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Magnesium in PDB 2dsd: Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Amp

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

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

Protein crystallography data

The structure of Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Amp, PDB code: 2dsd was solved by M.Zha, C.Zhong, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.01 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.076, 40.156, 100.124, 90.00, 121.68, 90.00
R / Rfree (%) 21.5 / 27.5

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 6 in 2dsd

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Magnesium binding site 1 out of 6 in the Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Amp


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 Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:54.6
occ:1.00
 OE1 A:GLU116 2.7 53.0 1.0
O2P A:AMP401 2.8 80.8 1.0
OE2 A:GLU116 2.9 53.3 1.0
O A:HOH417 3.0 45.2 1.0
CD A:GLU116 3.1 52.5 1.0
O A:HOH425 3.2 48.2 1.0
O A:ALA96 3.2 47.7 1.0
OE1 A:GLN82 3.2 66.0 1.0
N A:ALA96 3.4 43.0 1.0
NH2 A:ARG84 3.7 59.0 1.0
NE2 A:GLN82 3.7 65.0 1.0
CD A:GLN82 3.8 64.7 1.0
C A:ALA96 4.0 46.2 1.0
CA A:ALA96 4.0 44.5 1.0
CB A:ALA96 4.3 43.9 1.0
P A:AMP401 4.4 83.1 1.0
CG2 A:VAL80 4.4 48.0 1.0
C A:PRO95 4.4 41.3 1.0
O A:PHE94 4.5 36.6 1.0
CA A:PRO95 4.6 39.9 1.0
CG A:GLU116 4.6 50.8 1.0
OE2 A:GLU166 4.7 91.7 1.0
CZ A:ARG84 4.9 60.8 1.0
O3P A:AMP401 4.9 80.3 1.0

Magnesium binding site 2 out of 6 in 2dsd

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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 Amp


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 Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:89.6
occ:1.00
 O1P A:AMP401 2.6 81.4 1.0
OE2 A:GLU112 3.0 75.9 1.0
OE2 A:GLU116 3.0 53.3 1.0
OE2 A:GLU166 3.0 91.7 1.0
OE1 A:GLU166 3.0 93.1 1.0
OE2 A:GLU115 3.3 66.8 1.0
CD A:GLU166 3.4 92.5 1.0
CG A:GLU116 3.4 50.8 1.0
CD A:GLU116 3.6 52.5 1.0
P A:AMP401 3.7 83.1 1.0
O A:HOH431 3.7 54.9 1.0
CD A:GLU112 3.8 71.6 1.0
CG A:GLU112 3.8 66.8 1.0
O2P A:AMP401 4.0 80.8 1.0
O5' A:AMP401 4.2 84.1 1.0
CB A:GLU115 4.3 61.1 1.0
MG A:MG303 4.4 61.2 1.0
CD A:GLU115 4.5 67.0 1.0
O A:ALA96 4.6 47.7 1.0
O A:GLU112 4.8 53.7 1.0
OE1 A:GLU116 4.9 53.0 1.0
CB A:GLU116 4.9 50.9 1.0
CG A:GLU166 4.9 92.6 1.0
OE1 A:GLU112 5.0 73.0 1.0
CB A:GLU112 5.0 59.4 1.0
CA A:GLU112 5.0 54.4 1.0

Magnesium binding site 3 out of 6 in 2dsd

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Magnesium binding site 3 out of 6 in the Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Amp


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 Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:61.2
occ:1.00
 O1P A:AMP401 2.7 81.4 1.0
OE2 A:GLU112 2.9 75.9 1.0
O A:HOH431 3.1 54.9 1.0
CD A:GLU112 3.3 71.6 1.0
OE1 A:GLU112 3.3 73.0 1.0
N A:LEU98 3.3 61.8 1.0
P A:AMP401 3.6 83.1 1.0
O3P A:AMP401 3.8 80.3 1.0
CA A:GLY97 3.8 52.6 1.0
O5' A:AMP401 4.0 84.1 1.0
C5' A:AMP401 4.0 84.0 1.0
C A:GLY97 4.1 56.8 1.0
CB A:LEU98 4.2 67.6 1.0
CA A:LEU98 4.2 66.1 1.0
O A:LEU98 4.2 68.0 1.0
MG A:MG302 4.4 89.6 1.0
CG A:GLU112 4.4 66.8 1.0
CG A:LEU98 4.4 69.3 1.0
NH1 A:ARG111 4.6 53.2 1.0
CD1 A:LEU98 4.7 71.7 1.0
C A:LEU98 4.7 68.2 1.0

Magnesium binding site 4 out of 6 in 2dsd

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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 Amp


