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Magnesium in PDB 6o3p: Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions

Enzymatic activity of Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions:
3.6.1.22;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions, PDB code: 6o3p was solved by L.Tong, Y.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.67 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.207, 58.550, 61.707, 102.40, 115.19, 104.66
R / Rfree (%) 18 / 21.9

Other elements in 6o3p:

The structure of Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions (pdb code 6o3p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions, PDB code: 6o3p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6o3p

Go back to Magnesium Binding Sites List in 6o3p
Magnesium binding site 1 out of 6 in the Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions


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 the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:26.9
occ:1.00
 O A:ALA354 2.0 25.5 1.0
O A:HOH622 2.1 24.4 1.0
O3P A:AMP501 2.1 27.8 1.0
O A:HOH639 2.1 26.5 1.0
OE1 A:GLU415 2.1 32.5 1.0
OE2 A:GLU374 2.2 28.6 1.0
CD A:GLU374 3.0 27.8 1.0
CD A:GLU415 3.1 36.6 1.0
MG A:MG503 3.2 25.0 1.0
C A:ALA354 3.2 23.1 1.0
OE1 A:GLU374 3.3 29.4 1.0
P A:AMP501 3.3 26.6 1.0
OE2 A:GLU415 3.5 31.8 1.0
O1P A:AMP501 3.5 25.1 1.0
N A:ALA354 3.9 21.7 1.0
OE1 A:GLU370 4.0 28.0 1.0
CA A:GLY355 4.0 20.3 1.0
N A:GLY355 4.1 21.1 1.0
CA A:ALA354 4.1 19.9 1.0
O5' A:AMP501 4.2 29.9 1.0
CG A:GLU374 4.4 24.9 1.0
O2P A:AMP501 4.4 23.0 1.0
CG A:GLU415 4.4 42.3 1.0
O A:HOH673 4.5 42.0 1.0
CB A:ALA354 4.6 22.7 1.0
NE2 A:GLN342 4.7 57.1 1.0
O A:HOH694 4.7 27.5 1.0
CD A:GLU370 4.9 27.9 1.0

Magnesium binding site 2 out of 6 in 6o3p

Go back to Magnesium Binding Sites List in 6o3p
Magnesium binding site 2 out of 6 in the Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions


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 the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:25.0
occ:1.00
 OE1 A:GLU370 2.1 28.0 1.0
O A:HOH694 2.1 27.5 1.0
O3P A:AMP501 2.1 27.8 1.0
O A:HOH638 2.1 23.9 1.0
OE2 A:GLU374 2.1 28.6 1.0
OE2 A:GLU415 2.3 31.8 1.0
CD A:GLU370 3.1 27.9 1.0
CD A:GLU374 3.1 27.8 1.0
MG A:MG502 3.2 26.9 1.0
P A:AMP501 3.2 26.6 1.0
CD A:GLU415 3.3 36.6 1.0
CG A:GLU374 3.4 24.9 1.0
OE2 A:GLU370 3.5 25.2 1.0
O2P A:AMP501 3.5 23.0 1.0
MG A:MG504 3.5 25.0 1.0
OE1 A:GLU415 3.5 32.5 1.0
O5' A:AMP501 3.7 29.9 1.0
OE1 A:GLU373 4.0 28.2 1.0
O A:ALA354 4.0 25.5 1.0
O A:HOH674 4.2 29.1 1.0
O A:HOH739 4.2 39.0 1.0
O A:HOH610 4.3 40.8 1.0
OE1 A:GLU374 4.3 29.4 1.0
CG A:GLU370 4.5 26.6 1.0
O1P A:AMP501 4.6 25.1 1.0
CG A:GLU415 4.7 42.3 1.0
CA A:GLY355 4.7 20.3 1.0
CB A:GLU370 4.7 22.3 1.0
O A:HOH622 4.8 24.4 1.0
O A:HOH644 4.9 28.4 1.0
O A:HOH639 4.9 26.5 1.0
CB A:GLU374 5.0 23.7 1.0

