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Zinc in PDB 1gkq: D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121

Enzymatic activity of D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121

All present enzymatic activity of D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121:
3.5.2.2;

Protein crystallography data

The structure of D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121, PDB code: 1gkq was solved by J.Abendroth, K.Niefind, D.Schomburg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.200, 161.500, 168.500, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 21.1

Zinc Binding Sites:

The binding sites of Zinc atom in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121 (pdb code 1gkq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121, PDB code: 1gkq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1gkq

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Zinc binding site 1 out of 8 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1460

b:30.6
occ:1.00
 OD1 A:ASP315 2.2 21.5 1.0
NE2 A:HIS59 2.3 22.4 1.0
NE2 A:HIS61 2.3 25.4 1.0
OQ2 A:KCX150 2.6 13.1 1.0
CE1 A:HIS59 3.1 20.3 1.0
OQ1 A:KCX150 3.2 13.1 1.0
CX A:KCX150 3.2 13.1 1.0
CG A:ASP315 3.2 25.2 1.0
CD2 A:HIS61 3.3 23.5 1.0
ZN A:ZN1461 3.3 36.4 1.0
CE1 A:HIS61 3.3 24.7 1.0
CD2 A:HIS59 3.4 22.9 1.0
OD2 A:ASP315 3.7 26.2 1.0
ND1 A:HIS59 4.3 22.9 1.0
CB A:ASP315 4.4 20.7 1.0
CG A:HIS61 4.5 24.6 1.0
ND1 A:HIS61 4.5 26.2 1.0
CG A:HIS59 4.5 22.0 1.0
NZ A:KCX150 4.5 13.1 1.0
CD2 A:HIS239 4.5 21.3 1.0
NE2 A:HIS239 4.6 22.3 1.0
CG A:MET93 4.6 21.5 1.0
CA A:ASP315 4.8 21.4 1.0

Zinc binding site 2 out of 8 in 1gkq

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Zinc binding site 2 out of 8 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1461

b:36.4
occ:1.00
 OQ1 A:KCX150 1.9 13.1 1.0
NE2 A:HIS239 2.4 22.3 1.0
ND1 A:HIS183 2.4 18.2 1.0
CX A:KCX150 3.0 13.1 1.0
CE1 A:HIS183 3.2 18.9 1.0
CD2 A:HIS239 3.3 21.3 1.0
ZN A:ZN1460 3.3 30.6 1.0
CE1 A:HIS239 3.4 17.5 1.0
CG A:HIS183 3.5 16.6 1.0
OQ2 A:KCX150 3.6 13.1 1.0
CB A:HIS183 3.9 15.3 1.0
O A:SER288 3.9 24.2 1.0
NZ A:KCX150 4.1 13.1 1.0
OD2 A:ASP315 4.4 26.2 1.0
NE2 A:HIS183 4.4 18.9 1.0
CG A:HIS239 4.4 19.8 1.0
ND1 A:HIS239 4.5 20.6 1.0
CE2 A:PHE152 4.5 21.5 1.0
CE1 A:HIS59 4.5 20.3 1.0
CD2 A:HIS183 4.6 18.1 1.0
OH A:TYR155 4.6 28.0 1.0
OD1 A:ASP315 4.6 21.5 1.0
NE2 A:HIS59 4.7 22.4 1.0
CG2 A:VAL238 4.7 13.8 1.0
CD2 A:PHE152 4.8 21.1 1.0
CG A:ASP315 4.8 25.2 1.0
CA A:HIS183 4.9 15.9 1.0
CE2 A:TYR155 5.0 26.8 1.0
C A:SER288 5.0 23.5 1.0

Zinc binding site 3 out of 8 in 1gkq

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Zinc binding site 3 out of 8 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1460

b:30.6
occ:1.00
 OD1 B:ASP315 2.3 21.5 1.0
NE2 B:HIS61 2.3 25.4 1.0
NE2 B:HIS59 2.3 22.4 1.0
OQ2 B:KCX150 2.5 18.2 1.0
CE1 B:HIS59 3.1 20.3 1.0
CX B:KCX150 3.2 18.2 1.0
OQ1 B:KCX150 3.2 16.5 1.0
CD2 B:HIS61 3.2 23.5 1.0
CG B:ASP315 3.3 25.2 1.0
CE1 B:HIS61 3.3 24.7 1.0
CD2 B:HIS59 3.4 22.9 1.0
ZN B:ZN1461 3.4 36.4 1.0
OD2 B:ASP315 3.7 26.2 1.0
ND1 B:HIS59 4.3 22.9 1.0
ND1 B:HIS61 4.4 26.2 1.0
CG B:HIS61 4.4 24.6 1.0
CB B:ASP315 4.4 20.7 1.0
CG B:HIS59 4.5 22.0 1.0
NZ B:KCX150 4.5 13.1 1.0
CD2 B:HIS239 4.6 21.3 1.0
CG B:MET93 4.6 21.5 1.0
NE2 B:HIS239 4.6 22.3 1.0
CA B:ASP315 4.8 21.4 1.0

