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Sodium in PDB 8i1g: Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 9.1

Enzymatic activity of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 9.1

All present enzymatic activity of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 9.1:
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 9.1, PDB code: 8i1g 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 / 1.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.914, 48.009, 124.144, 90, 90, 90
R / Rfree (%) 13.8 / 17.1

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 9.1 (pdb code 8i1g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 9.1, PDB code: 8i1g:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 8i1g

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Sodium binding site 1 out of 5 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 9.1


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 9.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:10.9
occ:0.50
 N1 A:6U4201 1.1 28.3 0.5
C2 A:6U4201 1.4 27.6 0.5
O2 A:6U4201 1.6 25.7 0.5
OD1 A:ASP120 2.3 14.7 1.0
OD2 A:ASP119 2.4 11.8 1.0
O A:HOH432 2.4 26.3 0.5
O A:HOH402 2.4 21.0 0.5
O3 A:GOL203 2.4 16.3 0.5
C6 A:6U4201 2.4 29.0 0.5
HB2 A:TRP117 2.7 18.7 1.0
N3 A:6U4201 2.8 28.6 0.5
CG A:ASP119 3.0 11.6 1.0
OD1 A:ASP119 3.0 12.6 1.0
HB3 A:TRP117 3.2 18.7 1.0
N6 A:6U4201 3.3 28.5 0.5
HZ2 A:TRP123 3.3 14.7 1.0
CB A:TRP117 3.4 15.6 1.0
HZ A:PHE72 3.4 14.0 1.0
HE1 A:TRP123 3.4 12.8 1.0
CG A:ASP120 3.4 13.2 1.0
C5 A:6U4201 3.4 29.7 0.5
C4 A:6U4201 3.5 28.5 0.5
C3 A:GOL203 3.7 16.8 0.5
O2 A:GOL203 3.9 19.6 0.5
OD2 A:ASP120 3.9 15.2 1.0
CG A:TRP117 4.0 19.6 1.0
CZ A:PHE72 4.0 11.7 1.0
H A:ASP120 4.0 11.5 1.0
C2 A:GOL203 4.1 19.6 0.5
CZ2 A:TRP123 4.1 12.3 1.0
NE1 A:TRP123 4.1 10.6 1.0
O A:HOH326 4.2 13.5 1.0
HD21 A:ASN33 4.2 23.6 0.8
HE1 A:PHE72 4.4 14.7 1.0
N A:ASP120 4.4 9.6 1.0
CB A:ASP119 4.5 11.9 1.0
HD1 A:TRP117 4.5 26.7 1.0
CD1 A:TRP117 4.5 22.2 1.0
CE2 A:TRP123 4.5 10.3 1.0
CE1 A:PHE72 4.5 12.2 1.0
HA A:ASP120 4.6 11.8 1.0
CA A:TRP117 4.6 12.8 1.0
H A:ASP119 4.6 13.2 1.0
O A:HOH427 4.7 30.3 0.3
CB A:ASP120 4.7 10.6 1.0
H A:TRP117 4.7 14.2 1.0
ND2 A:ASN33 4.7 19.6 0.8
HB2 A:ASP119 4.7 14.3 1.0
CE2 A:PHE72 4.8 12.1 1.0
N7 A:6U4201 4.8 31.7 0.5
HE2 A:PHE72 4.8 14.5 1.0
CA A:ASP120 4.8 9.8 1.0
CD2 A:TRP117 4.8 20.7 1.0
HD22 A:LEU9 4.9 17.3 1.0
O A:TRP117 4.9 12.0 1.0
N9 A:6U4201 4.9 29.9 0.5
HD21 A:LEU9 4.9 17.3 1.0
C A:TRP117 4.9 12.0 1.0
C A:ASP119 5.0 10.3 1.0
HD22 A:ASN33 5.0 23.6 0.8

Sodium binding site 2 out of 5 in 8i1g

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Sodium binding site 2 out of 5 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 9.1


