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Sodium in PDB 7m07: Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp

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

All present enzymatic activity of Pre-Catalytic Ternary 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 Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp, PDB code: 7m07 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) 45.36 / 1.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.003, 59.665, 139.649, 90, 90, 90
R / Rfree (%) 17.1 / 18.8

Other elements in 7m07:

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

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp (pdb code 7m07). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp, PDB code: 7m07:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 7m07

Go back to Sodium Binding Sites List in 7m07
Sodium binding site 1 out of 5 in the Pre-Catalytic Ternary 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 Pre-Catalytic Ternary 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:Na704

b:11.4
occ:1.00
 O A:SER339 2.3 13.1 1.0
O A:HOH1052 2.3 22.4 1.0
O A:ALA344 2.4 12.9 1.0
OP1 P:DA5 2.4 14.1 1.0
O A:ILE341 2.5 11.8 1.0
O P:HOH103 2.7 19.8 1.0
C A:SER339 3.4 11.4 1.0
C A:ILE341 3.4 11.3 1.0
C A:ALA344 3.5 12.8 1.0
P P:DA5 3.5 12.3 1.0
O A:HOH992 3.6 24.3 1.0
OP2 P:DA5 3.7 13.3 1.0
O P:HOH126 3.7 21.1 0.5
N A:ALA344 3.8 12.5 1.0
CA A:TRP342 4.0 11.6 1.0
N A:GLY343 4.0 11.8 1.0
N A:ILE341 4.1 10.5 1.0
N A:TRP342 4.1 11.7 1.0
CA A:SER339 4.1 11.0 1.0
CA A:ALA344 4.2 11.7 1.0
C A:ASN340 4.2 12.2 1.0
N A:ASN340 4.3 11.1 1.0
C A:TRP342 4.4 12.4 1.0
CA A:ASN340 4.4 10.6 1.0
CA A:ILE341 4.4 10.7 1.0
O3' P:DT4 4.4 12.7 1.0
O P:HOH126 4.4 27.9 0.5
N A:GLY345 4.5 11.0 1.0
O5' P:DA5 4.7 10.8 1.0
CB A:ALA344 4.7 11.3 1.0
O A:HOH1001 4.7 30.3 1.0
CB A:SER339 4.7 20.3 1.0
CA A:GLY345 4.7 11.8 1.0
C A:GLY343 4.8 13.5 1.0
O A:ASN340 4.8 13.6 1.0
O A:HOH886 4.8 40.4 1.0
CA A:GLY343 4.9 13.4 1.0

Sodium binding site 2 out of 5 in 7m07

Go back to Sodium Binding Sites List in 7m07
Sodium binding site 2 out of 5 in the Pre-Catalytic Ternary 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 Pre-Catalytic Ternary 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:Na705

b:30.1
occ:1.00
 O A:CYS300 2.5 44.4 1.0
O A:ILE305 2.7 37.7 1.0
O A:ILE302 2.7 39.1 1.0
O A:HOH1030 2.8 40.1 1.0
OP1 D:DC3 2.9 34.5 1.0
O D:HOH104 3.5 33.9 1.0
C A:ILE302 3.6 45.1 1.0
C A:CYS300 3.7 43.0 1.0
OP2 D:DC3 3.7 41.3 1.0
C A:ILE305 3.8 33.5 1.0
P D:DC3 3.8 33.4 1.0
CA A:PRO303 4.1 41.6 1.0
N A:ILE305 4.1 33.0 1.0
N A:ILE302 4.2 43.9 1.0
N A:PRO303 4.2 41.5 1.0
C A:SER301 4.3 51.5 1.0
CA A:CYS300 4.4 48.4 1.0
N A:GLY304 4.4 31.9 1.0
CA A:ILE305 4.5 32.8 1.0
CA A:ILE302 4.6 41.9 1.0
O A:SER301 4.6 44.8 1.0
N A:SER301 4.6 49.0 1.0
C A:PRO303 4.7 39.2 1.0
N A:GLY306 4.7 35.1 1.0
CA A:SER301 4.7 50.7 1.0
O3' D:DC2 4.7 30.5 1.0
CA A:GLY306 4.9 36.2 1.0
O A:ALA299 4.9 49.1 1.0
CB A:ILE305 5.0 38.8 1.0
O D:HOH103 5.0 36.8 1.0

