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Sodium in PDB 8i1f: Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6

Enzymatic activity of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6

All present enzymatic activity of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6:
3.6.1.55; 3.6.1.56;

Protein crystallography data

The structure of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6, PDB code: 8i1f was solved by T.Nakamura, Y.Yamagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.18 / 1.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.978, 47.933, 124.048, 90, 90, 90
R / Rfree (%) 14.2 / 16.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6 (pdb code 8i1f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6, PDB code: 8i1f:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 8i1f

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Sodium binding site 1 out of 7 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6


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 Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:14.9
occ:0.20
 N1 A:6U4201 1.2 11.2 0.4
N1 A:6U4201 1.2 11.0 0.4
C2 A:6U4201 1.5 11.0 0.4
C2 A:6U4201 1.5 10.9 0.4
O2 A:6U4201 1.7 10.8 0.4
O2 A:6U4201 1.7 11.0 0.4
OD1 A:ASP120 2.4 11.0 1.0
OD2 A:ASP119 2.4 9.7 1.0
HB2 A:TRP117 2.4 12.5 1.0
C6 A:6U4201 2.5 11.3 0.4
C6 A:6U4201 2.5 11.2 0.4
N3 A:6U4201 2.8 11.9 0.4
HB3 A:TRP117 2.9 12.5 1.0
N3 A:6U4201 2.9 12.0 0.4
CB A:TRP117 3.0 10.4 1.0
CG A:ASP119 3.1 9.5 1.0
OD1 A:ASP119 3.2 10.4 1.0
N6 A:6U4201 3.2 12.2 0.4
N6 A:6U4201 3.2 12.1 0.4
HZ2 A:TRP123 3.3 12.0 1.0
HE1 A:TRP123 3.4 10.9 1.0
C5 A:6U4201 3.5 12.7 0.4
C5 A:6U4201 3.5 12.8 0.4
CG A:TRP117 3.5 11.6 1.0
CG A:ASP120 3.5 10.0 1.0
HZ A:PHE72 3.5 12.1 1.0
C4 A:6U4201 3.5 12.4 0.4
C4 A:6U4201 3.6 12.6 0.4
HD1 A:TRP117 3.8 15.4 1.0
CD1 A:TRP117 3.8 12.9 1.0
OD2 A:ASP120 4.0 13.0 1.0
H A:ASP120 4.0 10.2 1.0
HD21 A:ASN33 4.1 26.7 0.7
CZ A:PHE72 4.1 10.1 1.0
CZ2 A:TRP123 4.1 10.0 1.0
NE1 A:TRP123 4.2 9.1 1.0
O A:HOH334 4.2 10.9 1.0
CA A:TRP117 4.4 9.8 1.0
CD2 A:TRP117 4.4 12.5 1.0
N A:ASP120 4.4 8.5 1.0
CB A:ASP119 4.5 10.3 1.0
H A:TRP117 4.5 10.6 1.0
ND2 A:ASN33 4.5 22.2 0.7
CE2 A:TRP123 4.5 8.8 1.0
HD22 A:ASN33 4.6 26.7 0.7
HE1 A:PHE72 4.6 12.2 1.0
O A:HOH397 4.6 8.5 0.4
CE1 A:PHE72 4.6 10.2 1.0
H A:ASP119 4.7 11.2 1.0
CB A:ASP120 4.7 8.7 1.0
HD21 A:LEU9 4.7 13.9 1.0
HA A:ASP120 4.7 10.0 1.0
HE2 A:PHE72 4.7 12.4 1.0
CE2 A:PHE72 4.7 10.4 1.0
O A:TRP117 4.7 9.2 1.0
HD22 A:LEU9 4.8 13.9 1.0
HB2 A:ASP119 4.8 12.4 1.0
N7 A:6U4201 4.8 16.9 0.4
C A:TRP117 4.8 9.3 1.0
N7 A:6U4201 4.8 17.0 0.4
NE1 A:TRP117 4.8 14.0 1.0
N9 A:6U4201 4.9 14.1 0.4
N9 A:6U4201 4.9 14.3 0.4
CA A:ASP120 4.9 8.4 1.0
N A:TRP117 4.9 8.8 1.0
HE3 A:TRP117 5.0 15.2 1.0
HB2 A:ASN33 5.0 13.3 0.3

