Chlorine 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:

Calcium (Ca) 1 atom
Sodium (Na) 3 atoms
Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7m0a

Go back to Chlorine Binding Sites List in 7m0a
Chlorine binding site 1 out of 3 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 Chlorine with other atoms in the Cl 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:Cl709

b:50.6
occ:1.00
 NE2 A:GLN270 3.2 22.4 1.0
OG A:SER329 3.3 23.9 0.5
N A:SER329 3.3 17.6 0.5
N A:SER329 3.3 17.6 0.5
O A:HOH959 3.4 44.0 1.0
CB A:SER329 3.9 23.5 0.5
CB A:SER329 3.9 23.5 0.5
CA A:ILE328 3.9 22.4 1.0
CD A:GLN270 4.1 28.6 1.0
C A:ILE328 4.1 23.8 1.0
OE1 A:GLN270 4.1 31.5 1.0
CG2 A:ILE328 4.2 23.1 1.0
CA A:SER329 4.2 21.5 0.5
CA A:SER329 4.2 21.5 0.5
NZ A:LYS324 4.4 33.1 1.0
O A:HIS327 4.4 30.7 1.0
CE A:LYS324 4.6 41.5 1.0
CB A:ILE328 4.6 22.7 1.0
CE1 A:TYR267 4.9 25.1 1.0
CG1 A:ILE328 5.0 24.5 1.0

Chlorine binding site 2 out of 3 in 7m0a

Go back to Chlorine Binding Sites List in 7m0a
Chlorine binding site 2 out of 3 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 Chlorine with other atoms in the Cl 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:Cl710

b:51.1
occ:0.86
 O A:HOH1046 2.6 39.7 1.0
N A:SER408 3.1 22.6 1.0
O A:HOH874 3.2 35.3 0.7
OG A:SER408 3.5 30.6 1.0
CA A:ASN407 3.6 29.4 1.0
CB A:SER408 3.8 28.0 1.0
C A:ASN407 3.9 28.0 1.0
O A:HOH984 4.0 40.2 1.0
CA A:SER408 4.1 29.2 1.0
O A:PHE406 4.2 37.7 1.0
N A:ASN407 4.3 26.7 1.0
C A:PHE406 4.5 40.5 1.0
OD1 A:ASN407 4.5 31.2 1.0
CG A:ASN407 4.6 33.2 1.0
CB A:ASN407 4.7 32.5 1.0

Chlorine binding site 3 out of 3 in 7m0a

Go back to Chlorine Binding Sites List in 7m0a
Chlorine binding site 3 out of 3 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl711

b:43.7
occ:1.00
 N A:GLU556 3.1 21.1 1.0
O A:HOH1042 3.4 28.9 1.0
CA A:THR555 3.5 20.2 1.0
CB A:THR555 3.7 26.0 1.0
C A:THR555 3.8 19.0 1.0
O A:HOH898 3.8 36.0 1.0
CG A:GLU556 3.8 19.8 1.0
CB A:GLU556 4.0 20.6 1.0
CA A:GLU556 4.1 18.9 1.0
CD2 A:LEU503 4.1 26.4 1.0
CG2 A:THR555 4.4 29.4 1.0
O A:HOH1076 4.4 37.9 1.0
CD A:GLU556 4.6 23.0 1.0
OE1 A:GLU556 4.6 23.0 1.0
O A:PRO554 4.6 23.2 0.5
O A:PRO554 4.6 23.2 0.5
CB A:ALA500 4.7 20.3 1.0
N A:THR555 4.8 20.0 1.0
OG1 A:THR555 4.8 27.0 1.0
CA A:ALA500 4.9 20.4 1.0
O A:THR555 5.0 19.2 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 Apr 4 20:48:22 2023

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