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Sodium in PDB 5ws7: Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp

Enzymatic activity of Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp

All present enzymatic activity of Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp:
3.6.1.55; 3.6.1.56;

Protein crystallography data

The structure of Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp, PDB code: 5ws7 was solved by T.Nakamura, S.Waz, K.Hirata, Y.Nakabeppu, Y.Yamagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.61 / 1.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.620, 47.344, 123.818, 90.00, 90.00, 90.00
R / Rfree (%) 11.7 / 13.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp (pdb code 5ws7). 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/C87A/C104S Mutant) in Complex with 2-Oxo-Datp, PDB code: 5ws7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5ws7

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Sodium binding site 1 out of 5 in the Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp


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/C87A/C104S Mutant) in Complex with 2-Oxo-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:7.1
occ:0.46
 NA A:NA202 0.0 7.1 0.5
O1B A:6U4201 2.3 10.0 1.0
NA A:NA202 2.3 13.8 0.5
O2A A:6U4201 2.4 10.9 1.0
O A:HOH420 2.4 15.0 1.0
O A:HOH398 2.4 19.2 1.0
O A:HOH513 2.5 30.8 1.0
O A:HOH310 3.2 16.0 1.0
PB A:6U4201 3.5 8.4 1.0
PA A:6U4201 3.5 8.5 1.0
O3A A:6U4201 3.6 8.1 1.0
O A:HOH366 3.7 31.9 1.0
O A:HOH327 3.8 37.6 1.0
OE2 A:GLU56 3.8 13.3 0.1
O3B A:6U4201 4.1 9.7 1.0
O A:HOH478 4.2 44.9 1.0
O A:HOH475 4.2 44.5 1.0
O A:HOH313 4.3 15.4 1.0
OE1 A:GLU56 4.3 9.7 0.6
OE2 A:GLU56 4.4 11.3 0.6
O1G A:6U4201 4.5 13.1 1.0
OE1 A:GLU100 4.5 27.4 1.0
O5' A:6U4201 4.5 8.1 1.0
CD A:GLU56 4.6 9.6 0.6
O1A A:6U4201 4.6 9.9 1.0
HZ1 A:LYS23 4.7 27.5 0.3
CD A:GLU56 4.7 13.6 0.1
O2B A:6U4201 4.7 8.7 1.0
O A:GLY36 4.7 7.4 1.0
O2G A:6U4201 4.8 12.9 1.0
PG A:6U4201 4.8 10.4 1.0
O A:HOH404 4.8 43.0 1.0
OE1 A:GLU56 4.8 13.6 0.1
O A:HOH308 4.9 27.6 1.0
HA2 A:GLY37 5.0 7.2 1.0

Sodium binding site 2 out of 5 in 5ws7

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Sodium binding site 2 out of 5 in the Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp


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/C87A/C104S Mutant) in Complex with 2-Oxo-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:13.8
occ:0.54
 NA A:NA202 0.0 13.8 0.5
NA A:NA202 2.3 7.1 0.5
O A:HOH475 2.4 44.5 1.0
OE2 A:GLU56 2.5 13.3 0.1
O A:GLY36 2.7 7.4 1.0
OE1 A:GLU56 2.9 9.7 0.6
O2A A:6U4201 3.2 10.9 1.0
CD A:GLU56 3.3 13.6 0.1
CD A:GLU56 3.3 9.6 0.6
O1B A:6U4201 3.4 10.0 1.0
O A:HOH366 3.4 31.9 1.0
O A:HOH420 3.5 15.0 1.0
O A:HOH513 3.6 30.8 1.0
OE1 A:GLU56 3.6 13.6 0.1
O A:HOH408 3.7 9.4 0.6
OE2 A:GLU56 3.7 11.3 0.6
OE2 A:GLU56 3.8 12.8 0.4
C A:GLY36 3.9 6.3 1.0
HG3 A:GLU56 3.9 11.6 0.6
PA A:6U4201 4.0 8.5 1.0
HA2 A:GLY37 4.0 7.2 1.0
O3A A:6U4201 4.0 8.1 1.0
HA3 A:GLY37 4.1 7.2 1.0
H A:GLY36 4.1 7.6 1.0
O A:HOH319 4.1 12.1 1.0
O5' A:6U4201 4.2 8.1 1.0
CD A:GLU56 4.2 13.2 0.4
OE1 A:GLU56 4.2 13.9 0.4
O A:HOH313 4.2 15.4 1.0
CG A:GLU56 4.2 9.7 0.6
HG3 A:GLU56 4.3 16.5 0.1
PB A:6U4201 4.3 8.4 1.0
CA A:GLY37 4.4 6.0 1.0
CG A:GLU56 4.4 13.7 0.1
O A:HOH308 4.5 27.6 1.0
C4' A:6U4201 4.5 7.2 1.0
O A:HOH493 4.6 27.7 0.5
N A:GLY37 4.6 6.3 1.0
O A:HOH493 4.7 17.5 0.5
C5' A:6U4201 4.7 7.9 1.0
HZ1 A:LYS23 4.7 27.5 0.3
HG2 A:GLU56 4.8 11.6 0.6
O A:HOH398 4.8 19.2 1.0
OE1 A:GLU52 4.8 11.4 1.0
HB2 A:GLU56 4.9 16.6 0.4
N A:GLY36 4.9 6.3 1.0
O A:HOH327 4.9 37.6 1.0
HG2 A:GLU56 4.9 16.5 0.1
O A:HOH310 5.0 16.0 1.0
O A:HOH520 5.0 41.4 1.0
HG3 A:GLU56 5.0 16.0 0.4

