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Zinc in PDB 5n1p: Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide

Protein crystallography data

The structure of Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide, PDB code: 5n1p was solved by P.Giastas, A.Andreou, E.E.Eliopoulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.45 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 196.103, 44.347, 99.132, 90.00, 98.83, 90.00
R / Rfree (%) 16.1 / 18

Other elements in 5n1p:

The structure of Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide (pdb code 5n1p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide, PDB code: 5n1p:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5n1p

Go back to Zinc Binding Sites List in 5n1p
Zinc binding site 1 out of 4 in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide


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 Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:30.7
occ:1.00
O14 A:8GK301 2.1 49.5 1.0
NE2 A:HIS126 2.1 18.7 1.0
NE2 A:HIS130 2.1 23.8 1.0
OD1 A:ASP77 2.2 25.3 1.0
O A:HOH407 2.3 30.3 1.0
O12 A:8GK301 2.5 34.2 1.0
N13 A:8GK301 3.0 56.5 1.0
C1 A:8GK301 3.0 51.2 1.0
CD2 A:HIS130 3.1 22.9 1.0
CD2 A:HIS126 3.1 20.6 1.0
CG A:ASP77 3.1 28.8 1.0
CE1 A:HIS126 3.2 19.4 1.0
CE1 A:HIS130 3.2 24.1 1.0
OD2 A:ASP77 3.3 31.2 1.0
C11 A:8GK301 4.0 51.0 1.0
CG A:HIS130 4.2 24.2 1.0
CG A:HIS126 4.2 18.3 1.0
CB A:ASP76 4.2 20.9 1.0
ND1 A:HIS130 4.2 27.1 1.0
ND1 A:HIS126 4.3 19.0 1.0
OD2 A:ASP76 4.3 25.6 1.0
C2 A:8GK301 4.3 53.6 1.0
NE2 A:HIS230 4.5 36.6 1.0
CB A:ASP77 4.5 21.1 1.0
CD2 A:HIS230 4.5 29.6 1.0
CA A:PRO166 4.7 19.8 1.0
C3 A:8GK301 4.7 58.5 1.0
CG A:ASP76 4.7 24.0 1.0
CB A:PRO166 4.9 21.6 1.0
N A:ASP77 4.9 20.3 1.0
CA A:ASP77 4.9 20.6 1.0

Zinc binding site 2 out of 4 in 5n1p

Go back to Zinc Binding Sites List in 5n1p
Zinc binding site 2 out of 4 in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide


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 Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:23.9
occ:1.00
O B:HOH419 2.1 26.6 1.0
NE2 B:HIS126 2.1 18.5 1.0
OD1 B:ASP77 2.1 23.9 1.0
NE2 B:HIS130 2.1 21.1 1.0
O14 B:8GK301 2.2 26.0 0.9
O12 B:8GK301 2.4 23.3 0.9
C1 B:8GK301 3.0 40.2 0.9
CD2 B:HIS126 3.0 20.8 1.0
CD2 B:HIS130 3.1 21.5 1.0
N13 B:8GK301 3.1 42.0 0.9
CE1 B:HIS126 3.1 18.4 1.0
CG B:ASP77 3.1 28.0 1.0
CE1 B:HIS130 3.1 23.9 1.0
OD2 B:ASP77 3.4 29.1 1.0
ND1 B:HIS126 4.2 18.0 1.0
CG B:HIS126 4.2 18.1 1.0
ND1 B:HIS130 4.2 25.7 1.0
C11 B:8GK301 4.2 50.2 0.9
CG B:HIS130 4.2 23.2 1.0
OD2 B:ASP76 4.2 21.8 1.0
CB B:ASP76 4.2 18.8 1.0
C2 B:8GK301 4.3 45.0 0.9
NE2 B:HIS230 4.5 24.4 1.0
CB B:ASP77 4.5 19.2 1.0
CD2 B:HIS230 4.5 22.9 1.0
CA B:PRO166 4.6 20.9 1.0
CG B:ASP76 4.7 20.2 1.0
C3 B:8GK301 4.8 52.6 0.9
CB B:PRO166 4.9 19.6 1.0
N B:ASP77 4.9 17.3 1.0
CA B:ASP77 4.9 17.6 1.0

Zinc binding site 3 out of 4 in 5n1p

Go back to Zinc Binding Sites List in 5n1p
Zinc binding site 3 out of 4 in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide


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 Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:25.4
occ:1.00
NE2 C:HIS126 2.1 23.4 1.0
O14 C:8GK301 2.1 49.4 1.0
O C:HOH407 2.1 32.2 1.0
OD1 C:ASP77 2.1 23.2 1.0
NE2 C:HIS130 2.1 24.1 1.0
O12 C:8GK301 2.4 29.3 1.0
N13 C:8GK301 2.9 63.4 1.0
C1 C:8GK301 3.0 52.9 1.0
CD2 C:HIS126 3.1 23.6 1.0
CD2 C:HIS130 3.1 21.6 1.0
CG C:ASP77 3.1 29.6 1.0
CE1 C:HIS126 3.1 20.6 1.0
CE1 C:HIS130 3.1 24.6 1.0
OD2 C:ASP77 3.3 34.4 1.0
OD2 C:ASP76 4.2 31.1 1.0
ND1 C:HIS126 4.2 20.1 1.0
CG C:HIS126 4.2 19.9 1.0
CG C:HIS130 4.2 23.0 1.0
ND1 C:HIS130 4.2 24.2 1.0
CB C:ASP76 4.3 22.0 1.0
C2 C:8GK301 4.4 44.1 1.0
C11 C:8GK301 4.4 42.3 1.0
CB C:ASP77 4.5 22.1 1.0
NE2 C:HIS230 4.6 43.2 1.0
CA C:PRO166 4.6 20.2 1.0
CG C:ASP76 4.7 27.6 1.0
CD2 C:HIS230 4.7 41.4 1.0
N C:ASP77 4.9 24.7 1.0
C3 C:8GK301 4.9 38.7 1.0
CB C:PRO166 4.9 22.3 1.0
CA C:ASP77 4.9 22.0 1.0

Zinc binding site 4 out of 4 in 5n1p

Go back to Zinc Binding Sites List in 5n1p
Zinc binding site 4 out of 4 in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide


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 Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with N-Hydroxynaphthalene-1-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn304

b:23.8
occ:1.00
NE2 D:HIS130 2.1 25.9 1.0
OD1 D:ASP77 2.1 23.6 1.0
NE2 D:HIS126 2.1 20.5 1.0
O D:HOH408 2.1 25.6 1.0
O14 D:8GK301 2.1 27.4 0.9
O12 D:8GK301 2.4 23.4 0.9
C1 D:8GK301 3.0 43.2 0.9
CE1 D:HIS130 3.1 26.3 1.0
N13 D:8GK301 3.1 46.5 0.9
CD2 D:HIS126 3.1 21.4 1.0
CE1 D:HIS126 3.1 20.9 1.0
CG D:ASP77 3.1 27.6 1.0
CD2 D:HIS130 3.1 26.4 1.0
OD2 D:ASP77 3.4 28.6 1.0
ND1 D:HIS130 4.2 26.3 1.0
ND1 D:HIS126 4.2 20.3 1.0
CB D:ASP76 4.2 17.9 1.0
C11 D:8GK301 4.2 64.5 0.9
CG D:HIS126 4.2 21.1 1.0
CG D:HIS130 4.2 26.3 1.0
OD2 D:ASP76 4.3 22.7 1.0
C2 D:8GK301 4.4 48.8 0.9
NE2 D:HIS230 4.4 25.4 1.0
CD2 D:HIS230 4.5 25.8 1.0
CB D:ASP77 4.5 21.0 1.0
CA D:PRO166 4.5 21.3 1.0
CG D:ASP76 4.7 20.9 1.0
C3 D:8GK301 4.8 58.8 0.9
CB D:PRO166 4.9 21.4 1.0
N D:ASP77 4.9 18.0 1.0
CA D:ASP77 4.9 19.1 1.0

Reference:

P.Giastas, A.Andreou, A.Papakyriakou, D.Koutsioulis, S.Balomenou, S.J.Tzartos, V.Bouriotis, E.E.Eliopoulos. Structures of the Peptidoglycan N-Acetylglucosamine Deacetylase BC1974 and Its Complexes with Zinc Metalloenzyme Inhibitors. Biochemistry V. 57 753 2018.
ISSN: ISSN 1520-4995
PubMed: 29257674
DOI: 10.1021/ACS.BIOCHEM.7B00919
Page generated: Wed Dec 16 06:34:09 2020

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