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Chlorine in PDB 3gdx: Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp

Enzymatic activity of Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp

All present enzymatic activity of Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp, PDB code: 3gdx was solved by S.H.Wilson, V.K.Batra, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.58 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.500, 79.700, 55.300, 90.00, 107.90, 90.00
R / Rfree (%) 20.8 / 26.6

Other elements in 3gdx:

The structure of Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp (pdb code 3gdx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp, PDB code: 3gdx:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 3gdx

Go back to Chlorine Binding Sites List in 3gdx
Chlorine binding site 1 out of 2 in the Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl351

b:17.8
occ:1.00
ND2 A:ASN294 3.3 26.2 1.0
NH2 A:ARG299 3.3 24.6 0.5
OG1 A:THR297 3.3 24.6 1.0
NE A:ARG299 3.4 26.3 0.5
CZ A:ARG299 3.8 26.4 0.5
OD1 A:ASN294 4.0 26.5 1.0
CB A:TYR296 4.1 23.2 1.0
CG A:ASN294 4.1 25.4 1.0
CD2 A:TYR296 4.2 20.7 1.0
CZ A:ARG299 4.2 29.3 0.5
NE A:ARG299 4.2 28.8 0.5
NH2 A:ARG299 4.4 28.9 0.5
NH1 A:ARG299 4.5 29.4 0.5
CG A:TYR296 4.6 21.0 1.0
CB A:THR297 4.6 26.8 1.0
O A:HOH442 4.6 22.3 1.0
CD A:ARG299 4.6 26.1 0.5
CD A:ARG299 4.6 28.2 0.5
CG2 A:THR297 4.7 27.8 1.0
N A:THR297 4.8 24.1 1.0

Chlorine binding site 2 out of 2 in 3gdx

Go back to Chlorine Binding Sites List in 3gdx
Chlorine binding site 2 out of 2 in the Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dna Polymerase Beta with A Gapped Dnd Substrate and Dtmp(CF2)Pp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl352

b:33.7
occ:1.00
O A:HOH450 2.9 22.3 1.0
CA A:GLN264 3.5 22.8 1.0
N A:CYS267 3.5 24.8 1.0
C A:GLN264 3.6 22.1 1.0
O A:GLN264 3.6 23.1 1.0
CB A:VAL313 3.7 31.4 1.0
CG1 A:VAL313 3.8 32.5 1.0
SG A:CYS267 3.8 25.2 1.0
O A:ASP263 3.8 28.3 1.0
N A:TYR266 3.9 24.5 1.0
CB A:CYS267 4.0 25.0 1.0
CB A:TYR266 4.0 28.2 1.0
CA A:TYR266 4.2 26.7 1.0
N A:TYR265 4.3 22.2 1.0
CG2 A:VAL313 4.3 33.5 1.0
C A:TYR266 4.3 25.1 1.0
CA A:CYS267 4.4 24.0 1.0
O A:TYR296 4.4 21.0 1.0
CB A:GLN264 4.4 23.5 1.0
O A:VAL313 4.5 32.7 1.0
N A:GLN264 4.5 25.3 1.0
CD2 A:TYR266 4.5 33.3 1.0
C A:ASP263 4.5 26.3 1.0
C A:TYR265 4.7 24.7 1.0
CG A:TYR266 4.8 32.4 1.0
CG A:GLN264 4.8 27.3 1.0
CA A:VAL313 4.9 32.3 1.0
C A:VAL313 4.9 32.3 1.0

Reference:

T.G.Upton, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, G.K.Prakash, R.Kultyshev, V.K.Batra, D.D.Shock, L.C.Pedersen, W.A.Beard, S.H.Wilson. Alpha,Beta-Difluoromethylene Deoxynucleoside 5'-Triphosphates: A Convenient Synthesis of Useful Probes For Dna Polymerase Beta Structure and Function Org.Lett. V. 11 1883 2009.
ISSN: ISSN 1523-7060
PubMed: 19351147
DOI: 10.1021/OL701755K
Page generated: Sat Dec 12 09:44:06 2020

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