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Manganese in PDB 4ny8: Dna Polymerase Beta with O6MG in the Template Base Opposite to Incoming Non-Hydrolyzable Ctp with Manganese in the Active Site

Enzymatic activity of Dna Polymerase Beta with O6MG in the Template Base Opposite to Incoming Non-Hydrolyzable Ctp 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 Ctp 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 Ctp with Manganese in the Active Site, PDB code: 4ny8 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) 19.82 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.625, 79.288, 54.838, 90.00, 105.97, 90.00
R / Rfree (%) 20.6 / 26.5

Other elements in 4ny8:

The structure of Dna Polymerase Beta with O6MG in the Template Base Opposite to Incoming Non-Hydrolyzable Ctp 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 Ctp with Manganese in the Active Site (pdb code 4ny8). 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 Ctp with Manganese in the Active Site, PDB code: 4ny8:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4ny8

Go back to Manganese Binding Sites List in 4ny8
Manganese binding site 1 out of 2 in the Dna Polymerase Beta with O6MG in the Template Base Opposite to Incoming Non-Hydrolyzable Ctp 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 Ctp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:26.8
occ:1.00
O1A A:0KX405 1.7 34.9 1.0
OD1 A:ASP190 2.1 17.1 1.0
O A:HOH507 2.3 23.6 1.0
OD2 A:ASP192 2.3 26.0 1.0
O3G A:0KX405 2.6 40.9 1.0
O2B A:0KX405 2.6 26.1 1.0
O1G A:0KX405 3.1 38.1 1.0
PA A:0KX405 3.2 33.0 1.0
CG A:ASP190 3.2 19.6 1.0
CG A:ASP192 3.3 29.0 1.0
PG A:0KX405 3.4 27.0 1.0
MN A:MN402 3.5 53.7 1.0
PB A:0KX405 3.6 28.4 1.0
OD2 A:ASP190 3.6 22.8 1.0
OD1 A:ASP192 3.6 27.0 1.0
O3B A:0KX405 3.9 32.7 1.0
N3A A:0KX405 3.9 22.6 1.0
O5' A:0KX405 4.1 30.4 1.0
O A:ASP190 4.2 18.6 1.0
C5' A:0KX405 4.2 34.2 1.0
O2A A:0KX405 4.3 41.8 1.0
O A:HOH503 4.4 23.6 1.0
N A:ASP190 4.4 16.8 1.0
CA A:GLY179 4.4 26.5 1.0
C A:ASP190 4.5 20.1 1.0
CB A:ASP190 4.5 16.1 1.0
N A:SER180 4.5 24.6 1.0
CA A:ASP190 4.7 18.3 1.0
CB A:ASP192 4.7 16.8 1.0
O2G A:0KX405 4.7 37.8 1.0
OG A:SER180 4.8 25.9 1.0

Manganese binding site 2 out of 2 in 4ny8

Go back to Manganese Binding Sites List in 4ny8
Manganese binding site 2 out of 2 in the Dna Polymerase Beta with O6MG in the Template Base Opposite to Incoming Non-Hydrolyzable Ctp 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 Ctp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:53.7
occ:1.00
OD1 A:ASP192 2.5 27.0 1.0
O A:HOH584 2.5 26.0 1.0
O1A A:0KX405 2.7 34.9 1.0
OD2 A:ASP190 2.7 22.8 1.0
O3' P:DA10 3.1 48.1 1.0
O2A A:0KX405 3.2 41.8 1.0
PA A:0KX405 3.2 33.0 1.0
CG A:ASP190 3.4 19.6 1.0
CG A:ASP192 3.4 29.0 1.0
OD1 A:ASP190 3.5 17.1 1.0
MN A:MN401 3.5 26.8 1.0
O5' A:0KX405 3.6 30.4 1.0
OD2 A:ASP192 3.7 26.0 1.0
C3' P:DA10 4.0 40.4 1.0
C5' P:DA10 4.0 31.1 1.0
C4' P:DA10 4.3 28.2 1.0
C5' A:0KX405 4.3 34.2 1.0
OD2 A:ASP256 4.5 20.5 1.0
CB A:ASP190 4.8 16.1 1.0
CB A:ASP192 4.8 16.8 1.0
N3A A:0KX405 4.9 22.6 1.0
O1G A:0KX405 4.9 38.1 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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