Magnesium in PDB 8v4k: CCP5 in Complex with Microtubules CLASS1

The structure of CCP5 in Complex with Microtubules CLASS1 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the CCP5 in Complex with Microtubules CLASS1 (pdb code 8v4k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the CCP5 in Complex with Microtubules CLASS1, PDB code: 8v4k:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the CCP5 in Complex with Microtubules CLASS1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of CCP5 in Complex with Microtubules CLASS1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:83.7 occ:1.00 O2B A:GTP502 2.3 98.8 1.0 O3G A:GTP502 2.4 99.7 1.0 OE2 A:GLU71 3.2 116.4 1.0 PG A:GTP502 3.5 101.4 1.0 PB A:GTP502 3.5 100.6 1.0 O3B A:GTP502 3.7 101.9 1.0 OD2 A:ASP69 3.7 108.0 1.0 CD A:GLU71 3.8 116.7 1.0 O2G A:GTP502 3.8 98.2 1.0 CG A:GLU71 3.9 113.1 1.0 OD1 A:ASP69 4.0 110.2 1.0 OE1 A:GLN11 4.0 105.4 1.0 O3A A:GTP502 4.1 93.5 1.0 CB A:GLN11 4.1 89.5 1.0 CG A:ASP69 4.3 108.6 1.0 O2A A:GTP502 4.4 92.3 1.0 N A:GLN11 4.5 86.6 1.0 NZ B:LYS252 4.6 94.1 1.0 CB A:ASP98 4.7 114.0 1.0 OE1 A:GLU71 4.8 115.8 1.0 O1B A:GTP502 4.8 100.3 1.0 O1G A:GTP502 4.8 101.8 1.0 OD2 A:ASP98 4.8 120.3 1.0 CA A:GLN11 4.9 89.6 1.0 PA A:GTP502 4.9 91.2 1.0

Magnesium binding site 2 out of 4 in the CCP5 in Complex with Microtubules CLASS1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of CCP5 in Complex with Microtubules CLASS1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:98.6 occ:1.00 O2G B:G2P502 2.3 111.6 1.0 OE2 B:GLU69 2.6 135.3 1.0 PG B:G2P502 3.1 113.8 1.0 O3B B:G2P502 3.2 107.6 1.0 O1G B:G2P502 3.4 109.2 1.0 CD B:GLU69 3.4 134.7 1.0 O2B B:G2P502 3.5 100.5 1.0 O2A B:G2P502 3.5 106.7 1.0 PB B:G2P502 4.0 110.2 1.0 OE1 B:GLN11 4.0 116.6 1.0 OE1 B:GLU69 4.1 140.6 1.0 CB B:GLN11 4.2 100.6 1.0 CG B:GLU69 4.2 124.1 1.0 OD2 B:ASP67 4.3 114.5 1.0 OD1 B:ASP67 4.5 115.0 1.0 O3G B:G2P502 4.6 108.1 1.0 N B:GLN11 4.7 96.1 1.0 PA B:G2P502 4.7 102.4 1.0 CG B:ASP67 4.8 112.8 1.0 C3A B:G2P502 5.0 103.7 1.0

Magnesium binding site 3 out of 4 in the CCP5 in Complex with Microtubules CLASS1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of CCP5 in Complex with Microtubules CLASS1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:112.7 occ:1.00 O2B C:GTP502 2.2 105.5 1.0 O2G C:GTP502 2.4 110.8 1.0 O3G C:GTP502 2.6 115.1 1.0 OE2 C:GLU71 2.8 114.1 1.0 PG C:GTP502 2.8 112.3 1.0 PB C:GTP502 3.2 104.7 1.0 O3B C:GTP502 3.3 108.2 1.0 CD C:GLU71 3.4 117.9 1.0 O3A C:GTP502 3.5 106.4 1.0 NZ D:LYS252 3.8 102.0 1.0 OE1 C:GLU71 3.9 114.4 1.0 O2A C:GTP502 4.0 108.0 1.0 CG C:GLU71 4.2 117.5 1.0 O1G C:GTP502 4.3 110.4 1.0 PA C:GTP502 4.4 107.0 1.0 CB C:GLN11 4.4 97.9 1.0 OE1 C:GLN11 4.4 108.5 1.0 OD1 C:ASP69 4.6 109.7 1.0 O1B C:GTP502 4.6 105.3 1.0 OD2 C:ASP69 4.6 109.8 1.0 O D:ASN247 4.7 104.2 1.0 CE D:LYS252 4.7 101.7 1.0 N C:GLN11 4.8 94.4 1.0 OD2 C:ASP98 4.9 123.0 1.0 CB C:ASP98 4.9 117.8 1.0 OG1 C:THR145 5.0 103.9 1.0

Magnesium binding site 4 out of 4 in the CCP5 in Complex with Microtubules CLASS1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of CCP5 in Complex with Microtubules CLASS1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:98.0 occ:1.00 O2G D:G2P502 2.3 109.1 1.0 O2B D:G2P502 3.1 104.5 1.0 O2A D:G2P502 3.3 110.7 1.0 PG D:G2P502 3.4 117.4 1.0 O3B D:G2P502 3.4 114.3 1.0 PB D:G2P502 3.9 112.2 1.0 OE1 D:GLN11 3.9 123.6 1.0 CB D:GLN11 4.0 102.9 1.0 O1G D:G2P502 4.1 116.2 1.0 OE2 D:GLU69 4.2 131.2 1.0 N D:GLN11 4.4 100.2 1.0 PA D:G2P502 4.4 108.5 1.0 OD1 D:ASP67 4.5 115.4 1.0 OD2 D:ASP67 4.5 116.6 1.0 CG D:GLU69 4.6 124.8 1.0 O3G D:G2P502 4.7 111.4 1.0 C3A D:G2P502 4.8 107.1 1.0 O1A D:G2P502 4.8 106.6 1.0 CD D:GLU69 4.8 129.7 1.0 CA D:GLN11 4.9 100.5 1.0 CD D:GLN11 4.9 115.0 1.0 CG D:ASP67 4.9 113.0 1.0

J.Chen, E.A.Zehr, J.M.Gruschus, A.Szyk, Y.Liu, M.E.Tanner, N.Tjandra, A.Roll-Mecak. Tubulin Code Eraser CCP5 Binds Branch Glutamates By Substrate Deformation Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-024-07699-0