Atomistry » Sodium » PDB 6rzp-6set » 6s7x
Atomistry »
  Sodium »
    PDB 6rzp-6set »
      6s7x »

Sodium in PDB 6s7x: DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom

Protein crystallography data

The structure of DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom, PDB code: 6s7x was solved by M.A.Cottee, I.A.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.41 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.334, 70.386, 142.821, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.3

Other elements in 6s7x:

The structure of DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom (pdb code 6s7x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom, PDB code: 6s7x:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6s7x

Go back to Sodium Binding Sites List in 6s7x
Sodium binding site 1 out of 2 in the DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:39.5
occ:1.00
O A:GLU104 2.3 23.8 1.0
O A:HOH545 2.3 32.4 1.0
O A:HOH553 2.3 33.0 1.0
O B:HOH536 2.5 28.2 1.0
O A:HOH572 2.6 27.2 1.0
OE1 A:GLU110 2.8 26.0 1.0
CD A:GLU110 3.4 26.7 1.0
HG23 A:THR106 3.4 28.1 1.0
C A:GLU104 3.5 25.1 1.0
HE2 B:HIS189 3.6 29.0 0.0
HB3 A:GLU104 3.8 23.8 1.0
H A:THR106 3.8 25.8 1.0
HB3 A:GLU110 3.9 22.6 1.0
OE2 A:GLU110 3.9 31.7 1.0
HA A:ALA105 4.0 26.6 1.0
HA A:GLU104 4.1 23.8 1.0
HG2 A:GLU110 4.1 24.7 1.0
HD2 B:HIS189 4.2 28.2 1.0
O A:HOH409 4.2 25.6 1.0
NE2 B:HIS189 4.2 29.0 1.0
CG A:GLU110 4.2 24.9 1.0
CA A:GLU104 4.3 23.7 1.0
O A:HOH588 4.4 37.9 1.0
CG2 A:THR106 4.4 28.8 1.0
O A:HOH501 4.4 32.6 1.0
N A:ALA105 4.5 23.9 1.0
CB A:GLU104 4.5 23.2 1.0
CD2 B:HIS189 4.5 29.1 1.0
CB A:GLU110 4.5 22.5 1.0
N A:THR106 4.6 24.9 1.0
CA A:ALA105 4.7 26.9 1.0
O B:HOH562 4.7 34.7 1.0
HG22 A:THR106 4.8 28.0 1.0
HG21 A:THR106 4.8 28.0 1.0
HD12 A:LEU114 4.8 22.3 1.0
O A:HOH494 4.8 19.6 1.0
HB2 A:GLU110 4.8 22.6 1.0
OG1 A:THR106 4.9 27.0 1.0
HB2 A:GLU104 4.9 23.8 1.0
HG1 A:THR106 5.0 27.3 0.0

Sodium binding site 2 out of 2 in 6s7x

Go back to Sodium Binding Sites List in 6s7x
Sodium binding site 2 out of 2 in the DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of DARC1 Capsid Domain Dimer, Orthorhombic Form at 1.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:33.5
occ:1.00
O B:HOH532 2.3 35.1 1.0
O B:HOH454 2.5 26.4 1.0
O B:HIS182 2.5 21.6 1.0
O B:HOH503 2.5 22.2 1.0
C B:HIS182 3.2 19.6 1.0
H B:SER184 3.3 19.5 1.0
O B:HOH406 3.7 30.6 1.0
HB2 B:SER184 3.7 22.2 1.0
N B:SER184 3.8 19.3 1.0
HA B:HIS182 3.8 20.8 1.0
HA B:ILE183 3.9 18.5 1.0
N B:ILE183 4.0 18.1 1.0
CA B:HIS182 4.1 20.4 1.0
O B:HOH423 4.2 30.1 1.0
CA B:ILE183 4.3 18.2 1.0
C B:ILE183 4.3 19.2 1.0
HB3 B:SER184 4.3 22.2 1.0
CB B:SER184 4.4 21.2 1.0
O B:LYS181 4.5 23.0 1.0
O A:HOH504 4.5 30.3 1.0
O B:HOH563 4.5 37.8 1.0
CA B:SER184 4.6 20.0 1.0
H B:ILE183 4.7 18.5 1.0
HA B:SER184 4.8 19.8 1.0
N B:HIS182 4.9 20.2 1.0

Reference:

M.A.Cottee, S.C.Letham, G.R.Young, J.P.Stoye, I.A.Taylor. Structure of Drosophila Melanogaster ARC1 Reveals A Repurposed Molecule with Characteristics of Retroviral Gag Sci Adv 2020.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.AAY6354
Page generated: Tue Dec 15 12:58:00 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy