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Magnesium in PDB 6p1w: Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Cmpcpp

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

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 Cmpcpp:
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 Cmpcpp, PDB code: 6p1w 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) 29.90 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.802, 68.692, 110.065, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19

Other elements in 6p1w:

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Cmpcpp also contains other interesting chemical elements:

Chlorine (Cl) 4 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 Cmpcpp (pdb code 6p1w). 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 Cmpcpp, PDB code: 6p1w:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6p1w

Go back to Magnesium Binding Sites List in 6p1w
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 Cmpcpp


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 Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:11.4
occ:1.00
 OD2 A:ASP330 2.0 14.3 1.0
OD1 A:ASP332 2.1 13.5 1.0
OD1 A:ASP418 2.1 15.3 1.0
O A:HOH631 2.1 14.5 1.0
O2A A:2TM501 2.2 12.8 1.0
O3' P:DA4 2.2 12.7 1.0
CG A:ASP330 3.0 14.2 1.0
CG A:ASP332 3.1 12.2 1.0
CG A:ASP418 3.2 16.8 1.0
PA A:2TM501 3.3 12.2 1.0
C3' P:DA4 3.3 13.0 1.0
OD1 A:ASP330 3.4 13.5 1.0
OD2 A:ASP332 3.5 11.8 1.0
MG A:MG503 3.6 13.0 1.0
O1A A:2TM501 3.6 13.0 1.0
O5' A:2TM501 3.9 12.0 1.0
CB A:ASP418 3.9 12.9 1.0
C4' P:DA4 3.9 14.8 1.0
C5' P:DA4 3.9 13.3 1.0
O A:HOH771 4.0 12.0 0.5
C5' A:2TM501 4.0 10.4 1.0
CE1 A:HIS329 4.2 20.6 0.5
OD2 A:ASP418 4.2 16.2 1.0
CB A:ASP330 4.4 15.3 1.0
CB A:ASP332 4.4 11.1 1.0
OP1 P:DA4 4.5 14.3 1.0
O5' P:DA4 4.6 14.9 1.0
C2' P:DA4 4.6 13.5 1.0
NH2 A:ARG416 4.7 16.2 1.0
O2G A:2TM501 4.7 14.9 1.0
CZ3 A:TRP434 4.8 12.1 0.6
C1 A:2TM501 4.9 12.6 1.0
O2B A:2TM501 4.9 11.9 1.0
ND1 A:HIS329 5.0 20.9 0.5

Magnesium binding site 2 out of 2 in 6p1w

Go back to Magnesium Binding Sites List in 6p1w
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 Cmpcpp


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 Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:13.0
occ:1.00
 OD2 A:ASP332 2.0 11.8 1.0
O2B A:2TM501 2.0 11.9 1.0
OD1 A:ASP330 2.0 13.5 1.0
O2G A:2TM501 2.1 14.9 1.0
O A:HOH707 2.2 12.9 1.0
O2A A:2TM501 2.2 12.8 1.0
CG A:ASP332 3.1 12.2 1.0
CG A:ASP330 3.1 14.2 1.0
PB A:2TM501 3.1 12.5 1.0
PA A:2TM501 3.3 12.2 1.0
PG A:2TM501 3.3 17.1 1.0
OD1 A:ASP332 3.5 13.5 1.0
C1 A:2TM501 3.5 12.6 1.0
OD2 A:ASP330 3.5 14.3 1.0
O3B A:2TM501 3.6 13.7 1.0
MG A:MG502 3.6 11.4 1.0
O A:HOH771 3.8 12.0 0.5
C5' A:2TM501 4.0 10.4 1.0
O A:ASP330 4.1 13.7 1.0
ND1 A:HIS329 4.1 20.9 0.5
O5' A:2TM501 4.1 12.0 1.0
O A:HOH656 4.2 16.2 1.0
O3G A:2TM501 4.2 20.1 1.0
N A:GLY320 4.2 10.8 1.0
C A:ASP330 4.3 12.0 1.0
O A:HOH694 4.3 13.9 1.0
CE1 A:HIS329 4.3 20.6 0.5
CB A:ASP332 4.4 11.1 1.0
CB A:ASP330 4.4 15.3 1.0
O1B A:2TM501 4.5 14.5 1.0
O1G A:2TM501 4.5 20.7 1.0
O1A A:2TM501 4.5 13.0 1.0
N A:ASP330 4.6 13.0 1.0
CA A:GLY319 4.6 12.0 1.0
CA A:ASP330 4.7 13.9 1.0
O A:HOH631 4.7 14.5 1.0
N A:ASP332 4.7 12.8 1.0
N A:VAL331 4.8 12.2 1.0
C A:GLY319 5.0 12.8 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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