Atomistry » Sodium » PDB 4fpa-4gfi » 4fzz
Atomistry »
  Sodium »
    PDB 4fpa-4gfi »
      4fzz »

Sodium in PDB 4fzz: Exonuclease X in Complex with 5' Overhanging Duplex Dna

Protein crystallography data

The structure of Exonuclease X in Complex with 5' Overhanging Duplex Dna, PDB code: 4fzz was solved by T.Wang, H.Sun, F.Cheng, L.Bi, T.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.01 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.192, 79.009, 156.012, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 26

Sodium Binding Sites:

The binding sites of Sodium atom in the Exonuclease X in Complex with 5' Overhanging Duplex Dna (pdb code 4fzz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Exonuclease X in Complex with 5' Overhanging Duplex Dna, PDB code: 4fzz:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4fzz

Go back to Sodium Binding Sites List in 4fzz
Sodium binding site 1 out of 4 in the Exonuclease X in Complex with 5' Overhanging Duplex Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Exonuclease X in Complex with 5' Overhanging Duplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:22.4
occ:1.00
O B:HOH317 2.1 30.2 1.0
OD2 B:ASP6 2.2 28.6 1.0
O B:HOH301 2.3 14.2 1.0
O B:HOH319 2.6 29.0 1.0
O3' D:DA11 2.6 35.6 1.0
OP1 D:DG12 2.7 36.3 1.0
P D:DG12 3.3 36.3 1.0
CG B:ASP6 3.3 29.1 1.0
OD1 B:ASP6 3.8 31.2 1.0
OD2 B:ASP85 3.9 39.1 1.0
C3' D:DA11 3.9 35.3 1.0
O B:THR7 3.9 27.1 1.0
NA B:NA201 4.0 26.1 1.0
C5' D:DG12 4.0 35.0 1.0
O B:HOH304 4.1 22.4 1.0
C4' D:DA11 4.1 33.9 1.0
O5' D:DG12 4.2 32.8 1.0
O B:HOH313 4.3 19.5 1.0
N B:THR7 4.3 27.5 1.0
OD1 B:ASP85 4.4 35.6 1.0
OP2 D:DG12 4.4 36.8 1.0
CG B:ASP85 4.5 36.2 1.0
C2' D:DA11 4.6 35.2 1.0
CB B:ASP6 4.6 28.5 1.0
C5' D:DA11 4.6 32.4 1.0
O B:HIS80 4.7 27.8 1.0
O D:HOH201 4.7 35.7 1.0
CA B:ASP6 4.8 28.5 1.0
C B:THR7 4.9 26.8 1.0

Sodium binding site 2 out of 4 in 4fzz

Go back to Sodium Binding Sites List in 4fzz
Sodium binding site 2 out of 4 in the Exonuclease X in Complex with 5' Overhanging Duplex Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Exonuclease X in Complex with 5' Overhanging Duplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na101

b:29.4
occ:1.00
O A:HOH307 2.3 23.3 1.0
OD1 A:ASP6 2.4 24.8 1.0
OP1 C:DG12 2.4 20.6 1.0
O A:HOH301 2.4 19.4 1.0
O A:HOH303 2.4 38.3 1.0
O3' C:DA11 2.4 25.5 1.0
P C:DG12 3.0 23.1 1.0
CG A:ASP6 3.5 24.9 1.0
NA A:NA201 3.6 32.5 1.0
C3' C:DA11 3.7 26.6 1.0
O5' C:DG12 3.9 23.5 1.0
C5' C:DG12 3.9 24.8 1.0
OD2 A:ASP85 3.9 34.3 1.0
O A:THR7 3.9 28.1 1.0
OD2 A:ASP6 4.1 24.3 1.0
C4' C:DA11 4.1 27.4 1.0
OP2 C:DG12 4.2 21.7 1.0
OD1 A:ASP85 4.3 31.8 1.0
C2' C:DA11 4.3 27.2 1.0
N A:THR7 4.4 28.4 1.0
CG A:ASP85 4.5 32.5 1.0
O A:HOH306 4.7 21.6 1.0
O A:HIS80 4.7 25.1 1.0
CB A:ASP6 4.7 26.2 1.0
C5' C:DA11 4.8 24.1 1.0
CA A:ASP6 4.9 26.9 1.0
C A:THR7 5.0 28.2 1.0