Sodium binding site 3 out of 5 in 5ws7

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Sodium binding site 3 out of 5 in the Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp


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/C87A/C104S Mutant) in Complex with 2-Oxo-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:11.5
occ:1.00
 O A:HOH405 2.3 12.0 1.0
O A:HOH336 2.4 16.8 1.0
O A:HOH311 2.4 21.0 1.0
O2B A:6U4201 2.4 8.7 1.0
OE2 A:GLU52 2.4 11.0 1.0
O A:HOH313 2.5 15.4 1.0
CD A:GLU52 3.4 10.8 1.0
H A:LYS38 3.4 7.3 1.0
HH12 A:ARG51 3.4 14.4 1.0
PB A:6U4201 3.5 8.4 1.0
HE21 A:GLN40 3.6 16.9 1.0
OE1 A:GLU52 3.6 11.4 1.0
O1B A:6U4201 3.8 10.0 1.0
O A:HOH503 3.9 35.8 1.0
HA3 A:GLY37 3.9 7.2 1.0
HB2 A:LYS38 3.9 7.8 1.0
N A:LYS38 4.1 6.1 1.0
HH22 A:ARG51 4.1 14.2 1.0
O2G A:6U4201 4.1 12.9 1.0
O A:LYS38 4.2 8.4 1.0
NH1 A:ARG51 4.3 12.0 1.0
NE2 A:GLN40 4.3 14.1 1.0
OE1 A:GLU55 4.4 18.9 1.0
O A:HOH411 4.4 23.4 1.0
O3B A:6U4201 4.4 9.7 1.0
O A:HOH546 4.4 21.8 1.0
HE22 A:GLN40 4.5 16.9 1.0
O A:HOH310 4.6 16.0 1.0
CA A:GLY37 4.7 6.0 1.0
HH11 A:ARG51 4.7 14.4 1.0
CB A:LYS38 4.7 6.5 1.0
O3A A:6U4201 4.7 8.1 1.0
CG A:GLU52 4.8 10.3 1.0
C A:GLY37 4.8 5.9 1.0
CA A:LYS38 4.8 6.0 1.0
NH2 A:ARG51 4.8 11.8 1.0
PG A:6U4201 4.9 10.4 1.0
HG2 A:GLU52 4.9 12.4 1.0
C A:LYS38 4.9 6.3 1.0
HD2 A:LYS38 5.0 9.1 1.0

Sodium binding site 4 out of 5 in 5ws7

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Sodium binding site 4 out of 5 in the Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp


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/C87A/C104S Mutant) in Complex with 2-Oxo-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1002

