Magnesium in PDB 6e3v: Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Ttp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Ttp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Ttp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Ttp, PDB code: 6e3v was solved by M.-C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.71 / 1.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.134, 80.381, 55.674, 90.00, 107.41, 90.00
R / Rfree (%) 19.5 / 24

Other elements in 6e3v:

The structure of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Ttp also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Ttp (pdb code 6e3v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Ttp, PDB code: 6e3v:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6e3v

Go back to Magnesium Binding Sites List in 6e3v
Magnesium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Ttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg400

b:19.1
occ:1.00
 OD2 A:ASP192 2.0 20.2 1.0
OD1 A:ASP190 2.0 17.3 1.0
O2A A:1FZ404 2.1 16.8 1.0
O1B A:1FZ404 2.1 17.9 1.0
O1G A:1FZ404 2.1 18.2 1.0
O A:HOH535 2.2 18.9 1.0
CG A:ASP192 3.0 21.7 1.0
PB A:1FZ404 3.1 18.8 1.0
CG A:ASP190 3.1 21.2 1.0
PA A:1FZ404 3.3 19.2 1.0
MG A:MG401 3.3 25.0 1.0
PG A:1FZ404 3.4 22.2 1.0
OD1 A:ASP192 3.4 22.6 1.0
OD2 A:ASP190 3.5 28.9 1.0
N3A A:1FZ404 3.6 16.5 1.0
O3B A:1FZ404 3.6 18.3 1.0
O A:ASP190 4.0 24.0 1.0
C5' A:1FZ404 4.1 18.8 1.0
O3G A:1FZ404 4.2 19.1 1.0
O5' A:1FZ404 4.2 18.6 1.0
O A:HOH582 4.2 21.2 1.0
C A:ASP190 4.2 21.8 1.0
CB A:ASP192 4.3 18.8 1.0
N A:ASP190 4.4 18.4 1.0
CB A:ASP190 4.4 21.5 1.0
O2G A:1FZ404 4.4 22.0 1.0
OG A:SER180 4.4 23.1 1.0
CA A:GLY179 4.5 18.9 1.0
O1A A:1FZ404 4.5 16.7 1.0
O2B A:1FZ404 4.5 18.5 1.0
N A:SER180 4.5 21.1 1.0
CA A:ASP190 4.6 20.2 1.0
N A:ASP192 4.8 17.7 1.0
N A:MET191 4.8 18.3 1.0
O A:HOH623 4.9 27.6 1.0
C A:MET191 5.0 18.8 1.0

Magnesium binding site 2 out of 2 in 6e3v

Go back to Magnesium Binding Sites List in 6e3v
Magnesium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Ttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:25.0
occ:1.00
 OD1 A:ASP192 2.1 22.6 1.0
O2A A:1FZ404 2.3 16.8 1.0
OD2 A:ASP190 2.5 28.9 1.0
O A:HOH623 2.7 27.6 1.0
OD1 A:ASP190 2.9 17.3 1.0
CG A:ASP190 3.0 21.2 1.0
CG A:ASP192 3.1 21.7 1.0
OD2 A:ASP256 3.2 34.3 1.0
MG A:MG400 3.3 19.1 1.0
OD2 A:ASP192 3.3 20.2 1.0
PA A:1FZ404 3.4 19.2 1.0
O5' A:1FZ404 3.8 18.6 1.0
O1A A:1FZ404 3.9 16.7 1.0
CG A:ASP256 4.0 27.8 1.0
C5' A:1FZ404 4.1 18.8 1.0
C3' P:DA10 4.1 32.1 1.0
CB A:ASP190 4.3 21.5 1.0
O3' P:DA10 4.3 50.9 1.0
CB A:ASP192 4.4 18.8 1.0
O P:HOH101 4.5 25.4 1.0
CB A:ASP256 4.5 21.6 1.0
C5' P:DA10 4.5 37.0 1.0
O1G A:1FZ404 4.5 18.2 1.0
O A:MET191 4.7 18.9 1.0
O5' P:DA10 4.8 37.5 1.0
OD1 A:ASP256 4.8 26.6 1.0
O1B A:1FZ404 4.8 17.9 1.0
C4' P:DA10 4.8 38.9 1.0
N3A A:1FZ404 4.9 16.5 1.0
OP1 P:DA10 4.9 33.5 1.0
CA A:ASP192 5.0 19.6 1.0
C A:MET191 5.0 18.8 1.0

Reference:

M.C.Koag, H.Jung, S.Lee. Mutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-Oxoadenine By Human Dna Polymerases. J. Am. Chem. Soc. V. 141 4584 2019.
ISSN: ESSN 1520-5126
PubMed: 30817143
DOI: 10.1021/JACS.8B08551
Page generated: Mon Dec 14 22:37:53 2020

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