Magnesium binding site 3 out of 6 in 6o3p

Go back to Magnesium Binding Sites List in 6o3p
Magnesium binding site 3 out of 6 in the Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions


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 the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:25.0
occ:1.00
 OE2 A:GLU370 2.0 25.2 1.0
O A:HOH650 2.0 24.4 1.0
O2P A:AMP501 2.0 23.0 1.0
O A:HOH674 2.0 29.1 1.0
O A:HOH644 2.1 28.4 1.0
O A:HOH694 2.3 27.5 1.0
CD A:GLU370 3.1 27.9 1.0
P A:AMP501 3.2 26.6 1.0
OE1 A:GLU370 3.4 28.0 1.0
MG A:MG503 3.5 25.0 1.0
O5' A:AMP501 3.6 29.9 1.0
O3P A:AMP501 3.7 27.8 1.0
NH1 A:ARG369 4.0 25.6 1.0
N A:PHE356 4.1 20.6 1.0
OE1 A:GLU373 4.2 28.2 1.0
O A:HOH739 4.3 39.0 1.0
O4' A:AMP501 4.3 29.5 1.0
O A:HOH636 4.3 34.6 1.0
O A:PHE356 4.4 23.7 1.0
CG A:GLU370 4.4 26.6 1.0
O A:HOH638 4.5 23.9 1.0
O1P A:AMP501 4.6 25.1 1.0
CA A:GLY355 4.6 20.3 1.0
C5' A:AMP501 4.7 31.0 1.0
NH2 A:ARG369 4.7 22.1 1.0
C A:GLY355 4.8 20.3 1.0
CZ A:ARG369 4.8 26.1 1.0
C4' A:AMP501 4.8 31.0 1.0
CB A:PHE356 4.9 21.8 1.0
CA A:PHE356 4.9 19.6 1.0

Magnesium binding site 4 out of 6 in 6o3p

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Magnesium binding site 4 out of 6 in the Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions


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 the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:26.8
occ:1.00
 O B:ALA354 2.0 25.0 1.0
O B:HOH631 2.1 26.2 1.0
OE2 B:GLU374 2.1 24.7 1.0
O B:HOH625 2.1 22.5 1.0
O2P B:AMP502 2.2 28.6 1.0
OE1 B:GLU415 2.2 31.1 1.0
CD B:GLU374 3.0 31.3 1.0
CD B:GLU415 3.2 42.0 1.0
MG B:MG504 3.2 26.2 1.0
C B:ALA354 3.2 24.9 1.0
OE1 B:GLU374 3.3 27.9 1.0
P B:AMP502 3.4 27.7 1.0
O3P B:AMP502 3.5 27.4 1.0
OE2 B:GLU415 3.6 31.4 1.0
OE1 B:GLU370 3.9 25.0 1.0
N B:ALA354 3.9 21.9 1.0
CA B:GLY355 4.0 22.2 1.0
N B:GLY355 4.0 20.8 1.0
CA B:ALA354 4.1 20.3 1.0
O5' B:AMP502 4.2 25.7 1.0
CG B:GLU415 4.4 50.3 1.0
CG B:GLU374 4.4 26.2 1.0
O B:HOH741 4.4 37.9 1.0
O1P B:AMP502 4.6 23.6 1.0
CB B:ALA354 4.7 21.6 1.0
O B:HOH712 4.9 25.2 1.0
CD B:GLU370 4.9 26.0 1.0

Magnesium binding site 5 out of 6 in 6o3p

Go back to Magnesium Binding Sites List in 6o3p
Magnesium binding site 5 out of 6 in the Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions


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 the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:26.2
occ:1.00
 OE2 B:GLU374 2.0 24.7 1.0
OE1 B:GLU370 2.1 25.0 1.0
O B:HOH609 2.1 26.2 1.0
O2P B:AMP502 2.1 28.6 1.0
O B:HOH712 2.2 25.2 1.0
OE2 B:GLU415 2.2 31.4 1.0
CD B:GLU374 3.0 31.3 1.0
CD B:GLU415 3.0 42.0 1.0
CD B:GLU370 3.1 26.0 1.0
MG B:MG503 3.2 26.8 1.0
P B:AMP502 3.3 27.7 1.0
CG B:GLU374 3.3 26.2 1.0
OE1 B:GLU415 3.4 31.1 1.0
OE2 B:GLU370 3.6 24.2 1.0
MG B:MG505 3.6 26.0 1.0
O1P B:AMP502 3.7 23.6 1.0
O5' B:AMP502 3.7 25.7 1.0
OE1 B:GLU373 3.9 35.0 1.0
O B:ALA354 4.0 25.0 1.0
OE1 B:GLU374 4.2 27.9 1.0
CG B:GLU415 4.3 50.3 1.0
CG B:GLU370 4.5 25.1 1.0
O3P B:AMP502 4.6 27.4 1.0
CB B:GLU370 4.7 24.0 1.0
CA B:GLY355 4.7 22.2 1.0
CB B:GLU415 4.8 50.0 1.0
O B:HOH690 4.8 35.6 1.0
O B:HOH655 4.9 26.2 1.0
O B:HOH631 4.9 26.2 1.0
CB B:GLU374 4.9 26.6 1.0
O B:HOH625 4.9 22.5 1.0
O B:GLU370 4.9 23.4 1.0
CA B:GLU370 5.0 23.5 1.0

Magnesium binding site 6 out of 6 in 6o3p

Go back to Magnesium Binding Sites List in 6o3p
Magnesium binding site 6 out of 6 in the Crystal Structure of the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions


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 the Catalytic Domain of Mouse NUDT12 in Complex with Amp and 3 MG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg505

b:26.0
occ:1.00
 O B:HOH655 2.0 26.2 1.0
O1P B:AMP502 2.0 23.6 1.0
OE2 B:GLU370 2.1 24.2 1.0
O B:HOH652 2.1 23.7 1.0
O B:HOH712 2.2 25.2 1.0
O B:HOH690 2.2 35.6 1.0
CD B:GLU370 3.1 26.0 1.0
P B:AMP502 3.2 27.7 1.0
OE1 B:GLU370 3.5 25.0 1.0
MG B:MG504 3.6 26.2 1.0
O2P B:AMP502 3.7 28.6 1.0
O5' B:AMP502 3.7 25.7 1.0
NH1 B:ARG369 4.0 29.1 1.0
N B:PHE356 4.1 21.2 1.0
OE1 B:GLU373 4.2 35.0 1.0
O B:HOH727 4.2 38.4 1.0
O4' B:AMP502 4.3 28.9 1.0
O B:PHE356 4.3 24.2 1.0
CG B:GLU370 4.4 25.1 1.0
O B:HOH609 4.6 26.2 1.0
CA B:GLY355 4.6 22.2 1.0
O3P B:AMP502 4.6 27.4 1.0
NH2 B:ARG369 4.7 25.3 1.0
C5' B:AMP502 4.8 29.2 1.0
C B:GLY355 4.8 22.9 1.0
CZ B:ARG369 4.8 27.5 1.0
C4' B:AMP502 4.9 31.2 1.0
CB B:PHE356 4.9 22.9 1.0
CA B:PHE356 4.9 22.6 1.0
OE2 B:GLU358 4.9 36.0 1.0
O B:HOH736 5.0 38.9 1.0

Reference:

E.Grudzien-Nogalska, Y.Wu, X.Jiao, H.Cui, M.K.Mateyak, R.P.Hart, L.Tong, M.Kiledjian. Structural and Mechanistic Basis of Mammalian NUDT12 Rna Denadding. Nat.Chem.Biol. V. 15 575 2019.
ISSN: ESSN 1552-4469
PubMed: 31101919
DOI: 10.1038/S41589-019-0293-7
Page generated: Tue Oct 1 13:16:04 2024

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