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 9.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:21.4
occ:0.39
 OE2 A:GLU56 2.0 26.0 0.6
O2A A:6U4201 2.2 38.6 0.5
O A:HOH362 2.3 37.0 1.0
O A:GLY36 2.3 13.9 1.0
CD A:GLU56 3.1 24.2 0.6
O1B A:6U4201 3.3 45.0 0.5
PA A:6U4201 3.5 37.4 0.5
OE1 A:GLU56 3.5 23.7 0.6
C A:GLY36 3.5 11.2 1.0
HA3 A:GLY37 3.6 12.8 1.0
HA2 A:GLY37 3.6 12.8 1.0
OE1 A:GLU56 3.8 22.0 0.4
H A:GLY36 3.9 12.8 1.0
O3A A:6U4201 4.0 41.2 0.5
O5' A:6U4201 4.0 33.9 0.5
CA A:GLY37 4.0 10.6 1.0
PB A:6U4201 4.0 44.7 0.5
OE1 A:GLU52 4.2 25.4 1.0
N A:GLY37 4.2 11.1 1.0
O A:HOH380 4.3 30.3 1.0
CG A:GLU56 4.3 24.1 0.6
CD A:GLU56 4.4 22.8 0.4
O2B A:6U4201 4.4 40.0 0.5
HG2 A:GLU56 4.4 28.9 0.6
HG3 A:GLU56 4.5 28.9 0.6
C4' A:6U4201 4.6 30.7 0.5
N A:GLY36 4.6 10.7 1.0
OE2 A:GLU56 4.6 24.1 0.4
C5' A:6U4201 4.7 33.0 0.5
CA A:GLY36 4.7 11.5 1.0
O1A A:6U4201 4.8 39.0 0.5
HE3 A:MET101 4.9 32.1 0.4
HB2 A:GLU56 5.0 26.1 0.4

Sodium binding site 3 out of 5 in 8i1g

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Sodium binding site 3 out of 5 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 9.1


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 9.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:15.2
occ:1.00
 O B:HOH355 2.2 24.7 0.6
O3 B:GOL202 2.3 27.3 1.0
OD1 B:ASP120 2.3 15.5 1.0
OD2 B:ASP119 2.3 11.5 1.0
O B:HOH355 2.4 17.3 0.4
HB2 B:TRP117 2.8 18.4 1.0
OD1 B:ASP119 2.9 12.3 1.0
CG B:ASP119 2.9 11.1 1.0
HB3 B:TRP117 3.3 18.4 1.0
HZ2 B:TRP123 3.4 14.2 1.0
HZ B:PHE72 3.4 14.5 1.0
HE1 B:TRP123 3.4 11.9 1.0
CB B:TRP117 3.4 15.3 1.0
CG B:ASP120 3.5 12.4 1.0
C3 B:GOL202 3.5 31.1 1.0
O2 B:GOL202 3.6 37.3 1.0
OD2 B:ASP120 4.0 14.0 1.0
CZ B:PHE72 4.0 12.1 1.0
C2 B:GOL202 4.0 34.8 1.0
H B:ASP120 4.0 12.3 1.0
CG B:TRP117 4.1 17.9 1.0
NE1 B:TRP123 4.2 9.9 1.0
CZ2 B:TRP123 4.2 11.8 1.0
O B:HOH326 4.2 12.6 1.0
HD21 B:ASN33 4.2 25.1 0.9
HE1 B:PHE72 4.3 14.9 1.0
N B:ASP120 4.4 10.2 1.0
CB B:ASP119 4.4 11.1 1.0
CE1 B:PHE72 4.5 12.4 1.0
HD12 B:ILE70 4.5 14.1 0.1
H B:ASP119 4.5 13.6 1.0
CE2 B:TRP123 4.6 10.2 1.0
HD1 B:TRP117 4.6 23.3 1.0
HA B:ASP120 4.6 11.8 1.0
CD1 B:TRP117 4.6 19.4 1.0
HB2 B:ASP119 4.7 13.3 1.0
CB B:ASP120 4.7 10.5 1.0
CA B:TRP117 4.7 12.9 1.0
HD22 B:LEU9 4.7 15.5 1.0
ND2 B:ASN33 4.8 20.9 0.9
H B:TRP117 4.8 13.6 1.0
HD11 B:ILE70 4.8 14.1 0.1
CA B:ASP120 4.8 9.8 1.0
CE2 B:PHE72 4.8 12.9 1.0
O B:TRP117 4.9 12.1 1.0
HE2 B:PHE72 4.9 15.5 1.0
O B:HOH307 4.9 38.9 1.0
C B:ASP119 4.9 10.2 1.0
HB3 B:ASP119 5.0 13.3 1.0
C B:TRP117 5.0 11.6 1.0

