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Zinc in PDB 1gkr: L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens

Enzymatic activity of L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens

All present enzymatic activity of L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens:
3.5.2.2;

Protein crystallography data

The structure of L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens, PDB code: 1gkr 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) 30.00 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 111.500, 74.300, 146.900, 90.00, 106.57, 90.00
R / Rfree (%) 22.4 / 24.4

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 1gkr

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Zinc binding site 1 out of 8 in the L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1452

b:19.3
occ:1.00
 OQ1 A:KCX147 1.8 9.7 1.0
ND1 A:HIS183 2.0 3.0 1.0
NE2 A:HIS239 2.3 14.1 1.0
O A:HOH2124 2.7 20.7 1.0
CX A:KCX147 2.8 12.8 1.0
CE1 A:HIS183 2.8 6.6 1.0
OQ2 A:KCX147 3.1 9.2 1.0
CG A:HIS183 3.2 8.5 1.0
CD2 A:HIS239 3.2 11.5 1.0
CE1 A:HIS239 3.2 9.8 1.0
O A:HOH2123 3.2 20.7 1.0
ZN A:ZN1453 3.6 17.0 1.0
CB A:HIS183 3.7 8.5 1.0
O A:ALA285 3.9 20.4 1.0
NZ A:KCX147 4.0 10.8 1.0
NE2 A:HIS183 4.0 8.6 1.0
CD2 A:HIS183 4.2 3.6 1.0
ND1 A:HIS239 4.4 10.5 1.0
CG A:HIS239 4.4 9.6 1.0
CE1 A:HIS60 4.7 18.9 1.0
CA A:HIS183 4.7 10.0 1.0
NE2 A:HIS60 4.9 16.8 1.0
OD2 A:ASP312 4.9 18.3 1.0
C A:ALA285 5.0 15.7 1.0

Zinc binding site 2 out of 8 in 1gkr

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Zinc binding site 2 out of 8 in the L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1453

b:17.0
occ:1.00
 NE2 A:HIS60 2.1 16.8 1.0
OD1 A:ASP312 2.1 12.8 1.0
NE2 A:HIS62 2.1 10.4 1.0
OQ2 A:KCX147 2.2 9.2 1.0
O A:HOH2124 2.5 20.7 1.0
CE1 A:HIS60 2.9 18.9 1.0
CD2 A:HIS62 3.1 11.2 1.0
CG A:ASP312 3.1 14.0 1.0
CE1 A:HIS62 3.1 9.4 1.0
CD2 A:HIS60 3.2 18.0 1.0
CX A:KCX147 3.3 12.8 1.0
OD2 A:ASP312 3.4 18.3 1.0
ZN A:ZN1452 3.6 19.3 1.0
OQ1 A:KCX147 3.8 9.7 1.0
ND1 A:HIS60 4.1 15.8 1.0
CG A:HIS62 4.2 9.4 1.0
ND1 A:HIS62 4.2 8.6 1.0
CD2 A:HIS239 4.3 11.5 1.0
CG A:HIS60 4.3 16.8 1.0
CB A:ASP312 4.3 9.2 1.0
NZ A:KCX147 4.4 10.8 1.0
NE2 A:HIS239 4.4 14.1 1.0
CA A:ASP312 4.8 13.3 1.0
CE A:KCX147 4.8 10.2 1.0
O A:HOH2123 4.9 20.7 1.0
SD A:MET93 5.0 25.0 1.0

Zinc binding site 3 out of 8 in 1gkr

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Zinc binding site 3 out of 8 in the L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1452

b:19.3
occ:1.00
 OQ1 B:KCX147 1.8 9.7 1.0
ND1 B:HIS183 2.0 3.0 1.0
NE2 B:HIS239 2.3 14.1 1.0
O B:HOH2129 2.7 20.7 1.0
CX B:KCX147 2.8 12.8 1.0
CE1 B:HIS183 2.8 6.6 1.0
OQ2 B:KCX147 3.1 9.2 1.0
CG B:HIS183 3.2 8.5 1.0
CD2 B:HIS239 3.2 11.5 1.0
CE1 B:HIS239 3.2 9.8 1.0
O B:HOH2128 3.2 20.7 1.0
ZN B:ZN1453 3.6 17.0 1.0
CB B:HIS183 3.7 8.5 1.0
O B:ALA285 3.9 20.4 1.0
NZ B:KCX147 4.0 10.8 1.0
NE2 B:HIS183 4.0 8.6 1.0
CD2 B:HIS183 4.2 3.6 1.0
ND1 B:HIS239 4.4 10.5 1.0
CG B:HIS239 4.4 9.6 1.0
CE1 B:HIS60 4.7 18.9 1.0
CA B:HIS183 4.7 10.0 1.0
NE2 B:HIS60 4.9 16.8 1.0
OD2 B:ASP312 4.9 18.3 1.0
C B:ALA285 5.0 15.7 1.0

