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Sodium in PDB 8i19: Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp at pH 8.0

Enzymatic activity of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp at pH 8.0

All present enzymatic activity of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp at pH 8.0:
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 8.0, PDB code: 8i19 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) 36.63 / 1.48
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.498, 47.993, 123.489, 90, 90, 90
R / Rfree (%) 15.1 / 19

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 8.0 (pdb code 8i19). 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 8-Oxo-Dgtp at pH 8.0, PDB code: 8i19:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 8i19

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Sodium binding site 1 out of 5 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp at pH 8.0


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

b:13.6
occ:1.00
 OE2 A:GLU56 2.3 12.8 1.0
O1A A:8DG201 2.3 14.4 1.0
O2B A:8DG201 2.3 14.9 1.0
O A:GLY36 2.3 9.7 1.0
O A:HOH380 2.4 14.2 1.0
O A:HOH363 2.7 30.2 1.0
NA A:NA203 3.2 17.6 1.0
CD A:GLU56 3.2 12.1 1.0
PA A:8DG201 3.4 13.8 1.0
PB A:8DG201 3.5 14.7 1.0
OE1 A:GLU56 3.5 14.4 1.0
C A:GLY36 3.5 7.4 1.0
O3A A:8DG201 3.5 12.5 1.0
NZ A:LYS23 3.8 15.8 1.0
CE A:LYS23 4.0 15.7 1.0
CA A:GLY37 4.1 7.9 1.0
O5' A:8DG201 4.1 17.1 1.0
N A:GLY37 4.3 7.7 1.0
OE1 A:GLU52 4.3 13.6 1.0
O3B A:8DG201 4.4 20.5 1.0
O A:HOH355 4.4 14.1 1.0
O A:HOH306 4.5 21.2 1.0
N A:GLY36 4.5 7.5 1.0
CG A:GLU56 4.6 12.7 1.0
CA A:GLY36 4.7 7.1 1.0
O1B A:8DG201 4.7 11.8 1.0
CG A:GLU100 4.7 22.7 1.0
C4' A:8DG201 4.7 11.2 1.0
O2A A:8DG201 4.7 16.0 1.0
O1G A:8DG201 4.8 27.4 1.0
C5' A:8DG201 4.9 13.2 1.0

Sodium binding site 2 out of 5 in 8i19

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Sodium binding site 2 out of 5 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp at pH 8.0


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

b:17.6
occ:1.00
 O A:HOH306 2.4 21.2 1.0
O2B A:8DG201 2.4 14.9 1.0
OE1 A:GLU52 2.4 13.6 1.0
OE2 A:GLU56 2.4 12.8 1.0
O A:HOH312 2.5 23.7 1.0
O A:HOH319 2.9 18.5 1.0
NA A:NA202 3.2 13.6 1.0
CD A:GLU56 3.3 12.1 1.0
O A:HOH472 3.3 14.7 1.0
CD A:GLU52 3.3 15.1 1.0
OE2 A:GLU52 3.6 16.1 1.0
PB A:8DG201 3.7 14.7 1.0
CG A:GLU56 3.7 12.7 1.0
O A:GLY36 3.8 9.7 1.0
O A:HOH363 3.9 30.2 1.0
O1G A:8DG201 4.1 27.4 1.0
O1B A:8DG201 4.1 11.8 1.0
OE2 A:GLU100 4.2 26.1 1.0
CG A:GLU100 4.4 22.7 1.0
OE1 A:GLU56 4.4 14.4 1.0
CA A:GLY37 4.4 7.9 1.0
C A:GLY36 4.4 7.4 1.0
CD A:GLU100 4.5 24.5 1.0
CG A:GLU52 4.7 13.7 1.0
O3B A:8DG201 4.7 20.5 1.0
O3A A:8DG201 4.8 12.5 1.0
N A:GLY37 4.8 7.7 1.0
OE1 A:GLU55 4.8 23.4 1.0
O A:HOH412 4.9 29.8 1.0
O A:HOH428 5.0 34.5 1.0

Sodium binding site 3 out of 5 in 8i19

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Sodium binding site 3 out of 5 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp at pH 8.0