Sodium binding site 4 out of 5 in 8i1g

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Sodium binding site 4 out of 5 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 9.1


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 9.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:76.3
occ:1.00
 O B:HOH350 2.1 33.4 1.0
OE2 B:GLU52 2.2 26.8 1.0
HH12 B:ARG51 3.0 30.5 1.0
O B:HOH398 3.2 27.8 1.0
CD B:GLU52 3.2 23.7 1.0
OE1 B:GLU52 3.6 23.3 1.0
H B:LYS38 3.7 15.3 1.0
O B:HOH381 3.7 43.2 1.0
HE21 B:GLN40 3.7 32.1 1.0
HA3 B:GLY37 3.8 15.6 1.0
NH1 B:ARG51 3.8 25.4 1.0
HZ2 B:LYS38 3.8 45.5 1.0
NA B:NA204 4.1 43.1 0.8
HH22 B:ARG51 4.1 25.2 1.0
HB2 B:LYS38 4.1 21.6 1.0
O B:LYS38 4.2 15.5 1.0
N B:LYS38 4.2 12.7 1.0
HH11 B:ARG51 4.2 30.5 1.0
HZ3 B:LYS38 4.4 45.5 1.0
NZ B:LYS38 4.5 37.9 1.0
HZ1 B:LYS38 4.5 45.5 1.0
NE2 B:GLN40 4.5 26.7 1.0
CG B:GLU52 4.5 21.9 1.0
OE1 B:GLU55 4.6 33.0 1.0
CA B:GLY37 4.6 13.0 1.0
HG2 B:GLU52 4.7 26.2 1.0
HE22 B:GLN40 4.7 32.1 1.0
NH2 B:ARG51 4.7 21.0 1.0
CZ B:ARG51 4.7 21.6 1.0
C B:GLY37 4.8 12.4 1.0
HG3 B:GLU52 4.8 26.2 1.0
CB B:LYS38 4.9 17.9 1.0
CA B:LYS38 4.9 13.3 1.0
C B:LYS38 5.0 13.0 1.0

Sodium binding site 5 out of 5 in 8i1g

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Sodium binding site 5 out of 5 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 9.1


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 9.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na204

b:43.1
occ:0.76
 OE2 B:GLU56 2.3 20.5 0.7
O B:GLY36 2.5 14.6 1.0
OE1 B:GLU52 2.5 23.3 1.0
HA3 B:GLY37 3.0 15.6 1.0
CD B:GLU56 3.0 19.7 0.7
O B:HOH440 3.4 33.1 1.0
CD B:GLU52 3.5 23.7 1.0
O B:HOH381 3.5 43.2 1.0
O B:HOH305 3.5 26.1 1.0
C B:GLY36 3.5 13.3 1.0
O B:HOH309 3.5 58.2 1.0
HG3 B:GLU56 3.5 23.4 0.7
CA B:GLY37 3.7 13.0 1.0
CG B:GLU56 3.7 19.5 0.7
OE1 B:GLU56 3.8 20.3 0.7
HA2 B:GLY37 3.8 15.6 1.0
HG2 B:GLU56 3.9 23.4 0.7
OE2 B:GLU52 3.9 26.8 1.0
OE1 B:GLU56 4.0 21.3 0.3
O B:HOH398 4.0 27.8 1.0
N B:GLY37 4.1 12.8 1.0
NA B:NA203 4.1 76.3 1.0
H B:GLY36 4.2 14.7 1.0
HB3 B:GLU52 4.3 22.3 1.0
HB2 B:GLU56 4.5 24.4 0.3
CG B:GLU52 4.6 21.9 1.0
CA B:GLY36 4.7 12.4 1.0
HG3 B:GLU52 4.7 26.2 1.0
CD B:GLU56 4.8 22.1 0.3
N B:GLY36 4.8 12.2 1.0
H B:LYS38 4.8 15.3 1.0
H B:GLY37 4.9 15.4 1.0
CB B:GLU52 4.9 18.6 1.0
HA2 B:GLY36 5.0 14.9 1.0

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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