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Sodium in PDB 3hhq: Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae

Enzymatic activity of Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae

All present enzymatic activity of Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae:
3.6.1.23;

Protein crystallography data

The structure of Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae, PDB code: 3hhq was solved by A.U.Singer, E.Evdokimova, M.Kudritska, A.Dong, A.M.Edwards, A.F.Yakunin, A.Savchenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.62 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 95.461, 95.466, 97.594, 98.79, 97.42, 107.13
R / Rfree (%) 17.5 / 23.6

Other elements in 3hhq:

The structure of Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae also contains other interesting chemical elements:

Chlorine (Cl) 17 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae (pdb code 3hhq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae, PDB code: 3hhq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in 3hhq

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Sodium binding site 1 out of 14 in the Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na150

b:19.2
occ:1.00
 O A:HOH156 2.6 18.3 1.0
N A:ARG68 2.7 19.1 0.3
N A:ARG68 2.8 19.8 0.7
O A:VAL112 2.9 19.9 1.0
CA A:PRO67 3.2 19.1 1.0
C A:PRO67 3.5 19.1 1.0
CG A:ARG68 3.5 19.0 0.3
CB A:ARG68 3.6 18.9 0.3
CA A:ARG68 3.7 19.1 0.3
C A:VAL112 3.7 18.7 1.0
CA A:ARG68 3.8 20.1 0.7
CB A:PRO67 3.9 18.8 1.0
CA A:ALA113 3.9 18.5 1.0
CB A:ARG68 3.9 20.4 0.7
N A:ALA113 4.1 18.6 1.0
O A:ARG68 4.2 18.8 0.7
CG2 A:ILE77 4.2 18.5 1.0
O A:ARG68 4.2 18.6 0.3
O A:ALA66 4.2 17.8 1.0
CG A:ARG68 4.3 21.0 0.7
CD1 A:LEU71 4.3 16.8 1.0
CD2 A:LEU96 4.4 14.7 1.0
CB A:ALA113 4.5 17.5 1.0
C A:ARG68 4.5 18.7 0.3
N A:PRO67 4.5 19.0 1.0
C A:ARG68 4.5 19.0 0.7
CB A:LEU71 4.7 17.5 1.0
O A:PRO67 4.7 18.2 1.0
C A:ALA66 4.8 16.8 1.0
O A:ILE77 4.9 19.9 1.0
CA A:VAL112 5.0 19.1 1.0

Sodium binding site 2 out of 14 in 3hhq

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Sodium binding site 2 out of 14 in the Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na149

b:48.9
occ:1.00
 O C:ILE120 2.8 16.2 1.0
N C:ASP122 3.7 20.8 1.0
OD2 C:ASP122 3.8 30.3 1.0
CA C:VAL121 3.8 17.8 1.0
C C:ILE120 3.8 16.7 1.0
CA C:GLY60 4.0 18.1 1.0
NZ B:LYS119 4.0 18.4 1.0
CG C:ASP122 4.1 28.2 1.0
O B:HOH1225 4.2 25.0 1.0
C C:VAL121 4.3 19.6 1.0
N C:VAL121 4.3 17.5 1.0
CE B:LYS119 4.3 18.7 1.0
OD1 C:ASP122 4.4 33.9 1.0
O C:GLY60 4.4 16.9 1.0
OD2 C:ASP123 4.5 31.9 1.0
C C:GLY60 4.7 18.0 1.0
CA C:ASP122 4.8 23.9 1.0
CB C:VAL121 4.9 16.5 1.0
CG C:ASP123 4.9 28.2 1.0
CB C:ASP122 4.9 24.2 1.0
OD1 C:ASP123 4.9 29.4 1.0
CG1 C:VAL121 5.0 17.0 1.0

Sodium binding site 3 out of 14 in 3hhq

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Sodium binding site 3 out of 14 in the Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na152

