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Zinc in PDB 1nfg: Structure of D-Hydantoinase

Enzymatic activity of Structure of D-Hydantoinase

All present enzymatic activity of Structure of D-Hydantoinase:
3.5.2.2;

Protein crystallography data

The structure of Structure of D-Hydantoinase, PDB code: 1nfg was solved by Z.Xu, Y.Yang, W.Jiang, E.Arnold, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.94 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.700, 170.500, 87.300, 90.00, 95.20, 90.00
R / Rfree (%) 22 / 23.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of D-Hydantoinase (pdb code 1nfg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of D-Hydantoinase, PDB code: 1nfg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1nfg

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Zinc binding site 1 out of 8 in the Structure of D-Hydantoinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of D-Hydantoinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:21.0
occ:1.00
 OD1 A:ASP313 2.2 25.2 1.0
NE2 A:HIS59 2.3 31.3 1.0
NE2 A:HIS57 2.4 26.4 1.0
OQ2 A:KCX148 2.5 12.4 1.0
CG A:ASP313 3.1 27.5 1.0
ZN A:ZN502 3.2 22.7 1.0
CX A:KCX148 3.2 17.9 1.0
OQ1 A:KCX148 3.2 13.7 1.0
CD2 A:HIS59 3.3 29.6 1.0
O A:HOH579 3.3 24.0 1.0
CE1 A:HIS57 3.3 25.5 1.0
CE1 A:HIS59 3.3 29.5 1.0
O A:HOH581 3.3 13.7 1.0
CD2 A:HIS57 3.4 25.5 1.0
OD2 A:ASP313 3.6 29.6 1.0
CB A:ASP313 4.4 25.6 1.0
ND1 A:HIS59 4.4 28.8 1.0
CG A:HIS59 4.4 29.6 1.0
ND1 A:HIS57 4.4 24.9 1.0
NZ A:KCX148 4.5 14.6 1.0
CG A:HIS57 4.5 24.4 1.0
CD2 A:HIS237 4.6 27.0 1.0
CA A:ASP313 4.8 25.5 1.0
CE2 A:PHE91 4.8 21.4 1.0
NE2 A:HIS237 4.8 26.8 1.0
CD2 A:PHE91 4.9 23.3 1.0
O A:HOH580 5.0 21.0 1.0

Zinc binding site 2 out of 8 in 1nfg

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Zinc binding site 2 out of 8 in the Structure of D-Hydantoinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of D-Hydantoinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:22.7
occ:1.00
 OQ1 A:KCX148 2.0 13.7 1.0
O A:HOH579 2.2 24.0 1.0
ND1 A:HIS181 2.4 21.8 1.0
NE2 A:HIS237 2.6 26.8 1.0
CE1 A:HIS181 3.1 20.9 1.0
CX A:KCX148 3.1 17.9 1.0
ZN A:ZN501 3.2 21.0 1.0
CD2 A:HIS237 3.2 27.0 1.0
O A:HOH581 3.4 13.7 1.0
CG A:HIS181 3.6 20.3 1.0
OQ2 A:KCX148 3.7 12.4 1.0
CE1 A:HIS237 3.8 26.6 1.0
CE2 A:PHE150 4.0 22.6 1.0
CB A:HIS181 4.1 21.4 1.0
O A:THR286 4.2 21.6 1.0
NZ A:KCX148 4.2 14.6 1.0
NE2 A:HIS181 4.3 20.5 1.0
OD2 A:ASP313 4.4 29.6 1.0
CG A:HIS237 4.5 27.4 1.0
CD2 A:HIS181 4.6 21.9 1.0
OD1 A:ASP313 4.6 25.2 1.0
CG2 A:VAL236 4.7 19.1 1.0
NE2 A:HIS57 4.7 26.4 1.0
CZ A:PHE150 4.7 21.9 1.0
ND1 A:HIS237 4.7 28.3 1.0
CE1 A:HIS57 4.8 25.5 1.0
CD2 A:PHE150 4.8 22.6 1.0
OH A:TYR153 4.8 44.0 1.0
CG A:ASP313 4.9 27.5 1.0
CA A:HIS181 5.0 21.7 1.0

Zinc binding site 3 out of 8 in 1nfg

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Zinc binding site 3 out of 8 in the Structure of D-Hydantoinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of D-Hydantoinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:21.0
occ:1.00
 OD1 B:ASP313 2.2 24.9 1.0
NE2 B:HIS59 2.3 31.0 1.0
NE2 B:HIS57 2.4 26.1 1.0
OQ2 B:KCX148 2.5 12.2 1.0
CG B:ASP313 3.1 27.2 1.0
ZN B:ZN602 3.2 22.7 1.0
CX B:KCX148 3.2 17.6 1.0
OQ1 B:KCX148 3.2 13.5 1.0
CD2 B:HIS59 3.3 29.3 1.0
O B:HOH689 3.3 24.0 1.0
CE1 B:HIS57 3.3 25.2 1.0
CE1 B:HIS59 3.3 29.2 1.0
O B:HOH691 3.3 13.7 1.0
CD2 B:HIS57 3.4 25.2 1.0
OD2 B:ASP313 3.6 29.4 1.0
CB B:ASP313 4.4 25.4 1.0
ND1 B:HIS59 4.4 28.5 1.0
CG B:HIS59 4.4 29.4 1.0
ND1 B:HIS57 4.4 24.6 1.0
NZ B:KCX148 4.5 14.3 1.0
CG B:HIS57 4.5 24.2 1.0
CD2 B:HIS237 4.6 26.8 1.0
CA B:ASP313 4.8 25.2 1.0
CE2 B:PHE91 4.8 21.1 1.0
NE2 B:HIS237 4.8 26.5 1.0
CD2 B:PHE91 4.9 23.0 1.0
O B:HOH690 5.0 21.0 1.0

