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

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

All present enzymatic activity of Structure of Human Dna Polymerase Beta 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 Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp, PDB code: 4pgq 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) 19.27 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.898, 80.087, 55.077, 90.00, 106.15, 90.00
R / Rfree (%) 20.3 / 26

Other elements in 4pgq:

The structure of Structure of Human Dna Polymerase Beta 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 Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp (pdb code 4pgq). 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 G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp, PDB code: 4pgq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4pgq

Go back to Magnesium Binding Sites List in 4pgq
Magnesium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta 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 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:19.3
occ:1.00
O A:HOH557 1.9 35.9 1.0
O1G A:1FZ404 1.9 40.9 1.0
O1A A:1FZ404 1.9 39.9 1.0
O2B A:1FZ404 2.0 37.9 1.0
OD1 A:ASP190 2.1 33.3 1.0
OD1 A:ASP192 2.2 32.5 1.0
PB A:1FZ404 3.1 44.5 1.0
CG A:ASP190 3.1 31.3 1.0
CG A:ASP192 3.1 35.7 1.0
PA A:1FZ404 3.2 42.7 1.0
PG A:1FZ404 3.3 44.7 1.0
MG A:MG401 3.3 37.1 1.0
OD2 A:ASP190 3.4 35.0 1.0
OD2 A:ASP192 3.4 31.2 1.0
N3A A:1FZ404 3.6 41.4 1.0
O3B A:1FZ404 3.6 39.4 1.0
O A:HOH559 4.0 42.2 1.0
O3G A:1FZ404 4.1 43.5 1.0
O5' A:1FZ404 4.2 42.8 1.0
C5' A:1FZ404 4.2 48.4 1.0
O A:ASP190 4.3 30.1 1.0
O2G A:1FZ404 4.4 44.8 1.0
O1B A:1FZ404 4.4 43.7 1.0
CB A:ASP190 4.5 30.4 1.0
O2A A:1FZ404 4.5 45.7 1.0
O A:HOH530 4.5 32.0 1.0
CB A:ASP192 4.5 28.1 1.0
N A:ASP190 4.5 31.6 1.0
C A:ASP190 4.6 34.3 1.0
CA A:GLY179 4.6 36.5 1.0
N A:SER180 4.7 38.1 1.0
CA A:ASP190 4.8 30.1 1.0
N A:ASP192 5.0 26.8 1.0

Magnesium binding site 2 out of 2 in 4pgq

Go back to Magnesium Binding Sites List in 4pgq
Magnesium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta 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 2 of Structure of Human Dna Polymerase Beta 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:Mg401

b:37.1
occ:1.00
O1A A:1FZ404 2.3 39.9 1.0
OD2 A:ASP190 2.4 35.0 1.0
O A:HOH536 2.4 29.3 1.0
OD2 A:ASP192 2.5 31.2 1.0
O3' P:DA10 2.5 32.2 1.0
CG A:ASP190 3.3 31.3 1.0
PA A:1FZ404 3.3 42.7 1.0
C3' P:DA10 3.3 33.3 1.0
MG A:MG400 3.3 19.3 1.0
CG A:ASP192 3.4 35.7 1.0
OD1 A:ASP190 3.5 33.3 1.0
O2A A:1FZ404 3.5 45.7 1.0
OD1 A:ASP192 3.6 32.5 1.0
O A:HOH558 3.8 28.7 1.0
O5' A:1FZ404 4.0 42.8 1.0
C4' P:DA10 4.1 31.2 1.0
O A:HOH559 4.1 42.2 1.0
O1G A:1FZ404 4.4 40.9 1.0
CB A:ASP190 4.6 30.4 1.0
O A:HOH579 4.6 42.2 1.0
C5' A:1FZ404 4.7 48.4 1.0
OD2 A:ASP256 4.7 29.8 1.0
C2' P:DA10 4.7 34.0 1.0
N3A A:1FZ404 4.7 41.4 1.0
O2B A:1FZ404 4.7 37.9 1.0
CB A:ASP192 4.7 28.1 1.0
C5' P:DA10 4.8 27.9 1.0

Reference:

M.C.Koag, K.Nam, S.Lee. The Spontaneous Replication Error and the Mismatch Discrimination Mechanisms of Human Dna Polymerase Beta. Nucleic Acids Res. V. 42 11233 2015.
ISSN: ESSN 1362-4962
PubMed: 25200079
DOI: 10.1093/NAR/GKU789
Page generated: Mon Dec 14 19:19:45 2020

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