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

Other elements in 6rvd:

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

Calcium Binding Sites:

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 6rvd

Go back to Calcium Binding Sites List in 6rvd
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 6rvd

Go back to Calcium Binding Sites List in 6rvd
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

Reference:

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
Page generated: Sat Dec 12 07:31:08 2020

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