Atomistry » Magnesium » PDB 6whm-6wpf » 6wie
Atomistry »
  Magnesium »
    PDB 6whm-6wpf »
      6wie »

Magnesium in PDB 6wie: Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate

Enzymatic activity of Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate

All present enzymatic activity of Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate:
2.7.7.7;

Protein crystallography data

The structure of Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate, PDB code: 6wie was solved by A.M.Kaminski, T.A.Kunkel, L.C.Pedersen, K.Bebenek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.90 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.073, 62.247, 118.318, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 18.7

Other elements in 6wie:

The structure of Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate (pdb code 6wie). 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 Polymerase Mu on A Complementary Dna Double-Strand Break Substrate, PDB code: 6wie:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6wie

Go back to Magnesium Binding Sites List in 6wie
Magnesium binding site 1 out of 2 in the Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate


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 Polymerase Mu on A Complementary Dna Double-Strand Break Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:16.6
occ:0.60
NA A:NA502 0.1 17.8 0.4
OD2 A:ASP418 1.8 19.4 1.0
OD1 A:ASP332 1.9 15.0 1.0
OD2 A:ASP330 1.9 22.3 1.0
OP1 P:DT5 2.3 15.4 1.0
O3' P:DA4 2.6 17.2 1.0
CG A:ASP330 2.8 18.2 1.0
CG A:ASP332 2.9 13.2 1.0
CG A:ASP418 2.9 16.3 1.0
OD1 A:ASP330 3.1 14.3 1.0
P P:DT5 3.2 16.1 1.0
OD2 A:ASP332 3.2 14.6 1.0
MG A:MG503 3.5 13.6 1.0
CB A:ASP418 3.6 12.0 1.0
C3' P:DA4 3.8 13.4 1.0
C4' P:DA4 3.8 15.9 1.0
OD1 A:ASP418 3.9 17.1 1.0
C5' P:DA4 3.9 14.4 1.0
CB A:ASP330 4.0 12.9 1.0
OP2 P:DT5 4.2 13.8 1.0
O5' P:DT5 4.2 12.2 1.0
CB A:ASP332 4.2 10.7 1.0
C5' P:DT5 4.3 13.0 1.0
CZ3 A:TRP434 4.5 19.0 1.0
O32 A:PPV507 4.5 23.8 0.4
O A:HOH629 4.6 17.1 0.6
CE1 A:HIS329 4.6 28.4 1.0
NH2 A:ARG416 4.7 13.1 1.0
O A:VAL331 4.7 12.7 1.0
CA A:ASP332 4.7 10.4 1.0
C A:VAL331 4.9 12.7 1.0
N A:ASP418 4.9 11.1 1.0
CA A:ASP418 4.9 10.4 1.0
C2' P:DA4 4.9 15.3 1.0
N A:ASP332 4.9 10.5 1.0
O5' P:DA4 4.9 13.2 1.0

Magnesium binding site 2 out of 2 in 6wie

Go back to Magnesium Binding Sites List in 6wie
Magnesium binding site 2 out of 2 in the Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate


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 Polymerase Mu on A Complementary Dna Double-Strand Break Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:13.6
occ:1.00
O A:HOH629 1.9 17.1 0.6
O32 A:PPV507 2.0 23.8 0.4
O4 A:SO4506 2.1 14.7 0.6
OD1 A:ASP330 2.1 14.3 1.0
O11 A:PPV507 2.2 18.5 0.4
OP1 P:DT5 2.2 15.4 1.0
O A:HOH745 2.2 13.0 1.0
OD2 A:ASP332 2.2 14.6 1.0
P2 A:PPV507 3.1 18.8 0.4
CG A:ASP330 3.2 18.2 1.0
OPP A:PPV507 3.2 22.3 0.4
S A:SO4506 3.2 15.9 0.6
CG A:ASP332 3.3 13.2 1.0
P1 A:PPV507 3.3 31.3 0.4
O2 A:SO4506 3.3 22.4 0.6
NA A:NA502 3.5 17.8 0.4
OD2 A:ASP330 3.5 22.3 1.0
MG A:MG501 3.5 16.6 0.6
P P:DT5 3.5 16.1 1.0
OD1 A:ASP332 3.7 15.0 1.0
O12 A:PPV507 3.8 28.5 0.4
O3 A:SO4506 3.9 27.9 0.6
C5' P:DT5 4.0 13.0 1.0
O5' P:DT5 4.0 12.2 1.0
O A:ASP330 4.1 13.1 1.0
O21 A:PPV507 4.1 26.7 0.4
O A:HOH635 4.2 17.3 1.0
O A:HOH656 4.3 13.7 1.0
N A:GLY320 4.3 12.0 1.0
O22 A:PPV507 4.4 28.5 0.4
O31 A:PPV507 4.4 27.4 0.4
C A:ASP330 4.4 12.8 1.0
OP2 P:DT5 4.5 13.8 1.0
O1 A:SO4506 4.5 10.6 0.6
CB A:ASP330 4.5 12.9 1.0
O3' P:DA4 4.5 17.2 1.0
CA A:GLY319 4.5 11.1 1.0
CB A:ASP332 4.6 10.7 1.0
CE1 A:HIS329 4.6 28.4 1.0
ND1 A:HIS329 4.6 28.5 1.0
N A:ASP330 4.8 12.9 1.0
CA A:ASP330 4.8 11.7 1.0
N A:ASP332 4.9 10.5 1.0

Reference:

A.M.Kaminski, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, L.C.Pedersen, K.Bebenek. Structural Snapshots of Human Dna Polymerase Mu Engaged on A Dna Double-Strand Break. Nat Commun V. 11 4784 2020.
ISSN: ESSN 2041-1723
PubMed: 32963245
DOI: 10.1038/S41467-020-18506-5
Page generated: Tue Oct 1 23:00:17 2024

Last articles

Zn in 1B6Z
Zn in 1B71
Zn in 1B66
Zn in 1B55
Zn in 1B3D
Zn in 1B4E
Zn in 1B4T
Zn in 1B4L
Zn in 1B20
Zn in 1B0N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy