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Manganese in PDB 8i8s: Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgmp and MN2+

Enzymatic activity of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgmp and MN2+

All present enzymatic activity of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgmp and MN2+:
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-Dgmp and MN2+, PDB code: 8i8s 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) 33.24 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.408, 47.636, 123.681, 90, 90, 90
R / Rfree (%) 15.4 / 20.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgmp and MN2+ (pdb code 8i8s). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgmp and MN2+, PDB code: 8i8s:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 8i8s

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Manganese binding site 1 out of 6 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgmp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgmp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:13.3
occ:0.70
 OP3 A:8OG201 2.1 22.3 1.0
OE2 A:GLU56 2.1 18.3 1.0
O A:HOH420 2.1 23.1 1.0
O A:GLY36 2.2 15.2 1.0
O A:HOH366 2.2 15.3 1.0
O A:HOH441 2.3 23.8 1.0
MN A:MN204 3.0 17.2 0.3
CD A:GLU56 3.1 14.3 1.0
P A:8OG201 3.4 21.9 1.0
C A:GLY36 3.4 11.8 1.0
OE1 A:GLU56 3.5 14.4 1.0
OP2 A:8OG201 3.7 41.4 1.0
CA A:GLY37 4.0 12.7 1.0
NZ A:LYS23 4.0 20.1 1.0
OE1 A:GLU52 4.1 24.9 1.0
N A:GLY37 4.1 11.0 1.0
O A:HOH432 4.3 40.6 1.0
CE A:LYS23 4.3 19.4 1.0
O5' A:8OG201 4.3 19.4 1.0
O A:HOH365 4.4 12.9 1.0
OP1 A:8OG201 4.4 27.9 1.0
CG A:GLU56 4.4 13.2 1.0
N A:GLY36 4.4 10.2 1.0
CA A:GLY36 4.5 10.6 1.0
O A:HOH482 4.6 37.6 1.0
O A:HOH313 4.6 26.8 1.0
O A:HOH419 4.7 36.9 1.0
C4' A:8OG201 4.8 15.6 1.0
CD A:GLU52 5.0 20.3 1.0
O3' A:8OG201 5.0 12.8 1.0

Manganese binding site 2 out of 6 in 8i8s

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Manganese binding site 2 out of 6 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgmp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgmp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn203

b:18.3
occ:0.50
 O A:HOH482 2.1 37.6 1.0
O A:HOH330 2.2 29.5 1.0
O A:HOH357 2.2 30.3 1.0
OE2 A:GLU52 2.2 22.8 1.0
O A:HOH515 2.4 33.4 1.0
O A:HOH313 3.0 26.8 1.0
CD A:GLU52 3.2 20.3 1.0
OE1 A:GLU52 3.6 24.9 1.0
MN A:MN204 3.8 17.2 0.3
NH1 A:ARG51 3.8 23.2 1.0
O A:HOH420 3.9 23.1 1.0
O A:HOH502 4.2 30.8 1.0
NE2 A:GLN40 4.2 28.4 1.0
O A:LYS38 4.2 15.8 1.0
N A:LYS38 4.3 12.2 1.0
O A:HOH419 4.3 36.9 1.0
OE1 A:GLU55 4.3 27.4 1.0
CG A:GLU52 4.6 17.7 1.0
NH2 A:ARG51 4.6 20.0 1.0
CZ A:ARG51 4.7 20.6 1.0
CA A:GLY37 4.7 12.7 1.0
C A:GLY37 4.9 11.4 1.0
O A:HOH432 4.9 40.6 1.0
CB A:LYS38 4.9 12.2 1.0

Manganese binding site 3 out of 6 in 8i8s

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Manganese binding site 3 out of 6 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgmp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgmp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn204

b:17.2
occ:0.30
 O A:HOH419 1.9 36.9 1.0
O A:HOH420 2.0 23.1 1.0
OE1 A:GLU52 2.2 24.9 1.0
OE2 A:GLU56 2.3 18.3 1.0
O A:HOH482 2.5 37.6 1.0
MN A:MN202 3.0 13.3 0.7
CD A:GLU52 3.2 20.3 1.0
CD A:GLU56 3.2 14.3 1.0
O A:HOH441 3.6 23.8 1.0
CG A:GLU56 3.6 13.2 1.0
OE2 A:GLU52 3.6 22.8 1.0
O A:GLY36 3.7 15.2 1.0
MN A:MN203 3.8 18.3 0.5
O A:HOH357 4.2 30.3 1.0
O A:HOH313 4.2 26.8 1.0
OE1 A:GLU55 4.3 27.4 1.0
O A:HOH432 4.3 40.6 1.0
OE1 A:GLU56 4.3 14.4 1.0
C A:GLY36 4.5 11.8 1.0
CG A:GLU52 4.5 17.7 1.0
CA A:GLY37 4.6 12.7 1.0
CG A:GLU100 4.6 36.5 1.0
OP3 A:8OG201 4.7 22.3 1.0
CB A:GLU52 4.8 15.9 1.0
O A:HOH366 4.8 15.3 1.0
N A:GLY37 4.9 11.0 1.0

