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Sodium in PDB 4fzx: Exonuclease X in Complex with 3' Overhanging Duplex Dna

Protein crystallography data

The structure of Exonuclease X in Complex with 3' Overhanging Duplex Dna, PDB code: 4fzx 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) 20.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 33.475, 107.927, 117.124, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 23

Sodium Binding Sites:

The binding sites of Sodium atom in the Exonuclease X in Complex with 3' Overhanging Duplex Dna (pdb code 4fzx). 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 3' Overhanging Duplex Dna, PDB code: 4fzx:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4fzx

Go back to Sodium Binding Sites List in 4fzx
Sodium binding site 1 out of 4 in the Exonuclease X in Complex with 3' 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 3' Overhanging Duplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na101

b:25.5
occ:1.00
 O C:HOH376 2.2 19.3 1.0
O C:HOH308 2.3 16.9 1.0
OD1 C:ASP6 2.4 17.9 1.0
OP1 B:DG17 2.5 14.7 1.0
O C:HOH377 2.5 27.7 1.0
O3' B:DA16 2.9 9.3 1.0
P B:DG17 3.3 10.1 1.0
CG C:ASP6 3.6 15.6 1.0
NA C:NA201 3.6 24.1 1.0
O C:HOH303 3.6 15.2 1.0
O C:HOH321 4.1 20.2 1.0
OD2 C:ASP85 4.1 21.9 1.0
C3' B:DA16 4.2 12.8 1.0
OD2 C:ASP6 4.2 17.2 1.0
C5' B:DG17 4.3 11.4 1.0
O C:THR7 4.3 13.3 1.0
OD1 C:ASP85 4.3 18.5 1.0
O5' B:DG17 4.3 12.5 1.0
OP2 B:DG17 4.3 11.9 1.0
C4' B:DA16 4.4 9.4 1.0
O C:HIS80 4.4 12.4 1.0
O B:HOH202 4.6 16.5 1.0
CG C:ASP85 4.7 19.0 1.0
CB C:ASP6 4.7 14.1 1.0
N C:THR7 4.7 14.3 1.0
CA C:ASP6 4.9 14.5 1.0
C5' B:DA16 5.0 9.3 1.0

Sodium binding site 2 out of 4 in 4fzx

Go back to Sodium Binding Sites List in 4fzx
Sodium binding site 2 out of 4 in the Exonuclease X in Complex with 3' 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 3' Overhanging Duplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na101

b:30.8
occ:1.00
 O D:HOH360 2.1 20.0 1.0
O D:HOH307 2.3 16.6 1.0
OP1 A:DT17 2.4 17.0 1.0
O A:HOH204 2.5 22.8 1.0
O3' A:DC16 2.7 15.3 1.0
OD1 D:ASP6 2.8 24.4 1.0
P A:DT17 3.2 13.6 1.0
O D:HOH305 3.7 17.7 1.0
NA D:NA201 3.7 30.6 1.0
CG D:ASP6 3.7 18.9 1.0
C3' A:DC16 4.0 12.0 1.0
OD1 D:ASP85 4.1 30.1 1.0
O D:HOH336 4.1 21.4 1.0
C5' A:DT17 4.1 10.2 1.0
OD2 D:ASP6 4.1 26.6 1.0
O5' A:DT17 4.2 13.4 1.0
C4' A:DC16 4.2 13.5 1.0
OD2 D:ASP85 4.2 26.6 1.0
OP2 A:DT17 4.2 16.6 1.0
O D:THR7 4.3 15.2 1.0
O D:HIS80 4.3 15.4 1.0
O A:HOH201 4.5 26.8 1.0
CG D:ASP85 4.6 23.5 1.0
C5' A:DC16 4.7 10.6 1.0
N D:THR7 4.7 13.6 1.0
C2' A:DC16 4.7 12.9 1.0
CB D:ASP6 4.8 14.5 1.0
CA D:ASP6 4.9 14.1 1.0
CD2 D:PHE84 4.9 13.8 1.0

