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Zinc in PDB 1gkp: D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221

Enzymatic activity of D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221

All present enzymatic activity of D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221:
3.5.2.2;

Protein crystallography data

The structure of D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221, PDB code: 1gkp 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) 50.00 / 1.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 126.200, 215.900, 207.900, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 18.4

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221 (pdb code 1gkp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221, PDB code: 1gkp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 1gkp

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Zinc binding site 1 out of 12 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221


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 C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1460

b:19.6
occ:1.00
 OQ1 A:KCX150 2.0 16.2 1.0
O A:HOH2606 2.1 17.6 1.0
O A:HOH2605 2.2 23.9 1.0
ND1 A:HIS183 2.2 15.2 1.0
NE2 A:HIS239 2.3 15.9 1.0
CE1 A:HIS183 3.0 16.3 1.0
CX A:KCX150 3.1 17.6 1.0
CD2 A:HIS239 3.3 17.6 1.0
CE1 A:HIS239 3.3 12.4 1.0
CG A:HIS183 3.3 14.1 1.0
OQ2 A:KCX150 3.5 18.0 1.0
ZN A:ZN1461 3.6 19.5 1.0
CB A:HIS183 3.7 14.4 1.0
O A:SER288 3.9 20.4 1.0
NE2 A:HIS183 4.2 16.8 1.0
CE2 A:PHE152 4.2 17.1 1.0
NZ A:KCX150 4.3 14.3 1.0
OH A:TYR155 4.3 22.1 1.0
CD2 A:HIS183 4.4 14.8 1.0
ND1 A:HIS239 4.4 15.0 1.0
OD2 A:ASP315 4.4 21.9 1.0
CG A:HIS239 4.5 13.8 1.0
O A:HOH2113 4.5 30.1 1.0
CG2 A:VAL238 4.7 14.3 1.0
CE1 A:HIS59 4.7 13.8 1.0
CE A:KCX150 4.7 14.2 1.0
NE2 A:HIS59 4.7 15.2 1.0
CD2 A:PHE152 4.8 18.3 1.0
CA A:HIS183 4.8 13.0 1.0
OD1 A:ASP315 4.9 17.1 1.0
C A:SER288 4.9 18.2 1.0
CE2 A:TYR155 5.0 21.6 1.0

Zinc binding site 2 out of 12 in 1gkp

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Zinc binding site 2 out of 12 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221


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 C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1461

b:19.5
occ:1.00
 O A:HOH2606 2.0 17.6 1.0
OQ2 A:KCX150 2.1 18.0 1.0
NE2 A:HIS61 2.2 16.6 1.0
OD1 A:ASP315 2.2 17.1 1.0
NE2 A:HIS59 2.2 15.2 1.0
CX A:KCX150 3.1 17.6 1.0
CD2 A:HIS61 3.1 14.6 1.0
CE1 A:HIS59 3.2 13.8 1.0
CG A:ASP315 3.2 14.5 1.0
CE1 A:HIS61 3.2 15.2 1.0
CD2 A:HIS59 3.3 13.5 1.0
OQ1 A:KCX150 3.4 16.2 1.0
OD2 A:ASP315 3.5 21.9 1.0
ZN A:ZN1460 3.6 19.6 1.0
O A:HOH2113 4.1 30.1 1.0
NZ A:KCX150 4.2 14.3 1.0
O A:HOH2605 4.3 23.9 1.0
ND1 A:HIS59 4.3 15.0 1.0
CB A:ASP315 4.3 15.1 1.0
ND1 A:HIS61 4.3 15.9 1.0
CG A:HIS61 4.3 16.5 1.0
O A:HOH2114 4.4 34.5 1.0
CG A:HIS59 4.4 14.7 1.0
CG A:MET93 4.4 13.7 1.0
CD2 A:HIS239 4.4 17.6 1.0
NE2 A:HIS239 4.5 15.9 1.0
CA A:ASP315 4.7 13.3 1.0

Zinc binding site 3 out of 12 in 1gkp

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Zinc binding site 3 out of 12 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221


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 C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1460

b:18.8
occ:1.00
 O B:HOH2585 2.0 18.1 1.0
OQ1 B:KCX150 2.0 16.8 1.0
O B:HOH2584 2.1 20.6 1.0
ND1 B:HIS183 2.2 15.0 1.0
NE2 B:HIS239 2.2 12.8 1.0
CE1 B:HIS183 3.0 15.1 1.0
CX B:KCX150 3.1 16.6 1.0
CD2 B:HIS239 3.2 12.9 1.0
CE1 B:HIS239 3.3 12.1 1.0
CG B:HIS183 3.3 14.1 1.0
OQ2 B:KCX150 3.4 16.2 1.0
ZN B:ZN1461 3.6 18.5 1.0
CB B:HIS183 3.8 14.7 1.0
O B:SER288 3.8 20.6 1.0
NZ B:KCX150 4.2 16.3 1.0
NE2 B:HIS183 4.2 15.9 1.0
CE2 B:PHE152 4.3 18.9 1.0
O B:HOH2104 4.4 31.7 1.0
CG B:HIS239 4.4 12.4 1.0
OD2 B:ASP315 4.4 20.4 1.0
ND1 B:HIS239 4.4 13.3 1.0
OH B:TYR155 4.4 20.3 1.0
CD2 B:HIS183 4.4 16.3 1.0
CE1 B:HIS59 4.6 12.9 1.0
CG2 B:VAL238 4.7 13.2 1.0
NE2 B:HIS59 4.7 14.0 1.0
CD2 B:PHE152 4.7 18.8 1.0
CE B:KCX150 4.7 15.0 1.0
C B:SER288 4.8 17.2 1.0
OD1 B:ASP315 4.9 15.8 1.0
CA B:HIS183 4.9 13.9 1.0
CG B:ASP315 5.0 15.3 1.0

Zinc binding site 4 out of 12 in 1gkp

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Zinc binding site 4 out of 12 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221


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 C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1461

b:18.5
occ:1.00
 O B:HOH2585 2.1 18.1 1.0
OQ2 B:KCX150 2.1 16.2 1.0
OD1 B:ASP315 2.1 15.8 1.0
NE2 B:HIS61 2.2 15.4 1.0
NE2 B:HIS59 2.2 14.0 1.0
CX B:KCX150 3.0 16.6 1.0
CG B:ASP315 3.1 15.3 1.0
CE1 B:HIS61 3.1 16.0 1.0
CE1 B:HIS59 3.1 12.9 1.0
CD2 B:HIS61 3.2 14.8 1.0
CD2 B:HIS59 3.2 13.3 1.0
OQ1 B:KCX150 3.4 16.8 1.0
OD2 B:ASP315 3.5 20.4 1.0
ZN B:ZN1460 3.6 18.8 1.0
O B:HOH2104 3.9 31.7 1.0
NZ B:KCX150 4.1 16.3 1.0
O B:HOH2584 4.2 20.6 1.0
CB B:ASP315 4.2 13.9 1.0
ND1 B:HIS61 4.2 15.7 1.0
ND1 B:HIS59 4.3 13.7 1.0
CG B:HIS61 4.3 14.1 1.0
CG B:HIS59 4.3 12.2 1.0
CG B:MET93 4.4 15.9 1.0
CD2 B:HIS239 4.5 12.9 1.0
CA B:ASP315 4.6 13.1 1.0
NE2 B:HIS239 4.6 12.8 1.0

Zinc binding site 5 out of 12 in 1gkp

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Zinc binding site 5 out of 12 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221


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 C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1460

b:16.0
occ:1.00
 O C:HOH2655 2.0 13.9 1.0
OQ1 C:KCX150 2.0 13.2 1.0
O C:HOH2654 2.1 19.6 1.0
ND1 C:HIS183 2.2 12.8 1.0
NE2 C:HIS239 2.2 11.4 1.0
CE1 C:HIS183 3.1 12.6 1.0
CX C:KCX150 3.1 12.9 1.0
CD2 C:HIS239 3.2 12.2 1.0
CE1 C:HIS239 3.2 10.9 1.0
CG C:HIS183 3.3 11.1 1.0
OQ2 C:KCX150 3.4 14.2 1.0
ZN C:ZN1461 3.6 15.6 1.0
CB C:HIS183 3.8 11.1 1.0
O C:SER288 4.0 19.8 1.0
NE2 C:HIS183 4.3 13.8 1.0
NZ C:KCX150 4.3 12.3 1.0
CE2 C:PHE152 4.3 14.5 1.0
OH C:TYR155 4.3 19.7 1.0
ND1 C:HIS239 4.4 11.8 1.0
CG C:HIS239 4.4 11.8 1.0
O C:HOH2117 4.4 25.0 1.0
OD2 C:ASP315 4.4 16.8 1.0
CD2 C:HIS183 4.4 13.4 1.0
CG2 C:VAL238 4.6 11.6 1.0
CE1 C:HIS59 4.6 11.2 1.0
NE2 C:HIS59 4.7 11.8 1.0
CD2 C:PHE152 4.8 12.9 1.0
CE C:KCX150 4.8 12.3 1.0
CA C:HIS183 4.9 10.5 1.0
OD1 C:ASP315 4.9 13.4 1.0
CG C:ASP315 4.9 13.8 1.0
CE2 C:TYR155 4.9 17.4 1.0
C C:SER288 5.0 15.4 1.0

Zinc binding site 6 out of 12 in 1gkp

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Zinc binding site 6 out of 12 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221


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 C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1461

b:15.6
occ:1.00
 O C:HOH2655 2.1 13.9 1.0
OQ2 C:KCX150 2.1 14.2 1.0
OD1 C:ASP315 2.2 13.4 1.0
NE2 C:HIS61 2.2 12.7 1.0
NE2 C:HIS59 2.2 11.8 1.0
CX C:KCX150 3.1 12.9 1.0
CG C:ASP315 3.1 13.8 1.0
CE1 C:HIS61 3.1 13.3 1.0
CD2 C:HIS59 3.1 11.6 1.0
CE1 C:HIS59 3.1 11.2 1.0
CD2 C:HIS61 3.2 12.5 1.0
OQ1 C:KCX150 3.4 13.2 1.0
OD2 C:ASP315 3.5 16.8 1.0
ZN C:ZN1460 3.6 16.0 1.0
O C:HOH2117 4.0 25.0 1.0
NZ C:KCX150 4.1 12.3 1.0
CB C:ASP315 4.2 13.1 1.0
O C:HOH2654 4.3 19.6 1.0
ND1 C:HIS59 4.3 12.7 1.0
ND1 C:HIS61 4.3 12.8 1.0
CG C:HIS59 4.3 11.2 1.0
CG C:HIS61 4.3 12.5 1.0
CG C:MET93 4.4 12.4 1.0
CD2 C:HIS239 4.4 12.2 1.0
NE2 C:HIS239 4.6 11.4 1.0
CA C:ASP315 4.6 11.7 1.0

Zinc binding site 7 out of 12 in 1gkp

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Zinc binding site 7 out of 12 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221


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 C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1460

b:19.8
occ:1.00
 OQ1 D:KCX150 2.0 16.9 1.0
O D:HOH2556 2.1 18.5 1.0
O D:HOH2555 2.1 23.5 1.0
NE2 D:HIS239 2.2 14.5 1.0
ND1 D:HIS183 2.2 14.7 1.0
CE1 D:HIS183 3.0 15.4 1.0
CX D:KCX150 3.1 17.5 1.0
CD2 D:HIS239 3.2 14.9 1.0
CE1 D:HIS239 3.2 14.8 1.0
CG D:HIS183 3.3 13.8 1.0
OQ2 D:KCX150 3.4 17.6 1.0
ZN D:ZN1461 3.6 20.1 1.0
CB D:HIS183 3.8 13.8 1.0
O D:SER288 4.0 21.7 1.0
NE2 D:HIS183 4.2 16.9 1.0
NZ D:KCX150 4.3 16.2 1.0
CE2 D:PHE152 4.3 17.6 1.0
CG D:HIS239 4.3 14.7 1.0
OD2 D:ASP315 4.3 20.9 1.0
ND1 D:HIS239 4.4 14.4 1.0
OH D:TYR155 4.4 22.1 1.0
CD2 D:HIS183 4.4 17.0 1.0
O D:HOH2091 4.4 29.6 1.0
CE1 D:HIS59 4.6 14.3 1.0
NE2 D:HIS59 4.6 15.3 1.0
CG2 D:VAL238 4.7 13.3 1.0
CD2 D:PHE152 4.7 15.8 1.0
CE D:KCX150 4.8 15.6 1.0
OD1 D:ASP315 4.9 18.3 1.0
CA D:HIS183 4.9 13.3 1.0
CE2 D:TYR155 4.9 20.8 1.0
CG D:ASP315 5.0 17.3 1.0
C D:SER288 5.0 18.5 1.0

Zinc binding site 8 out of 12 in 1gkp

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Zinc binding site 8 out of 12 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221


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 C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1461

b:20.1
occ:1.00
 O D:HOH2556 2.0 18.5 1.0
OQ2 D:KCX150 2.1 17.6 1.0
NE2 D:HIS59 2.1 15.3 1.0
NE2 D:HIS61 2.2 17.5 1.0
OD1 D:ASP315 2.2 18.3 1.0
CX D:KCX150 3.1 17.5 1.0
CD2 D:HIS59 3.1 15.1 1.0
CG D:ASP315 3.1 17.3 1.0
CE1 D:HIS61 3.1 17.3 1.0
CE1 D:HIS59 3.1 14.3 1.0
CD2 D:HIS61 3.2 17.3 1.0
OQ1 D:KCX150 3.4 16.9 1.0
OD2 D:ASP315 3.5 20.9 1.0
ZN D:ZN1460 3.6 19.8 1.0
O D:HOH2091 4.0 29.6 1.0
NZ D:KCX150 4.1 16.2 1.0
O D:HOH2555 4.2 23.5 1.0
ND1 D:HIS59 4.2 13.9 1.0
CG D:HIS59 4.2 14.9 1.0
CB D:ASP315 4.3 15.5 1.0
ND1 D:HIS61 4.3 16.8 1.0
CG D:HIS61 4.3 16.9 1.0
CG D:MET93 4.4 16.5 1.0
CD2 D:HIS239 4.4 14.9 1.0
CA D:ASP315 4.6 15.4 1.0
NE2 D:HIS239 4.6 14.5 1.0
O D:HOH2092 5.0 33.3 1.0

Zinc binding site 9 out of 12 in 1gkp

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Zinc binding site 9 out of 12 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1460

b:16.0
occ:1.00
 OQ1 E:KCX150 2.1 13.3 1.0
O E:HOH2681 2.1 15.4 1.0
O E:HOH2680 2.1 19.1 1.0
ND1 E:HIS183 2.2 12.7 1.0
NE2 E:HIS239 2.3 11.7 1.0
CE1 E:HIS183 3.1 13.1 1.0
CX E:KCX150 3.1 13.7 1.0
CD2 E:HIS239 3.2 11.6 1.0
CE1 E:HIS239 3.3 10.1 1.0
CG E:HIS183 3.3 10.6 1.0
OQ2 E:KCX150 3.4 13.3 1.0
ZN E:ZN1461 3.6 15.8 1.0
CB E:HIS183 3.8 10.5 1.0
O E:SER288 3.9 19.0 1.0
NE2 E:HIS183 4.2 14.2 1.0
NZ E:KCX150 4.3 12.7 1.0
OH E:TYR155 4.3 17.3 1.0
CE2 E:PHE152 4.3 15.6 1.0
ND1 E:HIS239 4.4 11.4 1.0
OD2 E:ASP315 4.4 17.3 1.0
CD2 E:HIS183 4.4 13.3 1.0
CG E:HIS239 4.4 10.9 1.0
O E:HOH2133 4.5 27.4 1.0
CE1 E:HIS59 4.7 11.1 1.0
NE2 E:HIS59 4.7 11.7 1.0
CG2 E:VAL238 4.7 10.7 1.0
CE E:KCX150 4.8 12.5 1.0
CD2 E:PHE152 4.8 13.3 1.0
CA E:HIS183 4.9 10.1 1.0
OD1 E:ASP315 4.9 13.9 1.0
C E:SER288 4.9 15.8 1.0
CE2 E:TYR155 4.9 16.0 1.0
CG E:ASP315 5.0 13.8 1.0

Zinc binding site 10 out of 12 in 1gkp

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Zinc binding site 10 out of 12 in the D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of D-Hydantoinase (Dihydropyrimidinase) From Thermus Sp. in Space Group C2221 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1461

b:15.8
occ:1.00
 O E:HOH2681 2.0 15.4 1.0
OQ2 E:KCX150 2.1 13.3 1.0
OD1 E:ASP315 2.2 13.9 1.0
NE2 E:HIS61 2.2 13.4 1.0
NE2 E:HIS59 2.2 11.7 1.0
CX E:KCX150 3.1 13.7 1.0
CG E:ASP315 3.1 13.8 1.0
CD2 E:HIS61 3.2 12.7 1.0
CE1 E:HIS61 3.2 13.4 1.0
CE1 E:HIS59 3.2 11.1 1.0
CD2 E:HIS59 3.2 11.6 1.0
OQ1 E:KCX150 3.4 13.3 1.0
OD2 E:ASP315 3.5 17.3 1.0
ZN E:ZN1460 3.6 16.0 1.0
O E:HOH2133 4.0 27.4 1.0
NZ E:KCX150 4.1 12.7 1.0
CB E:ASP315 4.2 12.1 1.0
O E:HOH2680 4.2 19.1 1.0
ND1 E:HIS59 4.3 11.3 1.0
ND1 E:HIS61 4.3 12.9 1.0
CG E:HIS61 4.3 12.5 1.0
CG E:HIS59 4.3 11.1 1.0
CG E:MET93 4.4 12.0 1.0
CD2 E:HIS239 4.5 11.6 1.0
NE2 E:HIS239 4.6 11.7 1.0
CA E:ASP315 4.6 11.3 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: Sun Oct 13 01:33:30 2024

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