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Manganese in PDB 4yn4: Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site, PDB code: 4yn4 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) 19.80 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.774, 79.179, 55.031, 90.00, 106.53, 90.00
R / Rfree (%) 20.3 / 25.5

Other elements in 4yn4:

The structure of Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp 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 Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site (pdb code 4yn4). 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 Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site, PDB code: 4yn4:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4yn4

Go back to Manganese Binding Sites List in 4yn4
Manganese binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp 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 Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn400

b:58.5
occ:1.00
 O A:HOH588 2.4 34.1 1.0
OD1 A:ASP192 2.4 25.0 1.0
O2A A:1FZ404 2.5 32.3 1.0
OD2 A:ASP190 2.5 29.1 1.0
O3' P:DA10 2.6 27.1 1.0
CG A:ASP190 3.2 27.4 1.0
OD1 A:ASP190 3.3 22.6 1.0
CG A:ASP192 3.3 26.4 1.0
O A:HOH571 3.5 32.4 1.0
C3' P:DA10 3.5 31.0 1.0
PA A:1FZ404 3.5 33.5 1.0
MN A:MN401 3.5 32.9 1.0
OD2 A:ASP192 3.6 27.4 1.0
O1A A:1FZ404 3.7 36.5 1.0
O A:HOH543 4.0 34.0 1.0
O5' A:1FZ404 4.0 33.4 1.0
C4' P:DA10 4.1 27.6 1.0
C5' A:1FZ404 4.5 34.9 1.0
OD2 A:ASP256 4.6 33.6 1.0
CB A:ASP190 4.6 21.5 1.0
O1G A:1FZ404 4.6 29.2 1.0
CB A:ASP192 4.7 22.3 1.0
C5' P:DA10 4.8 31.1 1.0
C2' P:DA10 4.9 31.6 1.0

Manganese binding site 2 out of 2 in 4yn4

Go back to Manganese Binding Sites List in 4yn4
Manganese binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp 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 Beta Complexed with N7BG in the Template Opposite to Incoming Non-Hydrolyzable Dttp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:32.9
occ:1.00
 OD1 A:ASP190 2.1 22.6 1.0
O2A A:1FZ404 2.1 32.3 1.0
O1B A:1FZ404 2.2 29.9 1.0
O1G A:1FZ404 2.2 29.2 1.0
O A:HOH584 2.2 31.0 1.0
OD2 A:ASP192 2.3 27.4 1.0
PB A:1FZ404 3.2 30.7 1.0
CG A:ASP190 3.2 27.4 1.0
CG A:ASP192 3.2 26.4 1.0
PG A:1FZ404 3.3 30.7 1.0
PA A:1FZ404 3.4 33.5 1.0
OD1 A:ASP192 3.5 25.0 1.0
MN A:MN400 3.5 58.5 1.0
O3B A:1FZ404 3.6 28.6 1.0
OD2 A:ASP190 3.6 29.1 1.0
N3A A:1FZ404 3.8 32.4 1.0
O3G A:1FZ404 3.9 31.9 1.0
O A:HOH543 4.0 34.0 1.0
O A:ASP190 4.1 27.0 1.0
N A:ASP190 4.3 24.4 1.0
C5' A:1FZ404 4.4 34.9 1.0
O5' A:1FZ404 4.4 33.4 1.0
O A:HOH585 4.4 27.2 1.0
C A:ASP190 4.4 32.2 1.0
CA A:GLY179 4.4 31.3 1.0
CB A:ASP190 4.5 21.5 1.0
N A:SER180 4.5 31.7 1.0
CB A:ASP192 4.6 22.3 1.0
O1A A:1FZ404 4.6 36.5 1.0
O2G A:1FZ404 4.6 32.1 1.0
O2B A:1FZ404 4.6 34.2 1.0
CA A:ASP190 4.6 25.1 1.0
OG A:SER180 4.8 30.6 1.0
N A:ASP192 5.0 22.6 1.0

Reference:

Y.Kou, M.C.Koag, S.Lee. Structural and Kinetic Studies of the Effect of Guanine-N7 Alkylation and Metal Cofactors on Dna Replication. Biochemistry 2018.
ISSN: ISSN 1520-4995
PubMed: 29957995
DOI: 10.1021/ACS.BIOCHEM.8B00331
Page generated: Sat Aug 16 16:33:35 2025

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