Zinc in PDB 8v3o: CCP5 in Complex with Glu-P-Peptide 1 Transition State Analog

All present enzymatic activity of CCP5 in Complex with Glu-P-Peptide 1 Transition State Analog:
3.4.17.24;

The structure of CCP5 in Complex with Glu-P-Peptide 1 Transition State Analog, PDB code: 8v3o was solved by J.Chen, E.A.Zehr, J.M.Gruschus, A.Szyk, Y.Liu, M.E.Tanner, N.Tjandra, A.Roll-Mecak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.55 / 2.30
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.429, 81.372, 104, 90, 90, 90
R / Rfree (%)	20.3 / 22.7

The structure of CCP5 in Complex with Glu-P-Peptide 1 Transition State Analog also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Zinc atom in the CCP5 in Complex with Glu-P-Peptide 1 Transition State Analog (pdb code 8v3o). 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 Glu-P-Peptide 1 Transition State Analog, PDB code: 8v3o:

Zinc binding site 1 out of 1 in the CCP5 in Complex with Glu-P-Peptide 1 Transition State Analog


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 Glu-P-Peptide 1 Transition State Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:33.1 occ:1.00 OE1 A:GLU255 2.0 32.9 1.0 O6 I:BIX10 2.0 46.4 1.0 ND1 A:HIS434 2.3 36.5 1.0 ND1 A:HIS252 2.3 35.9 1.0 OE2 A:GLU255 2.5 43.6 1.0 CD A:GLU255 2.5 35.7 1.0 P6 I:BIX10 3.0 37.5 1.0 O61 I:BIX10 3.1 39.3 1.0 CG A:HIS434 3.1 31.6 1.0 CE1 A:HIS252 3.1 36.5 1.0 CB A:HIS434 3.2 30.6 1.0 CE1 A:HIS434 3.4 30.3 1.0 CG A:HIS252 3.4 32.9 1.0 CB A:HIS252 3.8 33.0 1.0 CG A:GLU255 4.0 31.1 1.0 O A:HOH916 4.0 31.4 1.0 C5 I:BIX10 4.0 40.0 1.0 O A:GLY435 4.0 44.1 1.0 CA A:HIS434 4.1 31.9 1.0 NH1 A:ARG303 4.2 41.1 1.0 N A:GLY435 4.2 37.2 1.0 NE2 A:HIS252 4.3 37.8 1.0 CD2 A:HIS434 4.3 31.8 1.0 NE2 A:HIS434 4.4 33.0 1.0 CD2 A:HIS252 4.5 36.0 1.0 C1 I:BIX10 4.5 45.9 1.0 CA I:BIX10 4.6 41.0 1.0 OC I:BIX10 4.6 38.8 1.0 C A:HIS434 4.7 34.0 1.0 CB A:GLU255 4.7 30.1 1.0 CG1 A:VAL251 4.9 31.3 1.0 C I:BIX10 5.0 44.1 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