Zinc binding site 4 out of 8 in 1gkq

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Zinc binding site 4 out of 8 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1461

b:36.4
occ:1.00
 OQ1 B:KCX150 1.9 16.5 1.0
ND1 B:HIS183 2.4 18.2 1.0
NE2 B:HIS239 2.5 22.3 1.0
CX B:KCX150 3.1 18.2 1.0
CE1 B:HIS183 3.2 18.9 1.0
CD2 B:HIS239 3.4 21.3 1.0
ZN B:ZN1460 3.4 30.6 1.0
CE1 B:HIS239 3.5 17.5 1.0
CG B:HIS183 3.5 16.6 1.0
OQ2 B:KCX150 3.6 18.2 1.0
CB B:HIS183 3.9 15.3 1.0
O B:SER288 4.0 24.2 1.0
NZ B:KCX150 4.1 13.1 1.0
NE2 B:HIS183 4.4 18.9 1.0
CE2 B:PHE152 4.4 21.5 1.0
OD2 B:ASP315 4.5 26.2 1.0
OH B:TYR155 4.5 28.0 1.0
CG B:HIS239 4.6 19.8 1.0
ND1 B:HIS239 4.6 20.6 1.0
CD2 B:HIS183 4.6 18.1 1.0
CE1 B:HIS59 4.6 20.3 1.0
OD1 B:ASP315 4.7 21.5 1.0
NE2 B:HIS59 4.7 22.4 1.0
CG2 B:VAL238 4.7 13.8 1.0
CD2 B:PHE152 4.8 21.1 1.0
CE2 B:TYR155 4.8 26.8 1.0
CG B:ASP315 4.9 25.2 1.0
CA B:HIS183 5.0 15.9 1.0
C B:SER288 5.0 23.5 1.0

Zinc binding site 5 out of 8 in 1gkq

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Zinc binding site 5 out of 8 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1460

b:30.6
occ:1.00
 OD1 C:ASP315 2.2 21.5 1.0
NE2 C:HIS59 2.3 22.4 1.0
NE2 C:HIS61 2.3 25.4 1.0
OQ2 C:KCX150 2.6 18.2 1.0
CE1 C:HIS59 3.1 20.3 1.0
OQ1 C:KCX150 3.2 16.5 1.0
CG C:ASP315 3.2 25.2 1.0
CX C:KCX150 3.2 18.2 1.0
CD2 C:HIS61 3.3 23.5 1.0
CE1 C:HIS61 3.3 24.7 1.0
ZN C:ZN1461 3.4 36.4 1.0
CD2 C:HIS59 3.4 22.9 1.0
OD2 C:ASP315 3.7 26.2 1.0
ND1 C:HIS59 4.3 22.9 1.0
CB C:ASP315 4.4 20.7 1.0
CG C:HIS61 4.4 24.6 1.0
ND1 C:HIS61 4.4 26.2 1.0
CG C:HIS59 4.5 22.0 1.0
NZ C:KCX150 4.5 13.1 1.0
CD2 C:HIS239 4.5 21.3 1.0
NE2 C:HIS239 4.6 22.3 1.0
CG C:MET93 4.6 21.5 1.0
CA C:ASP315 4.8 21.4 1.0

Zinc binding site 6 out of 8 in 1gkq

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Zinc binding site 6 out of 8 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1461

b:36.4
occ:1.00
 OQ1 C:KCX150 2.0 16.5 1.0
ND1 C:HIS183 2.4 18.2 1.0
NE2 C:HIS239 2.4 22.3 1.0
CX C:KCX150 3.1 18.2 1.0
CE1 C:HIS183 3.2 18.9 1.0
CD2 C:HIS239 3.3 21.3 1.0
ZN C:ZN1460 3.4 30.6 1.0
CE1 C:HIS239 3.4 17.5 1.0
CG C:HIS183 3.5 16.6 1.0
OQ2 C:KCX150 3.7 18.2 1.0
O C:SER288 3.9 24.2 1.0
CB C:HIS183 3.9 15.3 1.0
NZ C:KCX150 4.2 13.1 1.0
NE2 C:HIS183 4.4 18.9 1.0
OD2 C:ASP315 4.4 26.2 1.0
OH C:TYR155 4.5 28.0 1.0
CE2 C:PHE152 4.5 21.5 1.0
CG C:HIS239 4.5 19.8 1.0
ND1 C:HIS239 4.5 20.6 1.0
CD2 C:HIS183 4.6 18.1 1.0
CE1 C:HIS59 4.6 20.3 1.0
OD1 C:ASP315 4.7 21.5 1.0
NE2 C:HIS59 4.7 22.4 1.0
CG2 C:VAL238 4.8 13.8 1.0
CD2 C:PHE152 4.8 21.1 1.0
CG C:ASP315 4.9 25.2 1.0
CE2 C:TYR155 4.9 26.8 1.0
C C:SER288 4.9 23.5 1.0

Zinc binding site 7 out of 8 in 1gkq

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Zinc binding site 7 out of 8 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1460

b:30.6
occ:1.00
 OD1 D:ASP315 2.2 21.5 1.0
NE2 D:HIS61 2.3 25.4 1.0
NE2 D:HIS59 2.3 22.4 1.0
OQ2 D:KCX150 2.5 18.2 1.0
CE1 D:HIS59 3.1 20.3 1.0
CD2 D:HIS61 3.2 23.5 1.0
CX D:KCX150 3.2 18.2 1.0
CG D:ASP315 3.2 25.2 1.0
OQ1 D:KCX150 3.3 16.5 1.0
CE1 D:HIS61 3.3 24.7 1.0
CD2 D:HIS59 3.4 22.9 1.0
ZN D:ZN1461 3.4 36.4 1.0
OD2 D:ASP315 3.7 26.2 1.0
ND1 D:HIS59 4.3 22.9 1.0
ND1 D:HIS61 4.4 26.2 1.0
CG D:HIS61 4.4 24.6 1.0
CB D:ASP315 4.4 20.7 1.0
CG D:HIS59 4.4 22.0 1.0
NZ D:KCX150 4.5 13.1 1.0
CD2 D:HIS239 4.5 21.3 1.0
CG D:MET93 4.6 21.5 1.0
NE2 D:HIS239 4.6 22.3 1.0
CA D:ASP315 4.8 21.4 1.0

Zinc binding site 8 out of 8 in 1gkq

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Zinc binding site 8 out of 8 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1461

b:36.4
occ:1.00
 OQ1 D:KCX150 1.9 16.5 1.0
ND1 D:HIS183 2.4 18.2 1.0
NE2 D:HIS239 2.5 22.3 1.0
CX D:KCX150 3.1 18.2 1.0
CE1 D:HIS183 3.2 18.9 1.0
ZN D:ZN1460 3.4 30.6 1.0
CD2 D:HIS239 3.4 21.3 1.0
CE1 D:HIS239 3.5 17.5 1.0
CG D:HIS183 3.5 16.6 1.0
OQ2 D:KCX150 3.6 18.2 1.0
CB D:HIS183 3.9 15.3 1.0
O D:SER288 4.0 24.2 1.0
NZ D:KCX150 4.1 13.1 1.0
CE2 D:PHE152 4.4 21.5 1.0
NE2 D:HIS183 4.4 18.9 1.0
OD2 D:ASP315 4.5 26.2 1.0
OH D:TYR155 4.5 28.0 1.0
CD2 D:HIS183 4.6 18.1 1.0
CG D:HIS239 4.6 19.8 1.0
ND1 D:HIS239 4.6 20.6 1.0
CE1 D:HIS59 4.6 20.3 1.0
OD1 D:ASP315 4.6 21.5 1.0
NE2 D:HIS59 4.7 22.4 1.0
CD2 D:PHE152 4.8 21.1 1.0
CG2 D:VAL238 4.8 13.8 1.0
CE2 D:TYR155 4.8 26.8 1.0
CG D:ASP315 4.9 25.2 1.0
CA D:HIS183 5.0 15.9 1.0

Reference:

J.Abendroth, K.Niefind, D.Schomburg. X-Ray Structure of A Dihydropyrimidinase From Thermus Sp. at 1.3 A Resolution J.Mol.Biol. V. 320 143 2002.
ISSN: ISSN 0022-2836
PubMed: 12079340
DOI: 10.1016/S0022-2836(02)00422-9
Page generated: Wed Dec 16 02:50:10 2020

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