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Magnesium in PDB 3bm4: Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr

Enzymatic activity of Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr

All present enzymatic activity of Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr:
3.6.1.13;

Protein crystallography data

The structure of Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr, PDB code: 3bm4 was solved by M.Zha, Q.Guo, Y.Zhang, C.Zhong, Y.Ou, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.86 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.394, 41.168, 99.648, 90.00, 121.74, 90.00
R / Rfree (%) 19.8 / 23.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr (pdb code 3bm4). 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 Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr, PDB code: 3bm4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3bm4

Go back to Magnesium Binding Sites List in 3bm4
Magnesium binding site 1 out of 6 in the Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr


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 Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:20.9
occ:1.00
 OE2 A:GLU116 2.2 20.4 1.0
O2B B:ADV401 2.2 39.8 1.0
O A:ALA96 2.3 19.6 1.0
O A:HOH395 2.3 17.2 1.0
O1A B:ADV401 2.4 38.9 1.0
O A:HOH323 2.4 18.1 1.0
MG A:MG302 3.0 57.2 1.0
CD A:GLU116 3.1 23.3 1.0
C A:ALA96 3.3 19.9 1.0
O A:HOH443 3.4 39.1 1.0
OE1 A:GLU116 3.4 25.3 1.0
PB B:ADV401 3.6 39.8 1.0
PA B:ADV401 3.8 41.1 1.0
CA A:GLY97 4.1 18.2 1.0
N A:GLY97 4.2 16.9 1.0
O B:HOH437 4.2 34.9 1.0
OE2 A:GLU112 4.2 23.5 1.0
N A:ALA96 4.2 16.0 1.0
CX B:ADV401 4.2 42.1 1.0
NE2 A:GLN82 4.3 32.2 1.0
CA A:ALA96 4.3 16.5 1.0
O1B B:ADV401 4.4 44.0 1.0
O A:HOH334 4.4 18.2 1.0
CG A:GLU116 4.5 23.8 1.0
OE1 A:GLN82 4.5 30.6 1.0
NH2 A:ARG84 4.5 21.2 1.0
OR5 B:ADV401 4.7 45.1 1.0
O5' B:ADV401 4.7 39.4 1.0
O2A B:ADV401 4.8 40.4 1.0
CB A:ALA96 4.8 12.7 1.0
CR5 B:ADV401 4.8 48.7 1.0
CD A:GLN82 4.8 33.8 1.0

Magnesium binding site 2 out of 6 in 3bm4

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Magnesium binding site 2 out of 6 in the Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr


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 Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:57.2
occ:1.00
 OE2 A:GLU112 2.4 23.5 1.0
O1A B:ADV401 2.4 38.9 1.0
O A:HOH443 2.4 39.1 1.0
O A:HOH438 2.5 46.5 1.0
OE2 A:GLU116 2.6 20.4 1.0
MG A:MG301 3.0 20.9 1.0
O A:HOH434 3.0 30.4 1.0
MG A:MG303 3.3 37.4 1.0
CD A:GLU112 3.3 24.3 1.0
PA B:ADV401 3.6 41.1 1.0
CD A:GLU116 3.6 23.3 1.0
OE1 A:GLU112 3.6 22.4 1.0
O A:HOH323 3.7 18.1 1.0
O A:ALA96 3.7 19.6 1.0
OE2 A:GLU166 3.8 0.0 1.0
O2A B:ADV401 3.9 40.4 1.0
CG A:GLU116 4.0 23.8 1.0
O5' B:ADV401 4.3 39.4 1.0
CA A:GLY97 4.5 18.2 1.0
O2B B:ADV401 4.5 39.8 1.0
OE1 A:GLU116 4.6 25.3 1.0
OE2 A:GLU115 4.6 38.6 1.0
O A:HOH362 4.7 45.4 1.0
CG A:GLU112 4.7 20.4 1.0
CD A:GLU166 4.8 0.2 1.0
C A:ALA96 4.8 19.9 1.0
O A:HOH395 5.0 17.2 1.0

Magnesium binding site 3 out of 6 in 3bm4

Go back to Magnesium Binding Sites List in 3bm4
Magnesium binding site 3 out of 6 in the Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr


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 Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:37.4
occ:1.00
 O2A B:ADV401 2.3 40.4 1.0
OE1 A:GLU112 2.5 22.4 1.0
O A:HOH434 2.6 30.4 1.0
O A:HOH351 2.7 33.5 1.0
O A:HOH362 2.9 45.4 1.0
PA B:ADV401 3.3 41.1 1.0
MG A:MG302 3.3 57.2 1.0
CD A:GLU112 3.4 24.3 1.0
O A:HOH383 3.6 38.5 1.0
O1A B:ADV401 3.6 38.9 1.0
OE2 A:GLU112 3.7 23.5 1.0
O5' B:ADV401 3.9 39.4 1.0
O A:HOH438 4.1 46.5 1.0
NH1 A:ARG111 4.3 30.2 1.0
C5' B:ADV401 4.4 40.0 1.0
N A:LEU98 4.4 18.1 1.0
NH2 A:ARG111 4.5 28.5 1.0
CA A:GLY97 4.6 18.2 1.0
O A:LEU98 4.6 20.8 1.0
OE2 A:GLU115 4.6 38.6 1.0
CG A:GLU112 4.8 20.4 1.0
CZ A:ARG111 4.8 30.5 1.0
CX B:ADV401 4.9 42.1 1.0
C A:GLY97 5.0 18.1 1.0

Magnesium binding site 4 out of 6 in 3bm4

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Magnesium binding site 4 out of 6 in the Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr


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 Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:22.9
occ:1.00
 O2B B:ADV402 2.1 40.0 1.0
OE1 B:GLU116 2.2 21.7 1.0
O B:HOH448 2.2 19.0 1.0
O B:ALA96 2.3 19.5 1.0
O B:HOH452 2.3 18.5 1.0
O1A B:ADV402 2.4 40.9 1.0
MG B:MG305 3.1 47.8 1.0
CD B:GLU116 3.2 20.1 1.0
O B:HOH562 3.5 37.7 1.0
C B:ALA96 3.5 20.7 1.0
PB B:ADV402 3.5 43.0 1.0
OE2 B:GLU116 3.6 17.5 1.0
PA B:ADV402 3.8 43.9 1.0
O B:HOH425 4.0 33.7 1.0
CX B:ADV402 4.2 43.1 1.0
NH2 B:ARG84 4.2 20.2 1.0
CA B:GLY97 4.2 24.6 1.0
OE1 B:GLN82 4.3 30.5 1.0
N B:GLY97 4.3 23.2 1.0
O1B B:ADV402 4.3 44.4 1.0
NE2 B:GLN82 4.3 28.4 1.0
OE2 B:GLU112 4.4 33.7 1.0
N B:ALA96 4.4 18.0 1.0
O B:HOH405 4.4 20.5 1.0
CA B:ALA96 4.5 20.0 1.0
CG B:GLU116 4.5 21.0 1.0
OR5 B:ADV402 4.6 45.3 1.0
OE2 B:GLU166 4.6 95.9 1.0
O5' B:ADV402 4.7 41.6 1.0
O2A B:ADV402 4.7 40.1 1.0
CD B:GLN82 4.7 29.9 1.0
CR5 B:ADV402 4.8 48.3 1.0
CB B:ALA96 5.0 17.7 1.0

Magnesium binding site 5 out of 6 in 3bm4

Go back to Magnesium Binding Sites List in 3bm4
Magnesium binding site 5 out of 6 in the Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr


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 Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:47.8
occ:1.00
 O B:HOH562 2.4 37.7 1.0
OE1 B:GLU116 2.5 21.7 1.0
O B:HOH449 2.5 50.7 1.0
OE2 B:GLU112 2.5 33.7 1.0
O1A B:ADV402 2.7 40.9 1.0
O B:HOH512 3.0 39.3 1.0
MG B:MG304 3.1 22.9 1.0
MG B:MG306 3.2 41.4 1.0
OE2 B:GLU166 3.3 95.9 1.0
CD B:GLU112 3.5 33.3 1.0
CD B:GLU116 3.5 20.1 1.0
OE1 B:GLU166 3.7 96.8 1.0
OE1 B:GLU112 3.7 34.4 1.0
PA B:ADV402 3.7 43.9 1.0
O B:HOH452 3.7 18.5 1.0
CG B:GLU116 3.8 21.0 1.0
O B:ALA96 3.9 19.5 1.0
CD B:GLU166 3.9 96.2 1.0
O2A B:ADV402 4.0 40.1 1.0
O5' B:ADV402 4.5 41.6 1.0
O B:HOH450 4.5 51.3 1.0
OE2 B:GLU115 4.6 36.7 1.0
CA B:GLY97 4.6 24.6 1.0
OE2 B:GLU116 4.6 17.5 1.0
O2B B:ADV402 4.6 40.0 1.0
CG B:GLU112 4.8 31.0 1.0
C B:ALA96 4.9 20.7 1.0

Magnesium binding site 6 out of 6 in 3bm4

Go back to Magnesium Binding Sites List in 3bm4
Magnesium binding site 6 out of 6 in the Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr


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 Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Ampcpr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:41.4
occ:1.00
 O2A B:ADV402 2.5 40.1 1.0
O B:HOH512 2.5 39.3 1.0
O B:HOH491 2.6 32.5 1.0
OE1 B:GLU112 2.6 34.4 1.0
O B:HOH450 2.8 51.3 1.0
MG B:MG305 3.2 47.8 1.0
PA B:ADV402 3.4 43.9 1.0
CD B:GLU112 3.5 33.3 1.0
O B:HOH536 3.6 39.9 1.0
O1A B:ADV402 3.7 40.9 1.0
OE2 B:GLU112 3.7 33.7 1.0
O5' B:ADV402 3.9 41.6 1.0
O B:HOH449 4.2 50.7 1.0
NH1 B:ARG111 4.2 24.6 1.0
O B:HOH519 4.3 41.4 1.0
N B:LEU98 4.4 20.2 1.0
OE2 B:GLU166 4.5 95.9 1.0
C5' B:ADV402 4.6 40.1 1.0
OE2 B:GLU115 4.6 36.7 1.0
CA B:GLY97 4.6 24.6 1.0
NH2 B:ARG111 4.6 26.3 1.0
O B:LEU98 4.7 20.7 1.0
CG B:GLU112 4.9 31.0 1.0
CZ B:ARG111 4.9 28.0 1.0
C B:GLY97 5.0 24.7 1.0

Reference:

M.Zha, Q.Guo, Y.Zhang, B.Yu, Y.Ou, C.Zhong, J.Ding. Molecular Mechanism of Adp-Ribose Hydrolysis By Human NUDT5 From Structural and Kinetic Studies J.Mol.Biol. V. 379 568 2008.
ISSN: ISSN 0022-2836
PubMed: 18462755
DOI: 10.1016/J.JMB.2008.04.006
Page generated: Sun Aug 10 17:50:53 2025

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