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Magnesium in PDB 6p1o: Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Damp

Enzymatic activity of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Damp

All present enzymatic activity of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Damp:
2.7.7.7;

Protein crystallography data

The structure of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Damp, PDB code: 6p1o was solved by A.M.Kaminski, L.C.Pedersen, K.Bebenek, K.K.Chiruvella, D.A.Ramsden, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.15 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.947, 68.713, 110.724, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 18.7

Other elements in 6p1o:

The structure of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Damp also contains other interesting chemical elements:

Manganese (Mn) 1 atom
Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Damp (pdb code 6p1o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Damp, PDB code: 6p1o:

Magnesium binding site 1 out of 1 in 6p1o

Go back to Magnesium Binding Sites List in 6p1o
Magnesium binding site 1 out of 1 in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Damp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Damp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:19.6
occ:1.00
 O2G P:ATP701 2.0 19.2 0.4
OD2 A:ASP332 2.2 17.3 1.0
OD1 A:ASP330 2.2 18.2 1.0
O11 A:PPV507 2.2 21.0 0.6
O32 A:PPV507 2.3 35.2 0.6
O A:HOH745 2.3 22.6 1.0
O2B P:ATP701 2.4 35.2 0.4
OP1 P:DA5 2.5 21.1 1.0
CG A:ASP332 3.2 17.4 1.0
CG A:ASP330 3.3 24.4 1.0
PG P:ATP701 3.3 24.3 0.4
P1 A:PPV507 3.4 21.3 0.6
MN A:MN501 3.4 14.9 0.7
P2 A:PPV507 3.5 38.1 0.6
PB P:ATP701 3.5 37.0 0.4
OPP A:PPV507 3.5 26.0 0.6
O3B P:ATP701 3.6 27.9 0.4
OD1 A:ASP332 3.6 18.6 1.0
OD2 A:ASP330 3.7 22.4 1.0
P P:DA5 3.8 21.6 1.0
C5' P:DA5 3.9 16.2 1.0
O3G P:ATP701 4.0 30.5 0.4
O5' P:DA5 4.0 16.1 1.0
O A:HOH607 4.0 46.5 1.0
ND1 A:HIS329 4.2 27.9 0.5
O21 A:PPV507 4.2 24.6 0.6
O A:ASP330 4.2 18.5 1.0
O A:HOH658 4.3 20.1 1.0
CE1 A:HIS329 4.3 26.1 0.5
N A:GLY320 4.4 14.4 1.0
O22 A:PPV507 4.4 42.3 0.6
C A:ASP330 4.4 16.9 1.0
O P:HOH815 4.5 35.0 1.0
O1B P:ATP701 4.5 42.5 0.4
O1G P:ATP701 4.5 15.3 0.4
O12 A:PPV507 4.5 42.5 0.6
CB A:ASP332 4.5 13.7 1.0
CA A:GLY319 4.6 17.8 1.0
CB A:ASP330 4.6 19.7 1.0
O31 A:PPV507 4.6 23.2 0.6
OP2 P:DA5 4.7 21.6 1.0
O3A P:ATP701 4.7 43.0 0.4
N A:ASP330 4.8 17.2 1.0
O3' P:DA4 4.8 24.5 1.0
CA A:ASP330 4.9 19.0 1.0
N A:ASP332 4.9 13.8 1.0
N A:VAL331 5.0 16.1 1.0

Reference:

A.M.Kaminski, K.K.Chiruvella, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen. Unexpected Behavior of Dna Polymerase Mu Opposite Template 8-Oxo-7,8-Dihydro-2'-Guanosine. Nucleic Acids Res. V. 47 9410 2019.
ISSN: ESSN 1362-4962
PubMed: 31435651
DOI: 10.1093/NAR/GKZ680
Page generated: Tue Oct 1 13:49:15 2024

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