Chlorine in PDB 7m0b: Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Mismatched Dsb and Incoming Dumpnpp

Enzymatic activity of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Mismatched Dsb and Incoming Dumpnpp

All present enzymatic activity of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Mismatched Dsb and Incoming Dumpnpp:
2.7.7.7;

Protein crystallography data

The structure of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Mismatched Dsb and Incoming Dumpnpp, PDB code: 7m0b 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) 39.40 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.368, 59.961, 139.406, 90, 90, 90
R / Rfree (%) 17.1 / 20

Other elements in 7m0b:

The structure of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Mismatched Dsb and Incoming Dumpnpp also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Mismatched Dsb and Incoming Dumpnpp (pdb code 7m0b). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Mismatched Dsb and Incoming Dumpnpp, PDB code: 7m0b:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7m0b

Go back to Chlorine Binding Sites List in 7m0b
Chlorine binding site 1 out of 4 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Mismatched Dsb 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 Quaternary Complex of Dna Polymerase Lambda with Bound Mismatched Dsb and Incoming Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl706

b:45.9
occ:1.00
 OG A:SER515 3.1 23.4 1.0
CB A:SER515 3.5 20.1 1.0
O A:HOH1003 3.6 33.8 0.8
N A:VAL240 4.0 26.3 1.0
CG2 A:VAL240 4.1 22.0 1.0
CA A:SER515 4.1 18.1 1.0
CE3 A:TRP239 4.1 26.5 1.0
CG1 A:VAL240 4.2 27.8 1.0
O A:LYS238 4.3 37.9 1.0
NZ A:LYS281 4.4 38.0 1.0
CA A:TRP239 4.5 31.3 1.0
CZ3 A:TRP239 4.5 26.3 1.0
CE A:LYS281 4.6 29.6 1.0
O A:HOH915 4.6 30.8 1.0
CB A:VAL240 4.6 25.9 1.0
C A:TRP239 4.7 25.1 1.0
CA A:VAL240 4.9 24.0 1.0

Chlorine binding site 2 out of 4 in 7m0b

Go back to Chlorine Binding Sites List in 7m0b
Chlorine binding site 2 out of 4 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Mismatched Dsb 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 Quaternary Complex of Dna Polymerase Lambda with Bound Mismatched Dsb and Incoming Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl707

b:59.8
occ:1.00
 N A:SER408 3.4 23.1 1.0
OG A:SER408 3.5 28.6 1.0
CA A:ASN407 3.8 23.3 1.0
O A:PHE406 4.0 33.5 1.0
CB A:SER408 4.1 28.0 1.0
C A:ASN407 4.1 26.6 1.0
CA A:SER408 4.4 24.5 1.0
C A:PHE406 4.5 30.8 1.0
N A:ASN407 4.5 28.1 1.0
O A:HOH859 4.5 31.7 1.0
OD1 A:ASN407 4.6 27.7 1.0
CG A:ASN407 4.9 27.6 1.0
CB A:ASN407 4.9 24.1 1.0

Chlorine binding site 3 out of 4 in 7m0b

Go back to Chlorine Binding Sites List in 7m0b
Chlorine binding site 3 out of 4 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Mismatched Dsb and Incoming Dumpnpp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Mismatched Dsb and Incoming Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl708

b:62.9
occ:1.00
 NH1 A:ARG549 3.5 25.2 1.0
NH2 A:ARG549 3.9 27.6 1.0
O A:HOH886 3.9 38.9 1.0
CZ A:ARG549 4.1 30.0 1.0
CB A:THR534 4.6 26.0 1.0
CG2 A:THR534 4.8 25.1 1.0
OG1 A:THR534 4.9 25.4 1.0

Chlorine binding site 4 out of 4 in 7m0b

Go back to Chlorine Binding Sites List in 7m0b
Chlorine binding site 4 out of 4 in the Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Mismatched Dsb and Incoming Dumpnpp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Mismatched Dsb and Incoming Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl709

b:40.4
occ:0.84
 N A:GLU556 3.1 20.3 1.0
CA A:THR555 3.5 18.1 1.0
O A:HOH999 3.6 26.6 1.0
CB A:THR555 3.7 29.1 1.0
CG A:GLU556 3.7 18.0 1.0
C A:THR555 3.8 24.0 1.0
O A:HOH971 4.0 40.6 1.0
CB A:GLU556 4.0 20.3 1.0
CD2 A:LEU503 4.1 26.0 1.0
CA A:GLU556 4.1 25.4 1.0
CG2 A:THR555 4.4 27.1 1.0
OE1 A:GLU556 4.5 19.0 1.0
CD A:GLU556 4.5 23.0 1.0
CB A:ALA500 4.7 19.3 1.0
O A:PRO554 4.7 23.4 1.0
OG1 A:THR555 4.8 25.9 1.0
CA A:ALA500 4.8 17.4 1.0
O A:HOH1051 4.8 38.3 1.0
N A:THR555 4.8 17.7 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 00:19:59 2024

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