Magnesium in PDB 6rf8: Cryo-Em Structure of the N-Terminal Dc Repeat (Ndc) of Ndc-Ndc Chimera (Human Sequence) Bound to 13-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 13-Protofilament Gdp-Microtubule (pdb code 6rf8). 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 13-Protofilament Gdp-Microtubule, PDB code: 6rf8:
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 13-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 13-Protofilament Gdp-Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:78.2 occ:1.00 O2G A:GTP501 2.1 71.0 1.0 O1A A:GTP501 2.1 71.0 1.0 O1B A:GTP501 2.1 71.0 1.0 PA A:GTP501 2.4 71.0 1.0 PB A:GTP501 2.5 71.0 1.0 O3A A:GTP501 2.5 71.0 1.0 O2A A:GTP501 2.6 71.0 1.0 O3B A:GTP501 2.7 71.0 1.0 PG A:GTP501 2.9 71.0 1.0 N A:GLN11 3.2 65.0 1.0 CB A:GLN11 3.2 65.0 1.0 O1G A:GTP501 3.8 71.0 1.0 CA A:GLN11 3.8 65.0 1.0 O2B A:GTP501 3.9 71.0 1.0 OE2 A:GLU71 4.0 72.4 1.0 OE1 A:GLN11 4.0 65.0 1.0 O5' A:GTP501 4.0 71.0 1.0 O3G A:GTP501 4.1 71.0 1.0 C A:GLY10 4.2 64.3 1.0 CA A:GLY10 4.3 64.3 1.0 CG A:GLN11 4.5 65.0 1.0 CD A:GLN11 4.7 65.0 1.0 OD1 A:ASP69 4.7 69.7 1.0 CD A:GLU71 4.9 72.4 1.0 C5' A:GTP501 4.9 71.0 1.0 OG1 A:THR145 4.9 69.0 1.0 C A:GLN11 4.9 65.0 1.0 CB A:THR145 4.9 69.0 1.0 N A:ALA12 5.0 62.7 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 13-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 13-Protofilament Gdp-Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg502 b:81.0 occ:1.00 O2G a:GTP501 2.1 74.5 1.0 O1A a:GTP501 2.1 74.5 1.0 O1B a:GTP501 2.1 74.5 1.0 PA a:GTP501 2.4 74.5 1.0 PB a:GTP501 2.5 74.5 1.0 O3A a:GTP501 2.5 74.5 1.0 O2A a:GTP501 2.6 74.5 1.0 O3B a:GTP501 2.7 74.5 1.0 PG a:GTP501 2.9 74.5 1.0 N a:GLN11 3.2 69.8 1.0 CB a:GLN11 3.2 69.8 1.0 O1G a:GTP501 3.8 74.5 1.0 CA a:GLN11 3.8 69.8 1.0 O2B a:GTP501 3.9 74.5 1.0 OE2 a:GLU71 4.0 77.3 1.0 OE1 a:GLN11 4.0 69.8 1.0 O5' a:GTP501 4.0 74.5 1.0 O3G a:GTP501 4.1 74.5 1.0 C a:GLY10 4.2 67.9 1.0 CA a:GLY10 4.3 67.9 1.0 CG a:GLN11 4.5 69.8 1.0 CD a:GLN11 4.7 69.8 1.0 OD1 a:ASP69 4.7 74.4 1.0 CD a:GLU71 4.9 77.3 1.0 C5' a:GTP501 4.9 74.5 1.0 OG1 a:THR145 4.9 74.0 1.0 C a:GLN11 4.9 69.8 1.0 CB a:THR145 4.9 74.0 1.0 N a:ALA12 5.0 67.0 1.0

A.D.Cook, S.W.Manka, S.Wang, C.A.Moores, J.Atherton. A Microtubule Relion-Based Pipeline For Cryo-Em Image Processing. J.Struct.Biol. V. 209 07402 2020.
ISSN: ESSN 1095-8657
PubMed: 31610239
DOI: 10.1016/J.JSB.2019.10.004