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Manganese in PDB 6cu9: Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp and Manganese

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp 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 Ctp 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 Ctp and Manganese, PDB code: 6cu9 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) 19.82 / 2.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.707, 80.049, 55.602, 90.00, 107.70, 90.00
R / Rfree (%) 19.4 / 24.1

Other elements in 6cu9:

The structure of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp 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 Ctp and Manganese (pdb code 6cu9). 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 Ctp and Manganese, PDB code: 6cu9:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6cu9

Go back to Manganese Binding Sites List in 6cu9
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 Ctp 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 Ctp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:14.7
occ:1.00
OD2 A:ASP192 2.0 14.9 1.0
OD1 A:ASP190 2.1 16.1 1.0
O2A A:0KX405 2.1 17.3 1.0
O1B A:0KX405 2.1 14.3 1.0
O1G A:0KX405 2.1 16.2 1.0
O A:HOH540 2.3 11.6 1.0
CG A:ASP192 3.0 14.0 1.0
PB A:0KX405 3.1 16.8 1.0
CG A:ASP190 3.1 17.1 1.0
PA A:0KX405 3.3 17.8 1.0
OD1 A:ASP192 3.3 14.5 1.0
PG A:0KX405 3.5 17.4 1.0
OD2 A:ASP190 3.6 15.7 1.0
MN A:MN402 3.6 17.6 1.0
N3A A:0KX405 3.7 17.4 1.0
O3B A:0KX405 3.7 16.1 1.0
O A:ASP190 4.0 15.8 1.0
C5' A:0KX405 4.2 19.4 1.0
O5' A:0KX405 4.2 17.8 1.0
O A:HOH525 4.2 19.3 1.0
O2G A:0KX405 4.2 16.3 1.0
OG A:SER180 4.3 17.9 1.0
N A:ASP190 4.3 15.2 1.0
O A:HOH522 4.3 18.7 1.0
C A:ASP190 4.3 14.6 1.0
CB A:ASP192 4.4 17.3 1.0
N A:SER180 4.4 15.3 1.0
CB A:ASP190 4.4 15.4 1.0
CA A:GLY179 4.5 16.8 1.0
O2B A:0KX405 4.5 16.8 1.0
O1A A:0KX405 4.5 17.8 1.0
CA A:ASP190 4.6 15.2 1.0
O3G A:0KX405 4.6 19.1 1.0
O P:HOH104 4.7 17.9 1.0
N A:ASP192 4.7 16.1 1.0
N A:MET191 4.9 14.9 1.0
C A:MET191 4.9 14.9 1.0
C A:GLY179 5.0 17.6 1.0

Manganese binding site 2 out of 2 in 6cu9

Go back to Manganese Binding Sites List in 6cu9
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 Ctp 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 Ctp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:17.6
occ:1.00
OD2 A:ASP256 2.0 19.0 1.0
OD1 A:ASP192 2.1 14.5 1.0
OD2 A:ASP190 2.1 15.7 1.0
O P:HOH104 2.1 17.9 1.0
O3' P:DA10 2.3 13.9 1.0
O2A A:0KX405 2.3 17.3 1.0
CG A:ASP190 3.1 17.1 1.0
CG A:ASP256 3.1 20.5 1.0
CG A:ASP192 3.2 14.0 1.0
PA A:0KX405 3.3 17.8 1.0
OD1 A:ASP190 3.4 16.1 1.0
C3' P:DA10 3.5 17.7 1.0
OD2 A:ASP192 3.6 14.9 1.0
MN A:MN401 3.6 14.7 1.0
O5' A:0KX405 3.6 17.8 1.0
O1A A:0KX405 3.7 17.8 1.0
CB A:ASP256 3.9 22.5 1.0
C5' A:0KX405 4.1 19.4 1.0
OD1 A:ASP256 4.1 29.3 1.0
C4' P:DA10 4.2 19.0 1.0
C5' P:DA10 4.2 19.6 1.0
CB A:ASP190 4.5 15.4 1.0
OP1 P:DA10 4.5 20.7 1.0
CB A:ASP192 4.5 17.3 1.0
O A:HOH525 4.6 19.3 1.0
NH1 A:ARG254 4.7 24.9 1.0
O5' P:DA10 4.7 17.6 1.0
O A:MET191 4.7 15.6 1.0
C2' P:DA10 4.7 16.8 1.0
O1G A:0KX405 4.8 16.2 1.0
N3A A:0KX405 5.0 17.4 1.0
O1B A:0KX405 5.0 14.3 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 Ctp and Manganese To Be Published.
Page generated: Sun Oct 6 04:00:13 2024

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