Sodium in PDB 8can: Cryo-Em Structure of the Cora Homohexamer From Galleria Mellonella Saliva

Other elements in 8can:

The structure of Cryo-Em Structure of the Cora Homohexamer From Galleria Mellonella Saliva also contains other interesting chemical elements:

Copper (Cu) 24 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Cryo-Em Structure of the Cora Homohexamer From Galleria Mellonella Saliva (pdb code 8can). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Cryo-Em Structure of the Cora Homohexamer From Galleria Mellonella Saliva, PDB code: 8can:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 8can

Go back to Sodium Binding Sites List in 8can
Sodium binding site 1 out of 3 in the Cryo-Em Structure of the Cora Homohexamer From Galleria Mellonella Saliva


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 the Cora Homohexamer From Galleria Mellonella Saliva within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na806

b:13.6
occ:1.00
 HG3 D:MET327 3.2 7.5 1.0
HG3 B:MET327 3.2 7.4 1.0
HA B:MET327 3.3 7.4 1.0
HA D:MET327 3.3 7.5 1.0
HB2 B:TYR324 3.4 5.4 1.0
HB2 B:MET327 3.5 7.4 1.0
HB2 D:TYR324 3.5 5.2 1.0
HB2 D:MET327 3.5 7.5 1.0
O B:HOH946 3.8 9.5 1.0
O D:HOH939 4.0 9.5 1.0
CG D:MET327 4.0 7.5 1.0
CB B:MET327 4.0 7.4 1.0
CB D:MET327 4.0 7.5 1.0
CG B:MET327 4.0 7.4 1.0
CA B:MET327 4.0 7.4 1.0
CA D:MET327 4.0 7.5 1.0
O B:LYS326 4.1 7.8 1.0
O D:LYS326 4.2 7.5 1.0
O B:ASN325 4.3 7.4 1.0
CB B:TYR324 4.3 5.4 1.0
HB3 B:TYR324 4.4 5.4 1.0
CB D:TYR324 4.4 5.2 1.0
O D:ASN325 4.4 6.6 1.0
HB3 D:TYR324 4.5 5.2 1.0
HG2 D:MET327 4.5 7.5 1.0
N B:MET327 4.5 7.4 1.0
C B:LYS326 4.5 7.8 1.0
HG2 B:MET327 4.6 7.4 1.0
N D:MET327 4.6 7.5 1.0
C D:LYS326 4.6 7.5 1.0
H B:TYR324 4.7 5.4 1.0
O B:TYR324 4.7 5.4 1.0
H D:TYR324 4.7 5.2 1.0
O D:TYR324 4.8 5.2 1.0
H D:LYS328 4.8 7.7 1.0
H B:LYS328 4.9 7.2 1.0
HB3 B:MET327 4.9 7.4 1.0
HB3 D:MET327 4.9 7.5 1.0
C B:TYR324 4.9 5.4 1.0

Sodium binding site 2 out of 3 in 8can

Go back to Sodium Binding Sites List in 8can
Sodium binding site 2 out of 3 in the Cryo-Em Structure of the Cora Homohexamer From Galleria Mellonella Saliva


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 the Cora Homohexamer From Galleria Mellonella Saliva within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na806

