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Magnesium in PDB 3zvm: The Structural Basis For Substrate Recognition By Mammalian Polynucleotide Kinase 3' Phosphatase

Enzymatic activity of The Structural Basis For Substrate Recognition By Mammalian Polynucleotide Kinase 3' Phosphatase

All present enzymatic activity of The Structural Basis For Substrate Recognition By Mammalian Polynucleotide Kinase 3' Phosphatase:
2.7.1.78; 3.1.3.32;

Protein crystallography data

The structure of The Structural Basis For Substrate Recognition By Mammalian Polynucleotide Kinase 3' Phosphatase, PDB code: 3zvm was solved by F.Garces, L.H.Pearl, A.W.Oliver, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.49 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.817, 75.243, 135.199, 90.00, 96.30, 90.00
R / Rfree (%) 15.2 / 20.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structural Basis For Substrate Recognition By Mammalian Polynucleotide Kinase 3' Phosphatase (pdb code 3zvm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Structural Basis For Substrate Recognition By Mammalian Polynucleotide Kinase 3' Phosphatase, PDB code: 3zvm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3zvm

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Magnesium binding site 1 out of 4 in the The Structural Basis For Substrate Recognition By Mammalian Polynucleotide Kinase 3' Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structural Basis For Substrate Recognition By Mammalian Polynucleotide Kinase 3' Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1525

b:3.9
occ:1.00
 OD2 A:ASP170 2.2 9.1 1.0
O A:ASP172 2.3 11.2 1.0
O A:HOH2047 2.3 11.9 1.0
O A:HOH2050 2.3 23.2 1.0
OD1 A:ASP288 2.4 10.6 1.0
OP1 E:DC2 2.7 15.9 0.7
CG A:ASP170 3.2 8.2 1.0
CG A:ASP288 3.3 13.7 1.0
C A:ASP172 3.5 10.3 1.0
OD2 A:ASP288 3.5 15.4 1.0
OD1 A:ASP170 3.6 7.2 1.0
P E:DC2 4.0 28.3 0.7
OD2 A:ASP309 4.1 7.9 1.0
CA A:ASP172 4.3 9.7 1.0
OG1 A:THR174 4.3 6.4 1.0
O5' E:DC2 4.4 25.3 0.7
O A:HOH2114 4.4 30.5 1.0
CB A:ASP172 4.4 12.1 1.0
C5' E:DC2 4.4 27.2 0.7
O A:HOH2048 4.4 11.6 1.0
N A:ASP172 4.4 10.5 1.0
N A:GLY173 4.4 9.0 1.0
CB A:ASP170 4.4 5.7 1.0
CA A:GLY173 4.5 9.4 1.0
O A:HOH2113 4.5 33.4 1.0
CB A:ASP288 4.7 8.9 1.0
C A:GLY173 4.7 9.6 1.0
O A:HOH2049 4.7 8.7 1.0
N A:ALA289 4.8 5.9 1.0
N A:ASP288 4.8 7.9 1.0
N A:THR174 4.9 7.0 1.0
OP2 E:DC2 4.9 25.3 0.7

Magnesium binding site 2 out of 4 in 3zvm

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Magnesium binding site 2 out of 4 in the The Structural Basis For Substrate Recognition By Mammalian Polynucleotide Kinase 3' Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structural Basis For Substrate Recognition By Mammalian Polynucleotide Kinase 3' Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1526

b:9.7
occ:1.00
 O2B A:ADP1523 2.1 7.5 1.0
O A:HOH2424 2.2 6.9 1.0
O A:HOH2460 2.3 9.5 1.0
O A:HOH2423 2.3 8.3 1.0
OG A:SER378 2.3 6.9 1.0
OD2 A:ASP396 2.3 14.9 1.0
CB A:SER378 3.3 8.1 1.0
CG A:ASP396 3.3 24.0 1.0
PB A:ADP1523 3.3 7.4 1.0
O1B A:ADP1523 3.5 7.6 1.0
OD1 A:ASP396 3.6 26.8 1.0
O2A A:ADP1523 4.0 9.3 1.0
O A:HOH2452 4.0 23.7 1.0
N A:SER378 4.1 6.7 1.0
OD1 A:ASP421 4.2 10.6 1.0
OD2 A:ASP421 4.2 9.8 1.0
CA A:SER378 4.3 11.2 1.0
O A:HOH2421 4.3 9.6 1.0
O A:HOH2263 4.3 25.5 1.0
O3A A:ADP1523 4.3 8.5 1.0
NE2 A:HIS470 4.3 33.0 1.0
O3B A:ADP1523 4.4 6.8 1.0
PA A:ADP1523 4.5 8.9 1.0
CG A:ASP421 4.6 9.5 1.0
O1A A:ADP1523 4.7 10.5 1.0
CB A:ASP396 4.7 19.6 1.0
OD1 A:ASN394 4.7 14.0 1.0
CD2 A:HIS470 4.8 28.0 1.0
O8 A:EPE1524 4.8 30.2 0.9

Magnesium binding site 3 out of 4 in 3zvm

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Magnesium binding site 3 out of 4 in the The Structural Basis For Substrate Recognition By Mammalian Polynucleotide Kinase 3' Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structural Basis For Substrate Recognition By Mammalian Polynucleotide Kinase 3' Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1525

b:4.9
occ:1.00
 OD2 B:ASP170 2.2 10.8 1.0
O B:ASP172 2.3 8.4 1.0
O B:HOH2032 2.3 13.4 1.0
OD1 B:ASP288 2.3 8.2 1.0
O B:HOH2034 2.4 20.8 0.8
O B:HOH2035 2.4 20.1 1.0
OP1 F:DC2 2.8 19.1 0.7
CG B:ASP170 3.1 8.9 1.0
CG B:ASP288 3.3 10.4 1.0
OD1 B:ASP170 3.4 9.9 1.0
C B:ASP172 3.5 10.8 1.0
OD2 B:ASP288 3.5 14.9 1.0
OD2 B:ASP309 4.0 8.2 1.0
OG1 B:THR174 4.2 10.4 1.0
P F:DC2 4.3 29.8 0.7
CA B:ASP172 4.3 9.5 1.0
O F:HOH2004 4.4 33.1 1.0
N B:ASP172 4.4 11.2 1.0
C5' F:DC2 4.4 25.4 0.7
CB B:ASP170 4.4 7.4 1.0
CB B:ASP172 4.4 12.3 1.0
O B:HOH2033 4.4 9.4 1.0
N B:GLY173 4.5 9.2 1.0
O B:HOH2081 4.5 27.6 1.0
CA B:GLY173 4.6 11.7 1.0
CB B:ASP288 4.7 7.9 1.0
N B:ASP288 4.7 7.2 1.0
O B:HOH2031 4.7 11.7 1.0
N B:ALA289 4.7 5.9 1.0
O5' F:DC2 4.8 28.4 0.7
C B:GLY173 4.8 10.6 1.0
N B:THR174 4.9 6.7 1.0

Magnesium binding site 4 out of 4 in 3zvm

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Magnesium binding site 4 out of 4 in the The Structural Basis For Substrate Recognition By Mammalian Polynucleotide Kinase 3' Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structural Basis For Substrate Recognition By Mammalian Polynucleotide Kinase 3' Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1526

b:17.6
occ:1.00
 OD2 B:ASP396 2.2 14.5 1.0
O B:HOH2375 2.3 11.8 1.0
OG B:SER378 2.3 11.3 1.0
O B:HOH2395 2.3 15.5 1.0
O3B B:ADP1523 2.3 14.2 1.0
O B:HOH2374 2.3 14.3 1.0
CG B:ASP396 3.1 31.9 1.0
CB B:SER378 3.3 12.3 1.0
PB B:ADP1523 3.3 11.8 1.0
OD1 B:ASP396 3.4 31.8 1.0
O2B B:ADP1523 3.5 10.8 1.0
O2A B:ADP1523 4.1 12.4 1.0
O B:HOH2391 4.1 30.9 1.0
OD2 B:ASP421 4.1 12.6 1.0
O B:HOH2373 4.1 15.4 1.0
N B:SER378 4.1 11.1 1.0
OD1 B:ASP421 4.2 8.7 1.0
OD1 B:ASN394 4.3 22.5 1.0
CA B:SER378 4.3 13.9 1.0
O1B B:ADP1523 4.4 12.8 1.0
O3A B:ADP1523 4.4 11.4 1.0
O B:HOH2456 4.5 36.6 1.0
CB B:ASP396 4.5 24.5 1.0
CG B:ASP421 4.5 14.3 1.0
O B:HOH2214 4.6 28.9 1.0
O8 B:EPE1524 4.6 42.8 1.0
PA B:ADP1523 4.6 12.2 1.0
ND2 B:ASN394 4.7 21.6 1.0
O1A B:ADP1523 4.8 10.1 1.0
CG B:ASN394 5.0 19.6 1.0

Reference:

F.Garces, L.H.Pearl, A.W.Oliver. The Structural Basis For Substrate Recognition By Mammalian Polynucleotide Kinase 3' Phosphatase. Mol. Cell V. 44 385 2011.
ISSN: ISSN 1097-4164
PubMed: 22055185
DOI: 10.1016/J.MOLCEL.2011.08.036
Page generated: Mon Aug 11 05:22:15 2025

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