Chlorine 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:

Magnesium (Mg) 2 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8u0p

Go back to Chlorine Binding Sites List in 8u0p
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl604

b:60.8
occ:1.00
 O A:HOH913 3.0 51.2 1.0
O A:HOH908 3.5 39.6 1.0
NH2 A:ARG419 3.6 28.8 1.0
NE A:ARG419 3.7 22.7 1.0
CZ A:ARG419 4.0 26.6 1.0
CG A:PRO570 4.5 29.1 1.0
O A:HOH765 4.5 38.7 1.0
O A:HOH956 4.5 50.3 1.0
CD A:ARG419 4.7 22.4 1.0
CG A:ARG419 4.8 20.3 1.0
CD A:PRO570 4.9 30.2 1.0

Chlorine binding site 2 out of 4 in 8u0p

Go back to Chlorine Binding Sites List in 8u0p
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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:Cl605

b:63.4
occ:1.00
 NZ A:LYS287 3.6 40.4 1.0
NZ A:LYS248 3.6 42.6 1.0
CE A:LYS248 3.7 43.7 1.0
CD A:LYS287 4.1 42.9 1.0
CD A:LYS248 4.2 46.5 1.0
CE A:LYS287 4.2 43.2 1.0
CB A:LYS248 4.5 45.0 1.0
O A:HOH748 4.9 42.7 1.0

Chlorine binding site 3 out of 4 in 8u0p

Go back to Chlorine Binding Sites List in 8u0p
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl606

b:71.0
occ:1.00
 NH1 A:ARG549 3.4 38.9 1.0
NH2 A:ARG549 3.6 39.7 1.0
CZ A:ARG549 4.0 39.7 1.0
O A:HOH759 4.3 46.3 0.8
CG2 A:THR534 4.8 38.4 1.0

Chlorine binding site 4 out of 4 in 8u0p

Go back to Chlorine Binding Sites List in 8u0p
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl607

b:61.2
occ:0.81
 O A:HOH820 3.3 48.9 1.0
OG A:SER445 3.5 50.7 1.0
N A:SER445 3.5 35.5 1.0
CB A:SER445 3.6 37.3 1.0
O A:GLY442 3.7 48.5 1.0
CA A:GLY442 3.8 42.1 1.0
C A:GLY442 3.9 45.1 1.0
CB A:PHE444 4.1 38.8 1.0
CA A:SER445 4.2 37.9 1.0
N A:PHE444 4.4 38.3 1.0
O A:HOH720 4.4 44.0 1.0
N A:GLY442 4.4 48.3 1.0
C A:PHE444 4.5 39.1 1.0
CD2 A:PHE444 4.5 38.5 1.0
CA A:PHE444 4.5 37.5 1.0
N A:ILE443 4.7 42.7 1.0
CG A:PHE444 4.8 37.0 1.0

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: Tue Jul 30 12:57:50 2024

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