Calcium in PDB 6n7k: Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II)

Other elements in 6n7k:

The structure of Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II) (pdb code 6n7k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II), PDB code: 6n7k:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6n7k

Go back to Calcium Binding Sites List in 6n7k
Calcium binding site 1 out of 4 in the Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca203

b:18.7
occ:1.00
OE2 C:GLU90 2.7 15.6 1.0
CB C:ASP129 2.9 9.0 1.0
CA C:ASP129 3.2 10.8 1.0
CD C:GLU90 3.6 17.6 1.0
OD2 C:ASP129 3.7 16.0 1.0
CG C:ASP129 3.8 11.7 1.0
OE2 C:GLU89 3.9 19.8 1.0
OE1 C:GLU90 4.0 14.5 1.0
CA C:CA204 4.0 12.0 1.0
N C:ASP129 4.1 10.1 1.0
C C:ASP129 4.3 12.8 1.0
NE2 C:HIS134 4.4 15.4 1.0
ND1 C:HIS133 4.4 37.2 1.0
N C:GLU130 4.5 14.0 1.0
OD1 C:ASP95 4.5 10.8 1.0
O C:TRP128 4.7 12.0 1.0
CE1 C:HIS133 4.7 42.2 1.0
C C:TRP128 4.8 11.7 1.0
CG C:GLU90 4.8 16.4 1.0
CD C:GLU89 4.9 20.4 1.0
CG C:GLU126 4.9 20.1 1.0
OD1 C:ASP129 5.0 15.6 1.0
CB C:GLU126 5.0 13.9 1.0

Calcium binding site 2 out of 4 in 6n7k

Go back to Calcium Binding Sites List in 6n7k
Calcium binding site 2 out of 4 in the Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca204

b:12.0
occ:1.00
OE2 C:GLU89 2.4 19.8 1.0
O C:THR125 2.5 11.9 1.0
OD1 C:ASP95 2.5 10.8 1.0
OD2 C:ASP95 2.5 13.6 1.0
OE1 C:GLU89 2.5 19.2 1.0
CG C:ASP95 2.8 12.1 1.0
CD C:GLU89 2.8 20.4 1.0
CG C:GLU126 3.0 20.1 1.0
CA C:GLU126 3.0 9.9 1.0
CB C:GLU126 3.4 13.9 1.0
C C:THR125 3.4 10.1 1.0
N C:GLU126 3.6 8.3 1.0
OE1 C:GLU90 3.9 14.5 1.0
CA C:CA203 4.0 18.7 1.0
C C:GLU126 4.2 12.5 1.0
N C:GLY127 4.2 7.7 1.0
CB C:ASP95 4.2 9.0 1.0
OE2 C:GLU90 4.3 15.6 1.0
CD C:GLU126 4.3 20.4 1.0
CG C:GLU89 4.3 17.4 1.0
CD C:GLU90 4.5 17.6 1.0
OE2 C:GLU126 4.7 18.1 1.0
CA C:THR125 4.7 9.0 1.0
N C:GLU89 4.9 18.5 1.0

Calcium binding site 3 out of 4 in 6n7k

Go back to Calcium Binding Sites List in 6n7k
Calcium binding site 3 out of 4 in the Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca203

b:18.7
occ:1.00
OE2 F:GLU90 2.7 15.6 1.0
CB F:ASP129 2.9 9.0 1.0
CA F:ASP129 3.2 10.8 1.0
CD F:GLU90 3.6 17.6 1.0
OD2 F:ASP129 3.7 16.0 1.0
CG F:ASP129 3.8 11.7 1.0
OE2 F:GLU89 3.9 19.8 1.0
OE1 F:GLU90 4.0 14.5 1.0
CA F:CA204 4.0 12.0 1.0
N F:ASP129 4.1 10.1 1.0
C F:ASP129 4.3 12.8 1.0
NE2 F:HIS134 4.4 15.4 1.0
ND1 F:HIS133 4.4 37.2 1.0
N F:GLU130 4.5 14.0 1.0
OD1 F:ASP95 4.5 10.8 1.0
O F:TRP128 4.7 12.0 1.0
CE1 F:HIS133 4.7 42.2 1.0
C F:TRP128 4.8 11.7 1.0
CG F:GLU90 4.8 16.4 1.0
CD F:GLU89 4.9 20.4 1.0
CG F:GLU126 4.9 20.1 1.0
OD1 F:ASP129 5.0 15.6 1.0
CB F:GLU126 5.0 13.9 1.0

Calcium binding site 4 out of 4 in 6n7k

Go back to Calcium Binding Sites List in 6n7k
Calcium binding site 4 out of 4 in the Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca204

b:12.0
occ:1.00
OE2 F:GLU89 2.4 19.8 1.0
O F:THR125 2.5 11.9 1.0
OD1 F:ASP95 2.5 10.8 1.0
OD2 F:ASP95 2.5 13.6 1.0
OE1 F:GLU89 2.5 19.2 1.0
CG F:ASP95 2.8 12.1 1.0
CD F:GLU89 2.8 20.4 1.0
CG F:GLU126 3.0 20.1 1.0
CA F:GLU126 3.0 9.9 1.0
CB F:GLU126 3.4 13.9 1.0
C F:THR125 3.4 10.1 1.0
N F:GLU126 3.6 8.3 1.0
OE1 F:GLU90 3.9 14.5 1.0
CA F:CA203 4.0 18.7 1.0
C F:GLU126 4.2 12.5 1.0
N F:GLY127 4.2 7.7 1.0
CB F:ASP95 4.2 9.0 1.0
OE2 F:GLU90 4.3 15.6 1.0
CD F:GLU126 4.3 20.4 1.0
CG F:GLU89 4.3 17.4 1.0
CD F:GLU90 4.5 17.6 1.0
OE2 F:GLU126 4.7 18.1 1.0
CA F:THR125 4.7 9.0 1.0
N F:GLU89 4.9 18.5 1.0

Reference:

N.Yan, X.Gong, H.W.Qian. Cryo-Em Structure of the 2:1 HPTCH1-Shhp Complex To Be Published.
Page generated: Sat Dec 12 07:22:38 2020

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