Atomistry » Chlorine » PDB 3isv-3jpw » 3jpp
Atomistry »
  Chlorine »
    PDB 3isv-3jpw »
      3jpp »

Chlorine in PDB 3jpp: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate, PDB code: 3jpp was solved by V.K.Batra, J.Upton, B.Kashmerov, W.A.Beard, S.H.Wilson, M.F.Goodman, C.E.Mckenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.42 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.700, 80.110, 55.550, 90.00, 107.95, 90.00
R / Rfree (%) 19.8 / 25

Other elements in 3jpp:

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Sodium (Na) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate (pdb code 3jpp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate, PDB code: 3jpp:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3jpp

Go back to Chlorine Binding Sites List in 3jpp
Chlorine binding site 1 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl343

b:34.1
occ:1.00
NH2 A:ARG299 2.9 34.8 1.0
ND2 A:ASN294 3.1 23.1 1.0
NE A:ARG299 3.2 33.3 1.0
OG1 A:THR297 3.2 26.2 1.0
CZ A:ARG299 3.4 35.7 1.0
O A:HOH562 3.6 49.5 1.0
O A:HOH500 3.7 39.9 1.0
CG A:ASN294 4.0 22.9 1.0
OD1 A:ASN294 4.0 25.5 1.0
CB A:TYR296 4.1 24.6 1.0
CG2 A:THR297 4.3 23.5 1.0
CD2 A:TYR296 4.3 22.7 1.0
CB A:THR297 4.4 25.9 1.0
CD A:ARG299 4.4 30.2 1.0
O T:HOH266 4.5 44.2 1.0
CG A:TYR296 4.7 24.5 1.0
NH1 A:ARG299 4.7 35.5 1.0
O A:HOH390 4.7 25.7 1.0
N A:THR297 4.8 23.8 1.0
O T:HOH142 4.9 41.8 1.0

Chlorine binding site 2 out of 4 in 3jpp

Go back to Chlorine Binding Sites List in 3jpp
Chlorine binding site 2 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl344

b:32.9
occ:1.00
O A:HOH362 2.9 25.4 1.0
N A:CYS267 3.3 21.5 1.0
CA A:GLN264 3.5 26.4 1.0
C A:GLN264 3.6 24.9 1.0
N A:TYR266 3.6 21.5 1.0
CB A:TYR266 3.7 25.5 1.0
CB A:VAL313 3.8 30.3 1.0
CG1 A:VAL313 3.8 28.5 1.0
SG A:CYS267 3.8 22.9 1.0
O A:GLN264 3.9 25.6 1.0
O A:ASP263 3.9 25.4 1.0
CA A:TYR266 4.0 23.0 1.0
CB A:CYS267 4.0 23.0 1.0
N A:TYR265 4.1 24.8 1.0
C A:TYR266 4.1 22.9 1.0
CA A:CYS267 4.2 21.1 1.0
O A:TYR296 4.4 22.5 1.0
CD2 A:TYR266 4.4 31.8 1.0
CB A:GLN264 4.5 28.0 1.0
CG2 A:VAL313 4.5 27.2 1.0
N A:GLN264 4.5 25.9 1.0
C A:TYR265 4.5 24.0 1.0
O A:VAL313 4.5 31.0 1.0
CG A:TYR266 4.5 29.4 1.0
C A:ASP263 4.6 25.9 1.0
CA A:TYR265 4.9 23.6 1.0
CG A:GLN264 4.9 32.0 1.0
CA A:VAL313 5.0 31.5 1.0
C A:VAL313 5.0 31.8 1.0

Chlorine binding site 3 out of 4 in 3jpp

Go back to Chlorine Binding Sites List in 3jpp
Chlorine binding site 3 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl345

b:40.8
occ:1.00
N A:HIS34 3.2 30.7 1.0
CB A:HIS34 3.3 34.1 1.0
CB A:ALA32 3.4 24.8 1.0
C A:ALA32 3.4 29.4 1.0
CA A:ALA32 3.5 28.6 1.0
N A:LYS35 3.6 27.8 1.0
O A:ALA32 3.6 28.3 1.0
CA A:HIS34 3.7 31.5 1.0
N A:ILE33 3.9 31.0 1.0
CG A:HIS34 4.0 38.6 1.0
CD2 A:HIS34 4.0 38.7 1.0
C A:HIS34 4.1 30.4 1.0
CG A:LYS35 4.2 27.4 1.0
C A:ILE33 4.3 32.1 1.0
O A:HOH490 4.4 32.8 1.0
CB A:LYS35 4.6 24.7 1.0
CA A:ILE33 4.6 33.0 1.0
CA A:LYS35 4.7 25.4 1.0
O6 D:DG1 4.8 36.1 1.0
N A:ALA32 4.9 26.3 1.0

Chlorine binding site 4 out of 4 in 3jpp

Go back to Chlorine Binding Sites List in 3jpp
Chlorine binding site 4 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl346

b:57.4
occ:1.00
N A:LEU82 3.1 31.6 1.0
NH1 A:ARG89 3.3 42.9 1.0
NH2 A:ARG89 3.5 44.5 1.0
O A:HOH538 3.6 35.7 1.0
CA A:LYS81 3.6 35.2 1.0
CB A:LYS81 3.7 38.5 1.0
CD1 A:LEU85 3.8 31.2 1.0
OE2 A:GLU86 3.8 51.7 1.0
C A:LYS81 3.8 33.2 1.0
CZ A:ARG89 3.9 44.3 1.0
O A:LEU82 3.9 30.1 1.0
CB A:LEU85 4.0 31.2 1.0
CA A:LEU82 4.1 31.1 1.0
CB A:LEU82 4.1 31.1 1.0
C A:LEU82 4.4 31.1 1.0
CG A:LEU85 4.5 30.4 1.0
CD A:GLU86 4.8 50.8 1.0
CG A:GLU86 4.9 47.1 1.0
CG A:LYS81 5.0 40.4 1.0
N A:LYS81 5.0 34.7 1.0

Reference:

V.K.Batra, L.C.Pedersen, W.A.Beard, S.H.Wilson, B.A.Kashemirov, T.G.Upton, M.F.Goodman, C.E.Mckenna. Halogenated Beta,Gamma-Methylene- and Ethylidene-Dgtp-Dna Ternary Complexes with Dna Polymerase Beta: Structural Evidence For Stereospecific Binding of the Fluoromethylene Analogues. J.Am.Chem.Soc. V. 132 7617 2010.
ISSN: ISSN 0002-7863
PubMed: 20465217
DOI: 10.1021/JA909370K
Page generated: Sat Dec 12 09:49:21 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy