Chlorine 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:

Magnesium (Mg) 2 atoms
Sodium (Na) 5 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 2 in 7m07

Go back to Chlorine Binding Sites List in 7m07
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl707

b:42.4
occ:1.00
 N A:SER329 3.2 20.0 0.6
N A:SER329 3.2 20.0 0.5
OG A:SER329 3.2 22.2 0.6
NE2 A:GLN270 3.2 21.2 1.0
CA A:ILE328 3.8 22.4 1.0
CB A:SER329 3.9 20.8 0.5
CB A:SER329 3.9 20.8 0.6
C A:ILE328 4.0 24.3 1.0
CG2 A:ILE328 4.0 25.5 1.0
CA A:SER329 4.1 19.3 0.5
CA A:SER329 4.1 19.3 0.6
CD A:GLN270 4.1 22.3 1.0
OE1 A:GLN270 4.2 25.1 1.0
CB A:ILE328 4.4 24.1 1.0
O A:HIS327 4.4 28.7 1.0
CG1 A:ILE328 4.7 30.5 1.0
N A:ILE328 4.9 25.5 1.0
CE1 A:TYR267 5.0 26.1 1.0

Chlorine binding site 2 out of 2 in 7m07

Go back to Chlorine Binding Sites List in 7m07
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl709

b:42.3
occ:1.00
 O A:HOH1086 2.6 43.5 0.8
N A:GLU556 3.1 20.2 1.0
O A:HOH888 3.2 37.5 1.0
CA A:THR555 3.5 21.7 1.0
O A:HOH1033 3.5 26.8 1.0
CB A:THR555 3.7 25.9 1.0
O A:HOH1119 3.7 44.8 1.0
C A:THR555 3.8 21.8 1.0
CG A:GLU556 3.8 18.5 1.0
CB A:GLU556 4.1 18.8 1.0
CD2 A:LEU503 4.2 20.3 1.0
CA A:GLU556 4.2 20.4 1.0
CG2 A:THR555 4.4 26.5 1.0
O A:PRO554 4.5 24.9 1.0
OE1 A:GLU556 4.6 23.3 1.0
CD A:GLU556 4.6 20.4 1.0
CB A:ALA500 4.6 20.7 1.0
O A:HOH1084 4.8 31.9 1.0
N A:THR555 4.8 21.8 1.0
CA A:ALA500 4.9 20.4 1.0
OG1 A:THR555 4.9 27.9 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: Tue Jul 30 00:18:44 2024

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