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Zinc 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:

Magnesium (Mg) 7 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of the Yeast Nicotinamidase PNC1P Bound to the Inhibitor Nicotinaldehyde, PDB code: 3v8e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 3v8e

Go back to Zinc Binding Sites List in 3v8e
Zinc 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 Zinc with other atoms in the Zn 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:Zn300

b:84.0
occ:1.00
 OD2 A:ASP51 2.2 44.4 1.0
O A:HOH449 2.6 47.1 1.0
NE2 A:HIS94 2.6 26.8 1.0
NE2 A:HIS53 2.7 27.8 1.0
N1 A:JJJ167 2.7 50.0 1.0
C2 A:JJJ167 3.1 50.6 1.0
O A:HOH448 3.2 57.2 1.0
CG A:ASP51 3.4 37.2 1.0
CE1 A:HIS53 3.5 27.8 1.0
CE1 A:HIS94 3.5 26.6 1.0
CD2 A:HIS94 3.6 26.1 1.0
CD2 A:HIS53 3.7 28.0 1.0
C6 A:JJJ167 3.8 48.0 1.0
OD1 A:ASP51 4.1 38.7 1.0
OE1 A:GLU129 4.1 27.9 0.5
CB A:ASP51 4.4 33.4 1.0
OE2 A:GLU129 4.5 28.9 0.5
C3 A:JJJ167 4.5 47.3 1.0
CZ A:PHE13 4.5 27.4 1.0
ND1 A:HIS94 4.7 26.9 1.0
CD A:GLU129 4.7 29.1 0.5
ND1 A:HIS53 4.7 27.7 1.0
CG A:HIS94 4.8 26.4 1.0
CG A:HIS53 4.8 28.0 1.0
OG A:SER59 4.9 29.8 1.0

Zinc binding site 2 out of 7 in 3v8e

Go back to Zinc Binding Sites List in 3v8e
Zinc 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 Zinc with other atoms in the Zn 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:Zn300

b:95.8
occ:1.00
 OD2 B:ASP51 2.1 41.6 1.0
N1 B:JJJ167 2.5 53.4 1.0
NE2 B:HIS53 2.6 28.8 1.0
O B:HOH527 2.6 51.3 1.0
NE2 B:HIS94 2.7 29.0 1.0
O B:HOH520 3.1 45.1 1.0
C2 B:JJJ167 3.1 53.2 1.0
CE1 B:HIS53 3.3 28.9 1.0
CG B:ASP51 3.3 36.2 1.0
C6 B:JJJ167 3.6 51.1 1.0
CE1 B:HIS94 3.6 28.8 1.0
CD2 B:HIS53 3.7 28.0 1.0
CD2 B:HIS94 3.8 28.0 1.0
OD1 B:ASP51 4.1 37.2 1.0
OE1 B:GLU129 4.1 29.8 0.5
CB B:ASP51 4.3 31.9 1.0
OE2 B:GLU129 4.5 30.4 0.5
C3 B:JJJ167 4.5 51.3 1.0
ND1 B:HIS53 4.6 28.8 1.0
CD B:GLU129 4.7 30.8 0.5
ND1 B:HIS94 4.8 27.9 1.0
CZ B:PHE13 4.8 26.6 1.0
CG B:HIS53 4.8 27.8 1.0
OG B:SER59 4.8 28.7 1.0
C5 B:JJJ167 4.8 50.2 1.0
CG B:HIS94 4.9 27.1 1.0

Zinc binding site 3 out of 7 in 3v8e

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Zinc 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 Zinc with other atoms in the Zn 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:Zn300

b:0.1
occ:1.00
 OD2 C:ASP51 2.2 51.9 1.0
O C:HOH431 2.4 74.2 1.0
NE2 C:HIS94 2.7 42.1 1.0
NE2 C:HIS53 2.7 38.1 1.0
N1 C:JJJ167 2.7 64.5 1.0
O C:HOH432 3.1 48.6 1.0
C2 C:JJJ167 3.2 64.3 1.0
CG C:ASP51 3.4 44.9 1.0
CE1 C:HIS53 3.4 37.8 1.0
CE1 C:HIS94 3.6 42.4 1.0
CD2 C:HIS94 3.6 41.2 1.0
CD2 C:HIS53 3.8 38.3 1.0
C6 C:JJJ167 3.8 64.5 1.0
OE2 C:GLU129 4.0 40.1 0.5
OE1 C:GLU129 4.0 38.6 0.5
OD1 C:ASP51 4.0 44.3 1.0
CD C:GLU129 4.4 40.1 0.5
CB C:ASP51 4.5 41.1 1.0
C3 C:JJJ167 4.6 62.5 1.0
ND1 C:HIS53 4.7 37.1 1.0
CZ C:PHE13 4.7 38.3 1.0
ND1 C:HIS94 4.7 42.9 1.0
CG C:HIS94 4.8 41.6 1.0
CG C:HIS53 4.9 38.0 1.0
OG C:SER59 4.9 47.2 1.0

