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Sodium in PDB 6ijy: Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp Determined Using A Crystal Obtained Under Microgravity

Enzymatic activity of Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp Determined Using A Crystal Obtained Under Microgravity

All present enzymatic activity of Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp Determined Using A Crystal Obtained Under Microgravity:
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 8-Oxo-Dgtp Determined Using A Crystal Obtained Under Microgravity, PDB code: 6ijy 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) 38.00 / 1.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.492, 48.099, 123.936, 90.00, 90.00, 90.00
R / Rfree (%) 13.3 / 15.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp Determined Using A Crystal Obtained Under Microgravity (pdb code 6ijy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp Determined Using A Crystal Obtained Under Microgravity, PDB code: 6ijy:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6ijy

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Sodium binding site 1 out of 4 in the Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp Determined Using A Crystal Obtained Under Microgravity


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 8-Oxo-Dgtp Determined Using A Crystal Obtained Under Microgravity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:11.4
occ:0.78
 O A:GLY36 2.3 11.6 1.0
O2A A:8DG201 2.3 13.6 1.0
OE2 A:GLU56 2.3 15.4 1.0
O A:HOH395 2.3 13.0 1.0
O1B A:8DG201 2.4 14.2 1.0
CD A:GLU56 3.2 13.2 1.0
NA A:NA204 3.3 15.3 0.7
HE3 A:LYS23 3.3 17.6 1.0
HZ1 A:LYS23 3.4 15.8 1.0
PA A:8DG201 3.4 12.2 1.0
PB A:8DG201 3.5 13.2 1.0
C A:GLY36 3.5 9.4 1.0
OE1 A:GLU56 3.5 14.9 1.0
O3A A:8DG201 3.5 13.1 1.0
HZ2 A:LYS23 3.6 15.8 1.0
HA3 A:GLY37 3.6 11.4 1.0
HA2 A:GLY37 3.7 11.4 1.0
NZ A:LYS23 3.8 13.2 1.0
H A:GLY36 3.8 10.6 1.0
HG2 A:GLU100 4.0 28.1 1.0
CA A:GLY37 4.0 9.5 1.0
CE A:LYS23 4.0 14.6 1.0
O5' A:8DG201 4.1 11.7 1.0
N A:GLY37 4.2 9.4 1.0
OE1 A:GLU52 4.2 18.1 1.0
O3B A:8DG201 4.3 16.2 1.0
O A:HOH363 4.4 11.3 1.0
HB3 A:GLU100 4.5 21.0 1.0
N A:GLY36 4.5 8.8 1.0
O A:HOH314 4.6 24.2 1.0
CG A:GLU56 4.6 13.0 1.0
CA A:GLY36 4.6 9.4 1.0
HZ3 A:LYS23 4.7 15.8 1.0
O2B A:8DG201 4.7 13.2 1.0
O1A A:8DG201 4.7 13.4 1.0
HE2 A:LYS23 4.7 17.6 1.0
C4' A:8DG201 4.7 9.9 1.0
HD3 A:LYS23 4.7 13.9 1.0
HG2 A:GLU56 4.8 15.6 1.0
HG3 A:GLU56 4.9 15.6 1.0
C5' A:8DG201 4.9 11.3 1.0
CG A:GLU100 4.9 23.4 1.0
O3' A:8DG201 5.0 10.1 1.0

Sodium binding site 2 out of 4 in 6ijy

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Sodium binding site 2 out of 4 in the Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp Determined Using A Crystal Obtained Under Microgravity


