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Zinc in PDB 5nel: Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with Thiametg

Protein crystallography data

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

Resolution Low / High (Å) 48.34 / 2.73
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.437, 117.975, 98.199, 90.00, 102.10, 90.00
R / Rfree (%) 20.5 / 26.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with Thiametg (pdb code 5nel). 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 Thiametg, PDB code: 5nel:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5nel

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Zinc binding site 1 out of 4 in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with Thiametg


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 Thiametg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:63.6
occ:1.00
O A:HOH402 2.1 30.0 1.0
OD1 A:ASP77 2.1 66.9 1.0
NE2 A:HIS130 2.1 40.0 1.0
NE2 A:HIS126 2.3 52.6 1.0
O A:ACT302 2.4 96.9 1.0
OXT A:ACT302 2.6 89.8 1.0
C A:ACT302 2.9 89.2 1.0
CE1 A:HIS130 3.0 46.5 1.0
CG A:ASP77 3.0 67.0 1.0
OD2 A:ASP77 3.2 70.1 1.0
CE1 A:HIS126 3.2 56.5 1.0
CD2 A:HIS130 3.3 45.9 1.0
CD2 A:HIS126 3.3 52.5 1.0
OD2 A:ASP76 3.7 63.2 1.0
CB A:ASP76 4.1 55.7 1.0
ND1 A:HIS130 4.2 43.5 1.0
CG A:HIS130 4.3 44.2 1.0
CG A:ASP76 4.3 57.7 1.0
ND1 A:HIS126 4.4 54.5 1.0
CH3 A:ACT302 4.4 75.8 1.0
CG A:HIS126 4.4 55.7 1.0
CB A:ASP77 4.5 54.3 1.0
CA A:PRO166 4.6 59.9 1.0
CD2 A:HIS230 4.7 70.8 1.0
N A:ASP77 4.7 38.2 1.0
NE2 A:HIS230 4.7 69.4 1.0
N A:TYR167 4.9 64.8 1.0
CB A:PRO166 4.9 65.5 1.0
CA A:ASP77 4.9 47.2 1.0

Zinc binding site 2 out of 4 in 5nel

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Zinc binding site 2 out of 4 in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with Thiametg


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 Thiametg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:64.8
occ:1.00
NE2 B:HIS130 2.1 44.8 1.0
OD1 B:ASP77 2.2 74.5 1.0
NE2 B:HIS126 2.2 41.3 1.0
O4 B:NHT302 2.3 97.2 0.9
O6 B:NHT302 2.3 44.9 0.9
C6 B:NHT302 2.8 52.6 0.9
CD2 B:HIS130 3.0 43.1 1.0
CG B:ASP77 3.1 66.7 1.0
CE1 B:HIS126 3.2 39.4 1.0
CE1 B:HIS130 3.2 43.9 1.0
OD2 B:ASP77 3.2 65.1 1.0
CD2 B:HIS126 3.2 47.8 1.0
C4 B:NHT302 3.4 90.7 0.9
C5 B:NHT302 3.6 75.8 0.9
OD2 B:ASP76 4.1 64.8 1.0
CG B:HIS130 4.2 45.8 1.0
ND1 B:HIS130 4.2 43.3 1.0
ND1 B:HIS126 4.3 45.2 1.0
CA B:PRO166 4.3 63.8 1.0
CB B:ASP76 4.4 77.3 1.0
CG B:HIS126 4.4 47.4 1.0
CB B:PRO166 4.5 69.7 1.0
CB B:ASP77 4.5 58.9 1.0
CD2 B:HIS230 4.5 57.2 1.0
NE2 B:HIS230 4.6 63.9 1.0
C3 B:NHT302 4.7 93.4 0.9
CG B:ASP76 4.8 73.6 1.0
N B:TYR167 4.8 60.5 1.0
N B:ASP77 4.9 57.1 1.0
O5 B:NHT302 4.9 79.5 0.9
CG B:PRO166 5.0 68.7 1.0

