Magnesium in PDB 6rfd: Cryo-Em Structure of the N-Terminal Dc Repeat (Ndc) of Ndc-Ndc Chimera (Human Sequence) Bound to 14-Protofilament Gdp-Microtubule

The binding sites of Magnesium atom in the Cryo-Em Structure of the N-Terminal Dc Repeat (Ndc) of Ndc-Ndc Chimera (Human Sequence) Bound to 14-Protofilament Gdp-Microtubule (pdb code 6rfd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of the N-Terminal Dc Repeat (Ndc) of Ndc-Ndc Chimera (Human Sequence) Bound to 14-Protofilament Gdp-Microtubule, PDB code: 6rfd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of the N-Terminal Dc Repeat (Ndc) of Ndc-Ndc Chimera (Human Sequence) Bound to 14-Protofilament Gdp-Microtubule


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 the N-Terminal Dc Repeat (Ndc) of Ndc-Ndc Chimera (Human Sequence) Bound to 14-Protofilament Gdp-Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:0.8 occ:1.00 O1B A:GTP501 2.1 0.7 1.0 O2G A:GTP501 2.1 0.7 1.0 O1A A:GTP501 2.1 0.7 1.0 PA A:GTP501 2.4 0.7 1.0 O3A A:GTP501 2.5 0.7 1.0 PB A:GTP501 2.5 0.7 1.0 O2A A:GTP501 2.5 0.7 1.0 CB A:GLN11 2.7 0.4 1.0 N A:GLN11 2.8 0.4 1.0 O3B A:GTP501 2.9 0.7 1.0 PG A:GTP501 3.1 0.7 1.0 CA A:GLN11 3.3 0.4 1.0 OE1 A:GLN11 3.6 0.4 1.0 O3G A:GTP501 3.8 0.7 1.0 C A:GLY10 3.9 0.2 1.0 O2B A:GTP501 4.0 0.7 1.0 O5' A:GTP501 4.0 0.7 1.0 CG A:GLN11 4.0 0.4 1.0 CA A:GLY10 4.2 0.2 1.0 O1G A:GTP501 4.3 0.7 1.0 CD A:GLN11 4.3 0.4 1.0 C A:GLN11 4.4 0.4 1.0 OE2 A:GLU71 4.4 0.7 1.0 N A:ALA12 4.4 0.3 1.0 OD1 A:ASP69 4.8 0.3 1.0 C5' A:GTP501 4.9 0.7 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of the N-Terminal Dc Repeat (Ndc) of Ndc-Ndc Chimera (Human Sequence) Bound to 14-Protofilament Gdp-Microtubule


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 the N-Terminal Dc Repeat (Ndc) of Ndc-Ndc Chimera (Human Sequence) Bound to 14-Protofilament Gdp-Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg502 b:0.4 occ:1.00 O1B a:GTP501 2.1 0.3 1.0 O2G a:GTP501 2.1 0.3 1.0 O1A a:GTP501 2.1 0.3 1.0 PA a:GTP501 2.4 0.3 1.0 O3A a:GTP501 2.5 0.3 1.0 PB a:GTP501 2.5 0.3 1.0 O2A a:GTP501 2.5 0.3 1.0 CB a:GLN11 2.7 0.3 1.0 N a:GLN11 2.8 0.3 1.0 O3B a:GTP501 2.9 0.3 1.0 PG a:GTP501 3.1 0.3 1.0 CA a:GLN11 3.3 0.3 1.0 OE1 a:GLN11 3.6 0.3 1.0 O3G a:GTP501 3.8 0.3 1.0 C a:GLY10 3.9 0.4 1.0 O2B a:GTP501 4.0 0.3 1.0 O5' a:GTP501 4.0 0.3 1.0 CG a:GLN11 4.0 0.3 1.0 CA a:GLY10 4.2 0.4 1.0 O1G a:GTP501 4.3 0.3 1.0 CD a:GLN11 4.3 0.3 1.0 C a:GLN11 4.4 0.3 1.0 OE2 a:GLU71 4.4 1.0 1.0 N a:ALA12 4.4 0.5 1.0 OD1 a:ASP69 4.8 0.1 1.0 C5' a:GTP501 4.9 0.3 1.0

S.W.Manka, C.A.Moores. Tbc To Be Published.