Magnesium in PDB 4yd1: Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp

Enzymatic activity of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp

All present enzymatic activity of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp, PDB code: 4yd1 was solved by A.F.Moon, R.A.Gosavi, 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) 24.97 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.259, 69.042, 116.988, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19

Other elements in 4yd1:

The structure of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp 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 Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp (pdb code 4yd1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp, PDB code: 4yd1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4yd1

Go back to Magnesium Binding Sites List in 4yd1
Magnesium binding site 1 out of 3 in the Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:11.2
occ:1.00
OD2 A:ASP418 2.0 10.4 1.0
OD1 A:ASP332 2.0 8.6 1.0
OD2 A:ASP330 2.1 11.3 1.0
O A:HOH770 2.1 10.8 1.0
O3' P:DA4 2.2 12.4 1.0
O1A A:DUP607 2.3 10.5 1.0
CG A:ASP330 3.1 14.0 1.0
CG A:ASP332 3.1 10.0 1.0
CG A:ASP418 3.2 11.9 1.0
C3' P:DA4 3.3 12.4 1.0
PA A:DUP607 3.4 9.7 1.0
OD1 A:ASP330 3.4 12.3 1.0
OD2 A:ASP332 3.5 9.9 1.0
MG A:MG602 3.6 9.5 1.0
O5' A:DUP607 3.8 10.2 1.0
CB A:ASP418 3.8 10.6 1.0
O2A A:DUP607 3.8 11.0 1.0
C4' P:DA4 3.9 13.7 1.0
C5' P:DA4 4.1 14.1 1.0
O A:HOH950 4.1 14.5 0.4
C5' A:DUP607 4.2 9.8 1.0
CE1 A:HIS329 4.2 22.3 0.4
OD1 A:ASP418 4.2 11.3 1.0
CB A:ASP332 4.4 8.5 1.0
CB A:ASP330 4.4 8.5 1.0
OP1 P:DA4 4.5 14.7 1.0
NH2 A:ARG416 4.6 11.6 1.0
C2' P:DA4 4.6 12.0 1.0
CZ3 A:TRP434 4.6 10.3 1.0
O5' P:DA4 4.6 13.7 1.0
O3G A:DUP607 4.6 10.7 1.0
N3A A:DUP607 4.9 7.8 1.0
ND1 A:HIS329 4.9 20.7 0.4
O2B A:DUP607 5.0 8.6 1.0

Magnesium binding site 2 out of 3 in 4yd1

Go back to Magnesium Binding Sites List in 4yd1
Magnesium binding site 2 out of 3 in the Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:9.5
occ:1.00
O3G A:DUP607 2.0 10.7 1.0
O2B A:DUP607 2.0 8.6 1.0
OD1 A:ASP330 2.0 12.3 1.0
OD2 A:ASP332 2.0 9.9 1.0
O1A A:DUP607 2.1 10.5 1.0
O A:HOH850 2.2 10.5 1.0
PB A:DUP607 3.1 10.3 1.0
CG A:ASP332 3.1 10.0 1.0
CG A:ASP330 3.1 14.0 1.0
PA A:DUP607 3.3 9.7 1.0
PG A:DUP607 3.3 12.2 1.0
OD1 A:ASP332 3.4 8.6 1.0
N3A A:DUP607 3.5 7.8 1.0
OD2 A:ASP330 3.5 11.3 1.0
O3B A:DUP607 3.5 8.6 1.0
MG A:MG601 3.6 11.2 1.0
O A:ASP330 4.1 10.8 1.0
O A:HOH950 4.1 14.5 0.4
ND1 A:HIS329 4.1 20.7 0.4
O2G A:DUP607 4.2 13.2 1.0
C5' A:DUP607 4.2 9.8 1.0
O A:HOH749 4.2 13.7 1.0
O A:HOH849 4.3 9.9 1.0
O5' A:DUP607 4.3 10.2 1.0
N A:GLY320 4.3 9.9 1.0
C A:ASP330 4.3 9.0 1.0
O1B A:DUP607 4.4 10.2 1.0
CB A:ASP330 4.4 8.5 1.0
CB A:ASP332 4.4 8.5 1.0
O2A A:DUP607 4.4 11.0 1.0
CE1 A:HIS329 4.4 22.3 0.4
O1G A:DUP607 4.5 13.2 1.0
N A:ASP330 4.6 12.0 1.0
CA A:GLY319 4.6 9.5 1.0
O A:HOH770 4.6 10.8 1.0
CA A:ASP330 4.7 10.2 1.0
N A:ASP332 4.7 8.0 1.0
N A:VAL331 4.9 8.1 1.0
O3' P:DA4 5.0 12.4 1.0

Magnesium binding site 3 out of 3 in 4yd1

Go back to Magnesium Binding Sites List in 4yd1
Magnesium binding site 3 out of 3 in the Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg101

b:32.6
occ:1.00
O T:HOH216 1.9 23.0 1.0
O T:HOH223 2.0 26.9 1.0
O T:HOH207 2.1 30.1 1.0
O T:HOH255 2.1 33.2 1.0
O D:HOH116 2.1 40.6 1.0
O T:HOH211 4.0 41.8 1.0
O6 T:DG3 4.0 23.6 1.0
O D:HOH107 4.2 46.0 1.0
N7 T:DG2 4.2 23.2 1.0
O T:HOH210 4.2 31.8 1.0
O6 T:DG2 4.2 22.8 1.0
O T:HOH232 4.3 25.1 1.0
O D:HOH114 4.4 37.6 1.0
C5 T:DC1 4.5 28.5 1.0
N4 D:DC2 4.6 21.1 1.0
C6 T:DC1 4.9 29.9 1.0
C6 T:DG2 5.0 26.1 1.0
C5 T:DG2 5.0 22.8 1.0

Reference:

A.F.Moon, R.A.Gosavi, T.A.Kunkel, L.C.Pedersen, K.Bebenek. Creative Template-Dependent Synthesis By Human Polymerase Mu. Proc.Natl.Acad.Sci.Usa V. 112 E4530 2015.
ISSN: ESSN 1091-6490
PubMed: 26240373
DOI: 10.1073/PNAS.1505798112
Page generated: Mon Dec 14 19:53:32 2020

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