Magnesium in PDB 5vtp: X-Ray Diffraction Data of Dna Polymerase Eta (RAD30) of Saccharomyces Cerevisiae with A Single Magnesium Bound in Absence of Dna and Incoming Dntp

Enzymatic activity of X-Ray Diffraction Data of Dna Polymerase Eta (RAD30) of Saccharomyces Cerevisiae with A Single Magnesium Bound in Absence of Dna and Incoming Dntp

All present enzymatic activity of X-Ray Diffraction Data of Dna Polymerase Eta (RAD30) of Saccharomyces Cerevisiae with A Single Magnesium Bound in Absence of Dna and Incoming Dntp:
2.7.7.7;

Protein crystallography data

The structure of X-Ray Diffraction Data of Dna Polymerase Eta (RAD30) of Saccharomyces Cerevisiae with A Single Magnesium Bound in Absence of Dna and Incoming Dntp, PDB code: 5vtp was solved by K.T.Powers, M.T.Washington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.37 / 2.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 130.681, 130.681, 93.908, 90.00, 90.00, 120.00
R / Rfree (%) 22.1 / 24.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Diffraction Data of Dna Polymerase Eta (RAD30) of Saccharomyces Cerevisiae with A Single Magnesium Bound in Absence of Dna and Incoming Dntp (pdb code 5vtp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Diffraction Data of Dna Polymerase Eta (RAD30) of Saccharomyces Cerevisiae with A Single Magnesium Bound in Absence of Dna and Incoming Dntp, PDB code: 5vtp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5vtp

Go back to Magnesium Binding Sites List in 5vtp
Magnesium binding site 1 out of 2 in the X-Ray Diffraction Data of Dna Polymerase Eta (RAD30) of Saccharomyces Cerevisiae with A Single Magnesium Bound in Absence of Dna and Incoming Dntp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Diffraction Data of Dna Polymerase Eta (RAD30) of Saccharomyces Cerevisiae with A Single Magnesium Bound in Absence of Dna and Incoming Dntp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:94.9
occ:1.00
OD2 A:ASP30 2.2 77.9 1.0
OE1 A:GLU156 2.2 86.2 1.0
CG A:ASP30 3.1 68.7 1.0
CD A:GLU156 3.1 71.6 1.0
OD1 A:ASP30 3.3 68.4 1.0
HG2 A:GLU156 3.3 82.7 1.0
HG3 A:GLU156 3.4 82.7 1.0
CG A:GLU156 3.5 68.9 1.0
OD1 A:ASP155 4.1 57.4 1.0
OD2 A:ASP155 4.3 70.3 1.0
OE2 A:GLU156 4.3 63.9 1.0
CG A:ASP155 4.4 63.4 1.0
CB A:ASP30 4.5 50.1 1.0
HB2 A:ASP30 4.5 60.1 1.0
HG A:SER153 4.8 74.5 1.0
HZ1 A:LYS272 4.8 91.9 1.0
HE1 A:HIS28 4.8 65.2 1.0
HD22 A:ASN32 5.0 62.1 1.0
HB3 A:ASP30 5.0 60.1 1.0

Magnesium binding site 2 out of 2 in 5vtp

Go back to Magnesium Binding Sites List in 5vtp
Magnesium binding site 2 out of 2 in the X-Ray Diffraction Data of Dna Polymerase Eta (RAD30) of Saccharomyces Cerevisiae with A Single Magnesium Bound in Absence of Dna and Incoming Dntp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Diffraction Data of Dna Polymerase Eta (RAD30) of Saccharomyces Cerevisiae with A Single Magnesium Bound in Absence of Dna and Incoming Dntp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:93.4
occ:1.00
OE2 A:GLU417 2.1 91.0 1.0
O A:GLY98 2.2 85.2 1.0
CD A:GLU417 3.1 84.4 1.0
C A:GLY98 3.2 60.9 1.0
OE1 A:GLU417 3.4 95.9 1.0
HA2 A:GLY98 3.4 73.2 1.0
HA3 A:GLY98 3.7 73.2 1.0
CA A:GLY98 3.7 61.0 1.0
HA A:GLU99 4.1 81.3 1.0
N A:GLU99 4.3 61.2 1.0
CG A:GLU417 4.4 65.7 1.0
HA A:SER414 4.5 62.6 1.0
HB3 A:GLU417 4.6 66.4 1.0
HB2 A:GLU417 4.6 66.4 1.0
CA A:GLU99 4.7 67.8 1.0
CB A:GLU417 4.8 55.3 1.0
HG2 A:GLU417 4.8 78.8 1.0

Reference:

K.T.Powers, A.H.Elcock, M.T.Washington. The C-Terminal Region of Translesion Synthesis Dna Polymerase Eta Is Partially Unstructured and Has High Conformational Flexibility. Nucleic Acids Res. V. 46 2107 2018.
ISSN: ESSN 1362-4962
PubMed: 29385534
DOI: 10.1093/NAR/GKY031
Page generated: Mon Dec 14 21:19:09 2020

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