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Zinc in PDB 8hfd: Crystal Structure of Allantoinase From E. Coli BL21

Enzymatic activity of Crystal Structure of Allantoinase From E. Coli BL21

All present enzymatic activity of Crystal Structure of Allantoinase From E. Coli BL21:
3.5.2.5;

Protein crystallography data

The structure of Crystal Structure of Allantoinase From E. Coli BL21, PDB code: 8hfd was solved by E.S.Lin, H.Y.Huang, P.C.Yang, H.W.Liu, C.Y.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.92 / 2.07
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 203.158, 77.142, 144.847, 90, 100.8, 90
R / Rfree (%) 20.5 / 24.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Allantoinase From E. Coli BL21 (pdb code 8hfd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Allantoinase From E. Coli BL21, PDB code: 8hfd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8hfd

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Zinc binding site 1 out of 8 in the Crystal Structure of Allantoinase From E. Coli BL21


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 Allantoinase From E. Coli BL21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:25.7
occ:1.00
 NE2 A:HIS59 2.2 22.6 1.0
NE2 A:HIS61 2.2 21.1 1.0
OD1 A:ASP315 2.4 22.6 1.0
OQ1 A:KCX146 2.7 22.7 1.0
CD2 A:HIS59 3.1 22.0 1.0
CD2 A:HIS61 3.1 22.2 1.0
CX A:KCX146 3.2 30.0 1.0
CG A:ASP315 3.2 24.2 1.0
CE1 A:HIS59 3.2 25.6 1.0
CE1 A:HIS61 3.3 20.0 1.0
OQ2 A:KCX146 3.4 29.6 1.0
ZN A:ZN504 3.4 30.0 1.0
O A:HOH795 3.5 40.5 1.0
OD2 A:ASP315 3.6 26.4 1.0
NZ A:KCX146 4.2 34.1 1.0
CG A:HIS59 4.3 23.0 1.0
CG A:HIS61 4.3 26.0 1.0
ND1 A:HIS59 4.3 23.5 1.0
ND1 A:HIS61 4.3 23.4 1.0
OG A:SER317 4.4 27.7 1.0
CB A:ASP315 4.5 23.2 1.0
CD2 A:HIS242 4.5 22.3 1.0
NE2 A:HIS242 4.6 25.2 1.0
CA A:ASP315 4.7 25.4 1.0
CG A:MET91 4.8 22.7 1.0

Zinc binding site 2 out of 8 in 8hfd

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Zinc binding site 2 out of 8 in the Crystal Structure of Allantoinase From E. Coli BL21


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 Allantoinase From E. Coli BL21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:30.0
occ:1.00
 OQ2 A:KCX146 2.0 29.6 1.0
ND1 A:HIS186 2.1 28.8 1.0
NE2 A:HIS242 2.2 25.2 1.0
CE1 A:HIS186 3.0 28.5 1.0
CX A:KCX146 3.1 30.0 1.0
CD2 A:HIS242 3.2 22.3 1.0
CG A:HIS186 3.2 25.6 1.0
CE1 A:HIS242 3.2 28.0 1.0
OQ1 A:KCX146 3.4 22.7 1.0
ZN A:ZN503 3.4 25.7 1.0
CB A:HIS186 3.5 26.1 1.0
O A:HOH795 3.7 40.5 1.0
CZ A:PHE148 4.0 31.7 1.0
CE1 A:HIS59 4.1 25.6 1.0
NE2 A:HIS186 4.2 30.7 1.0
NE2 A:HIS59 4.2 22.6 1.0
NZ A:KCX146 4.2 34.1 1.0
CD2 A:HIS186 4.3 29.9 1.0
OD2 A:ASP315 4.3 26.4 1.0
ND1 A:HIS242 4.3 24.1 1.0
CG A:HIS242 4.3 24.7 1.0
CE2 A:PHE148 4.3 31.8 1.0
CA A:HIS186 4.5 26.1 1.0
OD1 A:ASP315 4.8 22.6 1.0
CG A:ASP315 4.8 24.2 1.0
CE1 A:PHE148 4.9 32.0 1.0

Zinc binding site 3 out of 8 in 8hfd

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Zinc binding site 3 out of 8 in the Crystal Structure of Allantoinase From E. Coli BL21


