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Magnesium in PDB 4ymn: Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 4ymn was solved by S.Lee, M.-C.Koag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.76 / 2.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.907, 79.020, 55.019, 90.00, 107.92, 90.00
R / Rfree (%) 20 / 26.9

Other elements in 4ymn:

The structure of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp 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 Beta Complexed with N7BG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp (pdb code 4ymn). 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 Beta Complexed with N7BG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 4ymn:

Magnesium binding site 1 out of 1 in 4ymn

Go back to Magnesium Binding Sites List in 4ymn
Magnesium binding site 1 out of 1 in the Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp


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 N7BG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:42.5
occ:1.00
 OD1 A:ASP190 2.3 33.2 1.0
O1B A:0KX404 2.3 64.6 1.0
O A:ASP190 3.0 28.9 1.0
O A:HOH516 3.3 29.6 1.0
O2G A:0KX404 3.3 55.6 1.0
O2A A:0KX404 3.3 79.2 1.0
CG A:ASP190 3.3 23.5 1.0
O1G A:0KX404 3.5 52.3 1.0
PB A:0KX404 3.7 61.9 1.0
C A:ASP190 3.7 25.2 1.0
N A:ASP190 3.9 25.1 1.0
PG A:0KX404 4.0 55.3 1.0
OD2 A:ASP190 4.0 38.3 1.0
CA A:ASP190 4.2 21.3 1.0
CA A:GLY179 4.3 32.7 1.0
O3B A:0KX404 4.3 58.9 1.0
CB A:ASP190 4.3 18.8 1.0
PA A:0KX404 4.5 84.5 1.0
N A:SER180 4.5 32.3 1.0
CB A:ASP192 4.5 26.2 1.0
N A:MET191 4.6 22.4 1.0
N A:ASP192 4.6 27.4 1.0
O2B A:0KX404 4.7 59.0 1.0
N3A A:0KX404 4.7 71.8 1.0
N A:GLY189 4.8 30.9 1.0
OG A:SER180 4.9 35.0 1.0
CA A:MET191 4.9 25.4 1.0
C A:GLY179 4.9 32.1 1.0
C A:MET191 4.9 26.5 1.0
C A:GLY189 5.0 27.4 1.0

Reference:

Y.Kou, M.C.Koag, S.Lee. Structural and Kinetic Studies of the Effect of Guanine-N7 Alkylation and Metal Cofactors on Dna Replication. Biochemistry 2018.
ISSN: ISSN 1520-4995
PubMed: 29957995
DOI: 10.1021/ACS.BIOCHEM.8B00331
Page generated: Sat Sep 28 23:22:05 2024

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