Magnesium in PDB 6wic: Pre-Catalytic Quaternary Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate

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

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

Protein crystallography data

The structure of Pre-Catalytic Quaternary Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate, PDB code: 6wic 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) 34.88 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.134, 62.233, 118.054, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 17.9

Other elements in 6wic:

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

Potassium (K) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 6wic

Go back to Magnesium Binding Sites List in 6wic
Magnesium binding site 1 out of 2 in the Pre-Catalytic Quaternary 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 Pre-Catalytic Quaternary 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:Mg702

b:13.5
occ:1.00
 OD1 A:ASP330 2.0 14.1 1.0
OD2 A:ASP332 2.1 13.1 1.0
O2B A:DUP701 2.1 12.3 1.0
O1G A:DUP701 2.1 15.1 1.0
O2A A:DUP701 2.1 13.1 1.0
O A:HOH917 2.2 13.5 1.0
CG A:ASP330 3.1 17.4 1.0
CG A:ASP332 3.1 13.1 1.0
PB A:DUP701 3.1 13.8 1.0
PA A:DUP701 3.3 12.7 1.0
PG A:DUP701 3.3 16.4 1.0
N3A A:DUP701 3.4 14.1 1.0
OD1 A:ASP332 3.5 13.9 1.0
OD2 A:ASP330 3.5 16.3 1.0
MG A:MG703 3.6 12.9 1.0
O3B A:DUP701 3.6 14.4 1.0
O A:HOH954 3.9 15.2 0.5
O A:ASP330 4.1 14.4 1.0
ND1 A:HIS329 4.1 20.3 0.5
O3G A:DUP701 4.2 19.4 1.0
O A:HOH870 4.2 19.3 1.0
C5' A:DUP701 4.2 14.1 1.0
O5' A:DUP701 4.2 12.4 1.0
O A:HOH812 4.3 14.7 1.0
C A:ASP330 4.3 14.0 1.0
N A:GLY320 4.3 14.8 1.0
O1A A:DUP701 4.4 14.0 1.0
CE1 A:HIS329 4.4 21.8 0.5
CB A:ASP330 4.4 16.0 1.0
CB A:ASP332 4.4 12.2 1.0
O2G A:DUP701 4.4 18.3 1.0
O1B A:DUP701 4.5 14.1 1.0
CA A:GLY319 4.5 13.3 1.0
N A:ASP330 4.6 15.6 1.0
O P:HOH103 4.6 14.8 1.0
CA A:ASP330 4.7 14.3 1.0
N A:ASP332 4.7 12.4 1.0
N A:VAL331 4.8 13.9 1.0

Magnesium binding site 2 out of 2 in 6wic

Go back to Magnesium Binding Sites List in 6wic
Magnesium binding site 2 out of 2 in the Pre-Catalytic Quaternary 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 Pre-Catalytic Quaternary 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:Mg703

b:12.9
occ:1.00
 OD2 A:ASP330 2.0 16.3 1.0
OD2 A:ASP418 2.0 16.8 1.0
OD1 A:ASP332 2.0 13.9 1.0
O P:HOH103 2.1 14.8 1.0
O3' P:DA4 2.2 14.6 1.0
O2A A:DUP701 2.2 13.1 1.0
CG A:ASP330 3.0 17.4 1.0
CG A:ASP332 3.1 13.1 1.0
CG A:ASP418 3.2 15.3 1.0
C3' P:DA4 3.3 14.0 1.0
PA A:DUP701 3.3 12.7 1.0
OD1 A:ASP330 3.4 14.1 1.0
OD2 A:ASP332 3.5 13.1 1.0
MG A:MG702 3.6 13.5 1.0
O5' A:DUP701 3.7 12.4 1.0
O1A A:DUP701 3.8 14.0 1.0
CB A:ASP418 3.8 14.3 1.0
C4' P:DA4 3.9 14.1 1.0
C5' P:DA4 4.0 14.7 1.0
O A:HOH954 4.0 15.2 0.5
C5' A:DUP701 4.1 14.1 1.0
CE1 A:HIS329 4.1 21.8 0.5
OD1 A:ASP418 4.2 16.0 1.0
CB A:ASP330 4.4 16.0 1.0
CB A:ASP332 4.4 12.2 1.0
OP1 P:DA4 4.5 16.7 1.0
O5' P:DA4 4.5 14.3 1.0
C2' P:DA4 4.6 14.6 1.0
NH2 A:ARG416 4.7 17.9 1.0
O1G A:DUP701 4.7 15.1 1.0
N3A A:DUP701 4.8 14.1 1.0
CZ3 A:TRP434 4.8 22.0 1.0
ND1 A:HIS329 4.8 20.3 0.5
O2B A:DUP701 4.9 12.3 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 Dec 15 01:33:11 2020

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