Sodium binding site 3 out of 4 in 4fzz

Go back to Sodium Binding Sites List in 4fzz
Sodium binding site 3 out of 4 in the Exonuclease X in Complex with 5' Overhanging Duplex Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Exonuclease X in Complex with 5' Overhanging Duplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:32.5
occ:1.00
OD2 A:ASP6 2.4 24.3 1.0
OP1 C:DG12 2.4 20.6 1.0
OD2 A:ASP139 2.4 21.3 1.0
OE2 A:GLU8 2.6 31.1 1.0
CG A:ASP6 3.2 24.9 1.0
OD1 A:ASP6 3.3 24.8 1.0
CG A:ASP139 3.3 23.1 1.0
CD A:GLU8 3.5 29.7 1.0
CB A:ASP139 3.6 23.7 1.0
NA C:NA101 3.6 29.4 1.0
OE1 A:GLU8 3.6 30.6 1.0
P C:DG12 3.8 23.1 1.0
ND1 A:HIS134 3.9 31.1 1.0
CA A:HIS134 4.0 28.5 1.0
O A:HOH307 4.1 23.3 1.0
O A:THR7 4.2 28.1 1.0
OD1 A:ASP139 4.5 25.1 1.0
OP2 C:DG12 4.5 21.7 1.0
N A:HIS134 4.6 29.2 1.0
C5' C:DG12 4.6 24.8 1.0
CE1 A:HIS134 4.6 30.8 1.0
N A:ALA136 4.6 21.7 1.0
CB A:ASP6 4.7 26.2 1.0
O5' C:DG12 4.7 23.5 1.0
CG A:HIS134 4.7 30.2 1.0
O3' C:DA11 4.8 25.5 1.0
O A:HOH306 4.8 21.6 1.0
C A:HIS134 4.8 27.5 1.0
CA A:ALA136 4.8 21.2 1.0
CB A:HIS134 4.8 28.6 1.0
CG A:GLU8 4.8 28.6 1.0
N A:ARG135 4.9 25.8 1.0
C A:THR7 4.9 28.2 1.0
O A:HOH303 5.0 38.3 1.0

Sodium binding site 4 out of 4 in 4fzz

Go back to Sodium Binding Sites List in 4fzz
Sodium binding site 4 out of 4 in the Exonuclease X in Complex with 5' Overhanging Duplex Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Exonuclease X in Complex with 5' Overhanging Duplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:26.1
occ:1.00
OE2 B:GLU8 2.4 26.7 1.0
OP1 D:DG12 2.4 36.3 1.0
OD2 B:ASP139 2.5 25.4 1.0
OD1 B:ASP6 2.7 31.2 1.0
CD B:GLU8 3.3 26.8 1.0
ND1 B:HIS134 3.3 47.4 1.0
CG B:ASP139 3.4 27.2 1.0
OE1 B:GLU8 3.6 29.8 1.0
CG B:ASP6 3.6 29.1 1.0
CB B:ASP139 3.7 28.5 1.0
CA B:HIS134 3.7 43.9 1.0
OD2 B:ASP6 3.8 28.6 1.0
P D:DG12 3.8 36.3 1.0
NA D:NA101 4.0 22.4 1.0
CE1 B:HIS134 4.0 46.8 1.0
C B:HIS134 4.2 41.4 1.0
O B:HOH317 4.3 30.2 1.0
O B:THR7 4.3 27.1 1.0
CG B:HIS134 4.3 46.0 1.0
N B:ARG135 4.3 38.5 1.0
O5' D:DG12 4.5 32.8 1.0
C5' D:DG12 4.5 35.0 1.0
N B:HIS134 4.5 46.6 1.0
OD1 B:ASP139 4.5 25.8 1.0
O D:HOH201 4.6 35.7 1.0
OP2 D:DG12 4.6 36.8 1.0
CB B:HIS134 4.6 44.2 1.0
CG B:GLU8 4.7 26.2 1.0
O B:HOH313 4.9 19.5 1.0
O3' D:DA11 4.9 35.6 1.0
N B:ALA136 4.9 32.8 1.0
C B:ARG135 4.9 34.5 1.0
O B:HIS134 4.9 41.0 1.0

Reference:

T.Wang, H.L.Sun, F.Cheng, X.E.Zhang, L.Bi, T.Jiang. Recognition and Processing of Double-Stranded Dna By Exox, A Distributive 3'-5' Exonuclease Nucleic Acids Res. V. 41 7556 2013.
ISSN: ISSN 0305-1048
PubMed: 23771145
DOI: 10.1093/NAR/GKT495
Page generated: Mon Oct 7 15:29:55 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy