Zinc in PDB 1k1d: Crystal Structure of D-Hydantoinase

The structure of Crystal Structure of D-Hydantoinase, PDB code: 1k1d was solved by Y.H.Cheon, H.S.Kim, K.H.Han, J.Abendroth, K.Niefind, D.Schomburg, J.Wang, Y.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 3.01
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	214.449, 182.890, 156.131, 90.00, 125.27, 90.00
R / Rfree (%)	26.3 / 28

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of D-Hydantoinase (pdb code 1k1d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of D-Hydantoinase, PDB code: 1k1d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Crystal 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 Crystal Structure of D-Hydantoinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:55.5 occ:1.00 ND1 A:HIS183 2.3 39.5 1.0 OQ1 A:KCX150 2.5 50.2 1.0 NE2 A:HIS239 2.5 40.9 1.0 CE1 A:HIS183 2.8 39.2 1.0 ZN A:ZN502 3.0 55.5 1.0 CD2 A:HIS239 3.4 40.5 1.0 CX A:KCX150 3.4 51.4 1.0 CG A:HIS183 3.5 39.6 1.0 OQ2 A:KCX150 3.6 52.0 1.0 CE1 A:HIS239 3.6 40.4 1.0 O A:SER288 4.0 48.9 1.0 NE2 A:HIS183 4.1 37.2 1.0 CB A:HIS183 4.1 40.5 1.0 OH A:TYR155 4.3 57.7 1.0 CE2 A:PHE152 4.3 39.5 1.0 CE2 A:TYR155 4.4 56.1 1.0 CD2 A:HIS183 4.4 38.2 1.0 NE2 A:HIS58 4.4 49.3 1.0 CE1 A:HIS58 4.5 49.2 1.0 NZ A:KCX150 4.6 49.6 1.0 OD1 A:ASP315 4.6 46.3 1.0 CG A:HIS239 4.6 40.1 1.0 OD2 A:ASP315 4.6 46.2 1.0 ND1 A:HIS239 4.7 40.4 1.0 CG2 A:VAL238 4.7 35.4 1.0 CD2 A:PHE152 4.8 39.9 1.0 CZ A:TYR155 4.8 56.9 1.0 CG A:ASP315 5.0 45.7 1.0

Zinc binding site 2 out of 16 in the Crystal 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 Crystal Structure of D-Hydantoinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:55.5 occ:1.00 NE2 A:HIS58 2.3 49.3 1.0 NE2 A:HIS60 2.4 55.3 1.0 OD1 A:ASP315 2.4 46.3 1.0 OQ2 A:KCX150 2.5 52.0 1.0 ZN A:ZN501 3.0 55.5 1.0 CD2 A:HIS60 3.1 55.5 1.0 CE1 A:HIS58 3.2 49.2 1.0 CD2 A:HIS58 3.4 48.6 1.0 CG A:ASP315 3.4 45.7 1.0 CX A:KCX150 3.5 51.4 1.0 CE1 A:HIS60 3.5 55.9 1.0 OQ1 A:KCX150 3.7 50.2 1.0 OD2 A:ASP315 3.9 46.2 1.0 CG A:HIS60 4.4 55.2 1.0 ND1 A:HIS58 4.4 49.5 1.0 CD2 A:HIS239 4.4 40.5 1.0 CG A:HIS58 4.5 49.4 1.0 NE2 A:HIS239 4.5 40.9 1.0 ND1 A:HIS60 4.5 55.5 1.0 NZ A:KCX150 4.6 49.6 1.0 CB A:ASP315 4.7 44.4 1.0 CA A:ASP315 4.9 43.9 1.0