Zinc binding site 4 out of 8 in 1gkr

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Zinc binding site 4 out of 8 in the L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1453

b:17.0
occ:1.00
 NE2 B:HIS60 2.1 16.8 1.0
OD1 B:ASP312 2.1 12.8 1.0
NE2 B:HIS62 2.1 10.4 1.0
OQ2 B:KCX147 2.2 9.2 1.0
O B:HOH2129 2.5 20.7 1.0
CE1 B:HIS60 2.9 18.9 1.0
CD2 B:HIS62 3.1 11.2 1.0
CG B:ASP312 3.1 14.0 1.0
CE1 B:HIS62 3.1 9.4 1.0
CD2 B:HIS60 3.2 18.0 1.0
CX B:KCX147 3.3 12.8 1.0
OD2 B:ASP312 3.4 18.3 1.0
ZN B:ZN1452 3.6 19.3 1.0
OQ1 B:KCX147 3.8 9.7 1.0
ND1 B:HIS60 4.1 15.8 1.0
CG B:HIS62 4.2 9.4 1.0
ND1 B:HIS62 4.2 8.6 1.0
CD2 B:HIS239 4.3 11.5 1.0
CG B:HIS60 4.3 16.8 1.0
CB B:ASP312 4.3 9.2 1.0
NZ B:KCX147 4.4 10.8 1.0
NE2 B:HIS239 4.4 14.1 1.0
CA B:ASP312 4.8 13.3 1.0
CE B:KCX147 4.8 10.2 1.0
O B:HOH2128 4.9 20.7 1.0
SD B:MET93 5.0 25.0 1.0

Zinc binding site 5 out of 8 in 1gkr

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Zinc binding site 5 out of 8 in the L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1452

b:19.3
occ:1.00
 OQ1 C:KCX147 1.8 9.7 1.0
ND1 C:HIS183 2.0 3.0 1.0
NE2 C:HIS239 2.3 14.1 1.0
O C:HOH2128 2.7 20.7 1.0
CX C:KCX147 2.8 12.8 1.0
CE1 C:HIS183 2.8 6.6 1.0
OQ2 C:KCX147 3.1 9.2 1.0
CG C:HIS183 3.2 8.5 1.0
CD2 C:HIS239 3.2 11.5 1.0
CE1 C:HIS239 3.2 9.8 1.0
O C:HOH2127 3.2 20.7 1.0
ZN C:ZN1453 3.6 17.0 1.0
CB C:HIS183 3.7 8.5 1.0
O C:ALA285 3.9 20.4 1.0
NZ C:KCX147 4.0 10.8 1.0
NE2 C:HIS183 4.0 8.6 1.0
CD2 C:HIS183 4.2 3.6 1.0
ND1 C:HIS239 4.4 10.5 1.0
CG C:HIS239 4.4 9.6 1.0
CE1 C:HIS60 4.7 18.9 1.0
CA C:HIS183 4.7 10.0 1.0
NE2 C:HIS60 4.9 16.8 1.0
OD2 C:ASP312 4.9 18.3 1.0
C C:ALA285 5.0 15.7 1.0

Zinc binding site 6 out of 8 in 1gkr

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Zinc binding site 6 out of 8 in the L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1453

b:17.0
occ:1.00
 NE2 C:HIS60 2.1 16.8 1.0
OD1 C:ASP312 2.1 12.8 1.0
NE2 C:HIS62 2.1 10.4 1.0
OQ2 C:KCX147 2.2 9.2 1.0
O C:HOH2128 2.5 20.7 1.0
CE1 C:HIS60 2.9 18.9 1.0
CD2 C:HIS62 3.1 11.2 1.0
CG C:ASP312 3.1 14.0 1.0
CE1 C:HIS62 3.1 9.4 1.0
CD2 C:HIS60 3.2 18.0 1.0
CX C:KCX147 3.3 12.8 1.0
OD2 C:ASP312 3.4 18.3 1.0
ZN C:ZN1452 3.6 19.3 1.0
OQ1 C:KCX147 3.8 9.7 1.0
ND1 C:HIS60 4.1 15.8 1.0
CG C:HIS62 4.2 9.4 1.0
ND1 C:HIS62 4.2 8.6 1.0
CD2 C:HIS239 4.3 11.5 1.0
CG C:HIS60 4.3 16.8 1.0
CB C:ASP312 4.3 9.2 1.0
NZ C:KCX147 4.4 10.8 1.0
NE2 C:HIS239 4.4 14.1 1.0
CA C:ASP312 4.8 13.3 1.0
CE C:KCX147 4.8 10.2 1.0
O C:HOH2127 4.9 20.7 1.0
SD C:MET93 5.0 25.0 1.0

Zinc binding site 7 out of 8 in 1gkr

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Zinc binding site 7 out of 8 in the L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1452

b:19.3
occ:1.00
 OQ1 D:KCX147 1.8 9.7 1.0
ND1 D:HIS183 2.0 3.0 1.0
NE2 D:HIS239 2.3 14.1 1.0
O D:HOH2127 2.7 20.7 1.0
CX D:KCX147 2.8 12.8 1.0
CE1 D:HIS183 2.8 6.6 1.0
OQ2 D:KCX147 3.1 9.2 1.0
CG D:HIS183 3.2 8.5 1.0
CD2 D:HIS239 3.2 11.5 1.0
CE1 D:HIS239 3.2 9.8 1.0
O D:HOH2126 3.2 20.7 1.0
ZN D:ZN1453 3.6 17.0 1.0
CB D:HIS183 3.7 8.5 1.0
O D:ALA285 3.9 20.4 1.0
NZ D:KCX147 4.0 10.8 1.0
NE2 D:HIS183 4.0 8.6 1.0
CD2 D:HIS183 4.2 3.6 1.0
ND1 D:HIS239 4.4 10.5 1.0
CG D:HIS239 4.4 9.6 1.0
CE1 D:HIS60 4.7 18.9 1.0
CA D:HIS183 4.7 10.0 1.0
NE2 D:HIS60 4.9 16.8 1.0
OD2 D:ASP312 4.9 18.3 1.0
C D:ALA285 5.0 15.7 1.0

Zinc binding site 8 out of 8 in 1gkr

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Zinc binding site 8 out of 8 in the L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of L-Hydantoinase (Dihydropyrimidinase) From Arthrobacter Aurescens within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1453

b:17.0
occ:1.00
 NE2 D:HIS60 2.1 16.8 1.0
OD1 D:ASP312 2.1 12.8 1.0
NE2 D:HIS62 2.1 10.4 1.0
OQ2 D:KCX147 2.2 9.2 1.0
O D:HOH2127 2.5 20.7 1.0
CE1 D:HIS60 2.9 18.9 1.0
CD2 D:HIS62 3.1 11.2 1.0
CG D:ASP312 3.1 14.0 1.0
CE1 D:HIS62 3.1 9.4 1.0
CD2 D:HIS60 3.2 18.0 1.0
CX D:KCX147 3.3 12.8 1.0
OD2 D:ASP312 3.4 18.3 1.0
ZN D:ZN1452 3.6 19.3 1.0
OQ1 D:KCX147 3.8 9.7 1.0
ND1 D:HIS60 4.1 15.8 1.0
CG D:HIS62 4.2 9.4 1.0
ND1 D:HIS62 4.2 8.6 1.0
CD2 D:HIS239 4.3 11.5 1.0
CG D:HIS60 4.3 16.8 1.0
CB D:ASP312 4.3 9.2 1.0
NZ D:KCX147 4.4 10.8 1.0
NE2 D:HIS239 4.4 14.1 1.0
CA D:ASP312 4.8 13.3 1.0
CE D:KCX147 4.8 10.2 1.0
O D:HOH2126 4.9 20.7 1.0
SD D:MET93 5.0 25.0 1.0

Reference:

J.Abendroth, K.Niefind, O.May, M.Siemann, C.Syldatk, D.Schomburg. The Structure of L-Hydantoinase From Arthobacter Aurescens Leads to An Understanding of Dihydropyrimidinase Substrate and Enantio Specificity. Biochemistry V. 41 8589 2002.
ISSN: ISSN 0006-2960
PubMed: 12093275
DOI: 10.1021/BI0157722
Page generated: Wed Dec 16 02:50:19 2020

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