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Sodium in PDB 7m09: Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Blunt- Ended Dsb Substrate and Incoming Dumpnpp

Enzymatic activity of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Blunt- Ended Dsb Substrate and Incoming Dumpnpp

All present enzymatic activity of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Blunt- Ended Dsb Substrate and Incoming Dumpnpp:
2.7.7.7;

Protein crystallography data

The structure of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Blunt- Ended Dsb Substrate and Incoming Dumpnpp, PDB code: 7m09 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) 39.17 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.941, 59.615, 140.042, 90, 90, 90
R / Rfree (%) 16.8 / 18.6

Other elements in 7m09:

The structure of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Blunt- Ended Dsb Substrate and Incoming Dumpnpp also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Blunt- Ended Dsb Substrate and Incoming Dumpnpp (pdb code 7m09). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Blunt- Ended Dsb Substrate and Incoming Dumpnpp, PDB code: 7m09:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7m09

Go back to Sodium Binding Sites List in 7m09
Sodium binding site 1 out of 3 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Blunt- Ended Dsb 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 Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Blunt- Ended Dsb Substrate and Incoming Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na705

b:13.0
occ:1.00
 O A:SER339 2.3 12.0 1.0
O A:ALA344 2.3 13.5 1.0
OP1 P:DG5 2.4 13.7 1.0
O A:ILE341 2.4 11.5 1.0
O A:HOH1054 2.4 18.8 1.0
O P:HOH209 2.8 20.8 1.0
C A:SER339 3.3 10.9 1.0
C A:ALA344 3.3 11.9 1.0
C A:ILE341 3.4 11.7 1.0
P P:DG5 3.4 12.6 1.0
OP2 P:DG5 3.7 13.0 1.0
N A:ALA344 3.8 10.7 1.0
N A:GLY343 4.0 11.4 1.0
CA A:SER339 4.0 10.7 1.0
CA A:TRP342 4.0 10.5 1.0
N A:ILE341 4.0 12.2 1.0
O A:HOH1036 4.0 44.6 1.0
N A:TRP342 4.1 11.9 1.0
CA A:ALA344 4.1 11.0 1.0
C A:ASN340 4.2 13.6 1.0
N A:ASN340 4.3 13.1 1.0
N A:GLY345 4.3 11.5 1.0
CA A:ILE341 4.3 11.1 1.0
CA A:ASN340 4.4 13.8 1.0
C A:TRP342 4.4 13.2 1.0
O3' P:DT4 4.4 13.4 1.0
O5' P:DG5 4.6 11.5 1.0
CA A:GLY345 4.6 11.6 1.0
CB A:ALA344 4.6 10.9 1.0
CB A:SER339 4.6 16.9 1.0
C A:GLY343 4.7 13.8 1.0
O A:ASN340 4.8 12.9 1.0
O A:HOH1009 4.9 25.0 0.6
CA A:GLY343 4.9 14.4 1.0
O A:PHE338 4.9 12.8 1.0

Sodium binding site 2 out of 3 in 7m09

Go back to Sodium Binding Sites List in 7m09
Sodium binding site 2 out of 3 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Blunt- Ended Dsb 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 Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Blunt- Ended Dsb Substrate and Incoming Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na706

b:32.6
occ:1.00
 O A:ILE305 2.4 29.2 1.0
O A:CYS300 2.4 36.8 1.0
O A:HOH1027 2.5 33.4 1.0
O A:ILE302 2.5 32.4 1.0
OP1 D:DC3 2.8 28.4 1.0
O D:HOH117 2.9 50.2 1.0
C A:ILE302 3.4 31.5 1.0
C A:ILE305 3.5 31.1 1.0
C A:CYS300 3.5 37.7 1.0
O D:HOH110 3.7 35.2 1.0
P D:DC3 3.8 28.3 1.0
OP2 D:DC3 3.9 32.4 1.0
N A:ILE305 3.9 24.2 1.0
N A:ILE302 3.9 34.4 1.0
N A:PRO303 4.0 29.7 1.0
CA A:PRO303 4.0 27.8 1.0
C A:SER301 4.1 42.6 1.0
N A:GLY304 4.2 26.4 1.0
O A:HOH1080 4.2 43.0 1.0
CA A:ILE305 4.2 26.7 1.0
CA A:CYS300 4.3 41.0 1.0
CA A:ILE302 4.3 31.3 1.0
O A:SER301 4.4 40.6 1.0
N A:SER301 4.4 37.8 1.0
C A:PRO303 4.5 30.1 1.0
N A:GLY306 4.5 29.3 1.0
CA A:SER301 4.5 41.2 1.0
O A:ALA299 4.6 36.7 1.0
CB A:ILE305 4.6 30.4 1.0
O3' D:DC2 4.6 29.2 1.0
CA A:GLY306 4.7 33.7 1.0
C A:GLY304 4.9 26.0 1.0

Sodium binding site 3 out of 3 in 7m09

Go back to Sodium Binding Sites List in 7m09
Sodium binding site 3 out of 3 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Blunt- Ended Dsb 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 Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Blunt- Ended Dsb Substrate and Incoming Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na709

b:27.2
occ:1.00
 O A:HOH1053 2.1 40.2 1.0
O A:HOH1022 2.1 40.6 1.0
O1G A:DUP701 2.2 13.5 1.0
O A:HOH833 2.4 27.7 1.0
O A:HOH1135 2.5 38.7 1.0
O A:HOH843 2.6 21.4 1.0
O A:HOH839 3.1 27.5 0.5
O P:HOH201 3.4 41.8 1.0
PG A:DUP701 3.5 13.7 1.0
O3G A:DUP701 3.7 13.5 1.0
O A:HOH948 3.9 26.1 1.0
O A:HOH955 4.1 29.4 1.0
O A:HOH907 4.2 34.7 1.0
NH1 A:ARG386 4.2 17.7 1.0
CA A:GLY426 4.2 12.7 1.0
O A:HOH968 4.5 30.8 1.0
O3B A:DUP701 4.5 14.5 1.0
O2G A:DUP701 4.5 14.3 1.0
O1A A:DUP701 4.7 13.4 1.0
C A:GLY426 4.9 14.3 1.0
N A:GLY426 5.0 12.9 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: Fri Apr 7 15:02:05 2023

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