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Magnesium in PDB 7mz1: Structure of Human Dna Polymerase Beta Complexed with Dza in the Template Base Paired with Incoming Non-Hydrolyzable Ttp

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

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with Dza 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 Dza in the Template Base Paired with Incoming Non-Hydrolyzable Ttp, PDB code: 7mz1 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) 19.96 / 2.18
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.319, 79.839, 55.324, 90, 107.29, 90
R / Rfree (%) 20.1 / 25.9

Other elements in 7mz1:

The structure of Structure of Human Dna Polymerase Beta Complexed with Dza 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 Dza in the Template Base Paired with Incoming Non-Hydrolyzable Ttp (pdb code 7mz1). 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 Dza in the Template Base Paired with Incoming Non-Hydrolyzable Ttp, PDB code: 7mz1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7mz1

Go back to Magnesium Binding Sites List in 7mz1
Magnesium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with Dza 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 Dza in the Template Base Paired with Incoming Non-Hydrolyzable Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg400

b:23.8
occ:1.00
 O1G A:1FZ404 2.0 22.3 1.0
OD1 A:ASP190 2.0 26.1 1.0
OD2 A:ASP192 2.0 22.6 1.0
O1A A:1FZ404 2.1 18.2 1.0
O2B A:1FZ404 2.1 17.6 1.0
O A:HOH515 2.2 23.3 1.0
PB A:1FZ404 3.1 18.8 1.0
CG A:ASP192 3.1 20.0 1.0
CG A:ASP190 3.2 24.6 1.0
PA A:1FZ404 3.3 20.2 1.0
PG A:1FZ404 3.3 21.8 1.0
OD1 A:ASP192 3.5 25.9 1.0
O3B A:1FZ404 3.5 20.4 1.0
N3A A:1FZ404 3.7 18.6 1.0
OD2 A:ASP190 3.7 29.9 1.0
MG A:MG401 3.7 30.1 1.0
O3G A:1FZ404 4.0 21.9 1.0
O A:ASP190 4.0 24.9 1.0
O A:HOH553 4.0 23.1 1.0
N A:ASP190 4.2 20.7 1.0
C A:ASP190 4.2 25.7 1.0
O A:HOH529 4.3 20.4 1.0
C5' A:1FZ404 4.3 20.1 1.0
O2G A:1FZ404 4.4 23.3 1.0
O5' A:1FZ404 4.4 20.1 1.0
CB A:ASP190 4.4 26.5 1.0
CB A:ASP192 4.4 26.2 1.0
OG A:SER180 4.5 22.6 1.0
O2A A:1FZ404 4.5 22.7 1.0
CA A:ASP190 4.5 24.5 1.0
O1B A:1FZ404 4.5 17.4 1.0
N A:SER180 4.5 22.9 1.0
CA A:GLY179 4.6 21.6 1.0
O A:HOH519 4.8 34.2 1.0
N A:MET191 4.8 23.6 1.0
N A:ASP192 4.9 23.9 1.0
C A:MET191 5.0 26.2 1.0

Magnesium binding site 2 out of 2 in 7mz1

Go back to Magnesium Binding Sites List in 7mz1
Magnesium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with Dza 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 Dza in the Template Base Paired with Incoming Non-Hydrolyzable Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:30.1
occ:1.00
 OD2 A:ASP256 2.2 34.5 1.0
OD1 A:ASP192 2.3 25.9 1.0
OD2 A:ASP190 2.3 29.9 1.0
O A:HOH519 2.5 34.2 1.0
O1A A:1FZ404 2.6 18.2 1.0
CG A:ASP190 3.0 24.6 1.0
OD1 A:ASP190 3.2 26.1 1.0
CG A:ASP192 3.3 20.0 1.0
CG A:ASP256 3.4 30.7 1.0
C3' P:DA10 3.4 31.8 1.0
O3' P:DA10 3.5 34.7 1.0
PA A:1FZ404 3.6 20.2 1.0
OD2 A:ASP192 3.6 22.6 1.0
MG A:MG400 3.7 23.8 1.0
O2A A:1FZ404 4.0 22.7 1.0
O5' A:1FZ404 4.0 20.1 1.0
CB A:ASP256 4.0 29.0 1.0
O A:HOH553 4.2 23.1 1.0
CB A:ASP190 4.3 26.5 1.0
C5' A:1FZ404 4.3 20.1 1.0
OD1 A:ASP256 4.3 28.1 1.0
OP1 P:DA10 4.4 31.0 1.0
C4' P:DA10 4.4 31.9 1.0
O A:MET191 4.5 22.9 1.0
C2' P:DA10 4.5 29.5 1.0
C5' P:DA10 4.5 29.9 1.0
NH2 A:ARG254 4.6 27.2 1.0
O5' P:DA10 4.6 30.9 1.0
CB A:ASP192 4.7 26.2 1.0
O1G A:1FZ404 4.9 22.3 1.0
N A:ASP256 5.0 22.7 1.0

Reference:

M.-C.Koag, S.Lee. Structure of Human Dna Polymerase Beta Complexed with Dza in the Template Base Paired with Incoming Non-Hydrolyzable Ttp To Be Published.
Page generated: Thu Oct 3 01:11:30 2024

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