b:30.1
occ:1.00
 O E:THR27 2.6 29.5 1.0
N F:ARG86 2.8 21.1 0.5
N F:ARG86 2.9 21.3 0.5
O F:THR61 3.3 18.5 1.0
CB F:ARG86 3.5 21.0 0.5
N E:ALA29 3.6 24.3 1.0
CB F:TYR62 3.6 15.8 1.0
CA F:ASP85 3.6 21.6 1.0
C F:ASP85 3.7 21.3 1.0
CB F:ARG86 3.7 21.6 0.5
CA F:ARG86 3.8 21.5 0.5
C E:THR27 3.8 28.9 1.0
CA F:ARG86 3.8 21.9 0.5
CA F:TYR62 3.9 16.8 1.0
CA E:ALA29 3.9 23.4 1.0
C E:ALA28 4.0 25.9 1.0
CB F:ASP85 4.0 22.0 1.0
CB E:ALA29 4.1 22.8 1.0
C F:THR61 4.1 18.0 1.0
OD2 F:ASP85 4.2 19.2 1.0
N F:TYR62 4.3 16.8 1.0
CD1 F:ILE120 4.3 15.4 1.0
CA E:ALA28 4.4 26.2 1.0
O F:VAL84 4.5 19.7 1.0
N E:ALA28 4.5 27.8 1.0
O E:ALA28 4.6 25.3 1.0
CG F:ASP85 4.6 24.9 1.0
N F:ASP85 4.8 20.1 1.0
CB E:THR27 4.8 29.0 1.0
O F:ASP85 4.9 20.8 1.0
NE F:ARG86 4.9 21.0 0.5
CA E:THR27 4.9 29.8 1.0
CG F:ARG86 4.9 21.0 0.5
CG F:TYR62 5.0 17.7 1.0

Sodium binding site 4 out of 14 in 3hhq

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Sodium binding site 4 out of 14 in the Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na149

b:27.4
occ:1.00
 O L:HOH208 2.6 15.7 1.0
O L:HOH205 2.8 12.1 1.0
OG1 L:THR79 2.9 21.4 1.0
O L:HOH209 3.0 16.1 1.0
O L:THR79 3.1 22.3 1.0
O K:HOH1249 3.7 16.7 1.0
C L:THR79 3.9 20.5 1.0
CB L:THR79 4.1 21.3 1.0
CD L:PRO67 4.1 20.8 1.0
NH2 L:ARG64 4.1 13.3 1.0
O L:ILE65 4.1 19.8 1.0
O J:HOH530 4.2 16.4 1.0
OE1 L:GLN78 4.4 21.9 1.0
CA L:THR79 4.4 20.3 1.0
OE1 K:GLN78 4.4 22.7 1.0
CD L:GLN78 4.4 22.7 1.0
N L:THR79 4.5 19.7 1.0
O K:HOH212 4.7 16.1 1.0
NE2 L:GLN78 4.7 25.6 1.0
O J:HOH448 4.8 19.6 1.0
CG L:GLN78 4.9 18.2 1.0
CG L:PRO67 4.9 18.9 1.0
N L:GLY80 4.9 19.8 1.0
CA L:ALA66 4.9 19.8 1.0
N L:PRO67 5.0 19.8 1.0
O L:ALA81 5.0 21.7 1.0

Sodium binding site 5 out of 14 in 3hhq

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Sodium binding site 5 out of 14 in the Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na150

b:28.5
occ:1.00
 OE2 M:GLU118 3.0 19.2 1.0
OE2 O:GLU118 3.2 20.8 1.0
OE2 N:GLU118 3.2 20.6 1.0
NE M:ARG64 3.4 17.5 1.0
NE O:ARG64 3.4 17.9 1.0
NE N:ARG64 3.4 16.4 1.0
CD M:ARG64 3.5 16.0 1.0
CD M:GLU118 3.6 17.4 1.0
CD N:ARG64 3.6 15.6 1.0
CD O:ARG64 3.7 19.4 1.0
OH N:TYR62 3.7 16.8 1.0
CD N:GLU118 3.8 19.4 1.0
CD O:GLU118 3.8 20.4 1.0
OH M:TYR62 3.9 16.6 1.0
OH O:TYR62 4.0 15.9 1.0
OE1 M:GLU118 4.0 17.7 1.0
CZ M:ARG64 4.0 19.4 1.0
CZ O:ARG64 4.1 20.0 1.0
CZ N:ARG64 4.2 18.7 1.0
OE1 N:GLU118 4.3 20.0 1.0
OE1 O:GLU118 4.3 21.4 1.0
NH1 M:ARG64 4.4 19.4 1.0
CG N:GLU118 4.4 14.6 1.0
CG M:GLU118 4.5 16.6 1.0
NH1 O:ARG64 4.5 18.6 1.0
NH1 N:ARG64 4.5 19.8 1.0
CG O:GLU118 4.6 19.5 1.0
NH2 M:ARG64 4.9 18.9 1.0
CG M:ARG64 5.0 13.5 1.0
NH2 O:ARG64 5.0 21.7 1.0

Sodium binding site 6 out of 14 in 3hhq

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Sodium binding site 6 out of 14 in the Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na150

b:36.8
occ:1.00
 O N:ASN75 2.4 20.7 1.0
OG N:SER100 2.8 18.3 1.0
O N:ARG102 3.0 22.4 1.0
OD1 N:ASN98 3.3 18.2 1.0
O N:HOH1092 3.3 31.4 1.0
C N:ASN75 3.4 19.4 1.0
ND2 N:ASN98 3.5 15.4 1.0
CB N:ASN75 3.6 19.7 1.0
CA N:ASN75 3.6 20.5 1.0
CB N:SER100 3.7 21.0 1.0
CG N:ASN98 3.7 19.6 1.0
CB N:PHE104 3.8 20.9 1.0
C N:ARG102 4.0 21.6 1.0
CB N:ARG102 4.1 21.2 1.0
O N:ASP103 4.3 19.0 1.0
OD1 N:ASN75 4.3 22.4 1.0
NH2 N:ARG102 4.3 26.2 1.0
CA N:PHE104 4.3 20.8 1.0
N N:PHE104 4.3 21.2 1.0
C N:ASP103 4.4 20.6 1.0
CD2 N:PHE104 4.4 22.9 1.0
CZ N:ARG102 4.4 28.7 1.0
CG N:PHE104 4.4 20.9 1.0
CG N:ASN75 4.4 22.9 1.0
NH1 N:ARG102 4.5 31.8 1.0
CA N:ARG102 4.5 21.6 1.0
CD1 N:ILE77 4.6 17.3 1.0
N N:GLY76 4.6 19.7 1.0
N N:ARG102 4.7 21.0 1.0
CA N:SER100 4.9 20.9 1.0
NE N:ARG102 5.0 28.7 1.0
CG1 N:ILE77 5.0 17.1 1.0
N N:ASP103 5.0 21.2 1.0

Sodium binding site 7 out of 14 in 3hhq

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Sodium binding site 7 out of 14 in the Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Na149

b:22.8
occ:1.00
 O O:ALA29 2.6 20.0 1.0
O M:VAL121 3.0 19.8 1.0
N O:LEU117 3.1 15.8 1.0
C O:ALA29 3.8 22.1 1.0
CB O:LEU117 3.9 17.6 1.0
CG O:LEU117 3.9 19.1 1.0
CA O:ILE116 4.0 16.2 1.0
CA O:LEU117 4.0 16.9 1.0
C O:ILE116 4.0 16.1 1.0
CD1 M:ILE120 4.1 16.2 1.0
CE1 O:TYR31 4.1 20.2 1.0
O O:HOH896 4.1 13.9 1.0
C M:VAL121 4.2 19.3 1.0
CG2 O:ILE116 4.3 14.5 1.0
CD1 O:LEU117 4.3 18.1 1.0
CB M:ILE120 4.4 15.0 1.0
O O:LEU115 4.4 16.7 1.0
O O:LEU117 4.5 15.4 1.0
CD1 O:TYR31 4.5 22.8 1.0
CE O:LYS23 4.6 29.9 1.0
C O:LEU117 4.6 16.4 1.0
CB O:ILE116 4.7 16.4 1.0
CA O:ALA29 4.7 22.8 1.0
CG1 M:ILE120 4.7 13.9 1.0
CA O:GLY30 4.8 20.3 1.0
N O:GLY30 4.8 20.4 1.0
CA M:ASP122 4.8 22.5 1.0
NZ O:LYS23 4.8 32.0 1.0
CG2 M:ILE120 4.9 17.5 1.0
N M:VAL121 4.9 16.6 1.0
N M:ASP122 5.0 20.2 1.0

Sodium binding site 8 out of 14 in 3hhq

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Sodium binding site 8 out of 14 in the Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Na151

b:49.4
occ:1.00
 O O:ALA18 3.0 19.2 1.0
O O:ALA16 3.4 23.2 1.0
O O:HOH1010 3.7 40.6 1.0
C O:ALA18 3.9 19.9 1.0
OG1 O:THR19 3.9 20.2 1.0
O O:HOH1372 4.1 22.4 1.0
O O:SER17 4.1 22.9 1.0
C O:SER17 4.2 21.8 1.0
C O:ALA16 4.4 22.1 1.0
CA O:SER17 4.5 22.9 1.0
N O:ALA18 4.6 20.0 1.0
N O:THR19 4.6 19.4 1.0
CA O:THR19 4.7 20.5 1.0
O O:HOH155 4.8 17.8 1.0
N O:SER17 4.8 22.5 1.0
CB O:THR19 4.9 20.6 1.0
CA O:ALA18 4.9 20.2 1.0
O O:HOH624 4.9 16.4 1.0

