Magnesium in PDB 8u0p: Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break

Enzymatic activity of Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break

All present enzymatic activity of Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break:
2.7.7.7;

Protein crystallography data

The structure of Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break, PDB code: 8u0p was solved by A.M.Kaminski, L.C.Pedersen, K.Bebenek, T.A.Kunkel, K.K.Chiruvella, D.A.Ramsden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.40 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.205, 60.068, 140.729, 90, 90, 90
R / Rfree (%) 17.2 / 19.3

Other elements in 8u0p:

The structure of Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break also contains other interesting chemical elements:

Sodium (Na) 1 atom
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break (pdb code 8u0p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break, PDB code: 8u0p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8u0p

Go back to Magnesium Binding Sites List in 8u0p
Magnesium binding site 1 out of 2 in the Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:17.5
occ:1.00
 OD1 A:ASP427 2.0 16.4 1.0
O2B A:DUP609 2.1 17.3 1.0
O3G A:DUP609 2.1 17.8 1.0
O2A A:DUP609 2.1 15.3 1.0
OD2 A:ASP429 2.1 17.9 1.0
O A:HOH777 2.1 18.6 1.0
CG A:ASP427 3.1 18.8 1.0
PB A:DUP609 3.1 18.3 1.0
CG A:ASP429 3.1 18.4 1.0
PA A:DUP609 3.2 17.0 1.0
PG A:DUP609 3.3 19.0 1.0
N3A A:DUP609 3.4 16.2 1.0
OD1 A:ASP429 3.5 20.1 1.0
OD2 A:ASP427 3.5 22.1 1.0
O3B A:DUP609 3.6 17.9 1.0
MG A:MG603 3.7 26.8 1.0
O A:HOH797 3.9 22.7 1.0
O2G A:DUP609 4.1 19.1 1.0
O A:ASP427 4.1 19.0 1.0
C5' A:DUP609 4.1 15.7 1.0
OG A:SER417 4.2 20.3 1.0
O5' A:DUP609 4.2 16.6 1.0
N A:ASP427 4.3 17.4 1.0
O A:HOH746 4.3 18.7 1.0
C A:ASP427 4.3 17.0 1.0
CB A:ASP427 4.3 18.2 1.0
N A:SER417 4.3 17.0 1.0
O1A A:DUP609 4.4 19.1 1.0
CB A:ASP429 4.4 19.7 1.0
O1B A:DUP609 4.5 19.0 1.0
CA A:GLY416 4.5 16.4 1.0
O1G A:DUP609 4.5 19.9 1.0
CA A:ASP427 4.6 17.1 1.0
O A:HOH779 4.6 18.6 1.0
N A:ASP429 4.9 16.0 1.0
N A:VAL428 5.0 16.6 1.0
C A:GLY416 5.0 18.1 1.0

Magnesium binding site 2 out of 2 in 8u0p

Go back to Magnesium Binding Sites List in 8u0p
Magnesium binding site 2 out of 2 in the Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Noncomplementary Dna Double-Strand Break within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:26.8
occ:1.00
 OD2 A:ASP427 2.0 22.1 1.0
OD2 A:ASP490 2.1 20.4 1.0
OD1 A:ASP429 2.2 20.1 1.0
O A:HOH779 2.2 18.6 1.0
O2A A:DUP609 2.4 15.3 1.0
O3' P:DC6 2.5 26.1 1.0
CG A:ASP427 3.0 18.8 1.0
CG A:ASP490 3.2 21.5 1.0
CG A:ASP429 3.2 18.4 1.0
C3' P:DC6 3.3 20.9 1.0
PA A:DUP609 3.4 17.0 1.0
OD1 A:ASP427 3.4 16.4 1.0
OD2 A:ASP429 3.6 17.9 1.0
MG A:MG601 3.7 17.5 1.0
O1A A:DUP609 3.7 19.1 1.0
O5' A:DUP609 3.8 16.6 1.0
CB A:ASP490 3.9 20.1 1.0
OD1 A:ASP490 4.1 20.3 1.0
C5' A:DUP609 4.1 15.7 1.0
C4' P:DC6 4.1 18.1 1.0
C5' P:DC6 4.2 17.6 1.0
O A:HOH797 4.3 22.7 1.0
CB A:ASP427 4.3 18.2 1.0
NH2 A:ARG488 4.3 20.1 1.0
CB A:ASP429 4.6 19.7 1.0
O5' P:DC6 4.6 18.9 1.0
C2' P:DC6 4.7 18.5 1.0
O3G A:DUP609 4.8 17.8 1.0
N3A A:DUP609 4.9 16.2 1.0
O A:HOH749 5.0 18.7 0.4

Reference:

A.M.Kaminski, K.K.Chiruvella, D.A.Ramsden, K.Bebenek, T.A.Kunkel, L.C.Pedersen. Dna Polymerase Lambda LOOP1 Variant Yields Unexpected Gain-of-Function Capabilities in Nonhomologous End-Joining. Dna Repair (Amst) V. 136 03645 2024.
ISSN: ISSN 1568-7856
PubMed: 38428373
DOI: 10.1016/J.DNAREP.2024.103645
Page generated: Fri Oct 4 21:08:26 2024

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