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

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

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the CCP5 in Complex with Microtubules CLASS3 (pdb code 8v4m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the CCP5 in Complex with Microtubules CLASS3, PDB code: 8v4m:

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of CCP5 in Complex with Microtubules CLASS3 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn701 b:189.7 occ:1.00 OE1 B:GLU503 2.1 173.1 1.0 OE2 E:GLU255 2.2 162.2 1.0 ND1 E:HIS252 2.3 154.2 1.0 ND1 E:HIS434 2.3 158.9 1.0 OE1 E:GLU255 2.4 155.0 1.0 CD E:GLU255 2.6 154.9 1.0 CE1 E:HIS252 2.8 157.8 1.0 CE1 E:HIS434 3.1 159.7 1.0 CD B:GLU503 3.2 169.6 1.0 CG E:HIS434 3.4 152.1 1.0 CG E:HIS252 3.4 146.9 1.0 NH2 E:ARG303 3.5 166.8 1.0 CB E:HIS434 3.8 148.7 1.0 NE2 E:HIS252 4.0 152.9 1.0 N B:GLU1001 4.0 173.7 1.0 CG B:GLU503 4.0 161.8 1.0 CG E:GLU255 4.1 145.9 1.0 CB E:HIS252 4.1 142.9 1.0 CB B:GLU503 4.1 162.9 1.0 CA B:GLU1001 4.1 174.8 1.0 OXT B:GLU1001 4.1 174.9 1.0 CD2 E:HIS252 4.3 148.4 1.0 NE2 E:HIS434 4.3 155.4 1.0 CZ E:ARG303 4.3 160.7 1.0 NH1 E:ARG303 4.4 158.9 1.0 O E:GLY435 4.4 159.0 1.0 CD2 E:HIS434 4.5 152.9 1.0 C B:GLU1001 4.5 175.0 1.0 N E:GLY435 4.7 144.8 1.0 ND2 E:ASN312 4.7 159.6 1.0 CA E:HIS434 4.8 144.7 1.0 CB E:GLU255 4.9 147.2 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