Zinc binding site 3 out of 4 in 5nel

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Zinc binding site 3 out of 4 in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with Thiametg


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 Thiametg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:65.6
occ:1.00
O C:HOH403 2.1 30.0 1.0
NE2 C:HIS130 2.1 47.5 1.0
OD1 C:ASP77 2.2 66.8 1.0
NE2 C:HIS126 2.2 71.1 1.0
OXT C:ACT302 2.4 76.9 1.0
O C:ACT302 2.7 81.7 1.0
C C:ACT302 2.9 79.6 1.0
CE1 C:HIS130 3.0 54.5 1.0
CG C:ASP77 3.1 65.5 1.0
CD2 C:HIS130 3.1 52.7 1.0
CD2 C:HIS126 3.2 74.5 1.0
CE1 C:HIS126 3.2 72.7 1.0
OD2 C:ASP77 3.3 68.7 1.0
OD2 C:ASP76 3.9 67.3 1.0
CB C:ASP76 4.1 75.0 1.0
ND1 C:HIS130 4.1 54.3 1.0
CG C:HIS130 4.2 52.7 1.0
ND1 C:HIS126 4.3 72.9 1.0
CG C:HIS126 4.3 71.7 1.0
CH3 C:ACT302 4.4 73.9 1.0
CG C:ASP76 4.4 72.6 1.0
CE1 C:HIS230 4.5 98.8 1.0
CB C:ASP77 4.5 62.6 1.0
CA C:PRO166 4.6 47.8 1.0
ND1 C:HIS230 4.7 0.4 1.0
N C:ASP77 4.7 56.8 1.0
N C:TYR167 4.9 53.7 1.0
CB C:PRO166 4.9 48.3 1.0
CA C:ASP77 4.9 57.9 1.0

Zinc binding site 4 out of 4 in 5nel

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Zinc binding site 4 out of 4 in the Crystal Structure of the Polysaccharide Deacetylase BC1974 From Bacillus Cereus in Complex with Thiametg


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 Thiametg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:72.4
occ:1.00
NE2 D:HIS130 2.1 29.6 1.0
O4 D:NHT302 2.1 90.7 0.8
NE2 D:HIS126 2.2 44.5 1.0
O6 D:NHT302 2.2 47.1 0.8
OD1 D:ASP77 2.2 63.2 1.0
CG D:ASP77 3.0 58.5 1.0
CD2 D:HIS130 3.0 35.1 1.0
OD2 D:ASP77 3.0 65.3 1.0
C6 D:NHT302 3.1 43.5 0.8
CE1 D:HIS130 3.1 48.4 1.0
CE1 D:HIS126 3.2 48.8 1.0
CD2 D:HIS126 3.2 50.3 1.0
C4 D:NHT302 3.3 83.7 0.8
C5 D:NHT302 3.7 64.2 0.8
CG D:HIS130 4.2 40.0 1.0
NE2 D:HIS230 4.2 72.0 1.0
ND1 D:HIS130 4.2 34.8 1.0
OD2 D:ASP76 4.2 55.0 1.0
ND1 D:HIS126 4.3 48.9 1.0
CB D:ASP76 4.3 69.0 1.0
CG D:HIS126 4.3 45.2 1.0
CD2 D:HIS230 4.4 65.2 1.0
CA D:PRO166 4.5 50.7 1.0
C3 D:NHT302 4.5 82.9 0.8
CB D:ASP77 4.5 52.3 1.0
CB D:PRO166 4.6 45.5 1.0
CG D:ASP76 4.8 67.6 1.0
O3 D:NHT302 4.9 76.1 0.8
N D:TYR167 4.9 61.8 1.0
N D:ASP77 4.9 55.5 1.0
O5 D:NHT302 5.0 67.0 0.8

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 06:35:24 2020

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