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Magnesium in PDB 6p1v: Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Dcmpnpp

Enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Dcmpnpp

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Dcmpnpp:
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 Undamaged Template Dg and Bound Incoming Dcmpnpp, PDB code: 6p1v 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) 31.30 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.902, 68.606, 110.125, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.4

Other elements in 6p1v:

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Dcmpnpp 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 Undamaged Template Dg and Bound Incoming Dcmpnpp (pdb code 6p1v). 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 Undamaged Template Dg and Bound Incoming Dcmpnpp, PDB code: 6p1v:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6p1v

Go back to Magnesium Binding Sites List in 6p1v
Magnesium binding site 1 out of 2 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Dcmpnpp


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 Undamaged Template Dg and Bound Incoming Dcmpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:15.1
occ:1.00
 OD2 A:ASP330 2.0 17.4 1.0
OD2 A:ASP418 2.0 16.7 1.0
OD1 A:ASP332 2.1 15.1 1.0
O P:HOH102 2.1 17.7 1.0
O3' P:DA4 2.2 14.3 1.0
O2A A:0KX501 2.4 13.7 1.0
CG A:ASP332 3.1 13.5 1.0
CG A:ASP330 3.1 15.8 1.0
CG A:ASP418 3.2 16.6 1.0
C3' P:DA4 3.3 15.0 1.0
PA A:0KX501 3.4 15.4 1.0
OD2 A:ASP332 3.5 13.4 1.0
OD1 A:ASP330 3.5 15.4 1.0
O1A A:0KX501 3.6 16.4 1.0
MG A:MG503 3.7 15.0 1.0
O5' A:0KX501 3.7 14.3 1.0
C4' P:DA4 3.9 15.4 1.0
CB A:ASP418 3.9 16.2 1.0
C5' P:DA4 3.9 17.3 1.0
C5' A:0KX501 4.0 12.9 1.0
CE1 A:HIS329 4.1 13.8 0.8
OD1 A:ASP418 4.2 18.0 1.0
OP1 P:DA4 4.3 17.9 1.0
CB A:ASP330 4.4 15.7 1.0
CB A:ASP332 4.4 13.0 1.0
O5' P:DA4 4.5 19.4 1.0
CZ3 A:TRP434 4.6 17.5 1.0
C2' P:DA4 4.6 14.6 1.0
NH2 A:ARG416 4.6 15.9 1.0
O1G A:0KX501 4.8 15.6 1.0
ND1 A:HIS329 4.8 15.1 0.5
N3A A:0KX501 4.9 15.7 1.0
O1B A:0KX501 4.9 15.2 1.0

Magnesium binding site 2 out of 2 in 6p1v

Go back to Magnesium Binding Sites List in 6p1v
Magnesium binding site 2 out of 2 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Dcmpnpp


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 Undamaged Template Dg and Bound Incoming Dcmpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:15.0
occ:1.00
 O1B A:0KX501 2.0 15.2 1.0
OD1 A:ASP330 2.0 15.4 1.0
O1G A:0KX501 2.1 15.6 1.0
OD2 A:ASP332 2.1 13.4 1.0
O2A A:0KX501 2.1 13.7 1.0
O A:HOH710 2.2 15.3 1.0
CG A:ASP330 3.1 15.8 1.0
PB A:0KX501 3.1 16.1 1.0
CG A:ASP332 3.2 13.5 1.0
PA A:0KX501 3.3 15.4 1.0
PG A:0KX501 3.3 18.3 1.0
OD2 A:ASP330 3.5 17.4 1.0
N3A A:0KX501 3.5 15.7 1.0
OD1 A:ASP332 3.5 15.1 1.0
O3B A:0KX501 3.6 16.0 1.0
MG A:MG502 3.7 15.1 1.0
O A:ASP330 4.1 16.2 1.0
O3G A:0KX501 4.1 16.9 1.0
C5' A:0KX501 4.1 12.9 1.0
ND1 A:HIS329 4.2 15.1 0.5
O A:HOH659 4.2 17.3 1.0
N A:GLY320 4.2 15.1 1.0
O5' A:0KX501 4.3 14.3 1.0
C A:ASP330 4.3 16.0 1.0
O A:HOH632 4.3 15.4 1.0
O1A A:0KX501 4.4 16.4 1.0
O2B A:0KX501 4.4 15.9 1.0
CB A:ASP330 4.4 15.7 1.0
O2G A:0KX501 4.4 17.6 1.0
CB A:ASP332 4.5 13.0 1.0
N A:ASP330 4.5 16.7 1.0
CA A:GLY319 4.5 13.9 1.0
CE1 A:HIS329 4.5 13.8 0.8
CA A:ASP330 4.7 15.9 1.0
O P:HOH102 4.7 17.7 1.0
N A:ASP332 4.8 16.5 1.0
N A:VAL331 4.9 15.1 1.0
C A:GLY319 4.9 15.4 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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