Sodium binding site 2 out of 7 in 8i1f

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Sodium binding site 2 out of 7 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6


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 Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:35.4
occ:0.50
 O A:HOH310 0.1 35.4 0.5
O A:HOH382 2.4 21.6 1.0
O2B A:6U4201 2.5 24.7 0.4
OE2 A:GLU52 2.5 22.6 1.0
O A:HOH443 2.5 35.6 1.0
O2B A:6U4201 2.7 12.1 0.4
O2G A:6U4201 3.4 34.3 0.4
CD A:GLU52 3.4 20.1 1.0
HH12 A:ARG51 3.4 20.4 1.0
NA A:NA205 3.5 31.7 0.8
H A:LYS38 3.5 11.2 1.0
PB A:6U4201 3.5 15.3 0.4
O1B A:6U4201 3.6 13.3 0.4
PB A:6U4201 3.6 25.7 0.4
OE1 A:GLU52 3.6 20.8 1.0
O A:HOH302 3.8 31.4 1.0
HA3 A:GLY37 3.8 11.6 1.0
HE21 A:GLN40 3.8 22.7 1.0
O A:HOH306 3.9 33.4 1.0
O1B A:6U4201 3.9 27.9 0.4
HB2 A:LYS38 4.0 13.1 1.0
N A:LYS38 4.1 9.4 1.0
NH1 A:ARG51 4.2 17.0 1.0
O2G A:6U4201 4.3 23.2 0.4
HH22 A:ARG51 4.3 17.3 1.0
O A:LYS38 4.3 11.8 1.0
O3B A:6U4201 4.5 18.5 0.4
O3B A:6U4201 4.5 29.9 0.4
OE1 A:GLU55 4.6 29.7 1.0
NE2 A:GLN40 4.6 18.9 1.0
O A:HOH458 4.6 34.2 1.0
PG A:6U4201 4.6 32.9 0.4
CA A:GLY37 4.7 9.7 1.0
HH11 A:ARG51 4.7 20.4 1.0
CG A:GLU52 4.8 17.6 1.0
C A:GLY37 4.8 9.0 1.0
CB A:LYS38 4.8 10.9 1.0
O3A A:6U4201 4.8 15.2 0.4
HE22 A:GLN40 4.8 22.7 1.0
O1G A:6U4201 4.8 24.0 0.4
O3A A:6U4201 4.8 20.8 0.4
PG A:6U4201 4.8 20.2 0.4
CA A:LYS38 4.9 9.8 1.0
HG2 A:GLU52 4.9 21.2 1.0
NH2 A:ARG51 5.0 14.4 1.0

Sodium binding site 3 out of 7 in 8i1f

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Sodium binding site 3 out of 7 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6


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 Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:21.6
occ:0.80
 OE2 A:GLU56 2.2 20.6 0.5
O2A A:6U4201 2.2 17.7 0.4
O2A A:6U4201 2.3 19.4 0.4
O1B A:6U4201 2.3 13.3 0.4
O A:HOH345 2.3 19.4 1.0
O A:HOH419 2.3 40.9 1.0
O A:GLY36 2.4 11.7 1.0
O1B A:6U4201 2.8 27.9 0.4
NA A:NA205 3.0 31.7 0.8
CD A:GLU56 3.1 20.2 0.5
OE1 A:GLU56 3.4 20.8 0.5
PA A:6U4201 3.4 17.0 0.4
PB A:6U4201 3.5 15.3 0.4
PA A:6U4201 3.5 19.9 0.4
C A:GLY36 3.6 10.3 1.0
O3A A:6U4201 3.6 15.2 0.4
HA3 A:GLY37 3.6 11.6 1.0
HA2 A:GLY37 3.7 11.6 1.0
O3A A:6U4201 3.7 20.8 0.4
PB A:6U4201 3.8 25.7 0.4
OE1 A:GLU56 3.8 13.5 0.5
O5' A:6U4201 3.9 16.2 0.4
H A:GLY36 4.0 11.2 1.0
CA A:GLY37 4.0 9.7 1.0
O5' A:6U4201 4.1 15.6 0.4
HZ1 A:LYS23 4.1 48.2 1.0
OE1 A:GLU52 4.2 20.8 1.0
O A:HOH380 4.2 37.2 1.0
N A:GLY37 4.3 9.1 1.0
CD A:GLU56 4.3 12.8 0.5
O A:HOH306 4.3 33.4 1.0
O3B A:6U4201 4.3 18.5 0.4
O1G A:6U4201 4.3 24.0 0.4
O A:HOH369 4.4 16.7 1.0
OE2 A:GLU56 4.4 16.0 0.5
CG A:GLU56 4.5 19.7 0.5
HE3 A:LYS23 4.5 46.0 1.0
C4' A:6U4201 4.6 12.7 0.4
HG2 A:GLU56 4.6 23.6 0.5
C4' A:6U4201 4.6 12.6 0.4
O2B A:6U4201 4.6 24.7 0.4
N A:GLY36 4.7 9.3 1.0
O2B A:6U4201 4.7 12.1 0.4
HG3 A:GLU56 4.7 23.6 0.5
CA A:GLY36 4.7 9.9 1.0
C5' A:6U4201 4.7 14.2 0.4
O1A A:6U4201 4.7 21.7 0.4
C5' A:6U4201 4.8 14.0 0.4
NZ A:LYS23 4.8 40.2 1.0
O1A A:6U4201 4.8 23.0 0.4
HZ2 A:LYS23 5.0 48.2 1.0