b:12.2
occ:1.00
 HG3 C:MET327 3.2 7.2 1.0
HG3 F:MET327 3.2 7.2 1.0
HA C:MET327 3.3 7.2 1.0
HA F:MET327 3.3 7.2 1.0
HB2 C:MET327 3.5 7.2 1.0
HB2 F:MET327 3.5 7.2 1.0
HB2 C:TYR324 3.5 5.2 1.0
HB2 F:TYR324 3.5 4.7 1.0
O C:HOH945 3.8 9.2 1.0
O F:HOH950 3.8 9.3 1.0
CB C:MET327 4.0 7.2 1.0
CB F:MET327 4.0 7.2 1.0
CG C:MET327 4.0 7.2 1.0
CG F:MET327 4.0 7.2 1.0
CA C:MET327 4.0 7.2 1.0
CA F:MET327 4.0 7.2 1.0
O C:LYS326 4.1 7.2 1.0
O F:LYS326 4.1 7.4 1.0
O C:ASN325 4.3 6.1 1.0
O F:ASN325 4.3 6.2 1.0
CB C:TYR324 4.4 5.2 1.0
CB F:TYR324 4.4 4.7 1.0
HB3 C:TYR324 4.5 5.2 1.0
HB3 F:TYR324 4.5 4.7 1.0
HG2 C:MET327 4.5 7.2 1.0
HG2 F:MET327 4.5 7.2 1.0
N C:MET327 4.5 7.2 1.0
N F:MET327 4.5 7.2 1.0
C C:LYS326 4.6 7.2 1.0
C F:LYS326 4.6 7.4 1.0
H C:TYR324 4.8 5.2 1.0
H F:TYR324 4.8 4.7 1.0
O C:TYR324 4.8 5.2 1.0
O F:TYR324 4.8 4.7 1.0
H F:LYS328 4.8 7.4 1.0
H C:LYS328 4.8 7.2 1.0
HB3 C:MET327 4.9 7.2 1.0
HB3 F:MET327 4.9 7.2 1.0

Sodium binding site 3 out of 3 in 8can

Go back to Sodium Binding Sites List in 8can
Sodium binding site 3 out of 3 in the Cryo-Em Structure of the Cora Homohexamer From Galleria Mellonella Saliva


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cryo-Em Structure of the Cora Homohexamer From Galleria Mellonella Saliva within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na806

b:14.4
occ:1.00
 HG3 E:MET327 3.2 7.2 1.0
HG3 A:MET327 3.2 7.9 1.0
HA E:MET327 3.3 7.2 1.0
HA A:MET327 3.4 7.9 1.0
HB2 E:TYR324 3.4 6.1 1.0
HB2 E:MET327 3.4 7.2 1.0
HB2 A:TYR324 3.5 5.7 1.0
HB2 A:MET327 3.6 7.9 1.0
O E:HOH922 3.8 9.6 1.0
CB E:MET327 3.9 7.2 1.0
CG E:MET327 3.9 7.2 1.0
O A:HOH939 4.0 9.4 1.0
CA E:MET327 4.0 7.2 1.0
CG A:MET327 4.0 7.9 1.0
CB A:MET327 4.0 7.9 1.0
O E:LYS326 4.1 7.4 1.0
CA A:MET327 4.1 7.9 1.0
O A:LYS326 4.2 7.5 1.0
O E:ASN325 4.3 6.5 1.0
CB E:TYR324 4.3 6.1 1.0
CB A:TYR324 4.4 5.7 1.0
HB3 E:TYR324 4.4 6.1 1.0
O A:ASN325 4.4 6.7 1.0
HB3 A:TYR324 4.4 5.7 1.0
N E:MET327 4.5 7.2 1.0
HG2 E:MET327 4.5 7.2 1.0
C E:LYS326 4.5 7.4 1.0
HG2 A:MET327 4.6 7.9 1.0
N A:MET327 4.6 7.9 1.0
H E:TYR324 4.7 6.1 1.0
C A:LYS326 4.7 7.5 1.0
O E:TYR324 4.7 6.1 1.0
H A:TYR324 4.7 5.7 1.0
O A:TYR324 4.8 5.7 1.0
H E:LYS328 4.9 7.2 1.0
HB3 E:MET327 4.9 7.2 1.0
H A:LYS328 4.9 7.8 1.0
C E:TYR324 4.9 6.1 1.0
HB3 A:MET327 5.0 7.9 1.0

Reference:

M.Spinola-Amilibia, R.Illanes-Vicioso, E.Ruiz-L Formula See Text Pez, P.Colomer-Vidal, F.V.Rodriguez, R.Peces Perez, C.F.Arias, T.Torroba, M.Sol Formula See Text, E.Arias-Palomo, F.Bertocchini. Plastic Degradation By Insect Hexamerins: Near-Atomic Resolution Structures of the Polyethylene-Degrading Proteins From the Wax Worm Saliva. Sci Adv V. 9 I6813 2023.
ISSN: ESSN 2375-2548
PubMed: 37729416
DOI: 10.1126/SCIADV.ADI6813
Page generated: Wed Oct 9 10:53:31 2024

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