Magnesium in PDB 8v4m: CCP5 in Complex with Microtubules CLASS3

The structure of CCP5 in Complex with Microtubules CLASS3 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the CCP5 in Complex with Microtubules CLASS3 (pdb code 8v4m). 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 CLASS3, PDB code: 8v4m:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the CCP5 in Complex with Microtubules CLASS3


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 CLASS3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:79.2 occ:1.00 O2B A:GTP502 2.2 90.6 1.0 O3G A:GTP502 2.5 97.1 1.0 OE2 A:GLU71 2.9 118.6 1.0 CD A:GLU71 3.3 117.0 1.0 PB A:GTP502 3.4 91.6 1.0 PG A:GTP502 3.5 98.2 1.0 O3B A:GTP502 3.7 90.5 1.0 OD2 A:ASP69 3.8 103.1 1.0 CG A:GLU71 3.8 109.8 1.0 O2G A:GTP502 3.9 92.6 1.0 OE1 A:GLU71 3.9 115.2 1.0 OD1 A:ASP69 4.0 104.7 1.0 OE1 A:GLN11 4.0 103.8 1.0 O3A A:GTP502 4.0 88.8 1.0 CB A:GLN11 4.1 85.4 1.0 CG A:ASP69 4.3 102.2 1.0 O2A A:GTP502 4.3 93.1 1.0 N A:GLN11 4.5 81.4 1.0 NZ B:LYS252 4.6 95.0 1.0 CB A:ASP98 4.7 108.1 1.0 O1B A:GTP502 4.7 93.5 1.0 O1G A:GTP502 4.9 98.6 1.0 PA A:GTP502 4.9 91.0 1.0 CA A:GLN11 4.9 85.2 1.0 OD2 A:ASP98 4.9 111.1 1.0 CB A:GLU71 5.0 103.8 1.0

Magnesium binding site 2 out of 4 in the CCP5 in Complex with Microtubules CLASS3


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 CLASS3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:79.5 occ:1.00 O2G B:G2P602 2.4 98.7 1.0 OE2 B:GLU69 2.8 124.5 1.0 O3B B:G2P602 3.0 89.4 1.0 PG B:G2P602 3.1 96.5 1.0 O2B B:G2P602 3.2 86.2 1.0 O2A B:G2P602 3.3 97.4 1.0 O1G B:G2P602 3.4 94.5 1.0 CD B:GLU69 3.6 123.8 1.0 PB B:G2P602 3.7 90.9 1.0 OE1 B:GLN11 4.0 110.4 1.0 CB B:GLN11 4.1 91.7 1.0 OE1 B:GLU69 4.3 128.6 1.0 OD2 B:ASP67 4.4 108.4 1.0 PA B:G2P602 4.4 95.6 1.0 CG B:GLU69 4.4 112.5 1.0 OD1 B:ASP67 4.4 104.6 1.0 N B:GLN11 4.5 88.0 1.0 O3G B:G2P602 4.5 93.0 1.0 C3A B:G2P602 4.7 87.8 1.0 O1A B:G2P602 4.8 92.7 1.0 CG B:ASP67 4.9 103.7 1.0 CA B:GLN11 4.9 90.9 1.0 CD B:GLN11 4.9 100.7 1.0 O1B B:G2P602 5.0 95.0 1.0

Magnesium binding site 3 out of 4 in the CCP5 in Complex with Microtubules CLASS3


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 CLASS3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:104.5 occ:1.00 O2B C:GTP502 2.4 99.7 1.0 OE2 C:GLU71 2.4 115.8 1.0 CD C:GLU71 2.9 121.6 1.0 O2G C:GTP502 2.9 109.1 1.0 O3G C:GTP502 2.9 118.2 1.0 PG C:GTP502 3.4 117.0 1.0 PB C:GTP502 3.5 105.2 1.0 OE1 C:GLU71 3.6 118.8 1.0 CG C:GLU71 3.7 120.4 1.0 O3B C:GTP502 3.7 109.6 1.0 O3A C:GTP502 4.0 109.3 1.0 OD1 C:ASP69 4.1 113.8 1.0 OD2 C:ASP69 4.2 112.1 1.0 NZ D:LYS252 4.4 104.3 1.0 CB C:GLN11 4.4 93.0 1.0 O2A C:GTP502 4.4 101.2 1.0 OE1 C:GLN11 4.5 107.5 1.0 CB C:GLU71 4.5 114.0 1.0 CG C:ASP69 4.6 110.9 1.0 CB C:ASP98 4.7 115.8 1.0 N C:GLN11 4.7 93.3 1.0 O1G C:GTP502 4.8 109.7 1.0 O1B C:GTP502 4.8 105.4 1.0 OG1 C:THR145 4.9 105.1 1.0 O D:ASN247 4.9 112.4 1.0 PA C:GTP502 4.9 104.7 1.0 OD2 C:ASP98 4.9 123.2 1.0

Magnesium binding site 4 out of 4 in the CCP5 in Complex with Microtubules CLASS3


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 CLASS3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:90.3 occ:1.00 O2G D:G2P502 2.5 102.8 1.0 O2B D:G2P502 2.8 98.7 1.0 PG D:G2P502 3.7 108.4 1.0 O3B D:G2P502 3.7 102.8 1.0 PB D:G2P502 3.8 99.0 1.0 CB D:GLN11 3.8 99.4 1.0 OE1 D:GLN11 3.9 114.0 1.0 OE2 D:GLU69 4.0 128.7 1.0 O1A D:G2P502 4.1 107.8 1.0 N D:GLN11 4.2 93.4 1.0 OD1 D:ASP67 4.2 111.0 1.0 OD2 D:ASP67 4.4 115.0 1.0 CG D:GLU69 4.4 115.9 1.0 O1G D:G2P502 4.5 106.8 1.0 O2A D:G2P502 4.5 111.7 1.0 CA D:GLN11 4.6 97.5 1.0 CD D:GLU69 4.7 124.6 1.0 PA D:G2P502 4.7 110.7 1.0 CG D:ASP67 4.8 110.6 1.0 O3G D:G2P502 4.8 106.9 1.0 CD D:GLN11 4.8 107.7 1.0 C3A D:G2P502 4.9 97.6 1.0 CG D:GLN11 4.9 100.0 1.0 O1B D:G2P502 5.0 104.5 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