Magnesium 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
Sodium (Na) 3 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7m09

Go back to Magnesium Binding Sites List in 7m09
Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg703

b:13.0
occ:0.30
 CA A:CA702 0.0 13.2 0.7
OD2 A:ASP427 2.0 14.4 1.0
OD2 A:ASP490 2.1 14.1 1.0
OD1 A:ASP429 2.1 12.9 1.0
O2A A:DUP701 2.3 10.7 1.0
O A:HOH878 2.3 14.4 1.0
O3' P:DC6 2.3 15.3 1.0
CG A:ASP427 3.0 14.4 1.0
CG A:ASP429 3.1 13.4 1.0
CG A:ASP490 3.2 14.1 1.0
OD1 A:ASP427 3.3 12.0 1.0
C3' P:DC6 3.4 17.2 1.0
PA A:DUP701 3.4 12.4 1.0
OD2 A:ASP429 3.6 12.2 1.0
MG A:MG704 3.6 12.4 1.0
O1A A:DUP701 3.8 13.4 1.0
CB A:ASP490 3.8 13.2 1.0
O5' A:DUP701 3.8 12.9 1.0
C5' A:DUP701 4.0 10.3 1.0
C4' P:DC6 4.1 13.4 1.0
OD1 A:ASP490 4.2 13.0 1.0
C5' P:DC6 4.2 14.8 1.0
CB A:ASP427 4.4 12.3 1.0
O A:HOH843 4.4 21.4 1.0
CB A:ASP429 4.4 12.5 1.0
NH2 A:ARG488 4.6 15.1 1.0
O5' P:DC6 4.6 14.2 1.0
O P:HOH220 4.6 23.0 1.0
C2' P:DC6 4.6 18.6 1.0
O3G A:DUP701 4.7 13.5 1.0
N3A A:DUP701 4.9 10.7 1.0
CA A:ASP429 5.0 12.0 1.0

Magnesium binding site 2 out of 2 in 7m09

Go back to Magnesium Binding Sites List in 7m09
Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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:Mg704

b:12.4
occ:1.00
 OD1 A:ASP427 2.0 12.0 1.0
OD2 A:ASP429 2.0 12.2 1.0
O2B A:DUP701 2.1 12.8 1.0
O3G A:DUP701 2.1 13.5 1.0
O A:HOH923 2.1 14.4 1.0
O2A A:DUP701 2.2 10.7 1.0
CG A:ASP429 3.0 13.4 1.0
CG A:ASP427 3.1 14.4 1.0
PB A:DUP701 3.1 13.4 1.0
PA A:DUP701 3.3 12.4 1.0
PG A:DUP701 3.4 13.7 1.0
OD1 A:ASP429 3.4 12.9 1.0
N3A A:DUP701 3.5 10.7 1.0
OD2 A:ASP427 3.5 14.4 1.0
CA A:CA702 3.6 13.2 0.7
MG A:MG703 3.6 13.0 0.3
O3B A:DUP701 3.6 14.5 1.0
O A:HOH843 3.9 21.4 1.0
O A:ASP427 4.0 12.5 1.0
O2G A:DUP701 4.1 14.3 1.0
C5' A:DUP701 4.1 10.3 1.0
OG A:SER417 4.3 15.3 1.0
O5' A:DUP701 4.3 12.9 1.0
N A:ASP427 4.3 13.5 1.0
O A:HOH936 4.3 13.6 1.0
C A:ASP427 4.3 13.0 1.0
CB A:ASP429 4.3 12.5 1.0
CB A:ASP427 4.3 12.3 1.0
O1A A:DUP701 4.4 13.4 1.0
N A:SER417 4.4 11.0 1.0
CA A:GLY416 4.5 12.2 1.0
O1B A:DUP701 4.5 14.4 1.0
CA A:ASP427 4.5 12.4 1.0
O A:HOH878 4.6 14.4 1.0
O1G A:DUP701 4.6 13.5 1.0
N A:ASP429 4.8 12.2 1.0
N A:VAL428 4.9 13.9 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: Wed Apr 5 13:17:38 2023

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