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 8-Oxo-Dgtp Determined Using A Crystal Obtained Under Microgravity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:24.8
occ:0.62
 O A:PHE113 2.2 11.9 1.0
O A:HOH388 2.7 13.1 1.0
O A:MET116 2.7 10.9 1.0
HA A:PRO118 3.2 12.7 1.0
HA A:LYS114 3.2 16.9 1.0
H A:MET116 3.2 10.0 1.0
C A:PHE113 3.3 9.9 1.0
C A:MET116 3.7 8.9 1.0
CA A:LYS114 3.8 14.1 1.0
C A:LYS114 3.8 11.9 1.0
O A:LYS114 3.9 14.6 1.0
HB2 A:MET116 4.0 10.3 1.0
N A:MET116 4.0 8.3 1.0
N A:LYS114 4.0 11.4 1.0
CA A:PRO118 4.0 10.6 1.0
HB3 A:PHE113 4.1 11.0 1.0
O A:TRP117 4.1 8.7 1.0
C A:TRP117 4.1 8.5 1.0
N A:PRO118 4.2 9.2 1.0
CA A:MET116 4.3 8.2 1.0
HA A:PHE113 4.4 10.8 1.0
CA A:PHE113 4.4 9.0 1.0
HG3 A:PRO118 4.4 18.5 1.0
N A:ASP115 4.4 9.4 1.0
HD3 A:PRO118 4.6 13.3 1.0
OG A:SER121 4.6 15.6 0.8
CB A:MET116 4.6 8.6 1.0
H A:ASP115 4.7 11.3 1.0
CB A:PHE113 4.7 9.1 1.0
N A:TRP117 4.8 8.6 1.0
HB3 A:PRO118 4.8 16.7 1.0
HG A:SER121 4.8 18.7 0.8
CD A:PRO118 4.8 11.1 1.0
CB A:PRO118 4.9 13.9 1.0
H A:LYS114 4.9 13.6 1.0
CG A:PRO118 4.9 15.4 1.0
HB3 A:SER121 5.0 15.5 0.2
CA A:TRP117 5.0 9.1 1.0

Sodium binding site 3 out of 4 in 6ijy

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Sodium binding site 3 out of 4 in the Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp Determined Using A Crystal Obtained Under Microgravity


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 8-Oxo-Dgtp Determined Using A Crystal Obtained Under Microgravity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:15.3
occ:0.74
 OE1 A:GLU52 2.3 18.1 1.0
O A:HOH314 2.4 24.2 1.0
O1B A:8DG201 2.4 14.2 1.0
OE2 A:GLU56 2.4 15.4 1.0
O A:HOH303 2.5 29.1 1.0
O A:HOH311 2.9 18.3 1.0
CD A:GLU52 3.2 16.4 1.0
NA A:NA202 3.3 11.4 0.8
O A:HOH452 3.3 20.9 1.0
CD A:GLU56 3.4 13.2 1.0
OE2 A:GLU52 3.5 21.1 1.0
HG3 A:GLU56 3.5 15.6 1.0
HA3 A:GLY37 3.5 11.4 1.0
HG2 A:GLU100 3.6 28.1 1.0
HG2 A:GLU56 3.6 15.6 1.0
PB A:8DG201 3.7 13.2 1.0
CG A:GLU56 3.8 13.0 1.0
O A:GLY36 3.8 11.6 1.0
O2B A:8DG201 4.0 13.2 1.0
O2G A:8DG201 4.3 24.9 1.0
OE2 A:GLU100 4.3 29.6 1.0
CA A:GLY37 4.4 9.5 1.0
OE1 A:GLU56 4.4 14.9 1.0
HB3 A:GLU52 4.4 16.5 1.0
C A:GLY36 4.5 9.4 1.0
CG A:GLU100 4.5 23.4 1.0
OE1 A:GLU55 4.6 27.7 1.0
CG A:GLU52 4.6 15.4 1.0
CD A:GLU100 4.6 26.6 1.0
HA A:GLU52 4.7 15.7 1.0
O3B A:8DG201 4.7 16.2 1.0
HA2 A:GLY37 4.8 11.4 1.0
O3A A:8DG201 4.8 13.1 1.0
N A:GLY37 4.8 9.4 1.0
HH12 A:ARG51 4.8 24.6 1.0
O A:HOH390 4.9 38.4 1.0
HB2 A:GLU55 4.9 19.1 1.0
CB A:GLU52 5.0 13.8 1.0

Sodium binding site 4 out of 4 in 6ijy

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Sodium binding site 4 out of 4 in the Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp Determined Using A Crystal Obtained Under Microgravity


