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Calcium 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:

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

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium was determined in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Blunt- Ended Dsb Substrate and Incoming Dumpnpp, PDB code: 7m09:

Calcium binding site 1 out of 1 in 7m09

Go back to Calcium Binding Sites List in 7m09
Calcium binding site 1 out of 1 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 Calcium with other atoms in the Ca 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:Ca702

b:13.2
occ:0.70
 MG A:MG703 0.0 13.0 0.3
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

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 Jul 9 23:22:00 2025

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