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Magnesium in PDB 4o5k: Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp

Enzymatic activity of Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp

All present enzymatic activity of Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 4o5k 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) 19.87 / 2.06
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.870, 79.568, 55.670, 90.00, 107.71, 90.00
R / Rfree (%) 20 / 25.2

Other elements in 4o5k:

The structure of Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp (pdb code 4o5k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 4o5k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4o5k

Go back to Magnesium Binding Sites List in 4o5k
Magnesium binding site 1 out of 2 in the Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:13.2
occ:1.00
O1A A:0KX405 1.9 14.7 1.0
O1G A:0KX405 2.0 18.2 1.0
OD1 A:ASP190 2.0 15.8 1.0
OD2 A:ASP192 2.1 13.3 1.0
O A:HOH621 2.1 10.0 1.0
O2B A:0KX405 2.1 12.9 1.0
CG A:ASP190 3.1 18.6 1.0
CG A:ASP192 3.1 14.0 1.0
PB A:0KX405 3.1 15.8 1.0
PA A:0KX405 3.2 15.2 1.0
PG A:0KX405 3.3 16.5 1.0
OD1 A:ASP192 3.4 17.0 1.0
OD2 A:ASP190 3.5 19.4 1.0
O3B A:0KX405 3.6 16.4 1.0
MG A:MG402 3.6 21.6 1.0
N3A A:0KX405 3.8 17.1 1.0
O A:ASP190 4.1 14.3 1.0
O5' A:0KX405 4.1 17.9 1.0
C5' A:0KX405 4.1 16.0 1.0
O3G A:0KX405 4.2 13.4 1.0
C A:ASP190 4.3 17.4 1.0
N A:ASP190 4.3 16.3 1.0
O A:HOH622 4.3 17.0 1.0
O2G A:0KX405 4.4 20.2 1.0
CB A:ASP190 4.4 14.3 1.0
O2A A:0KX405 4.4 17.7 1.0
OG A:SER180 4.4 15.7 1.0
CB A:ASP192 4.4 15.8 1.0
N A:SER180 4.5 16.3 1.0
CA A:ASP190 4.5 15.7 1.0
CA A:GLY179 4.6 15.8 1.0
O1B A:0KX405 4.6 17.5 1.0
O A:HOH626 4.7 30.4 1.0
N A:ASP192 4.8 14.4 1.0
N A:MET191 4.8 15.0 1.0
O A:HOH575 4.9 23.7 1.0
O A:HOH635 5.0 30.0 1.0

Magnesium binding site 2 out of 2 in 4o5k

Go back to Magnesium Binding Sites List in 4o5k
Magnesium binding site 2 out of 2 in the Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Dna Polymerase Complexed with N7MG in the Template Base Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:21.6
occ:1.00
OD1 A:ASP192 2.3 17.0 1.0
O A:HOH635 2.4 30.0 1.0
OD2 A:ASP190 2.4 19.4 1.0
O A:HOH575 2.5 23.7 1.0
OD2 A:ASP256 2.6 25.2 1.0
O1A A:0KX405 2.7 14.7 1.0
CG A:ASP190 3.0 18.6 1.0
OD1 A:ASP190 3.1 15.8 1.0
CG A:ASP192 3.3 14.0 1.0
O3' P:DA10 3.6 27.3 1.0
C3' P:DA10 3.6 21.7 1.0
PA A:0KX405 3.6 15.2 1.0
MG A:MG401 3.6 13.2 1.0
CG A:ASP256 3.6 23.2 1.0
OD2 A:ASP192 3.7 13.3 1.0
O5' A:0KX405 3.9 17.9 1.0
O2A A:0KX405 3.9 17.7 1.0
CB A:ASP256 4.2 18.0 1.0
CB A:ASP190 4.3 14.3 1.0
C5' A:0KX405 4.4 16.0 1.0
C4' P:DA10 4.6 20.9 1.0
OD1 A:ASP256 4.6 21.2 1.0
C2' P:DA10 4.6 21.3 1.0
OP1 P:DA10 4.6 20.7 1.0
CB A:ASP192 4.6 15.8 1.0
C5' P:DA10 4.7 20.8 1.0
O A:MET191 4.7 16.5 1.0
O5' P:DA10 4.7 24.1 1.0
NH2 A:ARG254 4.7 20.2 1.0
O1G A:0KX405 5.0 18.2 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: ISSN 0305-1048
PubMed: 24966350
DOI: 10.1093/NAR/GKU554
Page generated: Mon Dec 14 19:16:57 2020

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