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Magnesium in PDB 4z6d: Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp

Enzymatic activity of Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp

All present enzymatic activity of Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G 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 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp, PDB code: 4z6d 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) 19.85 / 2.51
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.283, 79.382, 54.859, 90.00, 110.18, 90.00
R / Rfree (%) 19.8 / 27

Other elements in 4z6d:

The structure of Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G 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 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp (pdb code 4z6d). 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 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp, PDB code: 4z6d:

Magnesium binding site 1 out of 1 in 4z6d

Go back to Magnesium Binding Sites List in 4z6d
Magnesium binding site 1 out of 1 in the Structure of Human Dna Polymerase Beta 279NA Mutant Complexed with G 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 279NA Mutant Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg400

b:30.6
occ:1.00
 O2B A:1FZ403 2.1 37.4 1.0
OD1 A:ASP190 2.1 26.2 1.0
O3G A:1FZ403 2.3 35.3 1.0
OD1 A:ASP192 2.3 32.0 1.0
O1A A:1FZ403 2.4 37.9 1.0
O A:HOH523 2.7 27.2 1.0
CG A:ASP190 3.3 27.5 1.0
PB A:1FZ403 3.4 38.5 1.0
O A:HOH515 3.5 28.4 1.0
CG A:ASP192 3.5 43.0 1.0
PA A:1FZ403 3.7 34.6 1.0
PG A:1FZ403 3.7 35.8 1.0
OD2 A:ASP190 3.9 32.1 1.0
O A:ASP190 3.9 23.1 1.0
N3A A:1FZ403 4.0 36.3 1.0
O3B A:1FZ403 4.1 35.0 1.0
CA A:GLY179 4.2 25.1 1.0
C A:ASP190 4.2 22.0 1.0
CB A:ASP192 4.3 33.9 1.0
N A:ASP190 4.4 21.5 1.0
O1G A:1FZ403 4.4 32.8 1.0
OD2 A:ASP192 4.4 44.8 1.0
N A:SER180 4.5 23.0 1.0
CB A:ASP190 4.5 20.9 1.0
N A:ASP192 4.5 25.1 1.0
O5' A:1FZ403 4.6 35.6 1.0
CA A:ASP190 4.6 20.5 1.0
O1B A:1FZ403 4.6 39.1 1.0
O2G A:1FZ403 4.7 36.6 1.0
OG A:SER180 4.8 21.1 1.0
N A:MET191 4.8 24.7 1.0
C5' A:1FZ403 4.9 35.6 1.0
O2A A:1FZ403 4.9 35.3 1.0
C A:GLY179 4.9 24.6 1.0

Reference:

M.C.Koag, S.Lee. Insights Into the Effect of Minor Groove Interactions and Metal Cofactors on Mutagenic Replication By Human Dna Polymerase Beta. Biochem. J. V. 475 571 2018.
ISSN: ESSN 1470-8728
PubMed: 29301983
DOI: 10.1042/BCJ20170787
Page generated: Sat Sep 28 23:57:04 2024

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