Sodium in PDB 7m08: Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp

Enzymatic activity of Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp

All present enzymatic activity of Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp:
2.7.7.7;

Protein crystallography data

The structure of Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp, PDB code: 7m08 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) 43.82 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.136, 59.862, 140.189, 90, 90, 90
R / Rfree (%) 18.6 / 20.9

Other elements in 7m08:

The structure of Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp (pdb code 7m08). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp, PDB code: 7m08:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7m08

Go back to Sodium Binding Sites List in 7m08
Sodium binding site 1 out of 3 in the Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:12.8
occ:1.00
 O A:SER339 2.4 16.4 1.0
O A:ALA344 2.4 17.3 1.0
O A:HOH897 2.5 24.7 1.0
OP1 P:DA5 2.5 16.8 1.0
O P:HOH109 2.6 25.3 1.0
O A:ILE341 2.6 15.7 1.0
C A:ILE341 3.5 15.4 1.0
C A:SER339 3.5 15.1 1.0
O A:HOH841 3.5 21.7 0.6
P P:DA5 3.6 15.7 1.0
C A:ALA344 3.6 17.7 1.0
OP2 P:DA5 3.7 16.1 1.0
N A:ALA344 3.9 16.7 1.0
CA A:TRP342 4.0 15.4 1.0
N A:GLY343 4.0 15.9 1.0
N A:TRP342 4.1 14.4 1.0
N A:ILE341 4.1 12.2 1.0
C A:ASN340 4.3 15.1 1.0
CA A:SER339 4.3 15.6 1.0
CA A:ALA344 4.3 12.4 1.0
O P:HOH122 4.3 34.2 1.0
N A:ASN340 4.3 13.9 1.0
CA A:ASN340 4.4 13.2 1.0
C A:TRP342 4.4 14.3 1.0
O3' P:DT4 4.4 16.3 1.0
CA A:ILE341 4.4 11.9 1.0
N A:GLY345 4.6 15.2 1.0
O A:HOH841 4.7 28.1 0.4
CB A:ALA344 4.8 14.9 1.0
O A:ASN340 4.8 16.8 1.0
O P:HOH134 4.8 40.3 1.0
O5' P:DA5 4.8 15.3 1.0
C A:GLY343 4.8 16.7 1.0
CA A:GLY345 4.9 15.4 1.0
O A:HOH866 4.9 35.4 1.0
CB A:SER339 4.9 23.1 1.0
CA A:GLY343 5.0 14.0 1.0

Sodium binding site 2 out of 3 in 7m08

Go back to Sodium Binding Sites List in 7m08
Sodium binding site 2 out of 3 in the Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:33.2
occ:1.00
 O A:CYS300 2.5 53.7 1.0
O A:HOH885 2.5 57.9 1.0
O A:ILE305 2.6 38.8 1.0
O A:ILE302 2.8 41.1 1.0
OP1 D:DC3 2.9 38.3 1.0
O D:HOH101 3.5 49.6 1.0
C A:CYS300 3.6 56.5 1.0
C A:ILE305 3.7 35.2 1.0
C A:ILE302 3.7 48.5 1.0
P D:DC3 3.8 39.4 1.0
OP2 D:DC3 3.8 40.0 1.0
N A:ILE305 4.1 35.6 1.0
CA A:CYS300 4.2 54.7 1.0
CA A:PRO303 4.2 46.4 1.0
N A:ILE302 4.3 53.4 1.0
N A:PRO303 4.3 47.2 1.0
CA A:ILE305 4.4 36.9 1.0
N A:GLY304 4.5 38.5 1.0
C A:SER301 4.5 59.2 1.0
N A:SER301 4.6 51.3 1.0
N A:GLY306 4.6 38.2 1.0
CA A:ILE302 4.7 48.5 1.0
C A:PRO303 4.7 40.5 1.0
O3' D:DC2 4.8 36.1 1.0
CA A:GLY306 4.8 35.5 1.0
CA A:SER301 4.8 57.4 1.0
CB A:ILE305 4.9 41.1 1.0
O A:ALA299 4.9 48.3 1.0
CB A:CYS300 4.9 63.8 1.0
O A:SER301 4.9 54.7 1.0

Sodium binding site 3 out of 3 in 7m08

Go back to Sodium Binding Sites List in 7m08
Sodium binding site 3 out of 3 in the Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:36.6
occ:1.00
 O A:LYS287 2.6 53.0 1.0
O A:THR250 2.6 82.0 1.0
O A:GLN247 2.6 66.1 1.0
O A:PHE289 2.8 50.1 1.0
O A:SER288 3.3 52.8 1.0
C A:SER288 3.4 52.9 1.0
CA A:SER288 3.7 46.8 1.0
O A:HOH736 3.7 47.1 1.0
C A:LYS287 3.7 46.6 1.0
C A:THR250 3.8 76.3 1.0
C A:PHE289 3.8 55.7 1.0
C A:GLN247 3.8 70.8 1.0
N A:PHE289 4.0 45.5 1.0
CD2 A:HIS252 4.0 61.4 1.0
N A:SER288 4.1 41.6 1.0
CA A:LYS248 4.4 66.5 1.0
CA A:PHE289 4.5 51.4 1.0
N A:LYS248 4.6 67.7 1.0
NE2 A:HIS252 4.6 64.2 1.0
N A:HIS290 4.6 55.9 1.0
N A:THR250 4.6 88.2 1.0
CA A:HIS290 4.6 61.8 1.0
CA A:ASN251 4.6 58.5 1.0
N A:ASN251 4.6 61.1 1.0
CA A:THR250 4.7 83.7 1.0
C A:LYS248 4.8 77.6 1.0
N A:HIS252 4.8 47.8 1.0
CA A:GLN247 4.9 64.1 1.0
CB A:THR250 4.9 78.7 1.0
CA A:LYS287 5.0 46.1 1.0

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: Tue Oct 8 17:46:34 2024

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