b:22.9
occ:1.00
 OE2 B:GLU56 2.2 15.8 0.6
O2B B:6U41001 2.3 25.8 1.0
O1A B:6U41001 2.3 17.1 1.0
O B:HOH1139 2.4 17.8 1.0
O B:GLY36 2.4 9.8 1.0
O B:HOH1229 2.5 42.6 1.0
O B:HOH1105 3.1 18.6 1.0
CD B:GLU56 3.2 15.6 0.6
PA B:6U41001 3.4 17.2 1.0
PB B:6U41001 3.5 25.1 1.0
O3A B:6U41001 3.6 20.9 1.0
OE1 B:GLU56 3.6 15.6 0.6
C B:GLY36 3.6 7.9 1.0
HZ1 B:LYS23 3.6 21.4 0.5
HE3 B:LYS23 3.6 21.4 0.5
HA3 B:GLY37 3.6 8.7 1.0
HA2 B:GLY37 3.7 8.7 1.0
HZ3 B:LYS23 3.7 21.4 0.5
O B:HOH1116 3.9 54.9 1.0
O5' B:6U41001 4.0 13.8 1.0
H B:GLY36 4.0 9.1 1.0
NZ B:LYS23 4.0 17.8 0.5
CA B:GLY37 4.0 7.2 1.0
OE2 B:GLU56 4.0 17.7 0.4
O B:HOH1207 4.1 36.0 1.0
OE1 B:GLU56 4.2 18.4 0.4
OE1 B:GLU52 4.2 17.3 1.0
CD B:GLU56 4.3 17.9 0.4
N B:GLY37 4.3 7.4 1.0
CE B:LYS23 4.3 17.9 0.5
O B:HOH1155 4.4 15.4 1.0
HE3 B:LYS23 4.5 29.7 0.5
O3B B:6U41001 4.5 33.5 1.0
CG B:GLU56 4.5 15.6 0.6
C4' B:6U41001 4.6 9.6 1.0
O1B B:6U41001 4.6 23.8 1.0
O3G B:6U41001 4.7 44.0 1.0
N B:GLY36 4.7 7.5 1.0
HG2 B:GLU56 4.7 18.7 0.6
HG3 B:GLU56 4.8 18.7 0.6
CA B:GLY36 4.8 7.6 1.0
O2A B:6U41001 4.8 18.1 1.0
C5' B:6U41001 4.8 11.1 1.0
HZ2 B:LYS23 4.9 21.4 0.5
HE2 B:LYS23 5.0 21.4 0.5

Sodium binding site 5 out of 5 in 5ws7

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Sodium binding site 5 out of 5 in the Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp


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/C87A/C104S Mutant) in Complex with 2-Oxo-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1003

b:33.1
occ:1.00
 O B:HOH1294 2.4 29.5 1.0
OE2 B:GLU52 2.5 17.6 1.0
O1B B:6U41001 2.6 23.8 1.0
O B:HOH1148 2.8 16.9 1.0
O B:HOH1105 2.8 18.6 1.0
O B:HOH1107 3.0 42.4 1.0
O2B B:6U41001 3.2 25.8 1.0
PB B:6U41001 3.3 25.1 1.0
CD B:GLU52 3.3 16.0 1.0
OE1 B:GLU52 3.4 17.3 1.0
HA3 B:GLY37 3.4 8.7 1.0
HH12 B:ARG51 3.4 18.7 1.0
O B:HOH1207 3.5 36.0 1.0
O B:HOH1146 3.5 36.5 1.0
O B:HOH1286 3.6 51.6 1.0
H B:LYS38 3.6 10.0 0.5
H B:LYS38 3.6 8.4 0.5
O1G B:6U41001 3.8 44.0 1.0
N B:LYS38 4.2 8.3 0.5
N B:LYS38 4.2 7.0 0.5
HZ3 B:LYS38 4.2 16.4 0.5
NH1 B:ARG51 4.3 15.6 1.0
HB2 B:LYS38 4.3 14.5 0.5
HB2 B:LYS38 4.3 9.3 0.5
CA B:GLY37 4.4 7.2 1.0
HE21 B:GLN40 4.4 17.9 0.5
O3B B:6U41001 4.4 33.5 1.0
HH22 B:ARG51 4.5 15.6 1.0
O B:LYS38 4.5 9.6 0.5
HZ1 B:LYS38 4.5 16.4 0.5
O3A B:6U41001 4.6 20.9 1.0
HH11 B:ARG51 4.6 18.7 1.0
O B:LYS38 4.7 7.9 0.5
HE2 B:LYS38 4.7 14.8 0.5
C B:GLY37 4.7 7.2 1.0
CG B:GLU52 4.8 14.0 1.0
NZ B:LYS38 4.8 13.7 0.5
PG B:6U41001 4.8 41.6 1.0
OE1 B:GLU55 4.8 18.7 0.4
HA2 B:GLY37 4.8 8.7 1.0
HG3 B:LYS38 4.9 9.8 0.5
HG2 B:GLU52 5.0 16.8 1.0

Reference:

S.Waz, T.Nakamura, K.Hirata, Y.Koga-Ogawa, M.Chirifu, T.Arimori, T.Tamada, S.Ikemizu, Y.Nakabeppu, Y.Yamagata. Structural and Kinetic Studies of the Human Nudix Hydrolase MTH1 Reveal the Mechanism For Its Broad Substrate Specificity J. Biol. Chem. V. 292 2785 2017.
ISSN: ESSN 1083-351X
PubMed: 28035004
DOI: 10.1074/JBC.M116.749713
Page generated: Tue Oct 8 01:06:14 2024

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