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 Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:48.3
occ:1.00
 O B:ALA96 2.5 37.3 1.0
OE1 B:GLU116 2.5 54.9 1.0
O3P B:AMP402 2.7 80.0 1.0
O B:HOH440 2.9 78.6 1.0
O B:HOH419 2.9 51.5 1.0
O1P B:AMP402 3.2 78.5 1.0
CD B:GLU116 3.3 52.0 1.0
OE1 B:GLU166 3.4 72.5 1.0
OE2 B:GLU116 3.4 49.4 1.0
P B:AMP402 3.4 79.3 1.0
C B:ALA96 3.7 37.0 1.0
O B:HOH411 3.7 47.1 1.0
NE2 B:GLN82 3.9 51.7 1.0
NH2 B:ARG84 3.9 48.5 1.0
OE1 B:GLN82 4.1 49.1 1.0
O5' B:AMP402 4.2 80.0 1.0
MG B:MG305 4.2 62.4 1.0
N B:ALA96 4.4 32.6 1.0
CD B:GLN82 4.4 49.1 1.0
CA B:ALA96 4.5 34.2 1.0
CG B:GLU116 4.6 49.8 1.0
N B:GLY97 4.6 40.8 1.0
CD B:GLU166 4.6 71.9 1.0
CA B:GLY97 4.7 44.0 1.0
O B:HOH452 4.8 68.6 1.0
O2P B:AMP402 4.9 78.7 1.0
CB B:ALA96 4.9 31.6 1.0
CZ B:ARG84 4.9 47.7 1.0

Magnesium binding site 5 out of 6 in 2dsd

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Magnesium binding site 5 out of 6 in the Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Amp


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 Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:62.4
occ:1.00
 OE1 B:GLU112 2.4 58.2 1.0
OE1 B:GLU116 2.7 54.9 1.0
O3P B:AMP402 2.7 80.0 1.0
OE1 B:GLU166 2.7 72.5 1.0
OE2 B:GLU166 3.0 70.8 1.0
CG B:GLU116 3.2 49.8 1.0
CD B:GLU166 3.2 71.9 1.0
CD B:GLU112 3.3 55.3 1.0
CD B:GLU116 3.3 52.0 1.0
MG B:MG306 3.9 62.2 1.0
OE2 B:GLU115 3.9 58.2 1.0
OE2 B:GLU112 4.0 57.6 1.0
CG B:GLU112 4.2 53.1 1.0
P B:AMP402 4.2 79.3 1.0
MG B:MG304 4.2 48.3 1.0
OE2 B:GLU116 4.6 49.4 1.0
O B:ALA96 4.6 37.3 1.0
CB B:GLU115 4.6 52.8 1.0
O5' B:AMP402 4.6 80.0 1.0
CB B:GLU116 4.6 49.8 1.0
CG B:GLU166 4.7 71.4 1.0
O2P B:AMP402 4.7 78.7 1.0
O B:GLU112 4.9 45.6 1.0
N B:GLU116 5.0 47.8 1.0
O B:HOH440 5.0 78.6 1.0

Magnesium binding site 6 out of 6 in 2dsd

Go back to Magnesium Binding Sites List in 2dsd
Magnesium binding site 6 out of 6 in the Crystal Structure of Human Adp-Ribose Pyrophosphatase NUDT5 in Complex with Magnesium and Amp


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 Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:62.2
occ:1.00
 OE2 B:GLU112 2.7 57.6 1.0
O2P B:AMP402 2.7 78.7 1.0
OE1 B:GLU112 3.4 58.2 1.0
CD B:GLU112 3.4 55.3 1.0
O3P B:AMP402 3.6 80.0 1.0
P B:AMP402 3.7 79.3 1.0
NH1 B:ARG111 3.7 42.3 1.0
MG B:MG305 3.9 62.4 1.0
O5' B:AMP402 4.0 80.0 1.0
OE2 B:GLU115 4.2 58.2 1.0
NH2 B:ARG111 4.6 44.4 1.0
N B:LEU98 4.6 49.6 1.0
CZ B:ARG111 4.7 43.9 1.0
C5' B:AMP402 4.7 81.5 1.0
O B:LEU98 4.7 49.2 1.0
CA B:GLY97 4.7 44.0 1.0
CG B:GLU112 4.9 53.1 1.0

Reference:

M.Zha, C.Zhong, Y.Peng, H.Hu, J.Ding. Crystal Structures of Human NUDT5 Reveal Insights Into the Structural Basis of the Substrate Specificity J.Mol.Biol. V. 364 1021 2006.
ISSN: ISSN 0022-2836
PubMed: 17052728
DOI: 10.1016/J.JMB.2006.09.078
Page generated: Tue Aug 13 22:35:27 2024

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