Atomistry » Magnesium » PDB 3bdh-3bre » 3bm4
Atomistry »
  Magnesium »
    PDB 3bdh-3bre »
      3bm4 »

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

Go back to Magnesium Binding Sites List in 3bm4
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

Go back to Magnesium Binding Sites List in 3bm4
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: Wed Aug 14 09:12:19 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy