Magnesium in PDB 6p1r: Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp

Enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp:
2.7.7.7;

Protein crystallography data

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp, PDB code: 6p1r 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) 31.37 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.889, 68.770, 110.489, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 19.4

Other elements in 6p1r:

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp 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 Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp (pdb code 6p1r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp, PDB code: 6p1r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6p1r

Go back to Magnesium Binding Sites List in 6p1r
Magnesium binding site 1 out of 2 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp


Mono view


Stereo pair view

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

b:14.4
occ:1.00
 OD2 A:ASP330 2.0 20.4 1.0
O A:HOH662 2.0 12.2 0.4
OD2 A:ASP418 2.0 20.2 1.0
OD1 A:ASP332 2.0 16.8 1.0
O P:HOH105 2.1 19.9 1.0
O2A A:ZAN501 2.3 16.5 1.0
O3' P:DA4 2.3 24.3 0.6
CG A:ASP330 3.0 18.3 1.0
CG A:ASP332 3.1 14.7 1.0
CG A:ASP418 3.1 18.8 1.0
C3' P:DA4 3.4 19.8 0.6
PA A:ZAN501 3.4 17.3 1.0
OD1 A:ASP330 3.4 15.8 1.0
OD2 A:ASP332 3.5 15.9 1.0
MG A:MG503 3.6 15.0 1.0
O5' A:ZAN501 3.8 17.9 1.0
CB A:ASP418 3.8 17.3 1.0
O1A A:ZAN501 3.8 19.4 1.0
C4' P:DA4 3.9 20.2 0.6
C5' P:DA4 4.0 18.9 0.6
C5' A:ZAN501 4.0 17.2 1.0
CE1 A:HIS329 4.1 18.0 0.8
OD1 A:ASP418 4.2 20.3 1.0
CB A:ASP330 4.4 16.4 1.0
CB A:ASP332 4.4 13.3 1.0
OP1 P:DA4 4.4 19.2 0.6
O5' P:DA4 4.4 23.2 0.6
OP1 P:DA4 4.5 19.1 0.4
NH2 A:ARG416 4.5 22.0 1.0
C2' P:DA4 4.7 18.8 0.6
ND1 A:HIS329 4.9 16.9 0.6
O2G A:ZAN501 4.9 18.3 1.0
N3A A:ZAN501 4.9 16.5 1.0

Magnesium binding site 2 out of 2 in 6p1r

Go back to Magnesium Binding Sites List in 6p1r
Magnesium binding site 2 out of 2 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:15.0
occ:1.00
 OD2 A:ASP332 2.0 15.9 1.0
OD1 A:ASP330 2.0 15.8 1.0
O2B A:ZAN501 2.1 15.8 1.0
O A:HOH725 2.1 18.3 1.0
O2G A:ZAN501 2.2 18.3 1.0
O2A A:ZAN501 2.2 16.5 1.0
CG A:ASP332 3.1 14.7 1.0
CG A:ASP330 3.1 18.3 1.0
PB A:ZAN501 3.1 16.9 1.0
PA A:ZAN501 3.3 17.3 1.0
PG A:ZAN501 3.4 17.8 1.0
OD1 A:ASP332 3.5 16.8 1.0
N3A A:ZAN501 3.5 16.5 1.0
OD2 A:ASP330 3.5 20.4 1.0
O3B A:ZAN501 3.6 16.2 1.0
MG A:MG502 3.6 14.4 1.0
O A:ASP330 4.0 17.4 1.0
ND1 A:HIS329 4.0 16.9 0.6
C5' A:ZAN501 4.1 17.2 1.0
O A:HOH621 4.2 19.4 1.0
O3G A:ZAN501 4.2 20.2 1.0
O A:HOH616 4.2 16.5 1.0
O5' A:ZAN501 4.3 17.9 1.0
C A:ASP330 4.3 17.0 1.0
N A:GLY320 4.3 14.5 1.0
CE1 A:HIS329 4.3 18.0 0.8
CB A:ASP332 4.4 13.3 1.0
CB A:ASP330 4.4 16.4 1.0
O1A A:ZAN501 4.5 19.4 1.0
O1B A:ZAN501 4.5 17.7 1.0
N A:ASP330 4.5 17.1 1.0
O1G A:ZAN501 4.6 19.6 1.0
CA A:ASP330 4.6 17.9 1.0
CA A:GLY319 4.6 14.7 1.0
N A:ASP332 4.7 14.9 1.0
O P:HOH105 4.8 19.9 1.0
N A:VAL331 4.8 15.3 1.0
O A:HOH662 4.9 12.2 0.4
C 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 23:45:38 2020

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