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 Allantoinase From E. Coli BL21 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:26.6
occ:1.00
 OQ1 B:KCX146 2.2 27.9 1.0
NE2 B:HIS61 2.2 26.4 1.0
NE2 B:HIS59 2.2 22.8 1.0
OD1 B:ASP315 2.3 23.5 1.0
CX B:KCX146 3.0 28.7 1.0
CG B:ASP315 3.1 23.7 1.0
CD2 B:HIS61 3.1 23.4 1.0
CD2 B:HIS59 3.2 21.5 1.0
CE1 B:HIS61 3.2 23.8 1.0
CE1 B:HIS59 3.2 26.9 1.0
OQ2 B:KCX146 3.4 29.3 1.0
ZN B:ZN503 3.4 30.9 1.0
OD2 B:ASP315 3.6 24.0 1.0
NZ B:KCX146 4.1 27.9 1.0
CG B:HIS61 4.3 26.0 1.0
ND1 B:HIS61 4.3 24.7 1.0
CG B:HIS59 4.3 24.5 1.0
ND1 B:HIS59 4.3 24.6 1.0
CB B:ASP315 4.3 22.2 1.0
OG B:SER317 4.4 32.4 1.0
CD2 B:HIS242 4.5 22.3 1.0
NE2 B:HIS242 4.6 22.4 1.0
CA B:ASP315 4.7 22.4 1.0
CG B:MET91 4.8 20.4 1.0

Zinc binding site 4 out of 8 in 8hfd

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Zinc binding site 4 out of 8 in the Crystal Structure of Allantoinase From E. Coli BL21


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 Allantoinase From E. Coli BL21 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:30.9
occ:1.00
 OQ2 B:KCX146 1.9 29.3 1.0
NE2 B:HIS242 2.2 22.4 1.0
ND1 B:HIS186 2.3 29.6 1.0
CX B:KCX146 2.8 28.7 1.0
OQ1 B:KCX146 3.1 27.9 1.0
CD2 B:HIS242 3.2 22.3 1.0
CE1 B:HIS186 3.2 25.9 1.0
CE1 B:HIS242 3.2 22.8 1.0
CG B:HIS186 3.2 25.1 1.0
ZN B:ZN502 3.4 26.6 1.0
CB B:HIS186 3.5 22.9 1.0
CE2 B:PHE148 3.9 29.4 1.0
CZ B:PHE148 4.0 32.6 1.0
NZ B:KCX146 4.1 27.9 1.0
CE1 B:HIS59 4.2 26.9 1.0
NE2 B:HIS186 4.3 23.1 1.0
NE2 B:HIS59 4.3 22.8 1.0
ND1 B:HIS242 4.3 26.1 1.0
CG B:HIS242 4.3 22.3 1.0
CD2 B:HIS186 4.4 26.2 1.0
OD2 B:ASP315 4.4 24.0 1.0
CA B:HIS186 4.5 23.0 1.0
CE B:KCX146 4.6 28.4 1.0
OD1 B:ASP315 4.8 23.5 1.0
CG B:ASP315 4.9 23.7 1.0
CD2 B:PHE148 4.9 33.3 1.0

Zinc binding site 5 out of 8 in 8hfd

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Zinc binding site 5 out of 8 in the Crystal Structure of Allantoinase From E. Coli BL21


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 Allantoinase From E. Coli BL21 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:31.4
occ:1.00
 NE2 C:HIS61 2.2 28.1 1.0
OQ2 C:KCX146 2.2 31.8 1.0
NE2 C:HIS59 2.2 26.0 1.0
OD1 C:ASP315 2.3 25.2 1.0
CD2 C:HIS59 3.1 25.4 1.0
CX C:KCX146 3.1 33.4 1.0
CD2 C:HIS61 3.1 26.2 1.0
CG C:ASP315 3.2 29.3 1.0
CE1 C:HIS59 3.3 28.7 1.0
CE1 C:HIS61 3.3 29.8 1.0
OQ1 C:KCX146 3.4 32.1 1.0
ZN C:ZN503 3.5 35.4 1.0
OD2 C:ASP315 3.6 26.8 1.0
NZ C:KCX146 4.2 29.7 1.0
OG C:SER317 4.2 36.1 1.0
CG C:HIS59 4.2 26.3 1.0
CG C:HIS61 4.3 30.4 1.0
ND1 C:HIS59 4.3 28.8 1.0
ND1 C:HIS61 4.3 34.2 1.0
CB C:ASP315 4.5 26.4 1.0
CD2 C:HIS242 4.5 27.0 1.0
NE2 C:HIS242 4.6 27.0 1.0
CG C:MET91 4.7 29.2 1.0
CA C:ASP315 4.8 28.9 1.0
O C:HOH742 4.8 35.7 1.0

Zinc binding site 6 out of 8 in 8hfd

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Zinc binding site 6 out of 8 in the Crystal Structure of Allantoinase From E. Coli BL21


