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Manganese in PDB 4nxz: Dna Polymerase Beta with O6MG in the Template Base Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site

Enzymatic activity of Dna Polymerase Beta with O6MG in the Template Base Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site

All present enzymatic activity of Dna Polymerase Beta with O6MG in the Template Base Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta with O6MG in the Template Base Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site, PDB code: 4nxz was solved by M.-C.Koag, K.Min, A.F.Monzingo, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 2.56
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.803, 79.842, 55.442, 90.00, 107.05, 90.00
R / Rfree (%) 19 / 25.5

Other elements in 4nxz:

The structure of Dna Polymerase Beta with O6MG in the Template Base Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Beta with O6MG in the Template Base Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site (pdb code 4nxz). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Dna Polymerase Beta with O6MG in the Template Base Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site, PDB code: 4nxz:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4nxz

Go back to Manganese Binding Sites List in 4nxz
Manganese binding site 1 out of 2 in the Dna Polymerase Beta with O6MG in the Template Base Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase Beta with O6MG in the Template Base Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn400

b:24.2
occ:1.00
O1A A:1FZ404 1.8 30.1 1.0
OD1 A:ASP190 2.1 26.3 1.0
O A:HOH559 2.1 26.2 1.0
OD2 A:ASP192 2.3 22.8 1.0
O2B A:1FZ404 2.6 19.6 1.0
O3G A:1FZ404 3.0 28.4 1.0
O1G A:1FZ404 3.1 32.1 1.0
PA A:1FZ404 3.2 28.9 1.0
CG A:ASP190 3.2 22.1 1.0
CG A:ASP192 3.2 20.3 1.0
PG A:1FZ404 3.3 17.8 1.0
PB A:1FZ404 3.6 25.6 1.0
OD1 A:ASP192 3.6 20.8 1.0
O A:ASP190 3.6 24.5 1.0
MN A:MN401 3.7 33.3 1.0
OD2 A:ASP190 3.8 23.4 1.0
O3B A:1FZ404 3.9 31.7 1.0
N3A A:1FZ404 3.9 27.7 1.0
C A:ASP190 4.0 25.7 1.0
O5' A:1FZ404 4.0 23.6 1.0
O A:HOH558 4.1 20.4 1.0
C5' A:1FZ404 4.2 27.9 1.0
N A:ASP190 4.2 27.3 1.0
O2A A:1FZ404 4.3 28.5 1.0
CB A:ASP190 4.4 23.8 1.0
CA A:ASP190 4.4 19.5 1.0
OG A:SER180 4.4 21.9 1.0
CB A:ASP192 4.5 17.2 1.0
N A:SER180 4.5 22.1 1.0
CA A:GLY179 4.6 22.8 1.0
N A:MET191 4.7 20.7 1.0
N A:ASP192 4.8 21.8 1.0
C A:MET191 4.8 23.0 1.0
O2G A:1FZ404 4.9 28.9 1.0
CA A:MET191 5.0 23.2 1.0

Manganese binding site 2 out of 2 in 4nxz

Go back to Manganese Binding Sites List in 4nxz
Manganese binding site 2 out of 2 in the Dna Polymerase Beta with O6MG in the Template Base Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase Beta with O6MG in the Template Base Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:33.3
occ:1.00
OD2 A:ASP256 2.2 23.2 1.0
OD2 A:ASP190 2.3 23.4 1.0
O3' P:DA10 2.5 24.8 1.0
OD1 A:ASP192 2.5 20.8 1.0
O1A A:1FZ404 2.7 30.1 1.0
O2A A:1FZ404 3.1 28.5 1.0
CG A:ASP190 3.2 22.1 1.0
PA A:1FZ404 3.2 28.9 1.0
OD1 A:ASP190 3.3 26.3 1.0
CG A:ASP256 3.4 26.3 1.0
CG A:ASP192 3.4 20.3 1.0
O5' A:1FZ404 3.5 23.6 1.0
C3' P:DA10 3.6 24.5 1.0
OD2 A:ASP192 3.6 22.8 1.0
MN A:MN400 3.7 24.2 1.0
C5' P:DA10 4.2 24.0 1.0
OD1 A:ASP256 4.2 24.1 1.0
C4' P:DA10 4.2 28.0 1.0
CB A:ASP256 4.2 20.0 1.0
O5' P:DA10 4.3 26.8 1.0
C5' A:1FZ404 4.3 27.9 1.0
OP1 P:DA10 4.4 37.3 1.0
CB A:ASP190 4.6 23.8 1.0
O A:MET191 4.8 20.8 1.0
CB A:ASP192 4.8 17.2 1.0
NH2 A:ARG254 4.8 30.9 1.0
O1G A:1FZ404 4.9 32.1 1.0
N3A A:1FZ404 4.9 27.7 1.0
C2' P:DA10 4.9 20.7 1.0
P P:DA10 4.9 21.7 1.0

Reference:

M.C.Koag, S.Lee. Metal-Dependent Conformational Activation Explains Highly Promutagenic Replication Across O6-Methylguanine By Human Dna Polymerase Beta. J.Am.Chem.Soc. V. 136 5709 2014.
ISSN: ISSN 0002-7863
PubMed: 24694247
DOI: 10.1021/JA500172D
Page generated: Tue Dec 15 04:25:32 2020

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