Magnesium in PDB 5bon: Crystal Structure of Human NUDT15 (MTH2)

All present enzymatic activity of Crystal Structure of Human NUDT15 (MTH2):
3.6.1.55;

The structure of Crystal Structure of Human NUDT15 (MTH2), PDB code: 5bon was solved by M.Carter, A.-S.Jemth, T.Helleday, P.Stenmark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.60 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.830, 71.676, 82.768, 90.07, 90.04, 73.08
R / Rfree (%)	19.3 / 22

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Human NUDT15 (MTH2) (pdb code 5bon). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 32 binding sites of Magnesium where determined in the Crystal Structure of Human NUDT15 (MTH2), PDB code: 5bon:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 32 in the Crystal Structure of Human NUDT15 (MTH2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human NUDT15 (MTH2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:29.1 occ:1.00 OE2 A:GLU63 2.0 26.3 1.0 O A:HOH335 2.1 25.0 1.0 O A:HOH403 2.1 29.6 1.0 O A:HOH383 2.1 26.1 1.0 O B:HOH412 2.2 26.2 1.0 O A:HOH323 2.2 28.4 1.0 MG A:MG204 2.9 27.2 1.0 CD A:GLU63 3.1 24.7 1.0 OE1 A:GLU63 3.6 26.7 1.0 O A:HOH337 3.7 23.5 1.0 MG A:MG203 3.7 26.5 1.0 NH1 A:ARG62 3.9 24.6 1.0 O A:HOH444 4.0 35.0 1.0 O A:HOH426 4.1 37.4 1.0 N A:HIS49 4.1 23.7 1.0 OE2 A:GLU51 4.3 34.1 1.0 OE1 A:GLU66 4.3 30.3 1.0 CG A:GLU63 4.4 23.3 1.0 O A:HOH333 4.4 24.8 1.0 O A:HIS49 4.5 22.8 1.0 O A:HOH423 4.5 40.3 1.0 NH2 A:ARG62 4.5 26.0 1.0 CA A:GLY48 4.5 25.2 1.0 CZ A:ARG62 4.7 25.2 1.0 C A:GLY48 4.7 22.9 1.0 CB A:HIS49 4.8 26.4 1.0 CA A:HIS49 4.9 26.3 1.0 ND1 A:HIS49 4.9 35.5 1.0

Magnesium binding site 2 out of 32 in the Crystal Structure of Human NUDT15 (MTH2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human NUDT15 (MTH2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:28.4 occ:1.00 O A:HOH337 2.0 23.5 1.0 O A:GLY47 2.0 25.5 1.0 OE2 A:GLU67 2.2 24.3 1.0 O A:HOH413 2.2 30.5 1.0 O A:HOH344 2.2 24.9 1.0 O A:HOH400 2.3 29.5 1.0 CD A:GLU67 3.1 25.3 1.0 MG A:MG203 3.2 26.5 1.0 C A:GLY47 3.2 24.4 1.0 O A:HOH423 3.4 40.3 1.0 OE1 A:GLU67 3.4 27.9 1.0 MG A:MG204 3.4 27.2 1.0 O A:HOH330 3.7 28.4 1.0 CA A:GLY48 3.8 25.2 1.0 N A:GLY48 3.9 28.0 1.0 OE1 A:GLU63 4.0 26.7 1.0 O A:HOH368 4.1 35.5 1.0 O A:HOH431 4.1 41.3 1.0 O A:HOH444 4.3 35.0 1.0 N A:GLY47 4.3 24.0 1.0 CA A:GLY47 4.4 23.4 1.0 O A:HOH415 4.4 44.1 1.0 O A:HOH403 4.4 29.6 1.0 O A:HOH323 4.5 28.4 1.0 CG A:GLU67 4.5 27.1 1.0 NH1 A:ARG34 4.6 40.9 1.0 OE1 A:GLN44 4.6 31.4 1.0 CD A:GLU63 4.7 24.7 1.0 O A:HOH436 4.8 41.3 1.0

Magnesium binding site 3 out of 32 in the Crystal Structure of Human NUDT15 (MTH2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human NUDT15 (MTH2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:26.5 occ:1.00 O A:HOH337 2.1 23.5 1.0 OE1 A:GLU63 2.1 26.7 1.0 O A:HOH403 2.1 29.6 1.0 O A:HOH333 2.1 24.8 1.0 OE2 A:GLU67 2.1 24.3 1.0 O A:HOH330 2.1 28.4 1.0 MG A:MG204 3.0 27.2 1.0 CD A:GLU67 3.1 25.3 1.0 CD A:GLU63 3.1 24.7 1.0 MG A:MG202 3.2 28.4 1.0 CG A:GLU67 3.4 27.1 1.0 OE2 A:GLU63 3.5 26.3 1.0 MG A:MG201 3.7 29.1 1.0 O A:HOH400 3.7 29.5 1.0 O A:GLY47 3.9 25.5 1.0 O A:HOH444 3.9 35.0 1.0 O A:HOH323 4.0 28.4 1.0 OE1 A:GLU113 4.0 36.3 1.0 OE1 A:GLU66 4.2 30.3 1.0 OE1 A:GLU67 4.2 27.9 1.0 OE2 A:GLU113 4.4 40.0 1.0 O A:HOH383 4.4 26.1 1.0 CG A:GLU63 4.4 23.3 1.0 O A:HOH423 4.5 40.3 1.0 CD A:GLU113 4.6 36.5 1.0 C A:GLY47 4.8 24.4 1.0 CB A:GLU63 4.8 24.3 1.0 CA A:GLY48 4.8 25.2 1.0 O A:HOH344 4.9 24.9 1.0 CB A:GLU67 4.9 29.1 1.0

Magnesium binding site 4 out of 32 in the Crystal Structure of Human NUDT15 (MTH2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human NUDT15 (MTH2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:27.2 occ:1.00 O A:HOH337 1.6 23.5 1.0 O A:HOH444 1.7 35.0 1.0 O A:HOH323 1.7 28.4 1.0 O A:HOH423 1.9 40.3 1.0 O A:HOH403 2.2 29.6 1.0 MG A:MG201 2.9 29.1 1.0 MG A:MG203 3.0 26.5 1.0 O A:HOH426 3.4 37.4 1.0 MG A:MG202 3.4 28.4 1.0 O A:HOH330 3.6 28.4 1.0 O B:HOH412 3.6 26.2 1.0 CA A:GLY48 3.7 25.2 1.0 O A:HOH411 3.8 42.4 1.0 OE2 A:GLU63 3.8 26.3 1.0 O A:HOH436 3.8 41.3 1.0 OE1 A:GLU63 4.0 26.7 1.0 O A:HOH413 4.0 30.5 1.0 ND1 A:HIS49 4.0 35.5 1.0 O A:HOH400 4.0 29.5 1.0 N A:HIS49 4.1 23.7 1.0 CD A:GLU63 4.2 24.7 1.0 OE2 A:GLU67 4.2 24.3 1.0 O A:GLY47 4.3 25.5 1.0 C A:GLY48 4.5 22.9 1.0 O A:HOH335 4.5 25.0 1.0 O A:HOH383 4.7 26.1 1.0 CE1 A:HIS49 4.7 32.5 1.0 O A:HOH415 4.7 44.1 1.0 O A:HOH333 4.7 24.8 1.0 N A:GLY48 4.9 28.0 1.0

Magnesium binding site 5 out of 32 in the Crystal Structure of Human NUDT15 (MTH2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human NUDT15 (MTH2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:28.2 occ:1.00 O B:HOH318 1.9 29.1 1.0 OE2 B:GLU67 2.1 28.0 1.0 O B:HOH375 2.1 33.5 1.0 OE1 B:GLU63 2.2 25.3 1.0 O B:HOH380 2.2 31.7 1.0 O B:HOH354 2.2 27.4 1.0 CD B:GLU67 3.0 37.7 1.0 MG B:MG203 3.0 37.1 1.0 CD B:GLU63 3.2 28.0 1.0 MG B:MG204 3.2 34.9 1.0 CG B:GLU67 3.4 30.5 1.0 OE2 B:GLU63 3.5 29.3 1.0 O B:HOH374 3.5 30.4 1.0 O B:GLY47 3.7 27.2 1.0 MG B:MG202 3.8 37.5 1.0 O B:HOH323 4.0 32.2 1.0 OE1 B:GLU113 4.1 33.5 1.0 O B:HOH409 4.1 47.6 1.0 OE1 B:GLU67 4.1 29.6 1.0 O B:HOH420 4.1 38.3 1.0 O B:HOH316 4.2 37.5 1.0 OE1 B:GLU66 4.2 29.2 1.0 OE2 B:GLU113 4.4 39.5 1.0 CG B:GLU63 4.5 25.2 1.0 C B:GLY47 4.6 27.7 1.0 CD B:GLU113 4.7 33.1 1.0 CA B:GLY48 4.7 27.8 1.0 O B:HOH393 4.7 39.9 1.0 CB B:GLU63 4.8 26.6 1.0 O B:HOH330 4.8 29.7 1.0 CB B:GLU67 4.9 27.0 1.0 O B:HOH403 5.0 32.5 1.0

Magnesium binding site 6 out of 32 in the Crystal Structure of Human NUDT15 (MTH2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Human NUDT15 (MTH2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:37.5 occ:1.00 O B:HOH380 2.0 31.7 1.0 O B:HOH316 2.0 37.5 1.0 OE2 B:GLU63 2.1 29.3 1.0 O B:HOH325 2.1 25.4 1.0 O B:HOH323 2.1 32.2 1.0 O A:HOH422 2.3 33.6 1.0 MG B:MG203 2.6 37.1 1.0 CD B:GLU63 3.1 28.0 1.0 OE1 B:GLU63 3.6 25.3 1.0 O B:HOH318 3.7 29.1 1.0 MG B:MG201 3.8 28.2 1.0 N B:HIS49 4.0 26.6 1.0 NH1 B:ARG62 4.0 23.6 1.0 O B:HOH409 4.0 47.6 1.0 O B:HOH420 4.0 38.3 1.0 O B:HOH413 4.1 40.8 1.0 OE1 B:GLU66 4.3 29.2 1.0 CA B:GLY48 4.4 27.8 1.0 OE2 B:GLU51 4.4 39.3 1.0 CG B:GLU63 4.4 25.2 1.0 O B:HIS49 4.5 23.9 1.0 C B:GLY48 4.6 29.1 1.0 O B:HOH354 4.6 27.4 1.0 NH2 B:ARG62 4.6 25.3 1.0 ND1 B:HIS49 4.6 34.9 1.0 CB B:HIS49 4.7 27.2 1.0 CZ B:ARG62 4.8 27.3 1.0 CA B:HIS49 4.8 28.2 1.0 O B:HOH375 4.9 33.5 1.0

Magnesium binding site 7 out of 32 in the Crystal Structure of Human NUDT15 (MTH2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Human NUDT15 (MTH2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:37.1 occ:1.00 O B:HOH316 1.7 37.5 1.0 O B:HOH318 1.8 29.1 1.0 O B:HOH420 1.8 38.3 1.0 O B:HOH380 2.0 31.7 1.0 MG B:MG202 2.6 37.5 1.0 O B:HOH408 2.8 44.3 1.0 MG B:MG201 3.0 28.2 1.0 O B:HOH413 3.5 40.8 1.0 CA B:GLY48 3.6 27.8 1.0 O B:HOH375 3.6 33.5 1.0 OE2 B:GLU63 3.6 29.3 1.0 O A:HOH422 3.7 33.6 1.0 MG B:MG204 3.7 34.9 1.0 O B:HOH393 3.8 39.9 1.0 ND1 B:HIS49 3.9 34.9 1.0 OE1 B:GLU63 3.9 25.3 1.0 N B:HIS49 3.9 26.6 1.0 O B:HOH374 4.0 30.4 1.0 CD B:GLU63 4.1 28.0 1.0 O B:HOH323 4.2 32.2 1.0 O B:HOH403 4.2 32.5 1.0 O B:HOH409 4.2 47.6 1.0 O B:HOH325 4.3 25.4 1.0 O B:GLY47 4.3 27.2 1.0 OE2 B:GLU67 4.3 28.0 1.0 C B:GLY48 4.3 29.1 1.0 CE1 B:HIS49 4.6 33.9 1.0 N B:GLY48 4.7 29.1 1.0 O B:HOH354 4.8 27.4 1.0 O B:HOH414 4.8 41.0 1.0 CG B:HIS49 4.9 28.3 1.0 O B:HOH421 4.9 46.6 1.0 C B:GLY47 5.0 27.7 1.0

Magnesium binding site 8 out of 32 in the Crystal Structure of Human NUDT15 (MTH2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Human NUDT15 (MTH2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:34.9 occ:1.00 O B:HOH403 2.1 32.5 1.0 O B:GLY47 2.1 27.2 1.0 O B:HOH330 2.1 29.7 1.0 O B:HOH318 2.2 29.1 1.0 OE2 B:GLU67 2.2 28.0 1.0 O B:HOH374 2.2 30.4 1.0 CD B:GLU67 3.1 37.7 1.0 MG B:MG201 3.2 28.2 1.0 C B:GLY47 3.2 27.7 1.0 OE1 B:GLU67 3.4 29.6 1.0 MG B:MG203 3.7 37.1 1.0 O B:HOH375 3.8 33.5 1.0 O B:HOH408 3.8 44.3 1.0 CA B:GLY48 3.9 27.8 1.0 N B:GLY48 4.0 29.1 1.0 OE1 B:GLU63 4.1 25.3 1.0 O B:HOH370 4.2 36.9 1.0 N B:GLY47 4.3 25.1 1.0 CA B:GLY47 4.3 25.6 1.0 O B:HOH420 4.4 38.3 1.0 OE1 B:GLN44 4.5 41.7 1.0 CG B:GLU67 4.5 30.5 1.0 O B:HOH380 4.6 31.7 1.0 NH1 B:ARG34 4.7 56.9 1.0 CD B:GLU63 4.9 28.0 1.0 O B:HOH316 5.0 37.5 1.0

