Magnesium in PDB 5v0d: Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (F2II)

Protein crystallography data

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (F2II), PDB code: 5v0d 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) 33.98 / 2.63
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 72.976, 72.976, 180.612, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 23.7

Other elements in 5v0d:

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (F2II) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (F2II) (pdb code 5v0d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (F2II), PDB code: 5v0d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5v0d

Go back to Magnesium Binding Sites List in 5v0d
Magnesium binding site 1 out of 2 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (F2II)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (F2II) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg401

b:67.7
occ:1.00
OD2 Z:ASP171 2.1 62.4 1.0
OP3 B:DG1 2.1 76.0 1.0
OD1 Z:ASP152 2.1 60.6 1.0
OD1 Z:ASP173 2.1 62.5 1.0
O Z:HOH513 2.1 69.7 1.0
OP2 B:DG1 2.1 75.1 1.0
P B:DG1 2.6 75.1 1.0
CG Z:ASP173 3.0 64.2 1.0
CG Z:ASP171 3.1 62.8 1.0
CB Z:ASP173 3.2 64.3 1.0
CG Z:ASP152 3.3 60.0 1.0
OD1 Z:ASP171 3.6 64.3 1.0
OP1 B:DG1 3.6 77.9 1.0
MG Z:MG402 3.7 69.8 1.0
O5' B:DG1 3.8 78.2 1.0
O Z:HOH537 3.9 62.4 1.0
OD2 Z:ASP225 3.9 68.4 1.0
OD2 Z:ASP152 3.9 58.5 1.0
O B:HOH102 3.9 64.3 1.0
N Z:GLY2 4.1 71.2 1.0
OD2 Z:ASP173 4.2 66.0 1.0
OE1 Z:GLU150 4.2 63.7 1.0
C5' B:DG1 4.3 82.4 1.0
CB Z:ASP171 4.4 61.5 1.0
CB Z:ASP152 4.4 61.7 1.0
O Z:HOH526 4.6 64.6 1.0
CA Z:ASP173 4.7 66.1 1.0
O3' E:DA2 4.7 85.3 1.0
CA Z:GLY2 4.8 74.5 1.0
NZ Z:LYS85 4.8 75.0 1.0
O Z:HOH527 5.0 64.4 1.0

Magnesium binding site 2 out of 2 in 5v0d

Go back to Magnesium Binding Sites List in 5v0d
Magnesium binding site 2 out of 2 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (F2II)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (F2II) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg402

b:69.8
occ:1.00
O Z:HOH526 2.1 64.6 1.0
O B:HOH102 2.1 64.3 1.0
OD2 Z:ASP152 2.1 58.5 1.0
OP2 B:DG1 2.1 75.1 1.0
O Z:HOH525 2.1 67.7 1.0
O3' E:DA2 2.2 85.3 1.0
CG Z:ASP152 3.0 60.0 1.0
OD1 Z:ASP152 3.1 60.6 1.0
P B:DG1 3.5 75.1 1.0
C3' E:DA2 3.6 97.0 1.0
MG Z:MG401 3.7 67.7 1.0
OD2 Z:ASP171 4.0 62.4 1.0
O Z:HOH511 4.0 76.7 1.0
O5' B:DG1 4.1 78.2 1.0
OP1 B:DG1 4.1 77.9 1.0
OD1 Z:ASP78 4.2 59.4 1.0
OD2 Z:ASP30 4.2 62.8 1.0
C4' E:DA2 4.2 0.6 1.0
C2' E:DA2 4.3 0.8 1.0
OD2 Z:ASP78 4.3 61.1 1.0
CB Z:ASP152 4.4 61.7 1.0
N Z:ASP152 4.4 60.1 1.0
OE1 Z:GLU150 4.5 63.7 1.0
OP3 B:DG1 4.5 76.0 1.0
O Z:HOH513 4.6 69.7 1.0
OD1 Z:ASP30 4.6 64.3 1.0
CG Z:ASP78 4.7 62.2 1.0
NZ Z:LYS85 4.7 75.0 1.0
CG Z:ASP30 4.9 64.0 1.0
CA Z:ASP152 4.9 60.9 1.0
CG Z:ASP171 4.9 62.8 1.0
C5' E:DA2 4.9 0.0 1.0
N Z:ALA151 4.9 61.8 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: Mon Dec 14 21:17:30 2020

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