Atomistry » Magnesium » PDB 6p1o-6p89 » 6p1w
Atomistry »
  Magnesium »
    PDB 6p1o-6p89 »
      6p1w »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy