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Sodium in PDB 8i1a: Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp at pH 8.6

Enzymatic activity of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp at pH 8.6

All present enzymatic activity of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp 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 8-Oxo-Dgtp at pH 8.6, PDB code: 8i1a 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) 31.35 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.783, 48.104, 123.988, 90, 90, 90
R / Rfree (%) 15 / 19.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp at pH 8.6 (pdb code 8i1a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp at pH 8.6, PDB code: 8i1a:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 8i1a

Go back to Sodium Binding Sites List in 8i1a
Sodium binding site 1 out of 6 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp 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 8-Oxo-Dgtp at pH 8.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:7.8
occ:0.60
 N1 A:8DG201 0.6 47.7 0.4
C6 A:8DG201 1.7 8.6 0.4
C2 A:8DG201 1.7 35.1 0.4
O6 A:8DG201 2.3 8.9 0.4
O A:HOH314 2.3 7.5 0.3
OD1 A:ASP120 2.4 10.4 1.0
O A:HOH458 2.4 20.5 0.6
N2 A:8DG201 2.4 31.6 0.4
O A:HOH386 2.4 14.5 0.6
OD2 A:ASP119 2.5 12.1 1.0
O A:HOH314 2.5 11.5 0.3
N3 A:8DG201 2.8 18.1 0.4
C5 A:8DG201 2.9 10.7 0.4
OD1 A:ASP119 3.1 10.8 1.0
CG A:ASP119 3.2 11.6 1.0
C4 A:8DG201 3.3 36.5 0.4
CG A:ASP120 3.5 9.6 1.0
CB A:TRP117 3.6 11.3 1.0
O A:HOH465 3.8 19.4 0.6
OD2 A:ASP120 3.9 12.2 1.0
CZ A:PHE72 3.9 9.9 1.0
NE1 A:TRP123 4.1 8.1 1.0
CZ2 A:TRP123 4.1 9.3 1.0
CG A:TRP117 4.1 13.8 1.0
N7 A:8DG201 4.2 16.1 0.4
O A:HOH325 4.2 10.3 1.0
O A:HOH457 4.4 30.2 0.6
CE2 A:PHE72 4.4 8.7 1.0
CE2 A:TRP123 4.5 7.7 1.0
N A:ASP120 4.5 8.0 1.0
N9 A:8DG201 4.6 30.5 0.4
CB A:ASP119 4.6 10.9 1.0
CD1 A:TRP117 4.6 16.2 1.0
CB A:ASP120 4.7 8.6 1.0
CE1 A:PHE72 4.8 9.5 1.0
OD1 A:ASN33 4.8 19.8 1.0
CA A:TRP117 4.8 9.6 1.0
CA A:ASP120 4.9 9.2 1.0
C8 A:8DG201 4.9 32.6 0.4
CD2 A:TRP117 4.9 13.7 1.0

Sodium binding site 2 out of 6 in 8i1a

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Sodium binding site 2 out of 6 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp 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 8-Oxo-Dgtp at pH 8.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:26.2
occ:1.00
 OE2 A:GLU56 2.2 25.4 1.0
O1A A:8DG201 2.3 18.2 0.4
O A:HOH456 2.3 23.1 0.6
O2B A:8DG201 2.3 82.4 0.4
O A:GLY36 2.4 11.8 1.0
O A:HOH346 2.4 31.4 1.0
NA A:NA205 3.1 60.4 1.0
CD A:GLU56 3.2 22.3 1.0
PA A:8DG201 3.4 18.4 0.4
O A:HOH324 3.4 53.0 1.0
NZ A:LYS23 3.5 42.9 1.0
PB A:8DG201 3.5 41.9 0.4
OE1 A:GLU56 3.6 19.5 1.0
C A:GLY36 3.6 9.6 1.0
O3A A:8DG201 3.6 27.7 0.4
CA A:GLY37 4.1 8.3 1.0
O5' A:8DG201 4.1 16.0 0.4
N A:GLY37 4.3 9.2 1.0
OE1 A:GLU52 4.3 21.7 1.0
O1B A:8DG201 4.3 39.7 0.4
O A:HOH336 4.4 25.1 1.0
O A:HOH301 4.4 67.9 1.0
CG A:GLU56 4.5 21.3 1.0
N A:GLY36 4.6 9.5 1.0
CE A:LYS23 4.6 41.2 1.0
C4' A:8DG201 4.6 16.5 0.4
C5' A:8DG201 4.7 19.4 0.4
CA A:GLY36 4.7 11.0 1.0
O A:HOH415 4.7 38.0 0.6
O3B A:8DG201 4.8 54.9 0.4
O2A A:8DG201 4.8 16.7 0.4
O1G A:8DG201 4.8 35.2 0.4

Sodium binding site 3 out of 6 in 8i1a

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Sodium binding site 3 out of 6 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp 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 8-Oxo-Dgtp at pH 8.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:23.0
occ:1.00
 O A:PHE113 2.1 15.2 1.0
O A:HOH376 2.6 13.1 1.0
O A:MET116 2.9 12.1 1.0
C A:PHE113 3.2 12.6 1.0
CA A:LYS114 3.8 18.0 1.0
C A:LYS114 3.9 14.7 1.0
C A:MET116 3.9 9.5 1.0
O A:LYS114 3.9 17.9 1.0
N A:LYS114 3.9 15.1 1.0
N A:MET116 4.1 8.5 1.0
O A:TRP117 4.2 9.3 1.0
CA A:PHE113 4.3 9.9 1.0
CA A:PRO118 4.4 10.7 1.0
C A:TRP117 4.4 9.1 1.0
OG A:SER121 4.4 17.7 1.0
CA A:MET116 4.5 8.2 1.0
N A:ASP115 4.5 11.4 1.0
N A:PRO118 4.5 9.2 1.0
CB A:PHE113 4.6 10.9 1.0
CB A:MET116 4.8 8.8 1.0
N A:TRP117 5.0 8.9 1.0
O A:HOH462 5.0 24.9 1.0