Zinc binding site 4 out of 8 in 1nfg

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Zinc binding site 4 out of 8 in the Structure of D-Hydantoinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of D-Hydantoinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:22.7
occ:1.00
 OQ1 B:KCX148 2.0 13.5 1.0
O B:HOH689 2.2 24.0 1.0
ND1 B:HIS181 2.4 21.5 1.0
NE2 B:HIS237 2.6 26.5 1.0
CE1 B:HIS181 3.1 20.7 1.0
CX B:KCX148 3.1 17.6 1.0
ZN B:ZN601 3.2 21.0 1.0
CD2 B:HIS237 3.2 26.8 1.0
O B:HOH691 3.4 13.7 1.0
CG B:HIS181 3.6 20.1 1.0
OQ2 B:KCX148 3.7 12.2 1.0
CE1 B:HIS237 3.8 26.4 1.0
CE2 B:PHE150 4.0 22.4 1.0
CB B:HIS181 4.1 21.2 1.0
O B:THR286 4.2 21.4 1.0
NZ B:KCX148 4.2 14.3 1.0
NE2 B:HIS181 4.3 20.2 1.0
OD2 B:ASP313 4.4 29.4 1.0
CG B:HIS237 4.5 27.1 1.0
CD2 B:HIS181 4.6 21.6 1.0
OD1 B:ASP313 4.6 24.9 1.0
CG2 B:VAL236 4.7 18.8 1.0
NE2 B:HIS57 4.7 26.1 1.0
CZ B:PHE150 4.7 21.6 1.0
ND1 B:HIS237 4.7 28.0 1.0
CE1 B:HIS57 4.8 25.2 1.0
CD2 B:PHE150 4.8 22.4 1.0
OH B:TYR153 4.8 43.8 1.0
CG B:ASP313 4.9 27.2 1.0
CA B:HIS181 5.0 21.4 1.0

Zinc binding site 5 out of 8 in 1nfg

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Zinc binding site 5 out of 8 in the Structure of D-Hydantoinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of D-Hydantoinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn701

b:21.0
occ:1.00
 OD1 C:ASP313 2.2 24.9 1.0
NE2 C:HIS59 2.3 31.0 1.0
NE2 C:HIS57 2.4 26.1 1.0
OQ2 C:KCX148 2.5 12.2 1.0
CG C:ASP313 3.1 27.2 1.0
ZN C:ZN702 3.2 22.7 1.0
CX C:KCX148 3.2 17.6 1.0
OQ1 C:KCX148 3.2 13.5 1.0
CD2 C:HIS59 3.3 29.3 1.0
O C:HOH782 3.3 24.0 1.0
CE1 C:HIS57 3.3 25.2 1.0
CE1 C:HIS59 3.3 29.2 1.0
O C:HOH784 3.3 13.7 1.0
CD2 C:HIS57 3.4 25.2 1.0
OD2 C:ASP313 3.6 29.4 1.0
CB C:ASP313 4.4 25.4 1.0
ND1 C:HIS59 4.4 28.5 1.0
CG C:HIS59 4.4 29.4 1.0
ND1 C:HIS57 4.4 24.6 1.0
NZ C:KCX148 4.5 14.3 1.0
CG C:HIS57 4.5 24.2 1.0
CD2 C:HIS237 4.6 26.8 1.0
CA C:ASP313 4.8 25.2 1.0
CE2 C:PHE91 4.8 21.1 1.0
NE2 C:HIS237 4.8 26.5 1.0
CD2 C:PHE91 4.9 23.0 1.0
O C:HOH783 5.0 21.0 1.0

Zinc binding site 6 out of 8 in 1nfg

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Zinc binding site 6 out of 8 in the Structure of D-Hydantoinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of D-Hydantoinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn702

b:22.7
occ:1.00
 OQ1 C:KCX148 2.0 13.5 1.0
O C:HOH782 2.2 24.0 1.0
ND1 C:HIS181 2.4 21.5 1.0
NE2 C:HIS237 2.6 26.5 1.0
CE1 C:HIS181 3.1 20.7 1.0
CX C:KCX148 3.1 17.6 1.0
ZN C:ZN701 3.2 21.0 1.0
CD2 C:HIS237 3.2 26.8 1.0
O C:HOH784 3.4 13.7 1.0
CG C:HIS181 3.6 20.1 1.0
OQ2 C:KCX148 3.7 12.2 1.0
CE1 C:HIS237 3.8 26.4 1.0
CE2 C:PHE150 4.0 22.4 1.0
CB C:HIS181 4.1 21.2 1.0
O C:THR286 4.2 21.4 1.0
NZ C:KCX148 4.2 14.3 1.0
NE2 C:HIS181 4.3 20.2 1.0
OD2 C:ASP313 4.4 29.4 1.0
CG C:HIS237 4.5 27.1 1.0
CD2 C:HIS181 4.6 21.6 1.0
OD1 C:ASP313 4.6 24.9 1.0
CG2 C:VAL236 4.7 18.8 1.0
NE2 C:HIS57 4.7 26.1 1.0
CZ C:PHE150 4.7 21.6 1.0
ND1 C:HIS237 4.7 28.0 1.0
CE1 C:HIS57 4.8 25.2 1.0
CD2 C:PHE150 4.8 22.4 1.0
OH C:TYR153 4.8 43.8 1.0
CG C:ASP313 4.9 27.2 1.0
CA C:HIS181 5.0 21.4 1.0

Zinc binding site 7 out of 8 in 1nfg

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Zinc binding site 7 out of 8 in the Structure of D-Hydantoinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of D-Hydantoinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:21.0
occ:1.00
 OD1 D:ASP313 2.2 24.9 1.0
NE2 D:HIS59 2.3 31.0 1.0
NE2 D:HIS57 2.4 26.1 1.0
OQ2 D:KCX148 2.5 12.2 1.0
CG D:ASP313 3.1 27.2 1.0
ZN D:ZN802 3.2 22.7 1.0
CX D:KCX148 3.2 17.6 1.0
OQ1 D:KCX148 3.2 13.5 1.0
CD2 D:HIS59 3.3 29.3 1.0
O D:HOH3085 3.3 24.0 1.0
CE1 D:HIS57 3.3 25.2 1.0
CE1 D:HIS59 3.3 29.2 1.0
O D:HOH3087 3.3 13.7 1.0
CD2 D:HIS57 3.4 25.2 1.0
OD2 D:ASP313 3.6 29.4 1.0
CB D:ASP313 4.4 25.4 1.0
ND1 D:HIS59 4.4 28.5 1.0
CG D:HIS59 4.4 29.4 1.0
ND1 D:HIS57 4.4 24.6 1.0
NZ D:KCX148 4.5 14.3 1.0
CG D:HIS57 4.5 24.2 1.0
CD2 D:HIS237 4.6 26.8 1.0
CA D:ASP313 4.8 25.2 1.0
CE2 D:PHE91 4.8 21.1 1.0
NE2 D:HIS237 4.8 26.5 1.0
CD2 D:PHE91 4.9 23.0 1.0
O D:HOH3086 5.0 21.0 1.0

Zinc binding site 8 out of 8 in 1nfg

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Zinc binding site 8 out of 8 in the Structure of D-Hydantoinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of D-Hydantoinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn802

b:22.7
occ:1.00
 OQ1 D:KCX148 2.0 13.5 1.0
O D:HOH3085 2.2 24.0 1.0
ND1 D:HIS181 2.4 21.5 1.0
NE2 D:HIS237 2.6 26.5 1.0
CE1 D:HIS181 3.1 20.7 1.0
CX D:KCX148 3.1 17.6 1.0
ZN D:ZN801 3.2 21.0 1.0
CD2 D:HIS237 3.2 26.8 1.0
O D:HOH3087 3.4 13.7 1.0
CG D:HIS181 3.6 20.1 1.0
OQ2 D:KCX148 3.7 12.2 1.0
CE1 D:HIS237 3.8 26.4 1.0
CE2 D:PHE150 4.0 22.4 1.0
CB D:HIS181 4.1 21.2 1.0
O D:THR286 4.2 21.4 1.0
NZ D:KCX148 4.2 14.3 1.0
NE2 D:HIS181 4.3 20.2 1.0
OD2 D:ASP313 4.4 29.4 1.0
CG D:HIS237 4.5 27.1 1.0
CD2 D:HIS181 4.6 21.6 1.0
OD1 D:ASP313 4.6 24.9 1.0
CG2 D:VAL236 4.7 18.8 1.0
NE2 D:HIS57 4.7 26.1 1.0
CZ D:PHE150 4.7 21.6 1.0
ND1 D:HIS237 4.7 28.0 1.0
CE1 D:HIS57 4.8 25.2 1.0
CD2 D:PHE150 4.8 22.4 1.0
OH D:TYR153 4.8 43.8 1.0
CG D:ASP313 4.9 27.2 1.0
CA D:HIS181 5.0 21.4 1.0

Reference:

Z.Xu, Y.Liu, Y.Yang, W.Jiang, E.Arnold, J.Ding. Crystal Structure of D-Hydantoinase From Burkholderia Pickettii at A Resolution of 2.7 Angstroms: Insights Into the Molecular Basis of Enzyme Thermostability. J.Bacteriol. V. 185 4038 2003.
ISSN: ISSN 0021-9193
PubMed: 12837777
DOI: 10.1128/JB.185.14.4038-4049.2003
Page generated: Wed Oct 16 17:15:44 2024

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