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Magnesium in PDB 4o5e: Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp

Enzymatic activity of Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp

All present enzymatic activity of Structure of Human Dna Polymerase Complexed with N7MG 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 Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp, PDB code: 4o5e 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) 19.73 / 2.53
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.425, 78.920, 54.819, 90.00, 105.97, 90.00
R / Rfree (%) 20.5 / 27.3

Other elements in 4o5e:

The structure of Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp also contains other interesting chemical elements:

Fluorine (F) 1 atom
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp (pdb code 4o5e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp, PDB code: 4o5e:

Magnesium binding site 1 out of 1 in 4o5e

Go back to Magnesium Binding Sites List in 4o5e
Magnesium binding site 1 out of 1 in the Structure of Human Dna Polymerase Complexed with N7MG 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 Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:41.5
occ:1.00
 O A:HOH563 2.1 42.7 1.0
OD1 A:ASP190 2.3 37.9 1.0
O A:HOH562 2.3 43.6 1.0
O2B A:1FZ404 2.5 56.7 1.0
O1G A:1FZ404 2.5 44.2 1.0
O1A A:1FZ404 2.8 55.1 1.0
CG A:ASP190 3.5 29.0 1.0
O A:ASP190 3.5 30.3 1.0
PB A:1FZ404 3.6 56.3 1.0
PG A:1FZ404 3.7 51.5 1.0
O3B A:1FZ404 3.9 60.0 1.0
C A:ASP190 4.0 32.9 1.0
PA A:1FZ404 4.1 63.6 1.0
CA A:GLY179 4.1 30.2 1.0
OD2 A:ASP190 4.2 32.2 1.0
O2G A:1FZ404 4.2 58.9 1.0
N A:ASP190 4.3 29.4 1.0
N A:SER180 4.3 33.6 1.0
CA A:ASP190 4.5 29.6 1.0
N3A A:1FZ404 4.5 52.2 1.0
N A:ASP192 4.5 32.0 1.0
CB A:ASP190 4.6 29.8 1.0
OG A:SER180 4.6 39.6 1.0
CB A:ASP192 4.7 28.7 1.0
N A:MET191 4.7 30.5 1.0
C A:GLY179 4.8 32.5 1.0
C5' A:1FZ404 4.8 56.9 1.0
CA A:MET191 4.9 25.1 1.0
O1B A:1FZ404 4.9 52.4 1.0
O5' A:1FZ404 4.9 54.3 1.0
CB A:SER188 5.0 29.7 1.0
O3G A:1FZ404 5.0 48.5 1.0

Reference:

M.C.Koag, Y.Kou, H.Ouzon-Shubeita, S.Lee. Transition-State Destabilization Reveals How Human Dna Polymerase Beta Proceeds Across the Chemically Unstable Lesion N7-Methylguanine. Nucleic Acids Res. V. 42 8755 2014.
ISSN: ISSN 0305-1048
PubMed: 24966350
DOI: 10.1093/NAR/GKU554
Page generated: Tue Aug 20 00:22:05 2024

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