Atomistry » Sodium » PDB 6myk-6nfp » 6n6i
Atomistry »
  Sodium »
    PDB 6myk-6nfp »
      6n6i »

Sodium in PDB 6n6i: Human REXO2 Bound to Pgg

Protein crystallography data

The structure of Human REXO2 Bound to Pgg, PDB code: 6n6i was solved by J.D.Lormand, H.Sondermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.97 / 1.43
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.814, 87.289, 123.797, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 17.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Human REXO2 Bound to Pgg (pdb code 6n6i). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human REXO2 Bound to Pgg, PDB code: 6n6i:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6n6i

Go back to Sodium Binding Sites List in 6n6i
Sodium binding site 1 out of 2 in the Human REXO2 Bound to Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human REXO2 Bound to Pgg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na701

b:11.7
occ:1.00
O A:HOH493 2.3 12.7 1.0
O A:HOH501 2.3 11.4 0.7
OD1 A:ASP15 2.3 13.6 1.0
O A:HOH433 2.4 13.4 0.4
OP1 D:G604 2.4 11.5 1.0
O A:HOH501 2.4 13.5 0.3
O A:HOH433 2.5 10.8 0.6
O3' D:G603 2.6 10.7 1.0
P D:G604 3.1 11.0 1.0
CG A:ASP15 3.5 14.2 1.0
O2' D:G603 3.8 12.0 1.0
C3' D:G603 3.8 10.2 1.0
O A:HOH413 3.9 12.7 1.0
O A:HOH576 3.9 18.0 0.6
OD2 A:ASP15 4.0 13.3 1.0
C5' D:G604 4.1 10.4 1.0
O A:HOH476 4.1 15.8 1.0
O5' D:G604 4.1 10.7 1.0
OD1 A:ASP115 4.2 10.6 1.0
C4' D:G603 4.2 10.2 1.0
OD2 A:ASP115 4.2 10.8 1.0
O A:LEU16 4.2 10.0 1.0
O A:ASN110 4.3 10.6 1.0
OP2 D:G604 4.4 12.7 1.0
O A:HOH576 4.4 19.9 0.4
C2' D:G603 4.5 10.2 1.0
O A:HOH499 4.5 18.9 1.0
CG A:ASP115 4.6 10.0 1.0
CB A:ASP15 4.7 10.9 1.0
O3 A:GOL301 4.8 17.1 1.0
N A:LEU16 4.8 8.3 1.0
C5' D:G603 4.9 11.5 1.0
C3 A:GOL301 4.9 27.6 1.0

Sodium binding site 2 out of 2 in 6n6i

Go back to Sodium Binding Sites List in 6n6i
Sodium binding site 2 out of 2 in the Human REXO2 Bound to Pgg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human REXO2 Bound to Pgg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na702

b:10.7
occ:1.00
O C:HOH801 2.3 10.7 0.5
OD1 B:ASP15 2.3 11.6 1.0
O C:HOH806 2.3 12.3 0.6
O B:HOH480 2.4 11.0 1.0
OP1 C:G604 2.4 12.1 1.0
O C:HOH806 2.5 14.6 0.4
O C:HOH801 2.6 9.2 0.5
O3' C:G603 2.6 10.1 1.0
P C:G604 3.2 11.1 1.0
CG B:ASP15 3.5 11.7 1.0
O2' C:G603 3.8 12.7 1.0
C3' C:G603 3.8 10.1 1.0
O B:HOH409 4.0 12.2 1.0
OD2 B:ASP15 4.0 11.3 1.0
C5' C:G604 4.0 11.6 1.0
O B:HOH450 4.1 8.4 0.4
O5' C:G604 4.1 10.6 1.0
OD2 B:ASP115 4.1 10.8 1.0
C4' C:G603 4.1 10.2 1.0
O B:LEU16 4.2 10.3 1.0
O B:HOH450 4.2 10.4 0.6
OD1 B:ASP115 4.2 11.6 1.0
O B:HOH501 4.2 14.4 0.4
O1 C:EDO701 4.3 21.8 0.5
O B:HOH501 4.3 13.4 0.6
O B:ASN110 4.3 9.8 1.0
OP2 C:G604 4.4 13.0 1.0
C2' C:G603 4.4 10.6 1.0
CG B:ASP115 4.6 11.5 1.0
CB B:ASP15 4.7 8.4 1.0
O2 C:EDO701 4.7 16.6 0.4
O2 C:EDO701 4.8 15.1 0.5
N B:LEU16 4.8 9.6 1.0
C5' C:G603 4.9 10.2 1.0

Reference:

S.K.Kim, J.D.Lormand, C.A.Weiss, K.A.Eger, H.Turdiev, A.Turdiev, W.C.Winkler, H.Sondermann, V.T.Lee. A Dedicated Diribonucleotidase Resolves A Key Bottleneck For the Terminal Step of Rna Degradation. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31225796
DOI: 10.7554/ELIFE.46313
Page generated: Tue Dec 15 12:38:07 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