ASP97 4.5 72.0 1.0 HB3 a:GLU70 4.6 66.9 1.0 H a:ALA98 4.6 62.4 1.0 HB3 a:GLN11 4.6 55.9 1.0 OD2 a:ASP68 4.6 66.8 1.0 OG1 a:THR144 4.6 70.8 1.0 OE1 a:GLN11 4.6 60.0 1.0 CB a:GLN11 4.7 50.9 1.0 CB a:GLU70 4.8 66.8 1.0 H a:THR144 4.8 62.2 1.0 HZ2 A:LYS252 4.8 70.3 1.0 O2B a:GTP501 4.8 33.4 1.0 HB3 a:ASP97 4.8 72.1 1.0 CG a:ASP68 4.9 69.4 1.0 N a:GLN11 4.9 53.5 1.0

Magnesium binding site 2 out of 6 in the Xenopus Borealis Undecorated Microtubule - 15 Protofilament, 3-Start Helix


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Xenopus Borealis Undecorated Microtubule - 15 Protofilament, 3-Start Helix within 5.0Å range: probe atom residue distance (Å) B Occ b:Mg502 b:44.2 occ:1.00 OE2 b:GLU70 1.9 71.1 1.0 O1G b:GTP501 2.0 39.3 1.0 OD2 b:ASP97 2.4 78.6 1.0 O1B b:GTP501 2.5 29.9 1.0 CD b:GLU70 2.8 74.6 1.0 OD1 b:ASP97 2.8 80.1 1.0 CG b:ASP97 2.9 78.4 1.0 PG b:GTP501 3.0 36.9 1.0 O2G b:GTP501 3.1 43.6 1.0 HG2 b:GLU70 3.3 68.1 1.0 OE1 b:GLU70 3.5 68.0 1.0 HZ1 B:LYS252 3.5 70.0 1.0 PB b:GTP501 3.5 25.8 1.0 O3B b:GTP501 3.6 26.6 1.0 CG b:GLU70 3.6 75.3 1.0 HB2 b:GLN11 3.9 56.9 1.0 H b:GLN11 4.2 56.9 1.0 O3A b:GTP501 4.2 28.8 1.0 HG3 b:GLU70 4.2 68.4 1.0 HG1 b:THR144 4.2 64.3 1.0 OD1 b:ASP68 4.3 72.1 1.0 O3G b:GTP501 4.3 31.5 1.0 NZ B:LYS252 4.3 74.4 1.0 CB b:ASP97 4.3 73.2 1.0 HZ3 B:LYS252 4.4 69.5 1.0 HB b:THR144 4.4 63.6 1.0 HB2 b:ASP97 4.5 72.0 1.0 HB3 b:GLU70 4.6 66.9 1.0 HB3 b:GLN11 4.6 55.9 1.0 H b:ALA98 4.6 62.4 1.0 OD2 b:ASP68 4.6 66.8 1.0 OG1 b:THR144 4.6 70.8 1.0 OE1 b:GLN11 4.6 60.0 1.0 CB b:GLN11 4.7 50.9 1.0 CB b:GLU70 4.8 66.8 1.0 H b:THR144 4.8 62.2 1.0 HZ2 B:LYS252 4.8 70.3 1.0 O2B b:GTP501 4.8 33.4 1.0 HB3 b:ASP97 4.8 72.1 1.0 CG b:ASP68 4.9 69.4 1.0 N b:GLN11 4.9 53.5 1.0

Magnesium binding site 3 out of 6 in the Xenopus Borealis Undecorated Microtubule - 15 Protofilament, 3-Start Helix


