Calcium in PDB 7rpk: Cryo-Em Structure of Murine Dispatched in Complex with Sonic Hedgehog

Other elements in 7rpk:

The structure of Cryo-Em Structure of Murine Dispatched in Complex with Sonic Hedgehog also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of Murine Dispatched in Complex with Sonic Hedgehog (pdb code 7rpk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cryo-Em Structure of Murine Dispatched in Complex with Sonic Hedgehog, PDB code: 7rpk:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7rpk

Go back to Calcium Binding Sites List in 7rpk
Calcium binding site 1 out of 2 in the Cryo-Em Structure of Murine Dispatched in Complex with Sonic Hedgehog


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 Murine Dispatched in Complex with Sonic Hedgehog within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca201

b:103.4
occ:1.00
OE2 H:GLU90 2.3 109.3 1.0
OE2 H:GLU127 2.3 100.1 1.0
OE2 H:GLU91 2.3 108.0 1.0
OD2 H:ASP96 2.3 97.0 1.0
OD1 H:ASP96 2.4 97.0 1.0
OE1 H:GLU91 2.6 108.0 1.0
O H:THR126 2.6 103.7 1.0
CG H:ASP96 2.7 97.0 1.0
CD H:GLU91 2.8 108.0 1.0
CD H:GLU90 2.9 109.3 1.0
OE1 H:GLU90 2.9 109.3 1.0
O H:LYS88 3.3 108.8 1.0
CD H:GLU127 3.4 100.1 1.0
CA H:ASP89 3.5 107.9 1.0
CA H:CA202 3.6 102.1 1.0
N H:GLU90 3.7 109.3 1.0
C H:THR126 3.7 103.7 1.0
C H:ASP89 4.1 107.9 1.0
CA H:GLU127 4.1 100.1 1.0
OE1 H:GLU127 4.1 100.1 1.0
C H:LYS88 4.2 108.8 1.0
OD2 H:ASP89 4.2 107.9 1.0
CB H:ASP96 4.2 97.0 1.0
CG H:GLU91 4.3 108.0 1.0
N H:ASP89 4.3 107.9 1.0
CG H:GLU90 4.3 109.3 1.0
CG H:GLU127 4.3 100.1 1.0
N H:GLU127 4.3 100.1 1.0
CG H:ASP89 4.4 107.9 1.0
CB H:ASP89 4.4 107.9 1.0
N H:GLU91 4.7 108.0 1.0
CA H:GLU90 4.7 109.3 1.0
CA H:THR126 4.8 103.7 1.0
CB H:GLU127 4.8 100.1 1.0
CB H:GLU90 4.8 109.3 1.0

Calcium binding site 2 out of 2 in 7rpk

Go back to Calcium Binding Sites List in 7rpk
Calcium binding site 2 out of 2 in the Cryo-Em Structure of Murine Dispatched in Complex with Sonic Hedgehog


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 Murine Dispatched in Complex with Sonic Hedgehog within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca202

b:102.1
occ:1.00
OD2 H:ASP132 2.3 103.5 1.0
OE1 H:GLU91 2.3 108.0 1.0
OE1 H:GLU127 2.3 100.1 1.0
OE2 H:GLU127 2.4 100.1 1.0
OD1 H:ASP130 2.4 97.8 1.0
OE1 H:GLU90 2.5 109.3 1.0
CD H:GLU127 2.7 100.1 1.0
CD H:GLU91 3.1 108.0 1.0
CG H:ASP132 3.3 103.5 1.0
CD2 H:HIS134 3.3 105.1 1.0
CG H:ASP130 3.3 97.8 1.0
NE2 H:HIS134 3.4 105.1 1.0
CA H:CA201 3.6 103.4 1.0
CG H:GLU91 3.6 108.0 1.0
CD H:GLU90 3.7 109.3 1.0
OD2 H:ASP130 4.0 97.8 1.0
OE2 H:GLU91 4.0 108.0 1.0
OD1 H:ASP132 4.0 103.5 1.0
CB H:ASP132 4.1 103.5 1.0
CG H:GLU127 4.2 100.1 1.0
CB H:ASP130 4.2 97.8 1.0
OE2 H:GLU90 4.3 109.3 1.0
OD1 H:ASP96 4.4 97.0 1.0
CA H:ASP130 4.5 97.8 1.0
CG H:HIS134 4.6 105.1 1.0
CE1 H:HIS134 4.8 105.1 1.0
CG H:GLU90 4.8 109.3 1.0
N H:ASP132 4.8 103.5 1.0
CE1 H:HIS135 5.0 102.6 1.0

Reference:

Q.Wang, D.E.Asarnow, K.Ding, R.Mann, J.Hatekeyama, Y.Zhang, Y.Ma, Y.Cheng, P.A.Beachy. Dispatched Uses Na+ Flux to Power Release of Lipid-Modified Hedgehog Nature 2021.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-021-03996-0
Page generated: Fri Nov 5 11:42:37 2021

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy