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Magnesium in PDB 3u7f: Crystal Structure of Mpnkp Catalytic Fragment (D170A) Bound to Single- Stranded Dna (Tcctcp)

Enzymatic activity of Crystal Structure of Mpnkp Catalytic Fragment (D170A) Bound to Single- Stranded Dna (Tcctcp)

All present enzymatic activity of Crystal Structure of Mpnkp Catalytic Fragment (D170A) Bound to Single- Stranded Dna (Tcctcp):
2.7.1.78; 3.1.3.32;

Protein crystallography data

The structure of Crystal Structure of Mpnkp Catalytic Fragment (D170A) Bound to Single- Stranded Dna (Tcctcp), PDB code: 3u7f was solved by N.Coquelle, Z.Havali, N.Bernstein, R.Green, J.N.M.Glover, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.93 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.600, 62.330, 67.970, 90.00, 91.81, 90.00
R / Rfree (%) 16.9 / 21.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mpnkp Catalytic Fragment (D170A) Bound to Single- Stranded Dna (Tcctcp) (pdb code 3u7f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Mpnkp Catalytic Fragment (D170A) Bound to Single- Stranded Dna (Tcctcp), PDB code: 3u7f:

Magnesium binding site 1 out of 1 in 3u7f

Go back to Magnesium Binding Sites List in 3u7f
Magnesium binding site 1 out of 1 in the Crystal Structure of Mpnkp Catalytic Fragment (D170A) Bound to Single- Stranded Dna (Tcctcp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Mpnkp Catalytic Fragment (D170A) Bound to Single- Stranded Dna (Tcctcp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:38.5
occ:0.91
 O B:HOH759 2.0 19.7 1.0
O B:HOH653 2.0 8.4 1.0
OD1 B:ASP288 2.2 8.2 1.0
O1 X:PO4523 2.2 8.8 1.0
O B:ASP172 2.3 8.2 1.0
OD2 B:ASP288 2.7 11.0 1.0
CG B:ASP288 2.7 6.9 1.0
H2'' X:DC402 3.2 8.0 1.0
HB1 B:ALA170 3.5 0.7 1.0
HG1 B:THR174 3.5 7.2 1.0
C B:ASP172 3.6 8.3 1.0
H B:ASP288 3.7 0.4 1.0
HE2 B:PHE305 3.7 15.8 1.0
P X:PO4523 3.7 1.7 1.0
H B:ALA289 3.8 2.1 1.0
HA3 B:GLY173 3.8 3.4 1.0
OD2 B:ASP309 3.8 0.3 1.0
HB3 B:ALA170 3.9 0.7 1.0
HZ B:PHE305 4.0 9.3 1.0
H1' X:DC402 4.1 10.0 0.9
C2' X:DC402 4.1 6.7 1.0
HB2 B:ALA289 4.1 1.0 1.0
CB B:ALA170 4.1 0.6 1.0
HB2 B:ASP172 4.2 6.7 1.0
CB B:ASP288 4.2 5.1 1.0
OG1 B:THR174 4.2 6.0 1.0
N B:ALA289 4.3 1.7 1.0
O3' X:DC402 4.3 6.9 1.0
O B:HOH651 4.4 4.8 1.0
O3 X:PO4523 4.4 0.2 1.0
HB2 B:ALA170 4.4 0.7 1.0
CE2 B:PHE305 4.4 13.2 1.0
CA B:GLY173 4.4 2.8 1.0
N B:GLY173 4.4 3.6 1.0
N B:ASP288 4.4 0.3 1.0
CA B:ASP172 4.5 6.6 1.0
O4 X:PO4523 4.6 1.8 1.0
CZ B:PHE305 4.6 7.8 1.0
O2 X:DC402 4.6 15.0 0.9
HB3 B:ASP288 4.6 6.1 1.0
C1' X:DC402 4.6 8.3 0.9
N B:ASP172 4.7 0.1 1.0
CA B:ASP288 4.7 2.7 1.0
H B:ASP172 4.7 0.1 1.0
H2' X:DC402 4.7 8.0 1.0
C B:GLY173 4.7 2.6 1.0
HB2 B:ASP288 4.7 6.1 1.0
CB B:ASP172 4.8 5.6 1.0
C B:ASP288 4.8 4.5 1.0
C3' X:DC402 4.8 7.3 0.9
HZ1 B:LYS259 4.8 0.8 1.0
CB B:ALA289 4.8 0.8 1.0
H B:THR174 4.9 2.1 1.0
N B:THR174 4.9 1.8 1.0
CG B:ASP309 4.9 0.3 1.0
HB3 B:ALA289 4.9 1.0 1.0
H B:LEU171 4.9 2.2 1.0
HB3 B:ASP172 4.9 6.7 1.0
HB B:THR174 5.0 0.1 1.0

Reference:

N.Coquelle, Z.Havali-Shahriari, N.Bernstein, R.Green, J.N.Glover. Structural Basis For the Phosphatase Activity of Polynucleotide Kinase/Phosphatase on Single- and Double-Stranded Dna Substrates. Proc.Natl.Acad.Sci.Usa V. 108 21022 2011.
ISSN: ISSN 0027-8424
PubMed: 22171004
DOI: 10.1073/PNAS.1112036108
Page generated: Thu Aug 15 12:24:30 2024

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