Sodium binding site 9 out of 14 in 3hhq

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Sodium binding site 9 out of 14 in the Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na150

b:26.9
occ:1.00
 O P:ALA29 2.7 25.2 1.0
O Q:VAL121 2.8 16.8 1.0
N P:LEU117 3.0 16.3 1.0
CB P:LEU117 3.6 15.5 1.0
CA P:LEU117 3.8 16.3 1.0
CG P:LEU117 3.8 16.6 1.0
CA P:ILE116 3.9 17.4 1.0
CE1 P:TYR31 3.9 25.0 1.0
C Q:VAL121 3.9 19.7 1.0
C P:ILE116 3.9 16.9 1.0
C P:ALA29 3.9 24.5 1.0
CG2 P:ILE116 4.0 17.7 1.0
CD1 Q:ILE120 4.1 14.2 1.0
O P:LEU117 4.2 15.1 1.0
CD1 P:LEU117 4.3 16.8 1.0
C P:LEU117 4.3 16.1 1.0
CA Q:ASP122 4.3 23.4 1.0
CB Q:ILE120 4.4 17.7 1.0
CD1 P:TYR31 4.4 23.1 1.0
O P:LEU115 4.4 19.2 1.0
CB P:ILE116 4.5 17.4 1.0
CG1 Q:ILE120 4.6 18.0 1.0
N Q:ASP122 4.6 20.5 1.0
N Q:VAL121 4.6 18.6 1.0
CA P:GLY30 4.7 22.6 1.0
N P:GLY30 4.7 23.2 1.0
CA Q:VAL121 4.9 18.7 1.0
CG2 Q:ILE120 4.9 17.5 1.0
CA P:ALA29 4.9 25.2 1.0
CB Q:ASP122 4.9 24.2 1.0
CE P:LYS23 5.0 31.6 1.0
N P:ILE116 5.0 17.5 1.0

Sodium binding site 10 out of 14 in 3hhq

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Sodium binding site 10 out of 14 in the Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Apo DUT1P From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Na150

b:24.4
occ:1.00
 OG1 S:THR79 2.6 21.0 1.0
O S:HOH232 2.8 15.9 1.0
O S:THR79 2.9 17.5 1.0
O U:HOH1368 2.9 20.3 1.0
C S:THR79 3.5 19.9 1.0
CB S:THR79 3.6 20.6 1.0
O U:HOH154 3.9 20.5 1.0
CA S:THR79 4.1 19.8 1.0
O S:ILE65 4.1 17.9 1.0
O S:HOH153 4.3 15.0 1.0
NE2 U:GLN78 4.3 19.6 1.0
CD S:PRO67 4.4 22.6 1.0
NH2 S:ARG64 4.4 15.2 1.0
N S:THR79 4.4 19.2 1.0
N S:GLY80 4.4 19.1 1.0
O S:HOH157 4.5 15.2 1.0
OE1 S:GLN78 4.5 23.9 1.0
O S:ALA81 4.7 21.0 1.0
CA S:GLY80 4.7 19.4 1.0
CD S:GLN78 4.7 21.1 1.0
O S:GLY80 4.8 22.5 1.0
O S:HOH2215 4.9 17.6 1.0
C S:GLY80 4.9 20.9 1.0
CG S:GLN78 4.9 19.2 1.0
CG2 S:THR79 4.9 19.2 1.0
OE1 U:GLN78 5.0 24.6 1.0

Reference:

A.Tchigvintsev, A.U.Singer, R.Flick, P.Petit, G.Brown, E.Evdokimova, A.Savchenko, A.F.Yakunin. Structure and Activity of the Saccharomyces Cerevisiae Dutp Pyrophosphatase DUT1, An Essential Housekeeping Enzyme. Biochem.J. V. 437 243 2011.
ISSN: ISSN 0264-6021
PubMed: 21548881
DOI: 10.1042/BJ20110304
Page generated: Mon Oct 7 10:23:40 2024

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