Zinc in PDB 8bgp: N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data

Protein crystallography data

The structure of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data, PDB code: 8bgp was solved by W.Rypniewski, K.Biniek-Antosiak, M.Bejger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.70 / 2.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.642, 158.654, 158.517, 90, 90, 90
R / Rfree (%) 21.8 / 26.1

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data (pdb code 8bgp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data, PDB code: 8bgp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 8bgp

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Zinc binding site 1 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:22.6
occ:1.00
OD2 A:ASP221 2.1 35.9 1.0
CG A:ASP221 2.9 37.6 1.0
OD1 A:ASP221 3.1 40.3 1.0
CB A:ASP221 4.4 35.6 1.0

Zinc binding site 2 out of 12 in 8bgp

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Zinc binding site 2 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:24.1
occ:1.00
OD2 A:ASP43 1.8 23.1 1.0
ND1 A:HIS40 2.0 25.5 1.0
O A:HOH401 2.2 12.7 1.0
NE2 A:HIS151 2.3 17.1 1.0
CG A:ASP43 2.7 24.3 1.0
OD1 A:ASP43 2.8 20.7 1.0
CE1 A:HIS40 2.9 30.7 1.0
CG A:HIS40 3.0 26.1 1.0
CD2 A:HIS151 3.2 16.6 1.0
CB A:HIS40 3.3 27.1 1.0
CE1 A:HIS151 3.3 18.1 1.0
NE2 C:HIS259 3.9 26.2 1.0
N A:HIS40 4.0 25.4 1.0
NE2 A:HIS40 4.1 28.3 1.0
CB A:ASP43 4.1 24.0 1.0
CD2 A:HIS40 4.1 26.7 1.0
CE1 C:HIS259 4.2 25.4 1.0
CB A:PRO39 4.3 25.6 1.0
CA A:HIS40 4.3 25.4 1.0
CG A:HIS151 4.4 18.4 1.0
ND1 A:HIS151 4.4 18.8 1.0
OD1 A:ASP42 4.7 39.7 1.0
CG A:PRO39 4.7 24.8 1.0
C A:PRO39 4.8 26.9 1.0
CD A:PRO39 5.0 24.7 1.0

Zinc binding site 3 out of 12 in 8bgp

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Zinc binding site 3 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:58.5
occ:1.00
ND1 A:HIS182 2.4 23.7 1.0
O A:HOH403 2.4 20.6 1.0
O A:HOH404 2.5 17.1 1.0
O A:HOH402 2.9 35.9 1.0
CG A:HIS182 3.3 23.6 1.0
CE1 A:HIS182 3.3 23.2 1.0
CB A:HIS182 3.5 24.2 1.0
CA A:HIS182 3.6 26.0 1.0
CG A:LYS132 3.8 44.5 1.0
O A:PRO181 3.9 30.0 1.0
CD A:LYS132 4.0 49.0 1.0
CD2 A:HIS182 4.4 24.1 1.0
NE2 A:HIS182 4.4 23.1 1.0
N A:SER183 4.5 26.9 1.0
CB A:LYS132 4.6 37.9 1.0
C A:HIS182 4.6 26.7 1.0
N A:HIS182 4.6 27.3 1.0
C A:PRO181 4.6 30.0 1.0

Zinc binding site 4 out of 12 in 8bgp

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Zinc binding site 4 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:30.1
occ:1.00
OD2 B:ASP43 2.0 19.1 1.0
ND1 B:HIS40 2.0 24.3 1.0
NE2 B:HIS151 2.3 24.9 1.0
O B:HOH401 2.5 37.0 1.0
CG B:ASP43 2.8 22.3 1.0
OD1 B:ASP43 2.9 23.7 1.0
CE1 B:HIS40 3.0 28.0 1.0
CG B:HIS40 3.1 24.6 1.0
CD2 B:HIS151 3.3 24.7 1.0
CE1 B:HIS151 3.4 24.1 1.0
CB B:HIS40 3.4 26.7 1.0
NE2 A:HIS259 3.7 38.4 1.0
CE1 A:HIS259 4.1 35.6 1.0
NE2 B:HIS40 4.1 29.8 1.0
CD2 B:HIS40 4.2 24.5 1.0
N B:HIS40 4.2 26.6 1.0
CB B:ASP43 4.2 22.8 1.0
CA B:HIS40 4.4 27.4 1.0
CG B:HIS151 4.4 23.1 1.0
CB B:PRO39 4.5 26.7 1.0
ND1 B:HIS151 4.5 22.6 1.0
OD1 B:ASP42 4.7 26.6 1.0
CG B:PRO39 4.9 27.0 1.0
C B:PRO39 5.0 26.3 1.0

Zinc binding site 5 out of 12 in 8bgp

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Zinc binding site 5 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:60.6
occ:1.00
O B:HOH403 2.4 12.8 1.0
ND1 B:HIS182 2.5 39.5 1.0
O B:HOH404 2.6 20.6 1.0
O B:HOH402 3.2 32.0 1.0
CE1 B:HIS182 3.4 41.2 1.0
CG B:HIS182 3.5 41.7 1.0
CD B:LYS132 3.5 51.1 1.0
CB B:HIS182 3.7 41.0 1.0
CG B:LYS132 3.7 49.9 1.0
CA B:HIS182 3.8 38.0 1.0
O B:PRO181 4.0 46.6 1.0
CB B:LYS132 4.5 42.2 1.0
NE2 B:HIS182 4.6 41.0 1.0
CD2 B:HIS182 4.6 38.6 1.0
N B:SER183 4.7 37.9 1.0
C B:PRO181 4.8 40.0 1.0
N B:HIS182 4.8 39.3 1.0
C B:HIS182 4.8 35.6 1.0
CE B:LYS132 4.9 60.8 1.0

Zinc binding site 6 out of 12 in 8bgp

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Zinc binding site 6 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:31.1
occ:1.00
OD2 C:ASP43 1.9 40.2 1.0
ND1 C:HIS40 2.3 27.5 1.0
NE2 C:HIS151 2.3 23.6 1.0
CG C:ASP43 2.6 39.5 1.0
OD1 C:ASP43 2.7 36.0 1.0
CE1 C:HIS40 3.2 25.6 1.0
O C:HOH402 3.2 17.4 1.0
CG C:HIS40 3.2 26.9 1.0
CE1 C:HIS151 3.3 25.5 1.0
CD2 C:HIS151 3.3 23.5 1.0
CB C:HIS40 3.5 29.6 1.0
NE2 B:HIS259 3.7 55.2 1.0
CB C:ASP43 4.1 38.4 1.0
CE1 B:HIS259 4.1 59.0 1.0
N C:HIS40 4.3 30.0 1.0
NE2 C:HIS40 4.3 25.5 1.0
CD2 C:HIS40 4.4 27.5 1.0
ND1 C:HIS151 4.4 26.4 1.0
CG C:HIS151 4.4 24.1 1.0
CA C:HIS40 4.5 30.7 1.0
CB C:PRO39 4.5 24.6 1.0
OD1 C:ASP42 4.6 40.0 1.0
CG C:PRO39 4.9 23.5 1.0

Zinc binding site 7 out of 12 in 8bgp

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Zinc binding site 7 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:58.6
occ:1.00
ND1 C:HIS182 2.5 47.3 1.0
CG C:HIS182 3.4 42.5 1.0
CB C:HIS182 3.5 37.7 1.0
CE1 C:HIS182 3.5 47.9 1.0
CG C:LYS132 3.5 37.7 1.0
CA C:HIS182 3.7 33.8 1.0
CD C:LYS132 3.7 36.3 1.0
O C:PRO181 3.8 40.3 1.0
CB C:LYS132 4.4 36.5 1.0
CD2 C:HIS182 4.5 45.5 1.0
C C:PRO181 4.6 36.0 1.0
N C:HIS182 4.6 34.9 1.0
NE2 C:HIS182 4.6 49.5 1.0
N C:SER183 4.7 32.2 1.0
C C:HIS182 4.8 31.2 1.0