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 8-Oxo-Dgtp Determined Using A Crystal Obtained Under Microgravity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:13.4
occ:0.32
 N1 B:8DG201 0.7 22.8 0.4
C2 B:8DG201 1.4 21.2 0.4
N2 B:8DG201 1.9 22.1 0.4
C6 B:8DG201 2.0 23.0 0.4
O B:HOH343 2.1 13.0 0.5
OD1 B:ASP120 2.3 19.0 1.0
OD2 B:ASP119 2.4 14.6 1.0
O6 B:8DG201 2.4 22.0 0.6
N3 B:8DG201 2.6 20.2 0.4
O6 B:8DG201 2.8 25.6 0.4
HB2 B:TRP117 2.9 16.7 1.0
OD1 B:ASP119 3.0 15.0 1.0
CG B:ASP119 3.0 13.6 1.0
N1 B:8DG201 3.0 18.0 0.6
C5 B:8DG201 3.1 21.8 0.4
C6 B:8DG201 3.1 19.2 0.6
C4 B:8DG201 3.2 19.7 0.4
HZ B:PHE72 3.2 13.0 0.4
HZ2 B:TRP123 3.4 14.2 1.0
HE1 B:TRP123 3.4 12.7 1.0
CG B:ASP120 3.4 11.5 1.0
HZ B:PHE72 3.6 15.0 0.6
HB3 B:TRP117 3.6 16.7 1.0
CB B:TRP117 3.6 13.9 1.0
OD2 B:ASP120 3.8 14.6 1.0
CZ B:PHE72 4.0 10.8 0.4
HD21 B:ASN33 4.1 20.6 1.0
O B:HOH327 4.2 11.4 1.0
NE1 B:TRP123 4.2 10.6 1.0
CZ B:PHE72 4.2 12.5 0.6
H B:ASP120 4.2 12.8 1.0
CZ2 B:TRP123 4.2 11.8 1.0
CG B:TRP117 4.3 16.4 1.0
C2 B:8DG201 4.3 18.7 0.6
N7 B:8DG201 4.4 23.6 0.4
HD12 B:ILE70 4.4 18.0 0.4
HD1 B:TRP117 4.4 26.3 1.0
CB B:ASP119 4.4 13.2 1.0
HD11 B:ILE70 4.5 18.0 0.4
N B:ASP120 4.5 10.7 1.0
HD22 B:LEU9 4.5 16.8 1.0
OD1 B:ASN33 4.5 14.5 1.0
C5 B:8DG201 4.5 18.0 0.6
N9 B:8DG201 4.5 20.1 0.4
HE1 B:PHE72 4.6 15.1 0.6
HE2 B:PHE72 4.6 13.4 0.4
CE2 B:TRP123 4.6 10.1 1.0
CD1 B:TRP117 4.6 21.9 1.0
HA B:ASP120 4.7 11.8 1.0
HE1 B:PHE72 4.7 12.9 0.4
CE2 B:PHE72 4.7 11.2 0.4
ND2 B:ASN33 4.7 17.2 1.0
HB2 B:ASP119 4.7 15.9 1.0
H B:ASP119 4.7 15.9 1.0
CB B:ASP120 4.7 9.8 1.0
CE1 B:PHE72 4.7 12.6 0.6
HD21 B:LEU9 4.7 16.8 1.0
H B:TRP117 4.7 12.5 1.0
CE1 B:PHE72 4.8 10.8 0.4
CA B:TRP117 4.8 11.2 1.0
N2 B:8DG201 4.8 21.5 0.6
CA B:ASP120 4.9 9.8 1.0
CD1 B:ILE70 4.9 15.0 0.4
CG B:ASN33 4.9 14.0 1.0
O B:TRP117 5.0 11.7 1.0
CE2 B:PHE72 5.0 13.2 0.6
HE2 B:PHE72 5.0 15.8 0.6

Reference:

T.Nakamura, K.Hirata, K.Fujimiya, M.Chirifu, T.Arimori, T.Tamada, S.Ikemizu, Y.Yamagata. X-Ray Structure Analysis of Human Oxidized Nucleotide Hydrolase MTH1 Using Crystals Obtained Under Microgravity. Int. J. Microgravity Sci. V. 36 2019APPL..
ISSN: ISSN 2188-9783
DOI: 10.15011//JASMA.36.360103
Page generated: Tue Oct 8 09:37:57 2024

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