Magnesium in PDB 6p1q: Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp

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

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 Dcmp:
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 Dcmp, PDB code: 6p1q was solved by L.C.Pedersen, A.M.Kaminski, 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) 25.07 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.768, 68.740, 110.479, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.6

Other elements in 6p1q:

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

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 Dcmp (pdb code 6p1q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp, PDB code: 6p1q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6p1q

Go back to Magnesium Binding Sites List in 6p1q
Magnesium binding site 1 out of 2 in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp


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 Dcmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:14.8
occ:1.00
 OD2 A:ASP330 1.8 29.8 1.0
OD1 A:ASP332 1.9 20.0 1.0
OD1 A:ASP418 2.1 20.2 1.0
OP1 P:DC5 2.3 22.0 1.0
O3' P:DA4 2.7 30.4 1.0
CG A:ASP330 2.7 26.7 1.0
CG A:ASP332 2.9 17.6 1.0
OD1 A:ASP330 3.0 17.9 1.0
P P:DC5 3.0 29.8 1.0
CG A:ASP418 3.1 20.6 1.0
OD2 A:ASP332 3.2 16.7 1.0
MG A:MG502 3.4 16.7 1.0
CB A:ASP418 3.7 17.3 1.0
C3' P:DA4 3.8 20.8 1.0
C4' P:DA4 3.9 23.9 1.0
C5' P:DA4 3.9 25.2 1.0
OP2 P:DC5 4.1 24.2 1.0
CB A:ASP330 4.1 18.7 1.0
OD2 A:ASP418 4.1 21.8 1.0
O5' P:DC5 4.2 25.6 1.0
CB A:ASP332 4.2 11.4 1.0
C5' P:DC5 4.3 18.6 1.0
CE1 A:HIS329 4.5 33.5 0.8
NH2 A:ARG416 4.6 22.0 1.0
O12 A:PPV507 4.7 35.0 0.9
CZ3 A:TRP434 4.8 25.2 1.0
CA A:ASP332 4.8 13.6 1.0
O A:VAL331 4.8 14.7 1.0
O5' P:DA4 4.9 29.4 1.0
C A:VAL331 4.9 16.5 1.0
CA A:ASP418 4.9 17.1 1.0
N A:ASP418 5.0 14.8 1.0
N A:ASP332 5.0 15.8 1.0
C2' P:DA4 5.0 27.8 1.0
OP1 P:DA4 5.0 18.8 1.0

Magnesium binding site 2 out of 2 in 6p1q

Go back to Magnesium Binding Sites List in 6p1q
Magnesium binding site 2 out of 2 in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:16.7
occ:1.00
 OD1 A:ASP330 2.1 17.9 1.0
OD2 A:ASP332 2.1 16.7 1.0
O21 A:PPV507 2.1 15.4 0.9
OP1 P:DC5 2.1 22.0 1.0
O A:HOH694 2.2 23.7 1.0
O12 A:PPV507 2.3 35.0 0.9
CG A:ASP332 3.1 17.6 1.0
CG A:ASP330 3.2 26.7 1.0
P1 A:PPV507 3.2 22.1 0.9
O31 A:PPV507 3.3 27.9 0.9
MG A:MG501 3.4 14.8 1.0
P2 A:PPV507 3.5 44.9 0.9
OD1 A:ASP332 3.6 20.0 1.0
P P:DC5 3.6 29.8 1.0
OD2 A:ASP330 3.6 29.8 1.0
OPP A:PPV507 3.8 37.5 0.9
O5' P:DC5 4.0 25.6 1.0
O32 A:PPV507 4.0 39.0 0.9
C5' P:DC5 4.1 18.6 1.0
O A:ASP330 4.1 16.1 1.0
O A:HOH621 4.2 16.6 1.0
ND1 A:HIS329 4.3 31.1 0.8
O A:HOH616 4.3 29.2 1.0
N A:GLY320 4.3 15.3 1.0
CE1 A:HIS329 4.3 33.5 0.8
C A:ASP330 4.4 15.5 1.0
CB A:ASP332 4.5 11.4 1.0
CB A:ASP330 4.5 18.7 1.0
O11 A:PPV507 4.5 19.3 0.9
O3' P:DA4 4.5 30.4 1.0
OP2 P:DC5 4.6 24.2 1.0
CA A:GLY319 4.6 15.3 1.0
O22 A:PPV507 4.7 45.5 0.9
N A:ASP330 4.8 16.0 1.0
CA A:ASP330 4.8 18.4 1.0
N A:ASP332 4.9 15.8 1.0
N A:VAL331 5.0 15.3 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: Mon Dec 14 23:45:37 2020

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