Zinc binding site 4 out of 7 in 3v8e

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Zinc 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 Zinc with other atoms in the Zn 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:Zn300

b:0.6
occ:1.00
 OD2 D:ASP51 2.4 58.4 1.0
NE2 D:HIS53 2.5 47.9 1.0
NE2 D:HIS94 2.6 56.3 1.0
N1 D:JJJ167 2.7 74.5 1.0
O D:HOH425 2.7 58.3 1.0
O D:HOH426 2.8 96.3 1.0
C2 D:JJJ167 3.2 72.2 1.0
CE1 D:HIS53 3.3 46.3 1.0
CG D:ASP51 3.4 54.3 1.0
CE1 D:HIS94 3.5 57.1 1.0
CD2 D:HIS94 3.6 55.0 1.0
CD2 D:HIS53 3.6 47.1 1.0
C6 D:JJJ167 3.8 74.5 1.0
OD1 D:ASP51 4.1 55.5 1.0
OE1 D:GLU129 4.1 48.3 0.5
CB D:ASP51 4.3 50.9 1.0
ND1 D:HIS53 4.5 45.4 1.0
C3 D:JJJ167 4.6 70.0 1.0
CZ D:PHE13 4.7 51.6 1.0
ND1 D:HIS94 4.7 57.4 1.0
CG D:HIS53 4.7 45.6 1.0
CG D:HIS94 4.7 55.4 1.0
CD D:GLU129 4.9 50.0 0.5
OE2 D:GLU129 4.9 50.5 0.5

Zinc binding site 5 out of 7 in 3v8e

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Zinc 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 Zinc with other atoms in the Zn 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:Zn300

b:0.1
occ:1.00
 OD2 E:ASP51 2.3 58.1 1.0
N1 E:JJJ167 2.3 68.9 1.0
NE2 E:HIS53 2.4 43.1 1.0
NE2 E:HIS94 2.6 44.5 1.0
O E:HOH419 2.8 60.1 1.0
C2 E:JJJ167 3.1 68.9 1.0
C6 E:JJJ167 3.2 69.3 1.0
O E:HOH420 3.3 62.5 1.0
CE1 E:HIS53 3.3 43.3 1.0
CG E:ASP51 3.5 51.5 1.0
CD2 E:HIS53 3.5 42.6 1.0
CD2 E:HIS94 3.5 42.4 1.0
CE1 E:HIS94 3.5 44.0 1.0
OE1 E:GLU129 4.2 44.2 0.5
OD1 E:ASP51 4.3 53.1 1.0
CB E:ASP51 4.4 45.6 1.0
C3 E:JJJ167 4.5 66.3 1.0
ND1 E:HIS53 4.5 43.0 1.0
C5 E:JJJ167 4.6 67.4 1.0
OE2 E:GLU129 4.6 46.7 0.5
CG E:HIS53 4.6 42.4 1.0
ND1 E:HIS94 4.7 43.5 1.0
CG E:HIS94 4.7 41.8 1.0
CZ E:PHE13 4.7 40.5 1.0
CD E:GLU129 4.8 46.6 0.5
OG E:SER59 5.0 50.6 1.0

Zinc binding site 6 out of 7 in 3v8e

Go back to Zinc Binding Sites List in 3v8e
Zinc 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 Zinc with other atoms in the Zn 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:Zn300

b:0.5
occ:1.00
 OD2 F:ASP51 2.2 75.6 1.0
O F:HOH412 2.3 95.0 1.0
NE2 F:HIS53 2.7 66.8 1.0
N1 F:JJJ167 2.8 90.3 1.0
NE2 F:HIS94 3.0 69.7 1.0
C2 F:JJJ167 3.1 89.5 1.0
CG F:ASP51 3.3 72.5 1.0
CE1 F:HIS53 3.4 66.4 1.0
OE1 F:GLU129 3.6 66.4 0.5
CE1 F:HIS94 3.8 71.4 1.0
CD2 F:HIS53 3.9 65.5 1.0
OD1 F:ASP51 3.9 75.5 1.0
C6 F:JJJ167 4.0 89.6 1.0
CD2 F:HIS94 4.1 68.0 1.0
OE2 F:GLU129 4.2 69.3 0.5
CD F:GLU129 4.3 68.7 0.5
CB F:ASP51 4.5 67.8 1.0
C3 F:JJJ167 4.5 88.7 1.0
ND1 F:HIS53 4.6 65.0 1.0
CZ F:PHE13 4.9 62.6 1.0
CE1 F:TYR131 4.9 76.0 1.0
CG F:HIS53 4.9 64.6 1.0
OG F:SER59 5.0 73.4 1.0
O F:TYR130 5.0 68.7 1.0

Zinc binding site 7 out of 7 in 3v8e

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Zinc 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 Zinc with other atoms in the Zn 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:Zn300

b:0.4
occ:1.00
 NE2 G:HIS53 2.5 69.8 1.0
OD2 G:ASP51 2.6 72.8 1.0
N1 G:JJJ167 2.7 91.7 1.0
NE2 G:HIS94 2.8 69.6 1.0
CE1 G:HIS53 3.0 69.6 1.0
C2 G:JJJ167 3.5 90.6 1.0
CE1 G:HIS94 3.5 70.4 1.0
CD2 G:HIS53 3.6 69.1 1.0
C6 G:JJJ167 3.6 92.8 1.0
OE2 G:GLU129 3.7 67.6 0.5
CG G:ASP51 3.8 70.2 1.0
CD2 G:HIS94 3.9 68.4 1.0
OG G:SER59 4.2 75.7 1.0
ND1 G:HIS53 4.2 67.1 1.0
CG G:HIS53 4.5 67.3 1.0
OD1 G:ASP51 4.6 70.3 1.0
CD G:GLU129 4.6 69.6 0.5
ND1 G:HIS94 4.7 70.1 1.0
OE1 G:GLU129 4.8 70.3 0.5
CD1 G:TRP91 4.8 79.0 1.0
CB G:ASP51 4.8 66.9 1.0
C3 G:JJJ167 4.8 90.6 1.0
CG G:HIS94 5.0 68.5 1.0
C5 G:JJJ167 5.0 92.1 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: Sat Oct 26 17:37:05 2024

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