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

b:25.2
occ:1.00
 O A:PHE113 2.2 10.5 1.0
O A:HOH374 2.6 11.8 1.0
O A:MET116 2.8 9.8 1.0
C A:PHE113 3.3 8.5 1.0
C A:MET116 3.8 7.5 1.0
CA A:LYS114 3.8 12.7 1.0
C A:LYS114 3.9 11.8 1.0
O A:LYS114 4.0 12.8 1.0
N A:MET116 4.0 8.0 1.0
N A:LYS114 4.0 11.0 1.0
O A:TRP117 4.1 8.2 1.0
CA A:PRO118 4.1 10.9 1.0
C A:TRP117 4.2 8.1 1.0
N A:PRO118 4.3 7.6 1.0
CA A:MET116 4.4 6.1 1.0
CA A:PHE113 4.4 6.7 1.0
N A:ASP115 4.5 9.4 1.0
OG A:SER121 4.6 15.1 1.0
CB A:MET116 4.7 8.0 1.0
CB A:PHE113 4.7 7.3 1.0
N A:TRP117 4.8 6.8 1.0
CD A:PRO118 4.9 8.4 1.0
CB A:PRO118 5.0 12.2 1.0

Sodium binding site 4 out of 5 in 8i19

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Sodium binding site 4 out of 5 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp at pH 8.0


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

b:13.5
occ:1.00
 O B:HOH390 2.3 17.6 1.0
OD1 B:ASP120 2.3 11.4 1.0
O6 B:8DG201 2.3 24.5 1.0
OD2 B:ASP119 2.4 12.3 1.0
OD1 B:ASP119 3.0 12.3 1.0
CG B:ASP119 3.0 12.5 1.0
C6 B:8DG201 3.2 30.6 1.0
N1 B:8DG201 3.3 17.4 1.0
CG B:ASP120 3.3 9.3 1.0
CB B:TRP117 3.6 10.6 0.5
CB B:TRP117 3.6 11.2 0.5
OD2 B:ASP120 3.8 11.0 1.0
CZ B:PHE72 3.9 15.5 1.0
O B:HOH326 4.0 35.5 1.0
CD1 B:TRP117 4.1 11.9 0.5
CG B:TRP117 4.1 12.1 0.5
O B:HOH356 4.1 9.4 1.0
CZ2 B:TRP123 4.2 8.9 1.0
NE1 B:TRP123 4.2 8.2 1.0
CG B:TRP117 4.3 13.3 0.5
N B:ASP120 4.4 8.9 1.0
CB B:ASP119 4.5 11.4 1.0
CE1 B:PHE72 4.6 16.1 1.0
C5 B:8DG201 4.6 20.5 1.0
CE2 B:TRP123 4.6 8.8 1.0
C2 B:8DG201 4.6 23.8 1.0
CB B:ASP120 4.6 8.8 1.0
CD1 B:TRP117 4.7 15.1 0.5
CE2 B:PHE72 4.7 15.8 1.0
OD1 B:ASN33 4.7 14.0 1.0
CA B:ASP120 4.8 8.8 1.0
CA B:TRP117 4.8 9.9 0.5
CA B:TRP117 4.8 10.1 0.5
CD1 B:ILE70 4.9 6.5 0.4
C B:ASP119 5.0 9.5 1.0
O B:TRP117 5.0 10.4 0.5

Sodium binding site 5 out of 5 in 8i19

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Sodium binding site 5 out of 5 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp at pH 8.0


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

b:38.1
occ:1.00
 OE2 B:GLU56 2.3 16.0 1.0
O B:GLY36 2.4 12.1 1.0
O B:HOH445 2.5 33.2 1.0
O B:HOH347 2.8 22.2 0.5
OE1 B:GLU52 3.0 26.1 1.0
O B:HOH324 3.2 32.1 1.0
CD B:GLU56 3.2 15.8 1.0
C B:GLY36 3.5 10.2 1.0
CA B:GLY37 3.7 9.9 1.0
CD B:GLU52 3.8 25.5 1.0
OE1 B:GLU56 3.9 16.6 1.0
O B:HOH347 4.0 22.8 0.5
O B:HOH384 4.0 13.5 0.6
N B:GLY37 4.1 9.7 1.0
OE2 B:GLU52 4.1 29.1 1.0
CG B:GLU56 4.1 14.0 1.0
O B:HOH384 4.2 23.2 0.5
O B:HOH481 4.3 41.0 1.0
CA B:GLY36 4.7 10.6 1.0
O3G B:8DG201 4.7 75.2 1.0
N B:GLY36 4.8 10.3 1.0
O3B B:8DG201 4.8 99.4 1.0
CG B:GLU52 4.9 23.2 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 12:19:20 2024

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