Magnesium 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
Calcium (Ca) 1 atom
Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp, PDB code: 7m0a:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7m0a

Go back to Magnesium Binding Sites List in 7m0a
Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg703

b:17.3
occ:0.20
 CA A:CA704 0.0 17.0 0.8
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 2.7 21.7 0.6
CG A:ASP427 2.9 27.3 1.0
P P:DT7 3.0 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 4.1 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
CB A:ASP427 4.3 16.5 1.0
C5' P:DC6 4.3 20.2 0.4
C5' A:TTP701 4.3 15.7 0.4
CB A:ASP429 4.3 14.6 1.0
C5' P:DC6 4.5 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
CA A:ASP490 4.9 14.1 1.0
CE1 A:PHE506 4.9 18.9 1.0
C A:VAL428 4.9 16.8 1.0
N A:ASP490 4.9 14.6 1.0
O2B A:TTP701 4.9 19.2 0.4
C2' P:DC6 5.0 22.8 0.6
O3A A:TTP701 5.0 25.1 0.4
O5' P:DC6 5.0 23.4 0.4
N A:ASP429 5.0 13.8 1.0

Magnesium binding site 2 out of 2 in 7m0a

Go back to Magnesium Binding Sites List in 7m0a
Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg binding site number 2 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:Mg705

b:16.4
occ:1.00
 O2B A:TTP701 2.0 19.2 0.4
O1A A:TTP701 2.0 15.7 0.4
O12 A:PPV702 2.0 19.2 0.6
OD2 A:ASP429 2.1 15.0 1.0
OD1 A:ASP427 2.1 18.4 1.0
O1G A:TTP701 2.1 22.5 0.4
O11 A:PPV702 2.2 22.5 0.6
OP1 P:DT7 2.2 14.9 0.6
O A:HOH887 2.2 20.6 1.0
PB A:TTP701 3.0 21.3 0.4
CG A:ASP429 3.1 17.0 1.0
PA A:TTP701 3.1 17.3 0.4
P2 A:PPV702 3.1 21.5 0.6
CG A:ASP427 3.2 27.3 1.0
O3A A:TTP701 3.2 25.1 0.4
O32 A:PPV702 3.3 25.3 0.6
PG A:TTP701 3.4 27.4 0.4
OD1 A:ASP429 3.4 16.8 1.0
CA A:CA704 3.4 17.0 0.8
P1 A:PPV702 3.4 27.6 0.6
MG A:MG703 3.4 17.3 0.2
O3B A:TTP701 3.6 27.0 0.4
P P:DT7 3.6 17.5 0.6
OPP A:PPV702 3.6 27.1 0.6
OD2 A:ASP427 3.6 26.8 1.0
O A:HOH865 3.9 37.1 1.0
C5' A:TTP701 4.0 15.7 0.4
O5' P:DT7 4.0 19.6 0.6
O31 A:PPV702 4.0 23.7 0.6
O5' A:TTP701 4.1 19.4 0.4
O A:ASP427 4.1 16.6 1.0
O3G A:TTP701 4.1 23.7 0.4
C5' P:DT7 4.2 16.1 0.6
O2A A:TTP701 4.2 15.9 0.4
C A:ASP427 4.4 17.2 1.0
CB A:ASP429 4.4 14.6 1.0
O1B A:TTP701 4.4 18.9 0.4
O A:HOH958 4.4 19.5 1.0
OP2 P:DT7 4.4 14.8 0.6
OG A:SER417 4.4 21.0 1.0
N A:SER417 4.4 13.8 1.0
CB A:ASP427 4.4 16.5 1.0
N A:ASP427 4.4 14.3 1.0
O A:HOH822 4.4 35.0 1.0
O22 A:PPV702 4.5 19.0 0.6
CA A:GLY416 4.5 13.5 1.0
O2G A:TTP701 4.6 27.9 0.4
O21 A:PPV702 4.6 28.0 0.6
O3' P:DC6 4.6 21.7 0.6
CA A:ASP427 4.7 16.5 1.0
N A:ASP429 4.9 13.8 1.0
O3' P:DC6 4.9 22.5 0.4
N A:VAL428 5.0 14.9 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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