Sodium 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:

Calcium (Ca) 2 atoms
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Cryo-Em Structure of Murine Dispatched in Complex with Sonic Hedgehog, PDB code: 7rpk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7rpk

Go back to Sodium Binding Sites List in 7rpk
Sodium 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 Sodium with other atoms in the Na 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
A:Na2129

b:30.0
occ:1.00
OD1 A:ASP1049 2.1 60.6 1.0
O A:GLY1045 2.2 54.0 1.0
OG1 A:THR613 2.3 56.1 1.0
O A:THR610 2.4 58.9 1.0
OG1 A:THR614 2.4 52.7 1.0
O A:HOH2202 2.8 30.0 1.0
CG A:ASP1049 3.1 60.6 1.0
C A:GLY1045 3.3 54.0 1.0
CB A:THR613 3.4 56.1 1.0
C A:THR610 3.4 58.9 1.0
OD2 A:ASP1049 3.4 60.6 1.0
CA A:THR610 3.7 58.9 1.0
N A:THR614 3.7 52.7 1.0
CB A:THR614 3.7 52.7 1.0
N A:LEU1046 4.0 55.8 1.0
CA A:LEU1046 4.0 55.8 1.0
O A:LEU1046 4.1 55.8 1.0
C A:THR613 4.1 56.1 1.0
CB A:VAL1048 4.1 59.4 1.0
N A:ASP1049 4.2 60.6 1.0
CA A:THR613 4.3 56.1 1.0
CA A:THR614 4.3 52.7 1.0
CA A:GLY1045 4.3 54.0 1.0
C A:LEU1046 4.3 55.8 1.0
CB A:THR610 4.3 58.9 1.0
CB A:ASP1049 4.4 60.6 1.0
O A:VAL609 4.4 60.0 1.0
CG2 A:THR613 4.5 56.1 1.0
CA A:ASP1049 4.5 60.6 1.0
N A:SER611 4.6 57.1 1.0
N A:THR613 4.7 56.1 1.0
CG2 A:VAL1048 4.7 59.4 1.0
O A:HOH2230 4.7 30.0 1.0
N A:VAL1048 4.8 59.4 1.0
CA A:VAL1048 4.8 59.4 1.0
O A:THR613 4.8 56.1 1.0
C A:VAL1048 4.8 59.4 1.0
CG2 A:THR614 4.8 52.7 1.0
N A:THR610 4.9 58.9 1.0

Sodium binding site 2 out of 2 in 7rpk

Go back to Sodium Binding Sites List in 7rpk
Sodium 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 Sodium with other atoms in the Na 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
A:Na2130

b:67.4
occ:1.00
OD1 A:ASP571 2.1 64.3 1.0
O A:GLY567 2.3 59.2 1.0
OG1 A:THR1088 2.3 60.1 1.0
O A:ALA1084 2.3 62.0 1.0
OD2 A:ASP571 2.4 64.3 1.0
OG1 A:THR1087 2.4 62.8 1.0
CG A:ASP571 2.6 64.3 1.0
N A:THR1088 3.2 60.1 1.0
C A:GLY567 3.3 59.2 1.0
C A:ALA1084 3.3 62.0 1.0
O A:HOH2204 3.3 30.0 1.0
CB A:THR1088 3.4 60.1 1.0
CB A:THR1087 3.5 62.8 1.0
CA A:ILE568 3.6 58.2 1.0
CA A:ALA1084 3.7 62.0 1.0
CA A:THR1088 3.8 60.1 1.0
C A:THR1087 3.8 62.8 1.0
N A:ILE568 3.9 58.2 1.0
CB A:ASP571 4.1 64.3 1.0
CA A:THR1087 4.1 62.8 1.0
C A:ILE568 4.3 58.2 1.0
O A:ILE568 4.4 58.2 1.0
CA A:GLY567 4.4 59.2 1.0
CB A:ALA1084 4.5 62.0 1.0
N A:ALA1085 4.5 62.4 1.0
N A:THR1087 4.5 62.8 1.0
O A:MET1083 4.6 65.6 1.0
CB A:ILE568 4.6 58.2 1.0
CG2 A:THR1088 4.6 60.1 1.0
O A:THR1087 4.7 62.8 1.0
CG2 A:THR1087 4.7 62.8 1.0
CG2 A:ILE568 4.7 58.2 1.0
N A:ASP571 4.8 64.3 1.0
CB A:ALA570 4.8 64.3 1.0
CA A:ASP571 4.8 64.3 1.0
N A:ALA1084 5.0 62.0 1.0
O A:ALA1085 5.0 62.4 1.0
CA A:ALA1085 5.0 62.4 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 16:05:14 2021

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