Sodium binding site 4 out of 7 in 8i1f

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Sodium binding site 4 out of 7 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6


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 Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:31.7
occ:0.76
 OE2 A:GLU56 2.2 20.6 0.5
OE1 A:GLU52 2.2 20.8 1.0
O1B A:6U4201 2.3 13.3 0.4
O A:HOH306 2.3 33.4 1.0
O A:HOH302 2.6 31.4 1.0
O1B A:6U4201 3.0 27.9 0.4
NA A:NA204 3.0 21.6 0.8
CD A:GLU56 3.1 20.2 0.5
HG2 A:GLU56 3.2 23.6 0.5
CD A:GLU52 3.3 20.1 1.0
O A:HOH443 3.3 35.6 1.0
HG3 A:GLU56 3.4 23.6 0.5
O A:HOH310 3.4 35.4 0.5
CG A:GLU56 3.5 19.7 0.5
NA A:NA203 3.5 35.4 0.5
HA3 A:GLY37 3.5 11.6 1.0
PB A:6U4201 3.6 15.3 0.4
OE2 A:GLU52 3.6 22.6 1.0
O A:HOH419 3.7 40.9 1.0
O A:GLY36 3.8 11.7 1.0
PB A:6U4201 3.9 25.7 0.4
O1G A:6U4201 4.0 24.0 0.4
O2B A:6U4201 4.0 24.7 0.4
O2B A:6U4201 4.1 12.1 0.4
OE1 A:GLU56 4.2 20.8 0.5
HB2 A:GLU56 4.3 16.0 0.5
HB3 A:GLU52 4.3 18.8 1.0
CA A:GLY37 4.4 9.7 1.0
C A:GLY36 4.5 10.3 1.0
OE1 A:GLU56 4.6 13.5 0.5
CG A:GLU52 4.6 17.6 1.0
O3B A:6U4201 4.6 18.5 0.4
HA A:GLU52 4.7 17.2 1.0
O3A A:6U4201 4.7 15.2 0.4
HA2 A:GLY37 4.7 11.6 1.0
OE1 A:GLU55 4.7 29.7 1.0
O2A A:6U4201 4.8 19.4 0.4
N A:GLY37 4.8 9.1 1.0
O3A A:6U4201 4.8 20.8 0.4
O2G A:6U4201 4.8 34.3 0.4
O2A A:6U4201 4.8 17.7 0.4
CB A:GLU52 4.9 15.7 1.0
HG3 A:GLU56 4.9 16.3 0.5
PG A:6U4201 4.9 20.2 0.4
CB A:GLU56 4.9 18.4 0.5
HB2 A:GLU55 5.0 25.0 1.0
O A:HOH345 5.0 19.4 1.0

Sodium binding site 5 out of 7 in 8i1f

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Sodium binding site 5 out of 7 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6


