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Sodium 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:

Magnesium (Mg) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 5 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 3hx0

Go back to Sodium Binding Sites List in 3hx0
Sodium binding site 1 out of 5 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 Sodium with other atoms in the Na 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
F:Na806

b:97.4
occ:1.00
 O F:HOH12 2.3 64.8 1.0
O F:SER339 2.3 80.5 1.0
O F:ILE341 2.3 77.1 1.0
OP1 H:DA5 2.4 75.4 1.0
O F:ALA344 2.5 77.5 1.0
C F:ILE341 3.1 77.8 1.0
N F:ALA344 3.3 79.0 1.0
C F:ALA344 3.5 77.4 1.0
C F:SER339 3.5 79.0 1.0
P H:DA5 3.7 75.8 1.0
N F:GLY343 3.7 79.3 1.0
N F:TRP342 3.8 77.7 1.0
N F:ILE341 3.8 78.0 1.0
CA F:TRP342 3.8 77.8 1.0
CA F:ALA344 3.8 77.4 1.0
C F:TRP342 4.0 79.0 1.0
OP2 H:DA5 4.1 74.2 1.0
CA F:ILE341 4.1 78.2 1.0
CB F:ALA344 4.1 76.1 1.0
C F:ASN340 4.2 78.8 1.0
CA F:SER339 4.3 77.7 1.0
C F:GLY343 4.4 79.8 1.0
N F:ASN340 4.5 78.9 1.0
CA F:ASN340 4.6 79.2 1.0
O5' H:DA5 4.6 75.3 1.0
CA F:GLY343 4.6 79.9 1.0
N F:GLY345 4.7 77.6 1.0
O3' H:DT4 4.8 75.8 1.0
O F:ASN340 4.8 79.7 1.0
CB F:ILE341 4.9 79.4 1.0
O F:TRP342 5.0 80.0 1.0
O F:PHE338 5.0 69.2 1.0

Sodium binding site 2 out of 5 in 3hx0

Go back to Sodium Binding Sites List in 3hx0
Sodium binding site 2 out of 5 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 Sodium with other atoms in the Na 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
K:Na807

b:83.8
occ:1.00
 O K:SER339 2.3 87.0 1.0
OP1 M:DT6 2.4 74.0 1.0
O K:ALA344 2.5 75.6 1.0
O K:HOH21 2.7 47.2 1.0
O K:ILE341 2.8 74.8 1.0
P M:DT6 3.5 73.1 1.0
C K:SER339 3.5 85.4 1.0
OP2 M:DT6 3.6 74.2 1.0
C K:ALA344 3.6 77.2 1.0
C K:ILE341 3.8 75.2 1.0
N K:ALA344 4.0 75.7 1.0
N K:ILE341 4.2 79.5 1.0
CA K:SER339 4.3 85.6 1.0
N K:GLY343 4.3 72.6 1.0
O3' M:DA5 4.3 71.0 1.0
CA K:ALA344 4.3 76.6 1.0
C K:ASN340 4.4 82.7 1.0
CA K:TRP342 4.5 73.7 1.0
N K:ASN340 4.5 84.0 1.0
N K:TRP342 4.5 74.7 1.0
CA K:ASN340 4.6 83.6 1.0
N K:GLY345 4.7 79.1 1.0
CA K:ILE341 4.7 75.5 1.0
O5' M:DT6 4.7 74.0 1.0
CB K:ALA344 4.8 76.5 1.0
CA K:GLY345 4.8 82.3 1.0
CB K:SER339 4.8 85.3 1.0
C K:TRP342 4.9 73.2 1.0
O K:ASN340 4.9 84.4 1.0