Magnesium binding site 9 out of 32 in the Crystal Structure of Human NUDT15 (MTH2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Human NUDT15 (MTH2) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:32.6 occ:1.00 O C:GLY47 2.0 28.6 1.0 O C:HOH340 2.2 28.1 1.0 O C:HOH419 2.2 31.7 1.0 O C:HOH383 2.2 33.3 1.0 OE2 C:GLU67 2.2 33.0 1.0 O C:HOH417 2.4 33.0 1.0 CD C:GLU67 3.1 29.9 1.0 C C:GLY47 3.2 27.0 1.0 MG C:MG203 3.2 29.1 1.0 OE1 C:GLU67 3.3 30.4 1.0 O C:HOH423 3.5 39.1 1.0 MG C:MG204 3.7 38.4 1.0 O C:HOH361 3.7 32.3 1.0 CA C:GLY48 3.8 32.1 1.0 N C:GLY48 3.9 32.8 1.0 OE1 C:GLU63 4.0 27.5 1.0 N C:GLY47 4.2 26.4 1.0 O C:HOH382 4.3 33.1 1.0 CA C:GLY47 4.3 26.7 1.0 OE1 C:GLN44 4.4 36.1 1.0 O C:HOH353 4.5 33.5 1.0 CG C:GLU67 4.5 28.3 1.0 NH1 C:ARG34 4.5 42.5 1.0 O C:HOH421 4.6 45.9 1.0 O C:HOH427 4.7 45.1 1.0 O C:HOH413 4.7 33.4 1.0 CD C:GLU63 4.8 28.0 1.0

Magnesium binding site 10 out of 32 in the Crystal Structure of Human NUDT15 (MTH2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Human NUDT15 (MTH2) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:34.1 occ:1.00 O C:HOH413 2.0 33.4 1.0 OE2 C:GLU63 2.1 28.1 1.0 O C:HOH343 2.1 25.7 1.0 O C:HOH353 2.1 33.5 1.0 O C:HOH365 2.1 34.5 1.0 O D:HOH388 2.2 35.7 1.0 MG C:MG204 3.0 38.4 1.0 CD C:GLU63 3.1 28.0 1.0 O D:HOH391 3.3 51.1 1.0 O C:HOH383 3.5 33.3 1.0 OE1 C:GLU63 3.5 27.5 1.0 MG C:MG203 3.6 29.1 1.0 O C:HOH445 3.8 43.1 1.0 N C:HIS49 4.1 27.5 1.0 NH1 C:ARG62 4.1 26.9 1.0 O C:HOH346 4.3 31.3 1.0 OE2 C:GLU51 4.3 40.9 1.0 CG C:GLU63 4.4 26.1 1.0 O C:HOH423 4.4 39.1 1.0 OE1 C:GLU66 4.4 33.1 1.0 CA C:GLY48 4.5 32.1 1.0 O C:HIS49 4.5 29.0 1.0 NH2 C:ARG62 4.6 26.6 1.0 O C:HOH433 4.6 48.0 1.0 C C:GLY48 4.7 31.6 1.0 O C:HOH429 4.8 46.8 1.0 CZ C:ARG62 4.8 26.2 1.0 CB C:HIS49 4.9 31.4 1.0 O C:HOH361 4.9 32.3 1.0 ND1 C:HIS49 4.9 41.3 1.0 CA C:HIS49 4.9 25.4 1.0

M.Carter, A.S.Jemth, A.Hagenkort, B.D.Page, R.Gustafsson, J.J.Griese, H.Gad, N.C.Valerie, M.Desroses, J.Bostrom, U.Warpman Berglund, T.Helleday, P.Stenmark. Crystal Structure, Biochemical and Cellular Activities Demonstrate Separate Functions of MTH1 and MTH2. Nat Commun V. 6 7871 2015.
ISSN: ESSN 2041-1723
PubMed: 26238318
DOI: 10.1038/NCOMMS8871