Zinc binding site 3 out of 16 in the Crystal 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 Crystal Structure of D-Hydantoinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:68.6 occ:1.00 ND1 B:HIS183 2.3 36.6 1.0 OQ1 B:KCX150 2.5 48.6 1.0 NE2 B:HIS239 2.7 37.3 1.0 CE1 B:HIS183 2.8 36.8 1.0 ZN B:ZN502 3.0 44.9 1.0 CX B:KCX150 3.4 47.7 1.0 CD2 B:HIS239 3.5 36.7 1.0 CG B:HIS183 3.5 37.3 1.0 OQ2 B:KCX150 3.5 46.5 1.0 CE1 B:HIS239 3.7 38.0 1.0 O B:SER288 4.0 47.3 1.0 NE2 B:HIS183 4.0 37.6 1.0 CB B:HIS183 4.1 38.0 1.0 CE2 B:PHE152 4.2 43.1 1.0 OH B:TYR155 4.2 53.5 1.0 CE2 B:TYR155 4.3 54.9 1.0 CD2 B:HIS183 4.4 37.3 1.0 NE2 B:HIS58 4.5 49.7 1.0 CE1 B:HIS58 4.5 49.8 1.0 OD1 B:ASP315 4.6 42.6 1.0 CD2 B:PHE152 4.7 42.2 1.0 OD2 B:ASP315 4.7 45.8 1.0 NZ B:KCX150 4.7 46.9 1.0 CG B:HIS239 4.7 38.7 1.0 CZ B:TYR155 4.8 54.5 1.0 ND1 B:HIS239 4.8 38.9 1.0 CG2 B:VAL238 4.8 34.6 1.0

Zinc binding site 4 out of 16 in the Crystal 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 Crystal Structure of D-Hydantoinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:44.9 occ:1.00 NE2 B:HIS58 2.2 49.7 1.0 OD1 B:ASP315 2.4 42.6 1.0 NE2 B:HIS60 2.4 57.9 1.0 OQ2 B:KCX150 2.5 46.5 1.0 ZN B:ZN501 3.0 68.6 1.0 CE1 B:HIS58 3.1 49.8 1.0 CD2 B:HIS60 3.2 57.2 1.0 CD2 B:HIS58 3.3 48.7 1.0 CG B:ASP315 3.4 43.8 1.0 CX B:KCX150 3.4 47.7 1.0 CE1 B:HIS60 3.6 56.7 1.0 OQ1 B:KCX150 3.6 48.6 1.0 OD2 B:ASP315 3.8 45.8 1.0 ND1 B:HIS58 4.2 48.9 1.0 CD2 B:HIS239 4.3 36.7 1.0 CG B:HIS58 4.4 48.1 1.0 NE2 B:HIS239 4.4 37.3 1.0 CG B:HIS60 4.4 56.3 1.0 ND1 B:HIS60 4.6 56.5 1.0 CB B:ASP315 4.6 42.9 1.0 NZ B:KCX150 4.7 46.9 1.0 CA B:ASP315 4.9 43.1 1.0

Zinc binding site 5 out of 16 in the Crystal 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 Crystal Structure of D-Hydantoinase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:69.9 occ:1.00 ND1 C:HIS183 2.3 38.2 1.0 OQ1 C:KCX150 2.6 56.5 1.0 NE2 C:HIS239 2.6 41.7 1.0 CE1 C:HIS183 2.8 38.0 1.0 ZN C:ZN502 3.1 50.6 1.0 CD2 C:HIS239 3.4 41.1 1.0 CG C:HIS183 3.5 39.4 1.0 CX C:KCX150 3.5 55.3 1.0 OQ2 C:KCX150 3.6 57.4 1.0 CE1 C:HIS239 3.7 42.9 1.0 O C:SER288 4.0 46.6 1.0 NE2 C:HIS183 4.0 37.0 1.0 OH C:TYR155 4.1 59.0 1.0 CB C:HIS183 4.2 39.1 1.0 CE2 C:PHE152 4.3 43.3 1.0 CE2 C:TYR155 4.3 57.0 1.0 CD2 C:HIS183 4.4 38.6 1.0 NE2 C:HIS58 4.5 45.0 1.0 CE1 C:HIS58 4.5 45.9 1.0 OD1 C:ASP315 4.6 50.9 1.0 OD2 C:ASP315 4.6 47.0 1.0 CG C:HIS239 4.7 40.5 1.0 NZ C:KCX150 4.7 53.0 1.0 CZ C:TYR155 4.7 57.4 1.0 ND1 C:HIS239 4.7 42.4 1.0 CD2 C:PHE152 4.8 42.8 1.0 CG2 C:VAL238 4.8 31.5 1.0 C C:SER288 5.0 44.8 1.0 CG C:ASP315 5.0 47.3 1.0

Zinc binding site 6 out of 16 in the Crystal 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 Crystal Structure of D-Hydantoinase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:50.6 occ:1.00 NE2 C:HIS58 2.3 45.0 1.0 OD1 C:ASP315 2.3 50.9 1.0 NE2 C:HIS60 2.4 58.7 1.0 OQ2 C:KCX150 2.6 57.4 1.0 ZN C:ZN501 3.1 69.9 1.0 CD2 C:HIS60 3.1 57.9 1.0 CE1 C:HIS58 3.2 45.9 1.0 CD2 C:HIS58 3.3 46.4 1.0 CG C:ASP315 3.4 47.3 1.0 CE1 C:HIS60 3.5 58.4 1.0 CX C:KCX150 3.5 55.3 1.0 OQ1 C:KCX150 3.7 56.5 1.0 OD2 C:ASP315 3.8 47.0 1.0 CG C:HIS60 4.3 57.0 1.0 ND1 C:HIS58 4.3 45.6 1.0 CD2 C:HIS239 4.4 41.1 1.0 CG C:HIS58 4.4 46.3 1.0 ND1 C:HIS60 4.5 58.9 1.0 NE2 C:HIS239 4.5 41.7 1.0 CB C:ASP315 4.6 43.5 1.0 NZ C:KCX150 4.7 53.0 1.0 CA C:ASP315 4.8 42.0 1.0

Zinc binding site 7 out of 16 in the Crystal 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 Crystal Structure of D-Hydantoinase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:64.3 occ:1.00 ND1 D:HIS183 2.3 38.7 1.0 NE2 D:HIS239 2.6 40.0 1.0 OQ1 D:KCX150 2.6 55.9 1.0 CE1 D:HIS183 2.8 38.5 1.0 ZN D:ZN502 3.0 48.4 1.0 CD2 D:HIS239 3.4 39.7 1.0 CG D:HIS183 3.5 40.4 1.0 CX D:KCX150 3.5 53.7 1.0 OQ2 D:KCX150 3.6 54.7 1.0 CE1 D:HIS239 3.6 39.5 1.0 O D:SER288 3.9 47.3 1.0 NE2 D:HIS183 4.0 38.9 1.0 CB D:HIS183 4.1 39.8 1.0 OH D:TYR155 4.2 54.6 1.0 CE2 D:PHE152 4.3 39.8 1.0 CE2 D:TYR155 4.3 55.3 1.0 CD2 D:HIS183 4.4 40.4 1.0 NE2 D:HIS58 4.4 48.1 1.0 CE1 D:HIS58 4.5 48.6 1.0 OD1 D:ASP315 4.6 50.9 1.0 OD2 D:ASP315 4.6 51.8 1.0 CG D:HIS239 4.6 38.8 1.0 ND1 D:HIS239 4.7 39.0 1.0 NZ D:KCX150 4.7 51.3 1.0 CG2 D:VAL238 4.7 33.2 1.0 CZ D:TYR155 4.8 55.3 1.0 CD2 D:PHE152 4.8 40.6 1.0 C D:SER288 5.0 47.0 1.0 CG D:ASP315 5.0 50.0 1.0

Zinc binding site 8 out of 16 in the Crystal 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 Crystal Structure of D-Hydantoinase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:48.4 occ:1.00 NE2 D:HIS58 2.2 48.1 1.0 OD1 D:ASP315 2.3 50.9 1.0 NE2 D:HIS60 2.5 52.5 1.0 OQ2 D:KCX150 2.6 54.7 1.0 ZN D:ZN501 3.0 64.3 1.0 CE1 D:HIS58 3.1 48.6 1.0 CD2 D:HIS60 3.2 53.2 1.0 CD2 D:HIS58 3.3 48.2 1.0 CG D:ASP315 3.3 50.0 1.0 CX D:KCX150 3.5 53.7 1.0 CE1 D:HIS60 3.6 54.3 1.0 OQ1 D:KCX150 3.6 55.9 1.0 OD2 D:ASP315 3.7 51.8 1.0 ND1 D:HIS58 4.2 48.8 1.0 CD2 D:HIS239 4.3 39.7 1.0 CG D:HIS58 4.4 48.7 1.0 NE2 D:HIS239 4.4 40.0 1.0 CG D:HIS60 4.4 53.2 1.0 CB D:ASP315 4.5 47.5 1.0 ND1 D:HIS60 4.6 54.1 1.0 NZ D:KCX150 4.7 51.3 1.0 CA D:ASP315 4.8 45.2 1.0