Zinc binding site 8 out of 12 in 8bgp

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Zinc binding site 8 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:37.5
occ:1.00
OD2 D:ASP43 2.0 36.9 1.0
NE2 D:HIS151 2.3 32.6 1.0
ND1 D:HIS40 2.3 26.3 1.0
CG D:ASP43 2.6 37.1 1.0
OD1 D:ASP43 2.6 39.3 1.0
O D:HOH403 2.9 18.1 1.0
CE1 D:HIS40 3.2 27.4 1.0
CE1 D:HIS151 3.2 31.8 1.0
CG D:HIS40 3.3 27.3 1.0
CD2 D:HIS151 3.3 30.8 1.0
CB D:HIS40 3.6 28.9 1.0
NE2 F:HIS259 3.7 53.8 1.0
CE1 F:HIS259 4.1 50.6 1.0
CB D:ASP43 4.1 36.5 1.0
N D:HIS40 4.4 29.6 1.0
NE2 D:HIS40 4.4 25.0 1.0
ND1 D:HIS151 4.4 34.2 1.0
CD2 D:HIS40 4.4 26.1 1.0
CG D:HIS151 4.5 30.4 1.0
OD1 D:ASP42 4.5 48.0 1.0
CA D:HIS40 4.6 30.9 1.0
CB D:PRO39 4.6 27.1 1.0
CG D:PRO39 5.0 26.9 1.0
CD2 F:HIS259 5.0 55.4 1.0

Zinc binding site 9 out of 12 in 8bgp

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Zinc binding site 9 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:65.0
occ:1.00
ND1 D:HIS182 2.4 29.5 1.0
CE1 D:HIS182 3.2 31.0 1.0
CG D:HIS182 3.5 29.6 1.0
CD D:LYS132 3.6 35.9 1.0
CG D:LYS132 3.7 37.1 1.0
CB D:HIS182 3.8 28.7 1.0
CA D:HIS182 4.0 30.2 1.0
O D:PRO181 4.3 46.9 1.0
CB D:LYS132 4.3 35.4 1.0
NE2 D:HIS182 4.4 31.6 1.0
CD2 D:HIS182 4.5 31.1 1.0
N D:SER183 4.8 32.8 1.0
C D:HIS182 5.0 29.6 1.0

Zinc binding site 10 out of 12 in 8bgp

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Zinc binding site 10 out of 12 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus Anomalous Data within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:28.3
occ:1.00
OD2 E:ASP43 1.9 35.6 1.0
ND1 E:HIS40 2.0 31.6 1.0
NE2 E:HIS151 2.3 14.4 1.0
O E:HOH402 2.6 14.8 1.0
CG E:ASP43 2.7 31.6 1.0
OD1 E:ASP43 2.8 33.8 1.0
CE1 E:HIS40 3.0 31.9 1.0
CG E:HIS40 3.0 30.1 1.0
CD2 E:HIS151 3.2 15.6 1.0
CE1 E:HIS151 3.3 16.5 1.0
CB E:HIS40 3.4 30.8 1.0
NE2 D:HIS259 3.8 32.5 1.0
CE1 D:HIS259 4.0 35.2 1.0
NE2 E:HIS40 4.1 31.2 1.0
N E:HIS40 4.1 27.5 1.0
CD2 E:HIS40 4.1 30.7 1.0
CB E:ASP43 4.2 30.3 1.0
CB E:PRO39 4.3 29.6 1.0
CA E:HIS40 4.4 28.8 1.0
CG E:HIS151 4.4 17.7 1.0
ND1 E:HIS151 4.4 15.8 1.0
OD1 E:ASP42 4.7 41.3 1.0
CG E:PRO39 4.8 28.9 1.0
C E:PRO39 4.9 28.3 1.0

Reference:

K.Biniek-Antosiak, M.Bejger, J.Sliwiak, D.Baranowski, A.S.A.Mohammed, D.I.Svergun, W.Rypniewski. Structural, Thermodynamic and Enzymatic Characterization of N , N -Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 36555375
DOI: 10.3390/IJMS232415736
Page generated: Sat Apr 8 07:52:38 2023

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