Magnesium in PDB 6wid: Nucleotide Incorporation Intermediate Into Quaternary Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate

Enzymatic activity of Nucleotide Incorporation Intermediate Into Quaternary Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate

All present enzymatic activity of Nucleotide Incorporation Intermediate Into Quaternary Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate:
2.7.7.7;

Protein crystallography data

The structure of Nucleotide Incorporation Intermediate Into Quaternary Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate, PDB code: 6wid 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) 31.02 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.186, 62.040, 118.320, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 17.7

Other elements in 6wid:

The structure of Nucleotide Incorporation Intermediate Into Quaternary 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) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Nucleotide Incorporation Intermediate Into Quaternary Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate (pdb code 6wid). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Nucleotide Incorporation Intermediate Into Quaternary Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate, PDB code: 6wid:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6wid

Go back to Magnesium Binding Sites List in 6wid
Magnesium binding site 1 out of 2 in the Nucleotide Incorporation Intermediate Into 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 Nucleotide Incorporation Intermediate Into 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:12.5
occ:1.00
 OD2 A:ASP330 1.9 15.6 1.0
OD2 A:ASP418 1.9 14.9 1.0
OD1 A:ASP332 2.0 10.6 1.0
O P:HOH102 2.1 15.2 1.0
OP1 P:DT5 2.2 12.8 0.4
O3' P:DA4 2.3 8.3 0.6
O2A A:DUP701 2.3 8.3 0.6
O3' P:DA4 2.4 10.6 0.4
CG A:ASP330 2.9 14.8 1.0
P P:DT5 3.0 9.8 0.4
CG A:ASP332 3.0 9.7 1.0
CG A:ASP418 3.1 13.0 1.0
OD1 A:ASP330 3.2 11.8 1.0
C3' P:DA4 3.4 8.2 0.6
PA A:DUP701 3.4 6.0 0.6
OD2 A:ASP332 3.4 10.2 1.0
C3' P:DA4 3.5 9.3 0.4
MG A:MG704 3.5 10.1 1.0
C4' P:DA4 3.6 10.2 0.4
O5' A:DUP701 3.7 5.1 0.6
CB A:ASP418 3.8 10.4 1.0
C5' P:DA4 3.8 11.4 0.4
O1A A:DUP701 3.8 6.9 0.6
OP2 P:DT5 3.9 12.8 0.4
C4' P:DA4 4.0 8.2 0.6
C5' P:DA4 4.1 8.1 0.6
OD1 A:ASP418 4.1 14.0 1.0
CE1 A:HIS329 4.1 11.1 0.6
C5' A:DUP701 4.1 7.0 0.6
O5' P:DT5 4.1 10.4 0.4
C5' P:DT5 4.2 14.4 0.4
CB A:ASP330 4.2 11.3 1.0
CB A:ASP332 4.3 9.8 1.0
OP1 P:DA4 4.5 12.1 0.6
CZ3 A:TRP434 4.6 23.8 1.0
O5' P:DA4 4.6 9.6 0.4
O1G A:DUP701 4.6 13.3 0.6
C2' P:DA4 4.6 12.5 0.4
O5' P:DA4 4.7 8.8 0.6
NH2 A:ARG416 4.7 12.8 1.0
C2' P:DA4 4.7 10.6 0.6
O12 A:PPV702 4.7 12.7 0.4
N3A A:DUP701 4.9 10.6 0.6
NE2 A:HIS329 4.9 18.1 0.6
O2B A:DUP701 4.9 9.7 0.6
ND1 A:HIS329 4.9 17.6 0.6
CA A:ASP332 5.0 8.7 1.0
OP1 P:DA4 5.0 10.8 0.4

Magnesium binding site 2 out of 2 in 6wid

Go back to Magnesium Binding Sites List in 6wid
Magnesium binding site 2 out of 2 in the Nucleotide Incorporation Intermediate Into 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 Nucleotide Incorporation Intermediate Into 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:Mg704

b:10.1
occ:1.00
 O2B A:DUP701 1.9 9.7 0.6
O2A A:DUP701 2.0 8.3 0.6
O1G A:DUP701 2.0 13.3 0.6
O12 A:PPV702 2.0 12.7 0.4
OD1 A:ASP330 2.1 11.8 1.0
OD2 A:ASP332 2.1 10.2 1.0
O A:HOH922 2.1 10.0 1.0
O21 A:PPV702 2.2 10.4 0.4
OP1 P:DT5 2.3 12.8 0.4
PB A:DUP701 3.1 11.6 0.6
CG A:ASP330 3.1 14.8 1.0
CG A:ASP332 3.1 9.7 1.0
P1 A:PPV702 3.1 13.8 0.4
PA A:DUP701 3.2 6.0 0.6
O31 A:PPV702 3.3 17.1 0.4
PG A:DUP701 3.3 16.4 0.6
P2 A:PPV702 3.3 17.6 0.4
N3A A:DUP701 3.4 10.6 0.6
OPP A:PPV702 3.5 15.3 0.4
O3B A:DUP701 3.5 15.6 0.6
MG A:MG703 3.5 12.5 1.0
OD1 A:ASP332 3.5 10.6 1.0
OD2 A:ASP330 3.6 15.6 1.0
P P:DT5 3.7 9.8 0.4
O3G A:DUP701 3.9 19.6 0.6
O A:ASP330 4.1 11.1 1.0
O5' P:DT5 4.1 10.4 0.4
C5' P:DT5 4.1 14.4 0.4
C5' A:DUP701 4.1 7.0 0.6
O5' A:DUP701 4.2 5.1 0.6
ND1 A:HIS329 4.2 17.6 0.6
O A:HOH809 4.2 15.2 1.0
O A:HOH838 4.3 10.7 1.0
CE1 A:HIS329 4.3 11.1 0.6
O22 A:PPV702 4.3 16.9 0.4
O1A A:DUP701 4.3 6.9 0.6
C A:ASP330 4.3 10.3 1.0
N A:GLY320 4.3 10.1 1.0
O32 A:PPV702 4.3 17.3 0.4
O1B A:DUP701 4.4 11.5 0.6
CB A:ASP330 4.4 11.3 1.0
CB A:ASP332 4.5 9.8 1.0
O2G A:DUP701 4.5 18.4 0.6
O11 A:PPV702 4.5 9.9 0.4
CA A:GLY319 4.5 8.4 1.0
O P:HOH102 4.6 15.2 1.0
O3' P:DA4 4.6 10.6 0.4
N A:ASP330 4.6 11.7 1.0
OP2 P:DT5 4.6 12.8 0.4
CA A:ASP330 4.7 10.0 1.0
N A:ASP332 4.7 7.7 1.0
N A:VAL331 4.9 9.3 0.3
N A:VAL331 4.9 8.6 0.7

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 01:33:19 2020

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