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Sodium in PDB 5v08: Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi)

Protein crystallography data

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi), PDB code: 5v08 was solved by Y.Shi, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.46 / 2.81
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.259, 74.259, 179.385, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 26.2

Other elements in 5v08:

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi) also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi) (pdb code 5v08). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi), PDB code: 5v08:

Sodium binding site 1 out of 1 in 5v08

Go back to Sodium Binding Sites List in 5v08
Sodium binding site 1 out of 1 in the Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Na402

b:97.9
occ:1.00
OP2 A:DT4 2.4 0.6 1.0
O Z:HOH527 2.4 98.2 1.0
OG Z:SER229 2.4 89.5 1.0
O Z:SER222 2.4 84.4 1.0
O Z:ILE233 2.5 91.0 1.0
CB Z:SER229 3.3 85.8 1.0
P A:DT4 3.3 0.1 1.0
OP1 A:DT4 3.5 0.6 1.0
C Z:SER222 3.6 78.6 1.0
C Z:ILE233 3.6 91.7 1.0
CA Z:GLY234 3.9 77.3 1.0
N Z:GLY234 4.2 87.3 1.0
O5' A:DT4 4.3 0.1 1.0
CA Z:GLY223 4.4 80.2 1.0
N Z:GLY223 4.4 73.6 1.0
CA Z:SER222 4.5 75.7 1.0
O3' A:DC3 4.6 0.8 1.0
O Z:HOH512 4.7 93.0 1.0
CA Z:SER229 4.7 83.8 1.0
O Z:HOH525 4.8 0.2 1.0
C3' A:DC3 4.8 0.6 1.0
CA Z:ILE233 4.8 95.0 1.0

Reference:

Y.Shi, H.W.Hellinga, L.S.Beese. Interplay of Catalysis, Fidelity, Threading, and Processivity in the Exo- and Endonucleolytic Reactions of Human Exonuclease I. Proc. Natl. Acad. Sci. V. 114 6010 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28533382
DOI: 10.1073/PNAS.1704845114
Page generated: Tue Dec 15 11:43:30 2020

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