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Chlorine in PDB 4rt3: Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp, PDB code: 4rt3 was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.26 / 1.92
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.735, 79.909, 55.337, 90.00, 107.52, 90.00
R / Rfree (%) 18 / 22.6

Other elements in 4rt3:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp (pdb code 4rt3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp, PDB code: 4rt3:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 4rt3

Go back to Chlorine Binding Sites List in 4rt3
Chlorine binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:42.8
occ:1.00
 N A:HIS34 3.3 31.0 1.0
C A:ALA32 3.4 34.6 1.0
CB A:ALA32 3.4 32.5 1.0
CB A:HIS34 3.5 35.4 1.0
CA A:ALA32 3.5 35.7 1.0
N A:LYS35 3.6 31.9 1.0
N A:ILE33 3.7 36.2 1.0
O A:ALA32 3.8 37.1 1.0
CA A:HIS34 3.8 34.0 1.0
CD2 A:HIS34 3.9 37.8 1.0
CG A:HIS34 4.0 37.7 1.0
C A:HIS34 4.2 33.3 1.0
CG A:LYS35 4.2 36.1 1.0
C A:ILE33 4.3 36.6 1.0
CB A:LYS35 4.6 32.6 1.0
CA A:ILE33 4.6 36.8 1.0
O T:HOH129 4.6 45.5 1.0
CA A:LYS35 4.7 30.6 1.0
O6 D:DG1 4.8 36.0 1.0
O A:HOH676 4.8 42.2 1.0
N A:ALA32 5.0 32.8 1.0

Chlorine binding site 2 out of 3 in 4rt3

Go back to Chlorine Binding Sites List in 4rt3
Chlorine binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:52.8
occ:1.00
 N A:LEU82 3.3 36.1 1.0
O A:HOH708 3.4 53.3 1.0
NH2 A:ARG89 3.5 55.2 1.0
NH1 A:ARG89 3.6 52.0 1.0
CA A:LYS81 3.8 35.1 1.0
CD1 A:LEU85 3.8 38.5 1.0
CZ A:ARG89 4.0 52.1 1.0
CB A:LYS81 4.0 44.7 1.0
CB A:LEU85 4.0 35.8 1.0
C A:LYS81 4.0 38.9 1.0
CB A:LEU82 4.2 39.0 1.0
O A:LEU82 4.2 41.5 1.0
CA A:LEU82 4.2 39.8 1.0
CG A:LEU85 4.5 34.8 1.0
C A:LEU82 4.7 40.8 1.0
O A:GLY80 4.8 37.7 1.0

Chlorine binding site 3 out of 3 in 4rt3

Go back to Chlorine Binding Sites List in 4rt3
Chlorine binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ternary Complex Crystal Structure of Dna Polymerase Beta with (Alpha, Beta)-Nh-(Beta,Gamma)-CH2-Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:38.8
occ:1.00
 O A:HOH727 3.0 43.6 1.0
OG1 A:THR297 3.0 29.3 1.0
ND2 A:ASN294 3.3 28.8 1.0
CG2 A:THR297 3.5 26.2 1.0
O T:HOH141 3.6 57.7 1.0
CB A:THR297 3.9 27.6 1.0
CB A:TYR296 3.9 29.4 1.0
NE A:ARG299 4.0 42.6 1.0
OD1 A:ASN294 4.0 30.2 1.0
CZ A:ARG299 4.1 45.5 1.0
CG A:ASN294 4.1 27.1 1.0
NH2 A:ARG299 4.1 40.3 1.0
CD2 A:TYR296 4.2 31.2 1.0
CG A:TYR296 4.5 29.3 1.0
N A:THR297 4.6 28.1 1.0
CD A:ARG299 4.6 39.3 1.0
NH1 A:ARG299 4.8 44.4 1.0
O A:HOH547 4.8 31.8 1.0
CA A:THR297 4.9 26.0 1.0

Reference:

A.P.Kadina, B.A.Kashemirov, K.Oertell, V.K.Batra, S.H.Wilson, M.F.Goodman, C.E.Mckenna. Two Scaffolds From Two Flips: (Alpha, Beta)/(Beta, Gamma) CH2/Nh "Met-Im" Analogues of Dttp. Org.Lett. V. 17 2586 2015.
ISSN: ISSN 1523-7060
PubMed: 25970636
DOI: 10.1021/ACS.ORGLETT.5B00799
Page generated: Fri Jul 26 01:34:49 2024

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