Sodium binding site 3 out of 4 in 4fzx

Go back to Sodium Binding Sites List in 4fzx
Sodium binding site 3 out of 4 in the Exonuclease X in Complex with 3' 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 3' Overhanging Duplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:24.1
occ:1.00
 OD2 C:ASP139 2.2 16.5 1.0
OE2 C:GLU8 2.2 18.7 1.0
OP1 B:DG17 2.3 14.7 1.0
O C:HOH378 2.6 34.9 1.0
OD2 C:ASP6 2.9 17.2 1.0
OD1 C:ASP6 3.0 17.9 1.0
CG C:ASP139 3.2 13.2 1.0
CD C:GLU8 3.3 16.7 1.0
CG C:ASP6 3.3 15.6 1.0
O C:HOH377 3.4 27.7 1.0
OE1 C:GLU8 3.6 15.4 1.0
NA B:NA101 3.6 25.5 1.0
CB C:ASP139 3.6 9.2 1.0
P B:DG17 3.6 10.1 1.0
O C:HOH340 4.1 24.3 1.0
OP2 B:DG17 4.2 11.9 1.0
CA C:HIS134 4.3 15.7 1.0
OD1 C:ASP139 4.3 14.9 1.0
O5' B:DG17 4.5 12.5 1.0
O B:HOH202 4.6 16.5 1.0
ND1 C:HIS134 4.6 23.9 1.0
CG C:GLU8 4.6 11.9 1.0
O C:HOH376 4.6 19.3 1.0
O C:HOH321 4.6 20.2 1.0
O C:THR7 4.7 13.3 1.0
O3' B:DA16 4.7 9.3 1.0
C C:HIS134 4.8 14.7 1.0
CB C:ASP6 4.8 14.1 1.0
C5' B:DG17 4.8 11.4 1.0
O C:HIS134 4.9 14.6 1.0
N C:HIS134 5.0 15.0 1.0

Sodium binding site 4 out of 4 in 4fzx

Go back to Sodium Binding Sites List in 4fzx
Sodium binding site 4 out of 4 in the Exonuclease X in Complex with 3' 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 3' Overhanging Duplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:30.6
occ:1.00
 OD2 D:ASP139 2.3 28.7 1.0
OP1 A:DT17 2.3 17.0 1.0
OE2 D:GLU8 2.5 20.9 1.0
OD1 D:ASP6 2.9 24.4 1.0
OD2 D:ASP6 3.0 26.6 1.0
O D:HOH363 3.1 37.4 1.0
CG D:ASP139 3.3 24.8 1.0
CG D:ASP6 3.3 18.9 1.0
CD D:GLU8 3.5 22.3 1.0
CB D:ASP139 3.5 17.8 1.0
P A:DT17 3.7 13.6 1.0
NA A:NA101 3.7 30.8 1.0
OE1 D:GLU8 3.8 23.4 1.0
O A:HOH204 3.8 22.8 1.0
O D:HOH358 4.0 35.5 1.0
OP2 A:DT17 4.2 16.6 1.0
CA D:HIS134 4.3 20.4 1.0
O5' A:DT17 4.4 13.4 1.0
OD1 D:ASP139 4.4 31.9 1.0
O A:HOH201 4.5 26.8 1.0
O D:HOH336 4.6 21.4 1.0
O D:THR7 4.6 15.2 1.0
C D:HIS134 4.7 19.1 1.0
ND1 D:HIS134 4.7 27.6 1.0
O3' A:DC16 4.8 15.3 1.0
C5' A:DT17 4.8 10.2 1.0
CB D:ASP6 4.8 14.5 1.0
CG D:GLU8 4.9 17.1 1.0
O D:HOH307 4.9 16.6 1.0
O D:HIS134 4.9 19.6 1.0
N D:HIS134 4.9 21.7 1.0
O D:ARG135 4.9 13.4 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 15:29:54 2024

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