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Magnesium in PDB 3v8e: Crystal Structure of the Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde

Enzymatic activity of Crystal Structure of the Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde

All present enzymatic activity of Crystal Structure of the Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde:
3.5.1.19;

Protein crystallography data

The structure of Crystal Structure of the Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde, PDB code: 3v8e was solved by K.A.Hoadley, B.C.Smith, J.M.Denu, J.L.Keck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.71
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 298.717, 298.717, 112.652, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 20.3

Other elements in 3v8e:

The structure of Crystal Structure of the Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde also contains other interesting chemical elements:

Zinc (Zn) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde (pdb code 3v8e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of the Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde, PDB code: 3v8e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3v8e

Go back to Magnesium Binding Sites List in 3v8e
Magnesium binding site 1 out of 7 in the Crystal Structure of the Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde


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 Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:51.2
occ:1.00
 O A:HOH421 2.3 46.3 1.0
O A:HOH440 2.4 43.8 1.0
OG1 A:THR21 2.4 34.1 1.0
O A:GLY18 2.4 33.0 1.0
O A:HOH439 2.5 28.5 1.0
O A:PRO16 2.7 32.3 1.0
CB A:THR21 3.5 33.5 1.0
C A:GLY18 3.6 32.2 1.0
C A:PRO16 3.7 32.7 1.0
N A:THR21 3.9 32.5 1.0
N A:GLY18 4.1 31.5 1.0
CA A:THR21 4.3 32.5 1.0
CA A:PRO16 4.3 32.8 1.0
O A:SER15 4.4 30.4 1.0
CA A:GLY18 4.4 31.4 1.0
C A:LEU17 4.5 31.9 1.0
N A:SER19 4.6 32.1 1.0
CG2 A:THR21 4.6 33.5 1.0
C A:SER19 4.6 31.9 1.0
N A:LEU20 4.6 31.1 1.0
CA A:SER19 4.7 31.9 1.0
N A:LEU17 4.7 32.8 1.0
O A:LEU17 4.9 32.5 1.0
CA A:LEU17 4.9 32.9 1.0

Magnesium binding site 2 out of 7 in 3v8e

Go back to Magnesium Binding Sites List in 3v8e
Magnesium binding site 2 out of 7 in the Crystal Structure of the Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde


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 Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:43.2
occ:1.00
 O B:HOH521 2.2 41.1 1.0
OG1 B:THR21 2.3 29.4 1.0
O B:GLY18 2.4 26.4 1.0
O B:HOH512 2.4 45.4 1.0
O B:PRO16 2.5 28.6 1.0
O B:HOH513 2.9 26.9 1.0
C B:GLY18 3.5 25.9 1.0
CB B:THR21 3.5 30.4 1.0
C B:PRO16 3.6 28.6 1.0
N B:THR21 4.0 28.9 1.0
N B:GLY18 4.0 26.4 1.0
O B:SER15 4.2 27.9 1.0
CA B:GLY18 4.3 25.6 1.0
CA B:PRO16 4.3 29.0 1.0
C B:LEU17 4.3 27.0 1.0
CA B:THR21 4.4 29.6 1.0
N B:SER19 4.5 25.8 1.0
N B:LEU17 4.6 28.2 1.0
C B:SER19 4.6 27.2 1.0
N B:LEU20 4.6 26.7 1.0
CG2 B:THR21 4.6 30.7 1.0
CA B:SER19 4.6 26.5 1.0
CA B:LEU17 4.8 27.9 1.0
O B:LEU17 4.8 26.8 1.0

Magnesium binding site 3 out of 7 in 3v8e

Go back to Magnesium Binding Sites List in 3v8e
Magnesium binding site 3 out of 7 in the Crystal Structure of the Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde


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 Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:60.4
occ:1.00
 O C:HOH429 2.5 52.9 1.0
O C:PRO16 2.5 44.7 1.0
O C:GLY18 2.5 45.8 1.0
OG1 C:THR21 2.6 45.0 1.0
O C:HOH430 2.7 53.5 1.0
O C:HOH423 2.8 38.2 1.0
C C:PRO16 3.6 44.6 1.0
C C:GLY18 3.7 43.8 1.0
CB C:THR21 3.8 44.3 1.0
N C:THR21 4.2 43.0 1.0
N C:GLY18 4.3 43.2 1.0
CA C:PRO16 4.3 44.6 1.0
O C:SER15 4.5 41.8 1.0
C C:LEU17 4.6 44.0 1.0
CA C:GLY18 4.6 42.1 1.0
CA C:THR21 4.6 42.7 1.0
N C:SER19 4.6 43.5 1.0
N C:LEU17 4.7 44.1 1.0
C C:SER19 4.7 44.1 1.0
CA C:SER19 4.7 43.9 1.0
N C:LEU20 4.7 42.5 1.0
CG2 C:THR21 4.8 43.4 1.0
CA C:LEU17 4.9 44.3 1.0

Magnesium binding site 4 out of 7 in 3v8e

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Magnesium binding site 4 out of 7 in the Crystal Structure of the Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde


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 Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:69.3
occ:1.00
 O D:GLY18 2.4 62.6 1.0
O D:HOH420 2.5 50.6 1.0
O D:HOH414 2.5 51.1 1.0
OG1 D:THR21 2.6 63.5 1.0
O D:PRO16 2.7 66.5 1.0
C D:GLY18 3.6 60.6 1.0
CB D:THR21 3.7 63.6 1.0
C D:PRO16 3.8 65.3 1.0
N D:THR21 4.2 61.3 1.0
N D:GLY18 4.4 61.6 1.0
CA D:PRO16 4.4 65.6 1.0
N D:SER19 4.5 59.5 1.0
CA D:SER19 4.5 60.1 1.0
C D:LEU17 4.5 62.7 1.0
CA D:GLY18 4.6 59.8 1.0
O D:SER15 4.6 60.8 1.0
C D:SER19 4.6 59.8 1.0
CA D:THR21 4.6 61.5 1.0
N D:LEU20 4.7 58.8 1.0
N D:LEU17 4.8 64.4 1.0
CG2 D:THR21 4.8 62.6 1.0
O D:LEU17 4.8 63.7 1.0
CA D:LEU17 5.0 64.0 1.0

Magnesium binding site 5 out of 7 in 3v8e

Go back to Magnesium Binding Sites List in 3v8e
Magnesium binding site 5 out of 7 in the Crystal Structure of the Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde


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 Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:45.3
occ:1.00
 OG1 E:THR21 2.3 39.5 1.0
O E:HOH415 2.4 44.5 1.0
O E:PRO16 2.4 39.6 1.0
O E:GLY18 2.6 40.3 1.0
O E:HOH414 2.9 33.2 1.0
CB E:THR21 3.4 40.0 1.0
C E:PRO16 3.5 38.6 1.0
C E:GLY18 3.7 38.5 1.0
CA E:PRO16 4.1 38.4 1.0
N E:THR21 4.2 39.1 1.0
N E:GLY18 4.2 37.1 1.0
O E:SER15 4.2 37.5 1.0
CA E:THR21 4.4 39.5 1.0
CG2 E:THR21 4.4 38.8 1.0
C E:LEU17 4.4 38.0 1.0
CA E:GLY18 4.5 37.2 1.0
N E:LEU17 4.5 37.8 1.0
N E:SER19 4.7 38.4 1.0
CA E:LEU17 4.8 38.0 1.0
C E:SER19 4.8 39.5 1.0
CA E:SER19 4.9 39.2 1.0
O E:LEU17 4.9 39.2 1.0
N E:LEU20 4.9 38.5 1.0

Magnesium binding site 6 out of 7 in 3v8e

Go back to Magnesium Binding Sites List in 3v8e
Magnesium binding site 6 out of 7 in the Crystal Structure of the Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde


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 Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:62.5
occ:1.00
 O F:GLY18 2.4 63.6 1.0
O F:HOH410 2.6 60.6 1.0
O F:HOH411 2.6 55.2 1.0
OG1 F:THR21 2.6 63.4 1.0
O F:PRO16 2.7 63.3 1.0
C F:GLY18 3.6 62.4 1.0
CB F:THR21 3.8 65.4 1.0
C F:PRO16 3.8 62.5 1.0
N F:GLY18 4.3 61.4 1.0
N F:THR21 4.4 66.2 1.0
C F:LEU17 4.4 61.5 1.0
N F:SER19 4.5 62.5 1.0
CA F:GLY18 4.5 60.5 1.0
CA F:SER19 4.5 63.4 1.0
C F:SER19 4.6 63.8 1.0
O F:SER15 4.6 60.8 1.0
CA F:PRO16 4.7 62.9 1.0
CA F:THR21 4.7 66.0 1.0
O F:LEU17 4.7 62.2 1.0
N F:LEU17 4.7 61.5 1.0
CG2 F:THR21 4.8 64.7 1.0
O F:SER19 4.8 64.7 1.0
CA F:LEU17 4.9 61.5 1.0
N F:LEU20 4.9 63.2 1.0

Magnesium binding site 7 out of 7 in 3v8e

Go back to Magnesium Binding Sites List in 3v8e
Magnesium binding site 7 out of 7 in the Crystal Structure of the Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde


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 the Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:79.2
occ:1.00
 O G:HOH409 2.1 63.7 1.0
O G:GLY18 2.2 79.8 1.0
O G:PRO16 2.6 80.4 1.0
O B:HOH469 2.7 72.2 1.0
OG1 G:THR21 2.8 80.1 1.0
C G:GLY18 3.5 77.6 1.0
C G:PRO16 3.8 80.1 1.0
CB G:THR21 3.9 80.7 1.0
N G:GLY18 4.2 77.3 1.0
C G:LEU17 4.2 78.0 1.0
N G:SER19 4.4 76.0 1.0
CA G:SER19 4.4 76.7 1.0
CA G:GLY18 4.4 76.1 1.0
O G:LEU17 4.5 78.7 1.0
N G:THR21 4.5 77.8 1.0
C G:SER19 4.6 76.2 1.0
N G:LEU17 4.7 79.4 1.0
CA G:LEU17 4.7 79.3 1.0
CA G:PRO16 4.7 80.5 1.0
O G:SER15 4.9 77.1 1.0
CA G:THR21 4.9 78.8 1.0
N G:LEU20 4.9 75.1 1.0
O G:SER19 5.0 77.2 1.0
CG2 G:THR21 5.0 80.3 1.0

Reference:

B.C.Smith, M.A.Anderson, K.A.Hoadley, J.L.Keck, W.W.Cleland, J.M.Denu. Structural and Kinetic Isotope Effect Studies of Nicotinamidase (PNC1) From Saccharomyces Cerevisiae. Biochemistry V. 51 243 2012.
ISSN: ISSN 0006-2960
PubMed: 22229411
DOI: 10.1021/BI2015508
Page generated: Thu Aug 15 12:46:26 2024

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