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Manganese in PDB 4p2h: Structure of Human Dna Polymerase Complexed with N7MG in the Template Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site

Enzymatic activity of Structure of Human Dna Polymerase Complexed with N7MG in the Template Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site

All present enzymatic activity of Structure of Human Dna Polymerase Complexed with N7MG in the Template Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Complexed with N7MG in the Template Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site, PDB code: 4p2h was solved by S.Lee, M.C.Koag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.79 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.767, 79.167, 54.982, 90.00, 106.18, 90.00
R / Rfree (%) 20.4 / 25

Other elements in 4p2h:

The structure of Structure of Human Dna Polymerase Complexed with N7MG in the Template Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site also contains other interesting chemical elements:

Fluorine (F) 1 atom
Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Human Dna Polymerase Complexed with N7MG in the Template Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site (pdb code 4p2h). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of Human Dna Polymerase Complexed with N7MG in the Template Opposite to Incoming Non-Hydrolyzable Ttp with Manganese in the Active Site, PDB code: 4p2h:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4p2h

Go back to Manganese Binding Sites List in 4p2h
Manganese binding site 1 out of 2 in the Structure of Human Dna Polymerase Complexed with N7MG in the Template 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 Structure of Human Dna Polymerase Complexed with N7MG in the Template 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:49.0
occ:1.00
OD1 A:ASP192 2.4 23.8 1.0
O3' P:DA10 2.4 24.5 1.0
O2A A:1FZ404 2.5 25.5 1.0
O A:HOH557 2.5 25.9 1.0
OD2 A:ASP190 2.7 23.4 1.0
C3' P:DA10 3.4 25.9 1.0
PA A:1FZ404 3.4 26.2 1.0
CG A:ASP190 3.4 24.7 1.0
CG A:ASP192 3.5 23.5 1.0
OD1 A:ASP190 3.5 20.0 1.0
MN A:MN401 3.5 25.0 1.0
O1A A:1FZ404 3.6 26.7 1.0
O A:HOH576 3.7 27.4 1.0
OD2 A:ASP192 3.9 26.0 1.0
O5' A:1FZ404 3.9 26.7 1.0
C4' P:DA10 4.0 22.1 1.0
O A:HOH542 4.1 32.7 1.0
O A:HOH560 4.2 30.1 1.0
OD2 A:ASP256 4.7 25.6 1.0
C5' A:1FZ404 4.7 28.7 1.0
O1G A:1FZ404 4.7 26.1 1.0
CB A:ASP192 4.7 20.1 1.0
C2' P:DA10 4.7 26.6 1.0
C5' P:DA10 4.7 23.0 1.0
CB A:ASP190 4.8 20.8 1.0
O P:HOH104 4.9 25.4 1.0
N3A A:1FZ404 4.9 22.7 1.0

Manganese binding site 2 out of 2 in 4p2h

Go back to Manganese Binding Sites List in 4p2h
Manganese binding site 2 out of 2 in the Structure of Human Dna Polymerase Complexed with N7MG in the Template 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 Structure of Human Dna Polymerase Complexed with N7MG in the Template 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:25.0
occ:1.00
O2A A:1FZ404 1.9 25.5 1.0
OD1 A:ASP190 2.1 20.0 1.0
O A:HOH544 2.2 22.8 1.0
O1B A:1FZ404 2.3 27.4 1.0
OD2 A:ASP192 2.3 26.0 1.0
O1G A:1FZ404 2.6 26.1 1.0
CG A:ASP192 3.2 23.5 1.0
PA A:1FZ404 3.2 26.2 1.0
CG A:ASP190 3.2 24.7 1.0
PG A:1FZ404 3.3 30.4 1.0
OD1 A:ASP192 3.3 23.8 1.0
PB A:1FZ404 3.3 28.9 1.0
O3G A:1FZ404 3.5 30.9 1.0
MN A:MN400 3.5 49.0 1.0
OD2 A:ASP190 3.7 23.4 1.0
O3B A:1FZ404 3.7 27.0 1.0
N3A A:1FZ404 3.7 22.7 1.0
O A:ASP190 4.1 23.0 1.0
O A:HOH560 4.1 30.1 1.0
O5' A:1FZ404 4.2 26.7 1.0
C5' A:1FZ404 4.3 28.7 1.0
O A:HOH547 4.4 23.8 1.0
O1A A:1FZ404 4.4 26.7 1.0
N A:ASP190 4.4 22.7 1.0
C A:ASP190 4.5 24.1 1.0
N A:SER180 4.5 25.0 1.0
CA A:GLY179 4.5 24.5 1.0
CB A:ASP190 4.5 20.8 1.0
CB A:ASP192 4.6 20.1 1.0
OG A:SER180 4.6 27.4 1.0
CA A:ASP190 4.7 19.3 1.0
O2G A:1FZ404 4.8 32.2 1.0
O2B A:1FZ404 4.8 27.4 1.0

Reference:

M.C.Koag, Y.Kou, H.Ouzon-Shubeita, S.Lee. Transition-State Destabilization Reveals How Human Dna Polymerase Beta Proceeds Across the Chemically Unstable Lesion N7-Methylguanine. Nucleic Acids Res. V. 42 8755 2014.
ISSN: ESSN 1362-4962
PubMed: 24966350
DOI: 10.1093/NAR/GKU554
Page generated: Sat Oct 5 20:43:49 2024

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