Sodium binding site 3 out of 5 in 7m07

Go back to Sodium Binding Sites List in 7m07
Sodium binding site 3 out of 5 in the Pre-Catalytic Ternary 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 Pre-Catalytic Ternary 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:Na706

b:34.4
occ:1.00
 O A:THR250 2.5 67.1 1.0
O A:GLN247 2.6 53.5 1.0
O A:LYS287 2.8 45.1 1.0
O A:PHE289 2.9 42.0 1.0
O A:SER288 3.1 45.9 1.0
C A:SER288 3.3 49.5 1.0
CA A:SER288 3.6 44.4 1.0
O A:HOH870 3.6 39.8 1.0
C A:THR250 3.7 72.8 1.0
C A:GLN247 3.8 57.7 1.0
C A:PHE289 3.8 55.7 1.0
C A:LYS287 3.9 42.1 1.0
N A:PHE289 4.0 39.1 1.0
CD2 A:HIS252 4.1 63.0 1.0
N A:SER288 4.2 40.2 1.0
NE2 A:HIS252 4.5 63.8 1.0
N A:ASN251 4.6 53.2 1.0
CA A:PHE289 4.6 40.4 1.0
CA A:THR250 4.6 90.8 1.0
CA A:ASN251 4.6 49.0 1.0
CA A:GLN247 4.7 51.8 1.0
CB A:THR250 4.7 85.4 1.0
N A:HIS290 4.7 53.2 1.0
CA A:LYS248 4.7 62.5 1.0
N A:THR250 4.7 82.7 1.0
CA A:HIS290 4.7 63.2 1.0
N A:LYS248 4.7 55.3 1.0
N A:HIS252 4.8 42.3 1.0
CB A:SER288 4.9 50.6 1.0
CB A:GLN247 4.9 44.1 1.0

Sodium binding site 4 out of 5 in 7m07

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Sodium binding site 4 out of 5 in the Pre-Catalytic Ternary 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 4 of Pre-Catalytic Ternary 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:Na708

b:36.2
occ:0.92
 O A:SER463 2.4 16.8 1.0
O A:HOH1094 2.6 35.5 1.0
O A:HOH1023 2.6 33.7 1.0
O A:HOH1116 2.6 38.7 1.0
O T:HOH216 3.0 37.7 1.0
O T:HOH208 3.0 27.3 1.0
C A:SER463 3.6 17.2 1.0
O T:HOH246 3.7 42.6 1.0
OP1 T:DT10 3.9 17.6 1.0
O T:HOH253 4.5 45.1 1.0
CA A:SER463 4.5 13.3 1.0
OP2 T:DT10 4.5 17.2 1.0
N A:GLN464 4.5 14.1 0.7
N A:GLN464 4.5 14.2 0.3
CB A:SER463 4.5 16.7 1.0
N A:GLU465 4.6 18.6 1.0
CA A:GLN464 4.6 16.0 0.7
CA A:GLN464 4.6 16.1 0.3
N A:SER463 4.7 14.0 1.0
P T:DT10 4.8 17.3 1.0
OE2 A:GLU465 4.9 21.3 1.0

Sodium binding site 5 out of 5 in 7m07

Go back to Sodium Binding Sites List in 7m07
Sodium binding site 5 out of 5 in the Pre-Catalytic Ternary 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 5 of Pre-Catalytic Ternary 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
T:Na101

b:44.8
occ:1.00
 OP2 T:DC4 2.7 34.3 1.0
O A:HOH1103 2.8 44.9 1.0
O T:HOH254 2.9 37.4 1.0
O5' T:DC4 3.0 36.7 1.0
C2' T:DG3 3.3 26.6 1.0
P T:DC4 3.4 40.3 1.0
O T:HOH220 3.7 31.7 1.0
C3' T:DG3 3.8 26.6 1.0
C2' T:DC4 3.8 30.2 1.0
C6 T:DC4 3.9 20.0 1.0
O T:HOH233 3.9 31.8 1.0
C3' T:DC4 4.0 29.4 1.0
O3' T:DG3 4.1 33.8 1.0
CH2 A:TRP274 4.1 30.6 1.0
C5' T:DC4 4.2 28.6 1.0
CZ2 A:TRP274 4.3 28.4 1.0
O4' T:DC4 4.4 23.7 1.0
C4' T:DC4 4.5 24.5 1.0
C1' T:DC4 4.6 31.8 1.0
C5 T:DC4 4.6 19.5 1.0
N1 T:DC4 4.7 22.9 1.0
C1' T:DG3 4.8 26.0 1.0
OP1 T:DC4 4.8 38.4 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: Mon Aug 18 10:48:50 2025

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