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Calcium in PDB 7m0a: Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp

Enzymatic activity of Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp

All present enzymatic activity of Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp:
2.7.7.7;

Protein crystallography data

The structure of Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp, PDB code: 7m0a 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) 43.71 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.768, 59.573, 140.726, 90, 90, 90
R / Rfree (%) 16.9 / 19.3

Other elements in 7m0a:

The structure of Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp (pdb code 7m0a). 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 Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp, PDB code: 7m0a:

Calcium binding site 1 out of 1 in 7m0a

Go back to Calcium Binding Sites List in 7m0a
Calcium binding site 1 out of 1 in the Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:17.0
occ:0.80
 MG A:MG703 0.0 17.3 0.2
OD1 A:ASP429 2.0 16.8 1.0
OD2 A:ASP427 2.0 26.8 1.0
OD2 A:ASP490 2.1 20.2 1.0
OP1 P:DT7 2.2 14.9 0.6
O1A A:TTP701 2.4 15.7 0.4
O A:HOH822 2.6 35.0 1.0
O3' P:DC6 2.6 22.5 0.4
O3' P:DC6 2.6 21.7 0.6
CG A:ASP427 2.9 27.3 1.0
P P:DT7 2.9 17.5 0.6
CG A:ASP429 3.0 17.0 1.0
OD1 A:ASP427 3.1 18.4 1.0
CG A:ASP490 3.1 17.5 1.0
OD2 A:ASP429 3.4 15.0 1.0
MG A:MG705 3.4 16.4 1.0
PA A:TTP701 3.6 17.3 0.4
CB A:ASP490 3.6 16.1 1.0
C3' P:DC6 3.8 21.6 0.4
C3' P:DC6 3.9 21.4 0.6
O5' A:TTP701 4.0 19.4 0.4
OP2 P:DT7 4.0 14.8 0.6
O5' P:DT7 4.1 19.6 0.6
O2A A:TTP701 4.1 15.9 0.4
OD1 A:ASP490 4.1 17.2 1.0
C5' P:DT7 4.2 16.1 0.6
C4' P:DC6 4.2 21.2 0.6
C4' P:DC6 4.2 21.2 0.4
C5' P:DC6 4.2 20.2 0.4
CB A:ASP427 4.3 16.5 1.0
C5' A:TTP701 4.3 15.7 0.4
CB A:ASP429 4.3 14.6 1.0
C5' P:DC6 4.4 20.2 0.6
O A:HOH865 4.5 37.1 1.0
NH2 A:ARG488 4.7 17.1 1.0
O A:VAL428 4.7 15.6 1.0
O1G A:TTP701 4.7 22.5 0.4
O11 A:PPV702 4.8 22.5 0.6
CA A:ASP429 4.8 15.8 1.0
CE1 A:PHE506 4.9 18.9 1.0
CA A:ASP490 4.9 14.1 1.0
O2B A:TTP701 4.9 19.2 0.4
C2' P:DC6 4.9 22.8 0.6
O3A A:TTP701 4.9 25.1 0.4
C A:VAL428 4.9 16.8 1.0
O5' P:DC6 5.0 23.4 0.4
N A:ASP490 5.0 14.6 1.0
O5' P:DC6 5.0 23.4 0.6
N A:ASP429 5.0 13.8 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 23:22:19 2025

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