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Sodium in PDB 7m0d: Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp

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

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

Protein crystallography data

The structure of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp, PDB code: 7m0d 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) 41.78 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.442, 151.989, 86.473, 90, 90, 90
R / Rfree (%) 16.4 / 18.9

Other elements in 7m0d:

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

Magnesium (Mg) 2 atoms
Potassium (K) 6 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp (pdb code 7m0d). 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 Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp, PDB code: 7m0d:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 7m0d

Go back to Sodium Binding Sites List in 7m0d
Sodium binding site 1 out of 5 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary 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 Bound Complementary Dsb Substrate and Incoming Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na702

b:15.2
occ:1.00
 OD1 A:ASP429 2.2 14.6 1.0
OD2 A:ASP427 2.3 17.5 1.0
OD2 A:ASP490 2.4 13.8 1.0
O1A A:DUP701 2.4 11.2 1.0
CG A:ASP427 3.0 17.8 1.0
OD1 A:ASP427 3.1 14.0 1.0
CG A:ASP490 3.2 15.3 1.0
CG A:ASP429 3.3 14.4 1.0
PA A:DUP701 3.4 12.5 1.0
MG A:MG703 3.5 12.5 1.0
O3' F:DC6 3.5 13.2 1.0
OD2 A:ASP429 3.6 11.2 1.0
C3' F:DC6 3.7 12.2 1.0
N A:TRS709 3.8 28.6 0.6
O5' A:DUP701 3.8 11.8 1.0
O2A A:DUP701 3.9 13.6 1.0
CB A:ASP490 3.9 10.8 1.0
C5' A:DUP701 4.0 11.2 1.0
OD1 A:ASP490 4.1 15.1 1.0
O2 A:TRS709 4.2 14.6 0.6
O A:HOH907 4.3 15.4 0.4
CB A:ASP427 4.4 12.4 1.0
CB A:ASP429 4.6 12.5 1.0
O1G A:DUP701 4.6 11.8 1.0
NH2 A:ARG488 4.7 13.0 1.0
C4' F:DC6 4.7 13.5 1.0
C2' F:DC6 4.8 12.4 1.0
C2 A:TRS709 4.8 19.1 0.6
O A:VAL428 4.8 12.0 1.0
C5' F:DC6 4.9 12.1 1.0
CE1 A:PHE506 4.9 11.3 1.0
N3A A:DUP701 4.9 10.1 1.0
C A:TRS709 4.9 25.4 0.6
O2B A:DUP701 4.9 12.4 1.0

Sodium binding site 2 out of 5 in 7m0d

Go back to Sodium Binding Sites List in 7m0d
Sodium binding site 2 out of 5 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary 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 Bound Complementary Dsb Substrate and Incoming Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na704

b:10.3
occ:1.00
 O2 F:EDO101 2.3 19.9 1.0
O A:SER339 2.4 13.3 1.0
O A:ALA344 2.5 13.6 1.0
OP1 F:DG5 2.5 15.3 1.0
O A:ILE341 2.6 12.9 1.0
O F:HOH406 2.7 17.0 1.0
C2 F:EDO101 3.2 22.9 1.0
C A:SER339 3.4 13.1 1.0
P F:DG5 3.5 12.5 1.0
C A:ALA344 3.5 12.9 1.0
C A:ILE341 3.5 11.0 1.0
K A:K706 3.6 18.6 0.8
OP2 F:DG5 3.7 13.9 1.0
N A:ALA344 3.9 10.2 1.0
N A:GLY343 4.0 11.1 1.0
CA A:SER339 4.1 13.9 1.0
CA A:TRP342 4.1 12.5 1.0
N A:TRP342 4.2 10.9 1.0
N A:ILE341 4.2 10.2 1.0
CA A:ALA344 4.2 9.9 1.0
C A:ASN340 4.3 15.2 1.0
O1 A:EDO714 4.4 27.9 1.0
O1 F:EDO101 4.4 28.3 1.0
C1 F:EDO101 4.4 31.8 1.0
C A:TRP342 4.4 10.4 1.0
N A:ASN340 4.4 12.3 1.0
N A:GLY345 4.4 14.1 1.0
CA A:ILE341 4.5 8.6 1.0
O3' F:DT4 4.5 11.3 1.0
CB A:SER339 4.6 13.0 1.0
CA A:ASN340 4.6 14.8 1.0
O5' F:DG5 4.6 13.8 1.0
CA A:GLY345 4.7 13.0 1.0
C A:GLY343 4.8 13.2 1.0
CB A:ALA344 4.8 10.9 1.0
O A:ASN340 4.8 12.4 1.0
CA A:GLY343 5.0 14.4 1.0