Manganese binding site 4 out of 6 in 8i8s

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Manganese binding site 4 out of 6 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgmp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgmp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn202

b:13.4
occ:0.40
 O B:HOH351 2.0 25.8 1.0
OE2 B:GLU56 2.0 21.0 1.0
O B:HOH373 2.1 21.2 1.0
O B:HOH394 2.2 31.4 1.0
O B:GLY36 2.3 16.6 1.0
OP2 B:8OG201 2.3 38.7 1.0
MN B:MN204 3.0 23.8 0.3
CD B:GLU56 3.1 18.6 1.0
P B:8OG201 3.3 26.6 1.0
OP1 B:8OG201 3.4 70.9 1.0
C B:GLY36 3.5 13.6 1.0
OE1 B:GLU56 3.5 17.2 1.0
OE1 B:GLU52 4.1 32.5 1.0
O5' B:8OG201 4.1 21.3 1.0
CA B:GLY37 4.1 12.8 1.0
N B:GLY37 4.3 13.1 1.0
CE B:LYS23 4.3 36.5 1.0
NZ B:LYS23 4.3 36.7 1.0
CG B:GLU56 4.4 16.0 1.0
O B:HOH338 4.4 17.9 1.0
N B:GLY36 4.4 11.9 1.0
CA B:GLY36 4.6 12.5 1.0
OP3 B:8OG201 4.6 52.4 1.0
O B:HOH306 4.7 27.6 1.0
C4' B:8OG201 4.8 19.4 1.0
C5' B:8OG201 4.9 22.4 1.0
CD B:GLU52 5.0 30.8 1.0

Manganese binding site 5 out of 6 in 8i8s

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Manganese binding site 5 out of 6 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgmp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgmp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn203

b:24.4
occ:0.30
 O B:HOH325 2.2 32.0 1.0
OE2 B:GLU52 2.4 33.2 1.0
O B:HOH306 2.8 27.6 1.0
O B:HOH453 3.1 52.3 1.0
CD B:GLU52 3.4 30.8 1.0
OE1 B:GLU52 3.7 32.5 1.0
MN B:MN204 3.7 23.8 0.3
O B:HOH351 3.8 25.8 1.0
NH1 B:ARG51 4.0 28.6 1.0
N B:LYS38 4.3 14.6 1.0
OE1 B:GLU55 4.4 39.7 1.0
O B:LYS38 4.4 20.1 1.0
CA B:GLY37 4.7 12.8 1.0
CG B:GLU52 4.7 26.0 1.0
OP1 B:8OG201 4.9 70.9 1.0
C B:GLY37 4.9 13.5 1.0
NH2 B:ARG51 4.9 27.6 1.0
CZ B:ARG51 5.0 26.9 1.0
CB B:LYS38 5.0 18.9 1.0

Manganese binding site 6 out of 6 in 8i8s

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Manganese binding site 6 out of 6 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgmp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgmp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn204

b:23.8
occ:0.30
 O B:HOH351 1.9 25.8 1.0
OE2 B:GLU56 2.3 21.0 1.0
OE1 B:GLU52 2.3 32.5 1.0
MN B:MN202 3.0 13.4 0.4
CD B:GLU56 3.2 18.6 1.0
CD B:GLU52 3.4 30.8 1.0
O B:HOH394 3.4 31.4 1.0
CG B:GLU56 3.5 16.0 1.0
MN B:MN203 3.7 24.4 0.3
OE2 B:GLU52 3.7 33.2 1.0
O B:GLY36 3.7 16.6 1.0
OE1 B:GLU55 4.3 39.7 1.0
OE1 B:GLU56 4.3 17.2 1.0
O B:HOH306 4.4 27.6 1.0
C B:GLY36 4.6 13.6 1.0
OP1 B:8OG201 4.6 70.9 1.0
CG B:GLU52 4.7 26.0 1.0
O B:HOH373 4.8 21.2 1.0
CA B:GLY37 4.8 12.8 1.0
CG B:GLU100 4.9 51.9 1.0
OP2 B:8OG201 4.9 38.7 1.0
CB B:GLU52 5.0 21.0 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: Sun Oct 6 12:29:47 2024

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