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Magnesium 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
Sodium (Na) 5 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 7m07

Go back to Magnesium Binding Sites List in 7m07
Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg702

b:11.7
occ:1.00
 OD2 A:ASP427 2.0 14.6 1.0
OD1 A:ASP429 2.0 12.6 1.0
OD2 A:ASP490 2.1 15.9 1.0
O A:HOH892 2.1 15.8 1.0
O2A A:DUP701 2.3 12.5 1.0
O3' P:DC6 2.3 15.6 1.0
CG A:ASP427 3.0 15.8 1.0
CG A:ASP429 3.1 12.6 1.0
CG A:ASP490 3.2 13.1 1.0
OD1 A:ASP427 3.3 13.5 1.0
PA A:DUP701 3.3 13.1 1.0
C3' P:DC6 3.4 14.1 1.0
OD2 A:ASP429 3.5 13.1 1.0
MG A:MG703 3.6 13.2 1.0
O1A A:DUP701 3.7 14.1 1.0
O5' A:DUP701 3.7 11.6 1.0
CB A:ASP490 3.9 13.0 1.0
C5' A:DUP701 4.0 11.8 1.0
C4' P:DC6 4.1 12.3 1.0
OD1 A:ASP490 4.1 15.3 1.0
C5' P:DC6 4.2 13.8 1.0
O A:HOH906 4.3 22.4 1.0
CB A:ASP427 4.3 13.4 1.0
CB A:ASP429 4.4 10.6 1.0
NH2 A:ARG488 4.6 17.0 1.0
O5' P:DC6 4.7 13.3 1.0
O3G A:DUP701 4.7 14.0 1.0
C2' P:DC6 4.7 16.3 1.0
N3A A:DUP701 4.8 14.1 1.0
O P:HOH127 4.9 27.3 1.0
CA A:ASP429 5.0 11.9 1.0
O2B A:DUP701 5.0 11.6 1.0

Magnesium binding site 2 out of 2 in 7m07

Go back to Magnesium Binding Sites List in 7m07
Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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:Mg703

b:13.2
occ:1.00
 O2B A:DUP701 2.0 11.6 1.0
OD1 A:ASP427 2.0 13.5 1.0
OD2 A:ASP429 2.1 13.1 1.0
O3G A:DUP701 2.1 14.0 1.0
O2A A:DUP701 2.1 12.5 1.0
O A:HOH909 2.2 13.6 1.0
CG A:ASP429 3.1 12.6 1.0
PB A:DUP701 3.1 13.7 1.0
CG A:ASP427 3.1 15.8 1.0
PA A:DUP701 3.3 13.1 1.0
PG A:DUP701 3.3 14.0 1.0
OD1 A:ASP429 3.4 12.6 1.0
N3A A:DUP701 3.4 14.1 1.0
O3B A:DUP701 3.6 14.6 1.0
MG A:MG702 3.6 11.7 1.0
OD2 A:ASP427 3.6 14.6 1.0
O2G A:DUP701 4.0 14.5 1.0
O A:HOH906 4.0 22.4 1.0
O A:ASP427 4.1 13.7 1.0
C5' A:DUP701 4.1 11.8 1.0
OG A:SER417 4.2 14.8 1.0
O5' A:DUP701 4.2 11.6 1.0
O A:HOH946 4.3 13.6 1.0
N A:ASP427 4.3 13.6 1.0
C A:ASP427 4.3 13.4 1.0
CB A:ASP429 4.4 10.6 1.0
N A:SER417 4.4 13.1 1.0
CB A:ASP427 4.4 13.4 1.0
O1A A:DUP701 4.4 14.1 1.0
O1B A:DUP701 4.5 15.2 1.0
CA A:GLY416 4.5 13.9 1.0
O1G A:DUP701 4.5 15.8 1.0
O A:HOH892 4.5 15.8 1.0
CA A:ASP427 4.6 12.8 1.0
N A:ASP429 4.8 11.5 1.0
N A:VAL428 5.0 12.1 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 23:36:38 2024

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