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Sodium in PDB 7m0a: Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp

Enzymatic activity of Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp

All present enzymatic activity of Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp:
2.7.7.7;

Protein crystallography data

The structure of Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp, PDB code: 7m0a was solved by A.M.Kaminski, K.Bebenek, L.C.Pedersen, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.71 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.768, 59.573, 140.726, 90, 90, 90
R / Rfree (%) 16.9 / 19.3

Other elements in 7m0a:

The structure of Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Calcium (Ca) 1 atom
Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp (pdb code 7m0a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp, PDB code: 7m0a:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7m0a

Go back to Sodium Binding Sites List in 7m0a
Sodium binding site 1 out of 3 in the Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na706

b:14.4
occ:1.00
 O A:SER339 2.3 12.6 1.0
O A:ALA344 2.3 14.1 1.0
OP1 P:DG5 2.3 15.6 1.0
O A:ILE341 2.4 14.0 1.0
O A:HOH1044 2.5 19.3 1.0
O P:HOH103 2.8 23.2 1.0
C A:SER339 3.3 15.4 1.0
C A:ILE341 3.3 12.8 1.0
C A:ALA344 3.4 14.7 1.0
P P:DG5 3.4 15.9 1.0
OP2 P:DG5 3.7 14.3 1.0
N A:ALA344 3.8 12.0 1.0
N A:GLY343 4.0 12.0 1.0
N A:ILE341 4.0 13.9 1.0
CA A:TRP342 4.0 12.2 1.0
CA A:SER339 4.0 10.7 1.0
N A:TRP342 4.0 12.5 1.0
CA A:ALA344 4.1 14.3 1.0
O A:HOH1004 4.1 45.4 1.0
C A:ASN340 4.2 14.8 1.0
N A:ASN340 4.2 15.0 1.0
CA A:ILE341 4.3 10.9 1.0
CA A:ASN340 4.3 16.0 1.0
N A:GLY345 4.3 14.1 1.0
C A:TRP342 4.4 15.7 1.0
O3' P:DT4 4.4 14.2 1.0
O P:HOH122 4.5 44.4 1.0
O5' P:DG5 4.6 15.4 1.0
CB A:ALA344 4.6 11.1 1.0
CA A:GLY345 4.6 14.8 1.0
CB A:SER339 4.6 16.2 1.0
C A:GLY343 4.7 14.3 1.0
O A:ASN340 4.7 14.9 1.0
CA A:GLY343 4.9 16.7 1.0
O A:PHE338 4.9 13.5 1.0

Sodium binding site 2 out of 3 in 7m0a

Go back to Sodium Binding Sites List in 7m0a
Sodium binding site 2 out of 3 in the Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na707

b:32.1
occ:1.00
 O A:ILE305 2.4 28.9 1.0
O A:CYS300 2.4 34.5 1.0
O A:HOH1018 2.5 32.6 1.0
O A:ILE302 2.5 29.5 1.0
O D:HOH114 2.6 42.0 1.0
OP1 D:DC3 2.8 29.3 1.0
C A:ILE302 3.4 31.5 1.0
C A:CYS300 3.5 32.9 1.0
C A:ILE305 3.5 26.6 1.0
O D:HOH107 3.8 35.6 1.0
P D:DC3 3.8 29.1 1.0
N A:ILE305 3.9 23.0 1.0
OP2 D:DC3 3.9 31.8 1.0
N A:ILE302 4.0 32.7 1.0
CA A:PRO303 4.0 25.5 1.0
N A:PRO303 4.0 28.6 1.0
C A:SER301 4.0 39.9 1.0
O A:HOH1054 4.1 39.6 1.0
CA A:ILE305 4.2 24.0 1.0
N A:GLY304 4.2 26.8 1.0
CA A:ILE302 4.3 31.4 1.0
CA A:CYS300 4.3 35.3 1.0
O A:SER301 4.3 33.5 1.0
N A:SER301 4.4 31.4 1.0
C A:PRO303 4.5 28.0 1.0
CA A:SER301 4.5 37.2 1.0
N A:GLY306 4.5 28.2 1.0
O A:ALA299 4.6 34.6 1.0
CB A:ILE305 4.6 28.7 1.0
O3' D:DC2 4.7 29.6 1.0
CA A:GLY306 4.8 34.0 1.0
C A:GLY304 4.9 25.3 1.0

Sodium binding site 3 out of 3 in 7m0a

Go back to Sodium Binding Sites List in 7m0a
Sodium binding site 3 out of 3 in the Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na708

b:55.5
occ:1.00
 O2G A:TTP701 2.6 27.9 0.4
O A:HOH865 2.6 37.1 1.0
O21 A:PPV702 2.6 28.0 0.6
O A:HOH849 2.9 44.0 1.0
PG A:TTP701 3.8 27.4 0.4
P1 A:PPV702 3.8 27.6 0.6
O A:HOH985 3.9 39.7 1.0
O11 A:PPV702 4.0 22.5 0.6
O1G A:TTP701 4.0 22.5 0.4
O A:HOH1001 4.3 33.0 1.0
O A:HOH937 4.4 38.4 1.0
NH1 A:ARG386 4.6 26.1 1.0
CA A:GLY426 4.7 20.0 1.0
O2A A:TTP701 4.7 15.9 0.4
O3B A:TTP701 4.7 27.0 0.4
OPP A:PPV702 4.8 27.1 0.6
OP2 P:DT7 4.8 14.8 0.6
O A:HOH839 4.9 38.7 1.0
O32 A:PPV702 4.9 25.3 0.6
O3G A:TTP701 4.9 23.7 0.4
O31 A:PPV702 4.9 23.7 0.6

Reference:

A.M.Kaminski, K.Bebenek, T.A.Kunkel, L.C.Pedersen. Comprehensive Structural Survey of Dna Double-Strand Break Synapsis By Dna Polymerase Lambda To Be Published.
Page generated: Fri Apr 7 15:02:05 2023

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