Calcium in PDB 6rvd: Revised Cryo-Em Structure of the Human 2:1 PTCH1-Shh Complex

The structure of Revised Cryo-Em Structure of the Human 2:1 PTCH1-Shh Complex also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Revised Cryo-Em Structure of the Human 2:1 PTCH1-Shh Complex (pdb code 6rvd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Revised Cryo-Em Structure of the Human 2:1 PTCH1-Shh Complex, PDB code: 6rvd:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Revised Cryo-Em Structure of the Human 2:1 PTCH1-Shh Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Revised Cryo-Em Structure of the Human 2:1 PTCH1-Shh Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca204 b:97.7 occ:1.00 OD1 C:ASP129 2.2 0.1 1.0 OE2 C:GLU90 2.2 95.9 1.0 OE1 C:GLU126 2.3 91.5 1.0 OD2 C:ASP131 2.5 0.5 1.0 OE2 C:GLU126 2.8 91.5 1.0 CD C:GLU126 2.9 91.5 1.0 CG C:ASP129 3.1 0.1 1.0 CD C:GLU90 3.4 95.9 1.0 CG C:ASP131 3.7 0.5 1.0 CB C:ASP129 3.7 0.1 1.0 CA C:ASP129 3.9 0.1 1.0 CA C:CA205 4.0 0.2 1.0 OD2 C:ASP129 4.1 0.1 1.0 CG C:GLU90 4.2 95.9 1.0 OE2 C:GLU89 4.2 95.8 1.0 OE1 C:GLU90 4.2 95.9 1.0 CB C:ASP131 4.3 0.5 1.0 OD1 C:ASP95 4.3 95.2 1.0 O C:TRP128 4.4 99.7 1.0 CG C:GLU126 4.4 91.5 1.0 N C:GLU130 4.6 0.5 1.0 OD1 C:ASP131 4.7 0.5 1.0 N C:ASP131 4.7 0.5 1.0 ND1 C:HIS133 4.8 94.5 1.0 C C:ASP129 4.8 0.1 1.0 N C:ASP129 5.0 0.1 1.0

Calcium binding site 2 out of 2 in the Revised Cryo-Em Structure of the Human 2:1 PTCH1-Shh Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Revised Cryo-Em Structure of the Human 2:1 PTCH1-Shh Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca205 b:0.2 occ:1.00 OD2 C:ASP95 2.1 95.2 1.0 OE2 C:GLU126 2.2 91.5 1.0 OE2 C:GLU89 2.2 95.8 1.0 OE1 C:GLU89 2.2 95.8 1.0 OD1 C:ASP95 2.4 95.2 1.0 CD C:GLU89 2.5 95.8 1.0 OE1 C:GLU90 2.5 95.9 1.0 CG C:ASP95 2.5 95.2 1.0 O C:THR125 2.5 86.0 1.0 OE2 C:GLU90 2.9 95.9 1.0 CD C:GLU90 3.1 95.9 1.0 CD C:GLU126 3.3 91.5 1.0 C C:THR125 3.7 86.0 1.0 CG C:GLU89 3.9 95.8 1.0 CA C:GLU126 4.0 91.5 1.0 CB C:ASP95 4.0 95.2 1.0 CA C:CA204 4.0 97.7 1.0 CG C:GLU126 4.1 91.5 1.0 OE1 C:GLU126 4.2 91.5 1.0 N C:GLU89 4.3 95.8 1.0 N C:GLU126 4.3 91.5 1.0 N C:ASP88 4.6 95.2 1.0 CG C:GLU90 4.6 95.9 1.0 CB C:GLU126 4.6 91.5 1.0 CA C:ASP88 4.7 95.2 1.0 CB C:GLU89 4.8 95.8 1.0 CA C:THR125 4.9 86.0 1.0 N C:GLU90 4.9 95.9 1.0 CA C:ASP95 4.9 95.2 1.0 C C:ASP88 4.9 95.2 1.0

A.F.Rudolf, M.Kinnebrew, C.Kowatsch, T.B.Ansell, K.El Omari, B.Bishop, E.Pardon, R.A.Schwab, T.Malinauskas, M.Qian, R.Duman, D.F.Covey, J.Steyaert, A.Wagner, M.S.P.Sansom, R.Rohatgi, C.Siebold. The Morphogen Sonic Hedgehog Inhibits Its Receptor Patched By A Pincer Grasp Mechanism. Nat.Chem.Biol. V. 15 975 2019.
ISSN: ESSN 1552-4469
PubMed: 31548691
DOI: 10.1038/S41589-019-0370-Y