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Xenopus Borealis Undecorated Microtubule - 15 Protofilament, 3-Start Helix within 5.0Å range: probe atom residue distance (Å) B Occ c:Mg502 b:44.2 occ:1.00 OE2 c:GLU70 1.9 71.1 1.0 O1G c:GTP501 2.0 39.3 1.0 OD2 c:ASP97 2.4 78.6 1.0 O1B c:GTP501 2.5 29.9 1.0 CD c:GLU70 2.8 74.6 1.0 OD1 c:ASP97 2.8 80.1 1.0 CG c:ASP97 2.9 78.4 1.0 PG c:GTP501 3.0 36.9 1.0 O2G c:GTP501 3.1 43.6 1.0 HG2 c:GLU70 3.3 68.1 1.0 OE1 c:GLU70 3.5 68.0 1.0 HZ1 C:LYS252 3.5 70.0 1.0 PB c:GTP501 3.5 25.8 1.0 O3B c:GTP501 3.6 26.6 1.0 CG c:GLU70 3.6 75.3 1.0 HB2 c:GLN11 3.9 56.9 1.0 H c:GLN11 4.2 56.9 1.0 O3A c:GTP501 4.2 28.8 1.0 HG3 c:GLU70 4.2 68.4 1.0 HG1 c:THR144 4.2 64.3 1.0 OD1 c:ASP68 4.3 72.1 1.0 O3G c:GTP501 4.3 31.5 1.0 CB c:ASP97 4.3 73.2 1.0 NZ C:LYS252 4.3 74.4 1.0 HZ3 C:LYS252 4.4 69.5 1.0 HB c:THR144 4.4 63.6 1.0 HB2 c:ASP97 4.5 72.0 1.0 HB3 c:GLU70 4.6 66.9 1.0 HB3 c:GLN11 4.6 55.9 1.0 H c:ALA98 4.6 62.4 1.0 OD2 c:ASP68 4.6 66.8 1.0 OG1 c:THR144 4.6 70.8 1.0 OE1 c:GLN11 4.6 60.0 1.0 CB c:GLN11 4.7 50.9 1.0 CB c:GLU70 4.8 66.8 1.0 HZ2 C:LYS252 4.8 70.3 1.0 H c:THR144 4.8 62.2 1.0 O2B c:GTP501 4.8 33.4 1.0 HB3 c:ASP97 4.8 72.1 1.0 CG c:ASP68 4.9 69.4 1.0 N c:GLN11 4.9 53.5 1.0

Magnesium binding site 4 out of 6 in the Xenopus Borealis Undecorated Microtubule - 15 Protofilament, 3-Start Helix


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Xenopus Borealis Undecorated Microtubule - 15 Protofilament, 3-Start Helix within 5.0Å range: probe atom residue distance (Å) B Occ d:Mg502 b:44.2 occ:1.00 OE2 d:GLU70 1.9 71.1 1.0 O1G d:GTP501 2.0 39.3 1.0 OD2 d:ASP97 2.4 78.6 1.0 O1B d:GTP501 2.5 29.9 1.0 CD d:GLU70 2.8 74.6 1.0 OD1 d:ASP97 2.8 80.1 1.0 CG d:ASP97 2.9 78.4 1.0 PG d:GTP501 3.0 36.9 1.0 O2G d:GTP501 3.1 43.6 1.0 HG2 d:GLU70 3.3 68.1 1.0 OE1 d:GLU70 3.5 68.0 1.0 HZ1 D:LYS252 3.5 70.0 1.0 PB d:GTP501 3.5 25.8 1.0 O3B d:GTP501 3.6 26.6 1.0 CG d:GLU70 3.6 75.3 1.0 HB2 d:GLN11 3.9 56.9 1.0 H d:GLN11 4.2 56.9 1.0 O3A d:GTP501 4.2 28.8 1.0 HG3 d:GLU70 4.2 68.4 1.0 HG1 d:THR144 4.2 64.3 1.0 OD1 d:ASP68 4.3 72.1 1.0 O3G d:GTP501 4.3 31.5 1.0 NZ D:LYS252 4.3 74.4 1.0 CB d:ASP97 4.3 73.2 1.0 HZ3 D:LYS252 4.4 69.5 1.0 HB d:THR144 4.4 63.6 1.0 HB2 d:ASP97 4.5 72.0 1.0 HB3 d:GLU70 4.6 66.9 1.0 H d:ALA98 4.6 62.4 1.0 HB3 d:GLN11 4.6 55.9 1.0 OD2 d:ASP68 4.6 66.8 1.0 OG1 d:THR144 4.6 70.8 1.0 OE1 d:GLN11 4.6 60.0 1.0 CB d:GLN11 4.7 50.9 1.0 CB d:GLU70 4.8 66.8 1.0 H d:THR144 4.8 62.2 1.0 HZ2 D:LYS252 4.8 70.3 1.0 O2B d:GTP501 4.8 33.4 1.0 HB3 d:ASP97 4.8 72.1 1.0 CG d:ASP68 4.9 69.4 1.0 N d:GLN11 4.9 53.5 1.0

Magnesium binding site 5 out of 6 in the Xenopus Borealis Undecorated Microtubule - 15 Protofilament, 3-Start Helix


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Xenopus Borealis Undecorated Microtubule - 15 Protofilament, 3-Start Helix within 5.0Å range: probe atom residue distance (Å) B Occ e:Mg501 b:44.2 occ:1.00 OE2 e:GLU70 1.9 71.1 1.0 O1G e:GTP502 2.0 39.3 1.0 OD2 e:ASP97 2.4 78.6 1.0 O1B e:GTP502 2.5 29.9 1.0 CD e:GLU70 2.8 74.6 1.0 OD1 e:ASP97 2.8 80.1 1.0 CG e:ASP97 2.9 78.4 1.0 PG e:GTP502 3.0 36.9 1.0 O2G e:GTP502 3.1 43.6 1.0 HG2 e:GLU70 3.3 68.1 1.0 OE1 e:GLU70 3.5 68.0 1.0 HZ1 E:LYS252 3.5 70.0 1.0 PB e:GTP502 3.5 25.8 1.0 O3B e:GTP502 3.6 26.6 1.0 CG e:GLU70 3.6 75.3 1.0 HB2 e:GLN11 3.9 56.9 1.0 H e:GLN11 4.2 56.9 1.0 O3A e:GTP502 4.2 28.8 1.0 HG3 e:GLU70 4.2 68.4 1.0 HG1 e:THR144 4.2 64.3 1.0 OD1 e:ASP68 4.3 72.1 1.0 O3G e:GTP502 4.3 31.5 1.0 NZ E:LYS252 4.3 74.4 1.0 CB e:ASP97 4.3 73.2 1.0 HZ3 E:LYS252 4.4 69.5 1.0 HB e:THR144 4.4 63.6 1.0 HB2 e:ASP97 4.5 72.0 1.0 HB3 e:GLU70 4.6 66.9 1.0 HB3 e:GLN11 4.6 55.9 1.0 H e:ALA98 4.6 62.4 1.0 OD2 e:ASP68 4.6 66.8 1.0 OG1 e:THR144 4.6 70.8 1.0 OE1 e:GLN11 4.6 60.0 1.0 CB e:GLN11 4.7 50.9 1.0 CB e:GLU70 4.8 66.8 1.0 H e:THR144 4.8 62.2 1.0 HZ2 E:LYS252 4.8 70.3 1.0 O2B e:GTP502 4.8 33.4 1.0 HB3 e:ASP97 4.8 72.1 1.0 CG e:ASP68 4.9 69.4 1.0 N e:GLN11 4.9 53.5 1.0

Magnesium binding site 6 out of 6 in the Xenopus Borealis Undecorated Microtubule - 15 Protofilament, 3-Start Helix


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Xenopus Borealis Undecorated Microtubule - 15 Protofilament, 3-Start Helix within 5.0Å range: probe atom residue distance (Å) B Occ f:Mg502 b:44.2 occ:1.00 OE2 f:GLU70 1.9 71.1 1.0 O1G f:GTP501 2.0 39.3 1.0 OD2 f:ASP97 2.4 78.6 1.0 O1B f:GTP501 2.5 29.9 1.0 CD f:GLU70 2.8 74.6 1.0 OD1 f:ASP97 2.8 80.1 1.0 CG f:ASP97 2.9 78.4 1.0 PG f:GTP501 3.0 36.9 1.0 O2G f:GTP501 3.1 43.6 1.0 HG2 f:GLU70 3.3 68.1 1.0 OE1 f:GLU70 3.5 68.0 1.0 HZ1 F:LYS252 3.5 70.0 1.0 PB f:GTP501 3.5 25.8 1.0 O3B f:GTP501 3.6 26.6 1.0 CG f:GLU70 3.6 75.3 1.0 HB2 f:GLN11 3.9 56.9 1.0 H f:GLN11 4.2 56.9 1.0 O3A f:GTP501 4.2 28.8 1.0 HG3 f:GLU70 4.2 68.4 1.0 HG1 f:THR144 4.2 64.3 1.0 OD1 f:ASP68 4.3 72.1 1.0 O3G f:GTP501 4.3 31.5 1.0 NZ F:LYS252 4.3 74.4 1.0 CB f:ASP97 4.3 73.2 1.0 HZ3 F:LYS252 4.4 69.5 1.0 HB f:THR144 4.4 63.6 1.0 HB2 f:ASP97 4.5 72.0 1.0 HB3 f:GLU70 4.6 66.9 1.0 HB3 f:GLN11 4.6 55.9 1.0 H f:ALA98 4.6 62.4 1.0 OD2 f:ASP68 4.6 66.8 1.0 OG1 f:THR144 4.6 70.8 1.0 OE1 f:GLN11 4.6 60.0 1.0 CB f:GLN11 4.7 50.9 1.0 CB f:GLU70 4.8 66.8 1.0 HZ2 F:LYS252 4.8 70.3 1.0 H f:THR144 4.8 62.2 1.0 O2B f:GTP501 4.8 33.4 1.0 HB3 f:ASP97 4.8 72.1 1.0 CG f:ASP68 4.9 69.4 1.0 N f:GLN11 4.9 53.5 1.0

L.A.Troman, E.De Gaulejac, C.A.Moores, S.Reber. Mechanistic Basis of Temperature Adaptation in Microtubule Dynamics Across Frog Species Current Biology V. 35 1 2025.
DOI: 10.1016/J.CUB.2024.12.022