Sodium binding site 4 out of 6 in 8i1a

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Sodium binding site 4 out of 6 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp 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 8-Oxo-Dgtp at pH 8.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:60.4
occ:1.00
 O A:HOH456 2.4 23.1 0.6
O A:HOH301 2.4 67.9 1.0
OE1 A:GLU52 2.5 21.7 1.0
OE2 A:GLU56 2.5 25.4 1.0
O A:HOH310 2.6 32.4 1.0
O2B A:8DG201 3.0 82.4 0.4
O A:HOH311 3.0 31.6 1.0
NA A:NA203 3.1 26.2 1.0
CD A:GLU56 3.3 22.3 1.0
O A:HOH471 3.4 35.3 1.0
CD A:GLU52 3.5 22.3 1.0
CG A:GLU56 3.5 21.3 1.0
O A:GLY36 3.7 11.8 1.0
OE2 A:GLU52 3.8 24.2 1.0
PB A:8DG201 3.9 41.9 0.4
O1B A:8DG201 3.9 39.7 0.4
O1G A:8DG201 4.0 35.2 0.4
O A:HOH324 4.3 53.0 1.0
OE1 A:GLU56 4.4 19.5 1.0
O A:HOH415 4.4 38.0 0.6
C A:GLY36 4.5 9.6 1.0
CA A:GLY37 4.6 8.3 1.0
CG A:GLU52 4.8 18.3 1.0
N A:GLY37 5.0 9.2 1.0
O1A A:8DG201 5.0 18.2 0.4
CB A:GLU56 5.0 20.2 1.0

Sodium binding site 5 out of 6 in 8i1a

Go back to Sodium Binding Sites List in 8i1a
Sodium binding site 5 out of 6 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp 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 8-Oxo-Dgtp at pH 8.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:11.1
occ:1.00
 OD1 B:ASP120 2.3 11.6 1.0
OD2 B:ASP119 2.4 11.3 1.0
O B:HOH359 2.4 18.9 1.0
O6 B:8DG201 2.4 70.7 1.0
OD1 B:ASP119 2.9 11.8 1.0
CG B:ASP119 3.0 12.0 1.0
C6 B:8DG201 3.2 37.1 1.0
N1 B:8DG201 3.3 18.6 1.0
CG B:ASP120 3.4 10.2 1.0
CB B:TRP117 3.6 12.6 0.5
CB B:TRP117 3.6 11.9 0.5
OD2 B:ASP120 3.9 10.7 1.0
CZ B:PHE72 3.9 8.2 0.4
CZ B:PHE72 4.0 7.8 0.6
CG B:TRP117 4.1 13.1 0.5
O B:HOH333 4.2 10.1 1.0
NE1 B:TRP123 4.2 8.1 1.0
O B:HOH321 4.2 28.1 1.0
CZ2 B:TRP123 4.2 8.8 1.0
CD1 B:TRP117 4.2 12.7 0.5
CG B:TRP117 4.3 12.7 0.5
N B:ASP120 4.4 9.6 1.0
CB B:ASP119 4.4 11.9 1.0
CE2 B:PHE72 4.5 8.2 0.6
CE2 B:TRP123 4.6 8.1 1.0
C2 B:8DG201 4.6 69.5 1.0
CB B:ASP120 4.6 9.3 1.0
C5 B:8DG201 4.7 44.7 1.0
CE2 B:PHE72 4.7 8.4 0.4
CE1 B:PHE72 4.7 9.3 0.4
OD1 B:ASN33 4.8 13.8 1.0
CA B:TRP117 4.8 11.4 0.5
CD1 B:TRP117 4.8 13.4 0.5
CA B:ASP120 4.8 9.1 1.0
CA B:TRP117 4.8 10.7 0.5
CE1 B:PHE72 4.8 6.2 0.6
O B:TRP117 4.9 11.6 0.5
C B:ASP119 5.0 9.8 1.0
O B:TRP117 5.0 10.3 0.5
C B:TRP117 5.0 12.6 0.5

Sodium binding site 6 out of 6 in 8i1a

Go back to Sodium Binding Sites List in 8i1a
Sodium binding site 6 out of 6 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp 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 8-Oxo-Dgtp at pH 8.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:34.6
occ:1.00
 OE2 B:GLU56 2.4 21.6 1.0
O B:GLY36 2.4 12.4 1.0
O B:HOH448 2.5 35.2 1.0
OE1 B:GLU52 2.7 26.5 1.0
CD B:GLU56 3.2 17.8 1.0
O B:HOH469 3.3 40.6 1.0
O B:HOH323 3.4 29.4 1.0
O B:HOH316 3.5 34.5 1.0
C B:GLY36 3.5 10.7 1.0
CD B:GLU52 3.6 26.1 1.0
CA B:GLY37 3.8 10.1 1.0
CG B:GLU56 4.0 18.0 1.0
OE2 B:GLU52 4.0 29.1 1.0
OE1 B:GLU56 4.0 18.1 1.0
N B:GLY37 4.1 10.1 1.0
O B:HOH402 4.1 22.0 1.0
O3G B:8DG201 4.5 87.2 1.0
CA B:GLY36 4.7 10.7 1.0
CG B:GLU52 4.7 22.0 1.0
N B:GLY36 4.8 11.0 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 12:19:30 2024

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