Sodium binding site 3 out of 5 in 3hx0

Go back to Sodium Binding Sites List in 3hx0
Sodium binding site 3 out of 5 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 Sodium with other atoms in the Na 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:Na808

b:64.8
occ:1.00
 O1A K:D3T703 2.4 83.8 1.0
OD1 K:ASP427 2.4 75.2 1.0
OD1 K:ASP429 2.5 66.9 1.0
OD2 K:ASP490 2.6 77.8 1.0
PA K:D3T703 3.3 81.0 1.0
CG K:ASP427 3.3 74.1 1.0
CG K:ASP429 3.4 68.8 1.0
MG K:MG803 3.5 62.7 1.0
OD2 K:ASP427 3.5 73.2 1.0
OD2 K:ASP429 3.6 69.7 1.0
O2A K:D3T703 3.6 81.5 1.0
O5' K:D3T703 3.7 83.7 1.0
CG K:ASP490 3.7 76.6 1.0
O3G K:D3T703 4.5 79.7 1.0
CB K:ASP490 4.6 72.3 1.0
OD1 K:ASP490 4.6 79.5 1.0
C5' K:D3T703 4.7 86.1 1.0
O3A K:D3T703 4.7 78.9 1.0
CB K:ASP427 4.7 72.1 1.0
NH1 K:ARG488 4.7 91.2 1.0
CB K:ASP429 4.8 67.6 1.0

Sodium binding site 4 out of 5 in 3hx0

Go back to Sodium Binding Sites List in 3hx0
Sodium binding site 4 out of 5 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 Sodium with other atoms in the Na 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:Na809

b:90.9
occ:1.00
 O P:SER339 2.4 88.8 1.0
O P:HOH29 2.4 79.7 1.0
O P:ALA344 2.4 87.7 1.0
O P:ILE341 2.5 86.3 1.0
OP1 R:DT6 2.9 81.4 1.0
C P:ILE341 3.4 86.9 1.0
C P:ALA344 3.5 87.5 1.0
N P:ALA344 3.5 84.8 1.0
C P:SER339 3.5 89.0 1.0
OP2 R:DT6 3.6 79.5 1.0
P R:DT6 3.6 81.0 1.0
O P:ASN340 3.8 89.4 1.0
C P:ASN340 3.9 89.0 1.0
CA P:ALA344 3.9 86.3 1.0
CA P:TRP342 3.9 86.7 1.0
N P:GLY343 4.0 85.4 1.0
N P:TRP342 4.0 86.5 1.0
N P:ILE341 4.2 88.2 1.0
CB P:ALA344 4.2 85.0 1.0
C P:TRP342 4.2 86.2 1.0
O3' R:DA5 4.3 80.4 1.0
N P:ASN340 4.4 88.4 1.0
CA P:ILE341 4.4 87.7 1.0
CA P:ASN340 4.4 88.7 1.0
CA P:SER339 4.4 89.9 1.0
N P:GLY345 4.6 88.2 1.0
C P:GLY343 4.7 84.0 1.0
CA P:GLY343 4.9 85.0 1.0

Sodium binding site 5 out of 5 in 3hx0

Go back to Sodium Binding Sites List in 3hx0
Sodium binding site 5 out of 5 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 Sodium with other atoms in the Na binding site number 5 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:Na810

b:69.7
occ:1.00
 OD1 P:ASP427 2.4 0.0 1.0
OD1 P:ASP429 2.5 86.5 1.0
OD2 P:ASP490 2.7 92.2 1.0
O1A P:D3T704 2.9 0.6 1.0
CG P:ASP490 3.3 91.9 1.0
CG P:ASP427 3.4 98.0 1.0
CG P:ASP429 3.6 87.9 1.0
OD1 P:ASP490 3.7 92.9 1.0
O5' P:D3T704 3.7 0.1 1.0
PA P:D3T704 3.8 0.1 1.0
OD2 P:ASP427 3.9 98.2 1.0
OD2 P:ASP429 3.9 87.2 1.0
MG P:MG804 4.0 76.6 1.0
CB P:ASP490 4.1 89.4 1.0
O2A P:D3T704 4.2 99.8 1.0
CB P:ASP427 4.7 95.7 1.0
C5' P:D3T704 4.9 0.3 1.0
CB P:ASP429 4.9 87.5 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: Mon Oct 7 10:29:06 2024

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