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Chlorine in PDB 3zvl: 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: 3zvl 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) 33.933 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.750, 63.500, 67.900, 90.00, 91.82, 90.00
R / Rfree (%) 17.05 / 21.82

Other elements in 3zvl:

The structure of The Structural Basis For Substrate Recognition By Mammalian Polynucleotide Kinase 3' Phosphatase also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 4 in 3zvl

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1525

b:17.3
occ:1.00
 O A:HOH2205 2.6 31.9 1.0
NZ A:LYS259 3.2 7.4 1.0
O A:HOH2033 3.2 9.8 1.0
OD1 A:ASP170 3.2 8.6 1.0
N A:ASN217 3.3 5.7 1.0
CE A:LYS259 3.3 11.6 1.0
O A:HOH2041 3.4 12.4 1.0
O A:HOH2032 3.4 7.3 1.0
CB A:ASN217 3.5 9.9 1.0
O A:HOH2134 3.8 36.3 1.0
O A:HOH2034 3.8 10.1 1.0
O A:HOH2118 3.8 18.9 1.0
CG A:ASN217 3.9 9.0 1.0
CA A:ASN217 3.9 8.9 1.0
ND2 A:ASN217 4.0 10.2 1.0
O A:ASN217 4.1 10.4 1.0
CG A:ASP170 4.3 8.8 1.0
C A:THR216 4.4 8.8 1.0
CA A:THR216 4.5 8.0 1.0
C A:ASN217 4.5 8.4 1.0
OD1 A:ASN217 4.6 7.6 1.0
MG A:MG1524 4.7 9.8 1.0
OG1 A:THR216 4.7 9.8 1.0
OD1 A:ASP309 4.7 9.9 1.0
OD2 A:ASP170 4.7 9.2 1.0
CD A:LYS259 4.8 8.1 1.0
O A:HOH2097 5.0 23.4 1.0

Chlorine binding site 2 out of 4 in 3zvl

Go back to Chlorine Binding Sites List in 3zvl
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1526

b:27.6
occ:1.00
 N A:MET219 3.0 12.1 1.0
NH1 A:ARG258 3.0 15.0 1.0
O A:ASN217 3.4 10.4 1.0
C A:ASN217 3.5 8.4 1.0
CB A:MET219 3.5 17.0 1.0
CB A:ASN217 3.5 9.9 1.0
N A:GLN218 3.7 6.7 1.0
CA A:GLN218 3.8 9.6 1.0
CA A:MET219 3.8 14.7 1.0
CZ A:ARG258 3.9 13.6 1.0
NH2 A:ARG258 3.9 17.4 1.0
C A:GLN218 3.9 12.4 1.0
O A:HOH2118 4.1 18.9 1.0
CA A:ASN217 4.2 8.9 1.0
O A:HOH2187 4.3 12.1 1.0
O A:HOH2122 4.6 15.1 1.0
CG A:ASN217 4.7 9.0 1.0
N A:GLY220 4.8 12.6 1.0
C A:MET219 4.8 11.9 1.0
O A:HOH2041 4.9 12.4 1.0
CG A:MET219 4.9 23.5 1.0
ND2 A:ASN217 5.0 10.2 1.0

Chlorine binding site 3 out of 4 in 3zvl

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Chlorine 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 Chlorine with other atoms in the Cl 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
A:Cl1527

b:47.2
occ:1.00
 O A:HOH2209 2.9 40.5 1.0
N A:PHE320 3.0 10.7 1.0
O A:HOH2290 3.4 35.0 1.0
O3 A:GOL1536 3.6 35.5 1.0
CA A:PRO319 3.6 11.1 1.0
O A:PHE320 3.7 12.3 1.0
C A:PRO319 3.8 12.7 1.0
O A:HOH2304 3.8 18.2 1.0
CA A:PHE320 3.9 10.0 1.0
CB A:PHE320 4.0 9.7 1.0
O A:HOH2305 4.2 30.8 1.0
C A:PHE320 4.3 14.0 1.0
O A:HOH2508 4.3 39.3 1.0
CB A:PRO319 4.4 12.6 1.0
O A:LEU318 4.5 10.8 1.0
O A:HOH2292 4.6 24.2 1.0
O A:HOH2306 4.6 37.2 1.0
C3 A:GOL1536 4.8 37.2 1.0
N A:PRO319 4.8 7.7 1.0
O A:HOH2289 4.8 14.2 1.0
O A:HOH2206 4.9 37.6 1.0
O A:HOH2202 5.0 43.9 1.0
O A:PRO319 5.0 8.9 1.0

Chlorine binding site 4 out of 4 in 3zvl

Go back to Chlorine Binding Sites List in 3zvl
Chlorine 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 Chlorine with other atoms in the Cl 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
A:Cl1537

b:40.0
occ:1.00
 O A:HOH2390 2.9 16.2 1.0
CG A:LYS416 3.8 18.3 1.0
CA A:LYS416 4.1 12.1 1.0
O A:GLY415 4.2 19.2 1.0
CB A:LYS416 4.3 15.0 1.0
NE A:ARG417 4.6 14.6 1.0
O A:GLY389 4.6 13.2 1.0
CD A:LYS416 4.6 20.1 1.0
NH2 A:ARG417 4.7 12.7 1.0
O A:HOH2389 4.7 35.5 1.0
C A:GLY415 4.8 16.2 1.0
N A:LYS416 4.8 15.6 1.0
CE A:LYS416 4.9 27.9 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 1097-2765
PubMed: 22055185
DOI: 10.1016/J.MOLCEL.2011.08.036
Page generated: Fri Jul 11 12:30:40 2025

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