Sodium binding site 3 out of 5 in 7m0d

Go back to Sodium Binding Sites List in 7m0d
Sodium binding site 3 out of 5 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary 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 Bound Complementary Dsb Substrate and Incoming Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:14.1
occ:1.00
 OD1 B:ASP429 2.2 12.4 1.0
OD2 B:ASP427 2.3 17.6 1.0
O2A B:DUP701 2.4 11.3 1.0
OD2 B:ASP490 2.4 13.8 1.0
CG B:ASP427 3.0 14.7 1.0
OD1 B:ASP427 3.0 12.5 1.0
CG B:ASP429 3.2 15.8 1.0
CG B:ASP490 3.2 13.8 1.0
O3' J:DC6 3.4 12.8 1.0
PA B:DUP701 3.4 12.2 1.0
MG B:MG703 3.4 12.5 1.0
OD2 B:ASP429 3.6 12.7 1.0
N J:TRS101 3.7 22.6 0.7
C3' J:DC6 3.7 13.0 1.0
O5' B:DUP701 3.8 10.9 1.0
O1A B:DUP701 3.9 11.5 1.0
CB B:ASP490 3.9 11.6 1.0
C5' B:DUP701 4.0 8.8 1.0
OD1 B:ASP490 4.1 14.6 1.0
O B:HOH1002 4.2 17.7 0.3
O1 J:TRS101 4.3 19.6 0.7
CB B:ASP427 4.4 10.4 1.0
CB B:ASP429 4.6 11.1 1.0
O1G B:DUP701 4.7 11.9 1.0
C4' J:DC6 4.7 9.7 1.0
C2' J:DC6 4.8 11.4 1.0
C J:TRS101 4.8 18.0 0.7
NH2 B:ARG488 4.8 11.3 1.0
C1 J:TRS101 4.8 20.1 0.7
N3A B:DUP701 4.9 10.8 1.0
C5' J:DC6 4.9 11.8 1.0
O B:VAL428 4.9 12.6 1.0
CE1 B:PHE506 4.9 12.6 1.0
O1B B:DUP701 4.9 10.9 1.0
O5' J:DC6 5.0 12.6 1.0

Sodium binding site 4 out of 5 in 7m0d

Go back to Sodium Binding Sites List in 7m0d
Sodium binding site 4 out of 5 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary 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 4 of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na704

b:10.2
occ:1.00
 O1 J:EDO102 2.4 22.2 1.0
O B:SER339 2.4 13.3 1.0
O B:ALA344 2.5 13.1 1.0
OP1 J:DG5 2.5 14.4 1.0
O B:ILE341 2.6 12.3 1.0
O J:HOH202 2.6 18.8 1.0
C1 J:EDO102 3.4 22.9 1.0
C B:SER339 3.5 15.2 1.0
C B:ALA344 3.5 13.2 1.0
P J:DG5 3.6 13.0 1.0
C B:ILE341 3.6 10.7 1.0
K B:K706 3.6 22.0 0.8
OP2 J:DG5 3.7 12.4 1.0
N B:ALA344 3.9 11.4 1.0
C2 J:EDO102 4.0 23.4 1.0
CA B:SER339 4.1 13.5 1.0
N B:GLY343 4.1 13.3 1.0
CA B:TRP342 4.1 12.5 1.0
N B:TRP342 4.2 12.7 1.0
N B:ILE341 4.3 9.6 1.0
CA B:ALA344 4.3 10.7 1.0
O2 J:EDO102 4.3 27.8 1.0
C B:ASN340 4.4 14.8 1.0
N B:GLY345 4.4 13.3 1.0
N B:ASN340 4.5 12.7 1.0
C B:TRP342 4.5 12.4 1.0
O1 B:FMT713 4.5 29.9 1.0
CB B:SER339 4.5 14.9 1.0
O3' J:DT4 4.5 11.5 1.0
CA B:ILE341 4.6 9.7 1.0
CA B:ASN340 4.6 15.7 1.0
CA B:GLY345 4.7 13.7 1.0
O5' J:DG5 4.7 13.2 1.0
C B:GLY343 4.8 12.1 1.0
CB B:ALA344 4.9 10.2 1.0
O B:ASN340 4.9 15.2 1.0
CA B:GLY343 5.0 14.8 1.0

Sodium binding site 5 out of 5 in 7m0d

Go back to Sodium Binding Sites List in 7m0d
Sodium binding site 5 out of 5 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary 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 5 of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na101

b:29.2
occ:1.00
 O K:HOH215 2.8 35.2 1.0
O6 L:DG1 2.9 18.0 1.0
O6 K:DG3 2.9 25.8 1.0
O L:HOH106 3.0 41.6 1.0
O L:HOH114 3.2 39.6 1.0
O K:HOH209 3.4 45.2 1.0
N4 L:DC2 3.7 22.4 1.0
C6 L:DG1 3.9 18.0 1.0
N4 K:DC4 4.0 17.6 1.0
C6 K:DG3 4.1 21.9 1.0
O L:HOH112 4.3 41.1 1.0
N7 K:DG2 4.5 38.9 1.0
N7 L:DG1 4.6 19.6 1.0
C5 L:DG1 4.6 20.4 1.0
N7 K:DG3 4.7 27.9 1.0
O K:HOH214 4.7 28.6 1.0
O6 K:DG2 4.7 31.2 1.0
C5 K:DG3 4.8 22.6 1.0
C4 L:DC2 5.0 25.1 1.0
C5 K:DG2 5.0 33.6 1.0
N1 L:DG1 5.0 14.2 1.0
O B:HOH1006 5.0 35.9 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: Tue Oct 8 17:47:35 2024

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