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 Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:15.8
occ:0.40
 N1 B:6U4201 1.1 15.2 0.6
C2 B:6U4201 1.6 12.0 0.6
O2 B:6U4201 1.8 11.3 0.6
O B:HOH368 2.1 20.8 0.4
OD2 B:ASP119 2.3 9.9 1.0
C6 B:6U4201 2.4 13.6 0.6
OD1 B:ASP120 2.4 13.8 1.0
HB2 B:TRP117 2.5 16.4 1.0
HB3 B:TRP117 2.8 16.4 1.0
N3 B:6U4201 2.9 13.0 0.6
CG B:ASP119 3.0 9.5 1.0
OD1 B:ASP119 3.0 10.6 1.0
CB B:TRP117 3.0 13.6 1.0
N6 B:6U4201 3.1 14.8 0.6
HE1 B:TRP123 3.4 11.1 1.0
C5 B:6U4201 3.4 16.0 0.6
HZ2 B:TRP123 3.4 12.3 1.0
CG B:ASP120 3.5 10.6 1.0
CG B:TRP117 3.5 15.8 1.0
HZ B:PHE72 3.5 13.3 1.0
C4 B:6U4201 3.5 12.3 0.6
HD1 B:TRP117 3.9 21.4 1.0
CD1 B:TRP117 3.9 17.8 1.0
OD2 B:ASP120 4.0 12.5 1.0
H B:ASP120 4.0 10.5 1.0
CZ B:PHE72 4.1 11.1 1.0
NE1 B:TRP123 4.1 9.2 1.0
O B:HOH330 4.2 11.3 1.0
CZ2 B:TRP123 4.2 10.3 1.0
HD21 B:ASN33 4.3 21.8 0.7
N B:ASP120 4.3 8.8 1.0
CD2 B:TRP117 4.4 19.8 1.0
CA B:TRP117 4.4 11.5 1.0
CB B:ASP119 4.4 10.1 1.0
HE1 B:PHE72 4.5 13.3 1.0
H B:ASP119 4.5 11.7 1.0
CE2 B:TRP123 4.6 9.1 1.0
H B:TRP117 4.6 11.7 1.0
HA B:ASP120 4.6 10.4 1.0
CE1 B:PHE72 4.6 11.1 1.0
CB B:ASP120 4.7 9.0 1.0
O B:TRP117 4.7 10.3 1.0
HB2 B:ASP119 4.7 12.1 1.0
ND2 B:ASN33 4.7 18.1 0.7
O B:HOH433 4.7 13.8 0.5
N7 B:6U4201 4.7 18.0 0.6
HD22 B:ASN33 4.8 21.8 0.7
C B:TRP117 4.8 10.5 1.0
HD22 B:LEU9 4.8 13.9 1.0
CA B:ASP120 4.8 8.7 1.0
N9 B:6U4201 4.9 13.8 0.6
CE2 B:PHE72 4.9 11.2 1.0
NE1 B:TRP117 4.9 22.4 1.0
HE2 B:PHE72 4.9 13.5 1.0
HE3 B:TRP117 4.9 24.9 1.0
HD21 B:LEU9 4.9 13.9 1.0
C B:ASP119 4.9 9.4 1.0
N B:TRP117 5.0 9.8 1.0

Sodium binding site 6 out of 7 in 8i1f

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Sodium binding site 6 out of 7 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6


