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Magnesium in PDB 3hx0: Ternary Complex of L277A, H511A, R514 Mutant Pol Lambda Bound to A 2 Nucleotide Gapped Dna Substrate with A Scrunched Da

Enzymatic activity of Ternary Complex of L277A, H511A, R514 Mutant Pol Lambda Bound to A 2 Nucleotide Gapped Dna Substrate with A Scrunched Da

All present enzymatic activity of Ternary Complex of L277A, H511A, R514 Mutant Pol Lambda Bound to A 2 Nucleotide Gapped Dna Substrate with A Scrunched Da:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of L277A, H511A, R514 Mutant Pol Lambda Bound to A 2 Nucleotide Gapped Dna Substrate with A Scrunched Da, PDB code: 3hx0 was solved by M.Garcia-Diaz, K.Bebenek, A.A.Larrea, J.M.Havener, L.Perera, J.M.Krahn, L.C.Pedersen, D.A.Ramsden, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.11 / 3.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 124.179, 131.912, 280.412, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 26.8

Other elements in 3hx0:

The structure of Ternary Complex of L277A, H511A, R514 Mutant Pol Lambda Bound to A 2 Nucleotide Gapped Dna Substrate with A Scrunched Da also contains other interesting chemical elements:

Sodium (Na) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex of L277A, H511A, R514 Mutant Pol Lambda Bound to A 2 Nucleotide Gapped Dna Substrate with A Scrunched Da (pdb code 3hx0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Ternary Complex of L277A, H511A, R514 Mutant Pol Lambda Bound to A 2 Nucleotide Gapped Dna Substrate with A Scrunched Da, PDB code: 3hx0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3hx0

Go back to Magnesium Binding Sites List in 3hx0
Magnesium binding site 1 out of 4 in the Ternary Complex of L277A, H511A, R514 Mutant Pol Lambda Bound to A 2 Nucleotide Gapped Dna Substrate with A Scrunched Da


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 L277A, H511A, R514 Mutant Pol Lambda Bound to A 2 Nucleotide Gapped Dna Substrate with A Scrunched Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:68.8
occ:1.00
 OD2 A:ASP427 1.8 67.6 1.0
O1A A:D3T701 2.0 58.7 1.0
O A:HOH7 2.0 76.8 1.0
O3G A:D3T701 2.0 70.5 1.0
O1B A:D3T701 2.1 64.8 1.0
OD2 A:ASP429 2.4 69.0 1.0
CG A:ASP427 2.9 67.2 1.0
PB A:D3T701 3.1 64.3 1.0
PA A:D3T701 3.2 62.2 1.0
PG A:D3T701 3.2 70.7 1.0
CG A:ASP429 3.2 68.6 1.0
OD1 A:ASP427 3.3 68.7 1.0
O3A A:D3T701 3.4 62.1 1.0
OD1 A:ASP429 3.4 68.7 1.0
O3B A:D3T701 3.4 66.9 1.0
O A:ASP427 3.7 69.2 1.0
O1G A:D3T701 3.7 66.5 1.0
O5' A:D3T701 4.0 62.0 1.0
C5' A:D3T701 4.0 61.1 1.0
N A:ASP427 4.1 64.7 1.0
C A:ASP427 4.1 67.1 1.0
CB A:ASP427 4.2 66.7 1.0
OG A:SER417 4.3 60.5 1.0
O2A A:D3T701 4.3 61.4 1.0
O2G A:D3T701 4.4 70.0 1.0
CA A:ASP427 4.4 66.1 1.0
N A:SER417 4.5 57.4 1.0
O2B A:D3T701 4.5 59.0 1.0
CB A:ASP429 4.6 67.9 1.0
CA A:GLY416 4.8 60.5 1.0
N A:ASP429 4.8 67.3 1.0
N A:VAL428 4.9 67.8 1.0
CB A:SER417 4.9 56.5 1.0

Magnesium binding site 2 out of 4 in 3hx0

Go back to Magnesium Binding Sites List in 3hx0
Magnesium binding site 2 out of 4 in the Ternary Complex of L277A, H511A, R514 Mutant Pol Lambda Bound to A 2 Nucleotide Gapped Dna Substrate with A Scrunched Da


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 L277A, H511A, R514 Mutant Pol Lambda Bound to A 2 Nucleotide Gapped Dna Substrate with A Scrunched Da within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg802

b:49.4
occ:1.00
 OD2 F:ASP427 1.9 65.0 1.0
O1A F:D3T702 1.9 63.0 1.0
OD2 F:ASP429 1.9 70.9 1.0
O1B F:D3T702 2.2 60.1 1.0
O F:HOH15 2.2 67.7 1.0
O3G F:D3T702 2.5 68.3 1.0
CG F:ASP429 2.8 70.3 1.0
CG F:ASP427 2.8 65.5 1.0
OD1 F:ASP429 3.1 67.1 1.0
PA F:D3T702 3.2 62.0 1.0
OD1 F:ASP427 3.2 67.2 1.0
PB F:D3T702 3.3 61.9 1.0
O3A F:D3T702 3.5 61.8 1.0
PG F:D3T702 3.6 70.8 1.0
C5' F:D3T702 3.8 60.8 1.0
O3B F:D3T702 3.8 65.3 1.0
O5' F:D3T702 3.9 61.4 1.0
O F:ASP427 3.9 68.8 1.0
O1G F:D3T702 4.1 67.9 1.0
C F:ASP427 4.2 66.0 1.0
CB F:ASP427 4.2 64.0 1.0
CB F:ASP429 4.2 71.0 1.0
N F:ASP427 4.3 61.9 1.0
O2A F:D3T702 4.4 63.3 1.0
N F:SER417 4.5 62.8 1.0
CA F:GLY416 4.5 65.2 1.0
CA F:ASP427 4.5 64.5 1.0
OG F:SER417 4.6 65.9 1.0
N F:ASP429 4.6 72.3 1.0
O2B F:D3T702 4.6 59.3 1.0
O2G F:D3T702 4.8 68.3 1.0
N F:VAL428 4.8 66.2 1.0

Magnesium binding site 3 out of 4 in 3hx0

Go back to Magnesium Binding Sites List in 3hx0
Magnesium binding site 3 out of 4 in the Ternary Complex of L277A, H511A, R514 Mutant Pol Lambda Bound to A 2 Nucleotide Gapped Dna Substrate with A Scrunched Da


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 L277A, H511A, R514 Mutant Pol Lambda Bound to A 2 Nucleotide Gapped Dna Substrate with A Scrunched Da within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg803

b:62.7
occ:1.00
 O1A K:D3T703 1.9 83.8 1.0
O K:HOH34 2.0 88.3 1.0
OD2 K:ASP427 2.1 73.2 1.0
O1B K:D3T703 2.1 78.3 1.0
O3G K:D3T703 2.3 79.7 1.0
OD2 K:ASP429 2.3 69.7 1.0
PB K:D3T703 3.1 76.2 1.0
CG K:ASP427 3.1 74.1 1.0
PA K:D3T703 3.2 81.0 1.0
PG K:D3T703 3.3 81.0 1.0
CG K:ASP429 3.3 68.8 1.0
O3A K:D3T703 3.4 78.9 1.0
NA K:NA808 3.5 64.8 1.0
O3B K:D3T703 3.5 78.7 1.0
OD1 K:ASP427 3.6 75.2 1.0
OD1 K:ASP429 3.7 66.9 1.0
O1G K:D3T703 3.7 78.3 1.0
O K:ASP427 3.8 70.5 1.0
O2A K:D3T703 4.2 81.5 1.0
O5' K:D3T703 4.2 83.7 1.0
OG K:SER417 4.2 69.5 1.0
C K:ASP427 4.3 68.3 1.0
N K:SER417 4.4 69.3 1.0
N K:ASP427 4.4 70.5 1.0
CB K:ASP427 4.4 72.1 1.0
O2B K:D3T703 4.5 76.0 1.0
CA K:GLY416 4.5 71.8 1.0
O2G K:D3T703 4.6 80.8 1.0
C5' K:D3T703 4.6 86.1 1.0
CA K:ASP427 4.6 70.1 1.0
CB K:ASP429 4.6 67.6 1.0
N K:ASP429 4.9 67.4 1.0
CB K:SER417 5.0 68.8 1.0
C K:GLY416 5.0 70.2 1.0
N K:VAL428 5.0 66.2 1.0

Magnesium binding site 4 out of 4 in 3hx0

Go back to Magnesium Binding Sites List in 3hx0
Magnesium binding site 4 out of 4 in the Ternary Complex of L277A, H511A, R514 Mutant Pol Lambda Bound to A 2 Nucleotide Gapped Dna Substrate with A Scrunched Da


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ternary Complex of L277A, H511A, R514 Mutant Pol Lambda Bound to A 2 Nucleotide Gapped Dna Substrate with A Scrunched Da within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg804

b:76.6
occ:1.00
 O1B P:D3T704 1.9 99.2 1.0
OD2 P:ASP429 2.0 87.2 1.0
OD2 P:ASP427 2.1 98.2 1.0
O1A P:D3T704 2.1 0.6 1.0
O P:HOH35 2.1 0.8 1.0
O3G P:D3T704 2.8 98.1 1.0
PB P:D3T704 3.0 99.5 1.0
CG P:ASP429 3.1 87.9 1.0
CG P:ASP427 3.1 98.0 1.0
PA P:D3T704 3.1 0.1 1.0
O3A P:D3T704 3.3 0.5 1.0
OD1 P:ASP429 3.5 86.5 1.0
OD1 P:ASP427 3.5 0.0 1.0
O3B P:D3T704 3.7 99.6 1.0
O P:ASP427 3.7 91.2 1.0
PG P:D3T704 3.7 0.4 1.0
O5' P:D3T704 3.7 0.1 1.0
NA P:NA810 4.0 69.7 1.0
CA P:GLY416 4.1 0.2 1.0
O1G P:D3T704 4.1 0.9 1.0
N P:SER417 4.1 0.8 1.0
C5' P:D3T704 4.1 0.3 1.0
C P:ASP427 4.2 91.5 1.0
OG P:SER417 4.3 0.5 1.0
O2B P:D3T704 4.3 98.8 1.0
CB P:ASP429 4.4 87.5 1.0
CB P:ASP427 4.4 95.7 1.0
O2A P:D3T704 4.5 99.8 1.0
N P:ASP427 4.6 96.3 1.0
C P:GLY416 4.6 0.9 1.0
CA P:ASP427 4.7 94.0 1.0
N P:ASP429 4.7 89.5 1.0
N P:VAL428 4.9 89.9 1.0
CB P:SER417 4.9 0.1 1.0
O2G P:D3T704 5.0 99.8 1.0

Reference:

M.Garcia-Diaz, K.Bebenek, A.A.Larrea, J.M.Havener, L.Perera, J.M.Krahn, L.C.Pedersen, D.A.Ramsden, T.A.Kunkel. Scrunching During Dna Repair Synthesis To Be Published.
Page generated: Wed Aug 14 15:28:12 2024

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