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Manganese in PDB 6cub: Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Atp and Manganese

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Atp and Manganese

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Atp and Manganese:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Atp and Manganese, PDB code: 6cub 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) 19.75 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.786, 78.993, 54.771, 90.00, 105.91, 90.00
R / Rfree (%) 19.7 / 25.4

Other elements in 6cub:

The structure of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Atp and Manganese also contains other interesting chemical elements:

Chlorine (Cl) 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 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Atp and Manganese (pdb code 6cub). 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 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Atp and Manganese, PDB code: 6cub:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6cub

Go back to Manganese Binding Sites List in 6cub
Manganese binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Atp and Manganese


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 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Atp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:22.7
occ:1.00
O1A A:DZ4401 2.1 22.7 1.0
OD1 A:ASP190 2.1 19.1 1.0
O1B A:DZ4401 2.2 24.2 1.0
O2G A:DZ4401 2.2 24.4 1.0
O A:HOH576 2.3 19.8 1.0
OD2 A:ASP192 2.3 26.2 1.0
CG A:ASP190 3.2 20.5 1.0
PB A:DZ4401 3.3 26.1 1.0
CG A:ASP192 3.3 25.3 1.0
PG A:DZ4401 3.3 27.1 1.0
PA A:DZ4401 3.4 26.9 1.0
MN A:MN403 3.5 49.3 1.0
OD1 A:ASP192 3.5 22.4 1.0
OD2 A:ASP190 3.6 20.7 1.0
O3B A:DZ4401 3.6 25.4 1.0
N3A A:DZ4401 3.8 21.3 1.0
O1G A:DZ4401 3.9 27.8 1.0
O A:ASP190 4.1 20.2 1.0
O A:HOH551 4.1 27.9 1.0
C5' A:DZ4401 4.3 29.4 1.0
O5' A:DZ4401 4.3 26.9 1.0
N A:ASP190 4.4 19.2 1.0
C A:ASP190 4.4 20.2 1.0
OG A:SER180 4.4 23.0 1.0
N A:SER180 4.5 24.6 1.0
CB A:ASP190 4.5 19.3 1.0
CA A:GLY179 4.5 23.2 1.0
O2A A:DZ4401 4.6 29.6 1.0
O A:HOH531 4.6 22.0 1.0
CB A:ASP192 4.6 18.3 1.0
O2B A:DZ4401 4.6 23.0 1.0
CA A:ASP190 4.7 19.1 1.0
O3G A:DZ4401 4.7 29.7 1.0

Manganese binding site 2 out of 2 in 6cub

Go back to Manganese Binding Sites List in 6cub
Manganese binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Atp and Manganese


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 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Atp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:49.3
occ:1.00
OD1 A:ASP192 2.4 22.4 1.0
O1A A:DZ4401 2.4 22.7 1.0
OD2 A:ASP190 2.5 20.7 1.0
O3' P:DA10 2.7 33.5 1.0
CG A:ASP190 3.2 20.5 1.0
OD1 A:ASP190 3.2 19.1 1.0
CG A:ASP192 3.4 25.3 1.0
PA A:DZ4401 3.5 26.9 1.0
MN A:MN402 3.5 22.7 1.0
OD2 A:ASP192 3.7 26.2 1.0
O2A A:DZ4401 3.8 29.6 1.0
O5' A:DZ4401 3.9 26.9 1.0
C3' P:DA10 4.0 41.0 1.0
O A:HOH551 4.2 27.9 1.0
C4' P:DA10 4.3 31.1 1.0
OD2 A:ASP256 4.4 25.7 1.0
C5' P:DA10 4.6 28.1 1.0
C5' A:DZ4401 4.6 29.4 1.0
CB A:ASP190 4.6 19.3 1.0
O2G A:DZ4401 4.6 24.4 1.0
O P:HOH106 4.7 26.9 1.0
CB A:ASP192 4.7 18.3 1.0
O1B A:DZ4401 4.9 24.2 1.0
CG A:ASP256 5.0 22.3 1.0

Reference:

M.-C.Koag, S.Lee. Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Atp and Manganese To Be Published.
Page generated: Tue Dec 15 04:51:26 2020

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