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Magnesium 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:

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

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total only one binding site of Magnesium was determined in the Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp, PDB code: 7m08:

Magnesium binding site 1 out of 1 in 7m08

Go back to Magnesium Binding Sites List in 7m08
Magnesium binding site 1 out of 1 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 Magnesium with other atoms in the Mg 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:Mg606

b:29.9
occ:0.60
 OD2 A:ASP490 1.8 32.3 1.0
OP1 P:DT7 1.9 21.3 1.0
OD1 A:ASP429 2.0 18.7 1.0
OD2 A:ASP427 2.1 42.0 1.0
O3' P:DC6 2.7 18.1 1.0
P P:DT7 2.8 18.6 1.0
CG A:ASP427 2.8 30.6 1.0
CG A:ASP490 2.9 21.8 1.0
OD1 A:ASP427 3.0 37.1 1.0
CG A:ASP429 3.1 21.7 1.0
OD2 A:ASP429 3.5 20.6 1.0
CB A:ASP490 3.5 16.4 1.0
OP2 P:DT7 3.8 18.8 1.0
O5' P:DT7 3.9 17.6 1.0
OD1 A:ASP490 4.0 25.0 1.0
CB A:ASP427 4.0 25.2 1.0
C3' P:DC6 4.1 16.7 1.0
C5' P:DT7 4.1 16.8 1.0
CB A:ASP429 4.4 16.2 1.0
C4' P:DC6 4.4 15.2 1.0
O A:HOH739 4.5 35.0 1.0
O P:HOH120 4.5 29.9 0.6
C5' P:DC6 4.6 17.2 1.0
O A:VAL428 4.6 17.8 1.0
CA A:ASP429 4.7 15.9 1.0
CE1 A:PHE506 4.8 24.6 1.0
C A:VAL428 4.8 17.9 1.0
CA A:ASP490 4.8 16.6 1.0
N A:ASP429 4.9 15.4 1.0
N A:ASP490 4.9 15.0 1.0
CZ A:PHE506 5.0 17.3 1.0
NH2 A:ARG488 5.0 22.0 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 Oct 2 23:36:48 2024

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