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 Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:28.2
occ:0.68
 NA B:NA203 0.0 28.2 0.7
NA B:NA203 1.6 12.2 0.3
O1A B:6U4201 2.1 24.0 0.6
OE2 B:GLU56 2.1 21.8 0.7
O B:HOH311 2.3 23.5 1.0
O B:GLY36 2.3 12.1 1.0
O2B B:6U4201 2.6 54.0 0.6
CD B:GLU56 3.2 20.2 0.7
O B:HOH304 3.2 45.7 1.0
PA B:6U4201 3.3 33.1 0.6
HA3 B:GLY37 3.4 12.2 1.0
C B:GLY36 3.5 10.4 1.0
O3A B:6U4201 3.6 42.6 0.6
HA2 B:GLY37 3.6 12.2 1.0
PB B:6U4201 3.7 51.7 0.6
OE1 B:GLU56 3.7 19.4 0.7
OE1 B:GLU56 3.8 20.7 0.3
OE1 B:GLU52 3.9 19.5 1.0
CA B:GLY37 3.9 10.2 1.0
O5' B:6U4201 4.1 22.5 0.6
H B:GLY36 4.1 12.7 1.0
N B:GLY37 4.2 10.7 1.0
CG B:GLU56 4.4 20.2 0.7
O B:HOH350 4.4 19.0 1.0
CD B:GLU56 4.4 19.6 0.3
HG2 B:GLU56 4.4 24.2 0.7
HG3 B:GLU56 4.5 24.2 0.7
O2A B:6U4201 4.6 36.1 0.6
OE2 B:GLU56 4.6 20.0 0.3
O3B B:6U4201 4.7 58.4 0.6
N B:GLY36 4.7 10.6 1.0
C4' B:6U4201 4.7 13.0 0.6
CA B:GLY36 4.7 11.1 1.0
O B:HOH452 4.8 32.4 1.0
CD B:GLU52 4.8 18.0 1.0
C5' B:6U4201 4.8 17.5 0.6
O1B B:6U4201 4.9 52.1 0.6
HB2 B:GLU56 5.0 22.7 0.3

Sodium binding site 7 out of 7 in 8i1f

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Sodium binding site 7 out of 7 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6


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 Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 8.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:12.2
occ:0.32
 NA B:NA203 0.0 12.2 0.3
NA B:NA203 1.6 28.2 0.7
OE2 B:GLU56 2.2 21.8 0.7
O2B B:6U4201 2.3 54.0 0.6
OE1 B:GLU52 2.4 19.5 1.0
O B:GLY36 2.5 12.1 1.0
HA3 B:GLY37 2.8 12.2 1.0
CD B:GLU56 3.1 20.2 0.7
O1A B:6U4201 3.3 24.0 0.6
CD B:GLU52 3.4 18.0 1.0
C B:GLY36 3.4 10.4 1.0
O B:HOH304 3.4 45.7 1.0
O B:HOH311 3.5 23.5 1.0
PB B:6U4201 3.5 51.7 0.6
CA B:GLY37 3.6 10.2 1.0
O B:HOH395 3.7 31.0 1.0
HG3 B:GLU56 3.7 24.2 0.7
HA2 B:GLY37 3.7 12.2 1.0
O3A B:6U4201 3.8 42.6 0.6
OE2 B:GLU52 3.8 20.8 1.0
CG B:GLU56 3.9 20.2 0.7
OE1 B:GLU56 3.9 19.4 0.7
N B:GLY37 3.9 10.7 1.0
HG2 B:GLU56 3.9 24.2 0.7
OE1 B:GLU56 4.0 20.7 0.3
O B:HOH302 4.0 39.2 1.0
HB3 B:GLU52 4.1 17.6 1.0
H B:GLY36 4.2 12.7 1.0
PA B:6U4201 4.2 33.1 0.6
O1B B:6U4201 4.3 52.1 0.6
HB2 B:GLU56 4.4 22.7 0.3
CG B:GLU52 4.5 16.7 1.0
HG3 B:GLU52 4.6 20.0 1.0
CA B:GLY36 4.6 11.1 1.0
H B:LYS38 4.7 12.3 1.0
CD B:GLU56 4.7 19.6 0.3
H B:GLY37 4.7 12.8 1.0
CB B:GLU52 4.8 14.7 1.0
N B:GLY36 4.8 10.6 1.0
O3B B:6U4201 4.8 58.4 0.6
C B:GLY37 4.9 9.9 1.0
HA2 B:GLY36 4.9 13.3 1.0
O5' B:6U4201 4.9 22.5 0.6
O1G B:6U4201 4.9 65.1 0.6

Reference:

T.Nakamura, Y.Koga-Ogawa, K.Fujimiya, M.Chirifu, M.Goto, S.Ikemizu, Y.Nakabeppu, Y.Yamagata. Protonation States of Asp Residues in the Human Nudix Hydrolase MTH1 Contribute to Its Broad Substrate Recognition. Febs Lett. 2023.
ISSN: ISSN 0014-5793
PubMed: 36914375
DOI: 10.1002/1873-3468.14611
Page generated: Wed Oct 9 12:22:51 2024

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Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
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