Zinc binding site 9 out of 16 in the Crystal Structure of D-Hydantoinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of D-Hydantoinase within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:68.5 occ:1.00 ND1 E:HIS183 2.3 39.5 1.0 OQ1 E:KCX150 2.6 56.5 1.0 NE2 E:HIS239 2.6 36.6 1.0 CE1 E:HIS183 2.9 39.6 1.0 ZN E:ZN502 2.9 49.9 1.0 CD2 E:HIS239 3.4 36.3 1.0 CX E:KCX150 3.5 54.0 1.0 CG E:HIS183 3.6 40.5 1.0 OQ2 E:KCX150 3.6 54.4 1.0 CE1 E:HIS239 3.7 37.4 1.0 O E:SER288 4.0 46.2 1.0 NE2 E:HIS183 4.1 38.9 1.0 OH E:TYR155 4.2 59.2 1.0 CB E:HIS183 4.2 39.5 1.0 CE2 E:PHE152 4.3 41.9 1.0 NE2 E:HIS58 4.4 45.1 1.0 CE2 E:TYR155 4.4 55.7 1.0 CD2 E:HIS183 4.4 40.8 1.0 CE1 E:HIS58 4.5 45.9 1.0 OD1 E:ASP315 4.5 46.5 1.0 OD2 E:ASP315 4.6 48.1 1.0 CG E:HIS239 4.6 36.6 1.0 NZ E:KCX150 4.7 52.3 1.0 ND1 E:HIS239 4.7 37.3 1.0 CG2 E:VAL238 4.8 33.8 1.0 CZ E:TYR155 4.8 56.8 1.0 CD2 E:PHE152 4.8 41.4 1.0 CG E:ASP315 4.9 45.6 1.0

Zinc binding site 10 out of 16 in the Crystal Structure of D-Hydantoinase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of D-Hydantoinase within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn502 b:49.9 occ:1.00 NE2 E:HIS58 2.3 45.1 1.0 OD1 E:ASP315 2.3 46.5 1.0 NE2 E:HIS60 2.5 55.6 1.0 OQ2 E:KCX150 2.6 54.4 1.0 ZN E:ZN501 2.9 68.5 1.0 CE1 E:HIS58 3.1 45.9 1.0 CD2 E:HIS60 3.2 54.8 1.0 CD2 E:HIS58 3.3 45.4 1.0 CG E:ASP315 3.3 45.6 1.0 CX E:KCX150 3.5 54.0 1.0 CE1 E:HIS60 3.6 55.6 1.0 OQ1 E:KCX150 3.6 56.5 1.0 OD2 E:ASP315 3.8 48.1 1.0 CD2 E:HIS239 4.2 36.3 1.0 ND1 E:HIS58 4.3 44.8 1.0 NE2 E:HIS239 4.4 36.6 1.0 CG E:HIS58 4.4 45.0 1.0 CG E:HIS60 4.5 54.4 1.0 CB E:ASP315 4.6 42.8 1.0 ND1 E:HIS60 4.6 55.8 1.0 NZ E:KCX150 4.7 52.3 1.0 CA E:ASP315 4.8 41.8 1.0

Y.H.Cheon, H.S.Kim, K.H.Han, J.Abendroth, K.Niefind, D.Schomburg, J.Wang, Y.Kim. Crystal Structure of D-Hydantoinase From Bacillus Stearothermophilus: Insight Into the Stereochemistry of Enantioselectivity. Biochemistry V. 41 9410 2002.
ISSN: ISSN 0006-2960
PubMed: 12135362
DOI: 10.1021/BI0201567