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 Allantoinase From E. Coli BL21 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn503

b:35.4
occ:1.00
 OQ1 C:KCX146 2.0 32.1 1.0
NE2 C:HIS242 2.2 27.0 1.0
ND1 C:HIS186 2.3 29.6 1.0
CX C:KCX146 3.0 33.4 1.0
CE1 C:HIS242 3.1 27.8 1.0
CD2 C:HIS242 3.2 27.0 1.0
CE1 C:HIS186 3.2 28.9 1.0
CG C:HIS186 3.3 28.2 1.0
OQ2 C:KCX146 3.4 31.8 1.0
ZN C:ZN502 3.5 31.4 1.0
CB C:HIS186 3.6 29.4 1.0
CZ C:PHE148 3.9 33.4 1.0
CE2 C:PHE148 4.2 38.4 1.0
NZ C:KCX146 4.2 29.7 1.0
CE1 C:HIS59 4.2 28.7 1.0
ND1 C:HIS242 4.3 29.5 1.0
CG C:HIS242 4.3 27.6 1.0
NE2 C:HIS186 4.3 30.1 1.0
NE2 C:HIS59 4.3 26.0 1.0
OD2 C:ASP315 4.3 26.8 1.0
CD2 C:HIS186 4.4 27.7 1.0
CA C:HIS186 4.6 27.5 1.0
CE C:KCX146 4.7 31.6 1.0
OD1 C:ASP315 4.8 25.2 1.0
CG C:PRO289 4.9 31.1 1.0
CG C:ASP315 4.9 29.3 1.0
CE1 C:PHE148 4.9 36.9 1.0
CD C:PRO289 5.0 33.0 1.0

Zinc binding site 7 out of 8 in 8hfd

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Zinc binding site 7 out of 8 in the Crystal Structure of Allantoinase From E. Coli BL21


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 Allantoinase From E. Coli BL21 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn503

b:37.0
occ:1.00
 OQ1 D:KCX146 2.1 40.0 1.0
NE2 D:HIS242 2.3 26.7 1.0
ND1 D:HIS186 2.3 35.6 1.0
ZN D:ZN504 3.0 36.6 1.0
CD2 D:HIS242 3.1 23.1 1.0
CE1 D:HIS186 3.1 31.7 1.0
CX D:KCX146 3.1 40.0 1.0
CE1 D:HIS242 3.3 26.3 1.0
CG D:HIS186 3.5 27.7 1.0
OQ2 D:KCX146 3.5 35.2 1.0
CB D:HIS186 3.9 28.2 1.0
CE1 D:HIS59 4.0 29.9 1.0
CE2 D:PHE148 4.1 31.9 1.0
NE2 D:HIS59 4.1 33.1 1.0
CZ D:PHE148 4.1 36.2 1.0
NZ D:KCX146 4.2 40.4 1.0
OD2 D:ASP315 4.3 30.9 1.0
NE2 D:HIS186 4.3 31.4 1.0
CG D:HIS242 4.3 28.3 1.0
ND1 D:HIS242 4.4 28.5 1.0
OD1 D:ASP315 4.4 29.5 1.0
CD2 D:HIS186 4.5 28.8 1.0
CG D:ASP315 4.6 26.1 1.0
CE D:KCX146 4.8 35.0 1.0
CA D:HIS186 4.9 31.3 1.0

Zinc binding site 8 out of 8 in 8hfd

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Zinc binding site 8 out of 8 in the Crystal Structure of Allantoinase From E. Coli BL21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Allantoinase From E. Coli BL21 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn504

b:36.6
occ:1.00
 OD1 D:ASP315 2.1 29.5 1.0
NE2 D:HIS61 2.2 31.9 1.0
NE2 D:HIS59 2.3 33.1 1.0
OQ2 D:KCX146 2.7 35.2 1.0
CE1 D:HIS61 3.0 30.7 1.0
ZN D:ZN503 3.0 37.0 1.0
CG D:ASP315 3.1 26.1 1.0
CE1 D:HIS59 3.1 29.9 1.0
CD2 D:HIS59 3.3 28.7 1.0
CD2 D:HIS61 3.3 22.8 1.0
OQ1 D:KCX146 3.3 40.0 1.0
CX D:KCX146 3.4 40.0 1.0
OD2 D:ASP315 3.5 30.9 1.0
ND1 D:HIS61 4.2 32.4 1.0
ND1 D:HIS59 4.3 29.6 1.0
CG D:HIS61 4.4 31.8 1.0
CD2 D:HIS242 4.4 23.1 1.0
CB D:ASP315 4.4 26.4 1.0
CG D:HIS59 4.4 28.9 1.0
NE2 D:HIS242 4.4 26.7 1.0
NZ D:KCX146 4.7 40.4 1.0
CA D:ASP315 4.7 25.2 1.0

Reference:

Y.H.Huang, P.C.Yang, E.S.Lin, Y.Y.Ho, W.F.Peng, H.P.Lu, C.C.Huang, C.Y.Huang. Crystal Structure of Allantoinase From Escherichia Coli BL21: A Molecular Insight Into A Role of the Active Site Loops in Catalysis. Molecules V. 28 2023.
ISSN: ESSN 1420-3049
PubMed: 36677881
DOI: 10.3390/MOLECULES28020827
Page generated: Thu Dec 28 13:11:36 2023

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