Zinc in PDB 6dk9: Yeast DDI2 Cyanamide Hydratase

The structure of Yeast DDI2 Cyanamide Hydratase, PDB code: 6dk9 was solved by S.A.Moore, W.Xiao, J.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.70 / 2.60
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	264.456, 264.456, 119.152, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 21.7

The binding sites of Zinc atom in the Yeast DDI2 Cyanamide Hydratase (pdb code 6dk9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Yeast DDI2 Cyanamide Hydratase, PDB code: 6dk9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Yeast DDI2 Cyanamide Hydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast DDI2 Cyanamide Hydratase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:68.2 occ:0.60 HE2 A:HIS88 1.4 59.1 1.0 O A:HOH426 2.0 52.5 0.6 OD2 A:ASP89 2.1 61.7 1.0 NE2 A:HIS55 2.2 50.7 1.0 NE2 A:HIS88 2.2 49.3 1.0 CD2 A:HIS88 3.0 50.5 1.0 CE1 A:HIS55 3.0 47.9 1.0 CG A:ASP89 3.0 49.1 1.0 HD2 A:HIS88 3.0 60.6 1.0 HE1 A:HIS55 3.1 57.5 1.0 CD2 A:HIS55 3.3 48.3 1.0 CE1 A:HIS88 3.3 49.2 1.0 HD21 A:ASN161 3.3 53.9 1.0 OD1 A:ASP89 3.4 53.7 1.0 O A:HOH412 3.4 44.0 1.0 HD2 A:HIS55 3.5 58.0 1.0 HE1 A:HIS88 3.6 59.1 1.0 HZ2 A:TRP186 3.9 49.5 1.0 CG2 A:THR157 4.0 38.2 1.0 ND1 A:HIS55 4.1 51.4 1.0 ND2 A:ASN161 4.2 44.9 1.0 CG A:HIS88 4.2 48.2 1.0 HE1 A:PHE190 4.2 58.1 1.0 HB2 A:ASP89 4.3 55.4 1.0 ND1 A:HIS88 4.3 49.3 1.0 CG A:HIS55 4.3 50.4 1.0 CB A:ASP89 4.3 46.2 1.0 CB A:THR157 4.4 40.4 1.0 HG22 A:VAL59 4.5 59.4 1.0 CE1 A:PHE190 4.6 48.5 1.0 HD22 A:ASN161 4.7 53.9 1.0 NE2 A:HIS137 4.7 43.2 1.0 HD2 A:HIS137 4.8 53.0 1.0 CZ2 A:TRP186 4.8 41.2 1.0 OD1 A:ASN161 4.8 54.6 1.0 HA A:THR157 4.9 54.9 1.0 HB3 A:ASP89 4.9 55.4 1.0 HD1 A:HIS55 4.9 61.7 1.0 CG A:ASN161 5.0 51.1 1.0

Zinc binding site 2 out of 9 in the Yeast DDI2 Cyanamide Hydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast DDI2 Cyanamide Hydratase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:71.1 occ:0.60 HE2 B:HIS88 1.5 51.3 1.0 O B:HOH443 2.0 70.5 0.6 OD2 B:ASP89 2.1 69.8 1.0 NE2 B:HIS55 2.2 52.2 1.0 NE2 B:HIS88 2.2 42.8 1.0 CD2 B:HIS88 3.0 40.6 1.0 HD2 B:HIS88 3.0 48.8 1.0 CG B:ASP89 3.0 61.1 1.0 CE1 B:HIS55 3.0 53.5 1.0 HE1 B:HIS55 3.2 64.2 1.0 HD21 B:ASN161 3.2 57.9 1.0 CD2 B:HIS55 3.2 48.3 1.0 CE1 B:HIS88 3.3 47.6 1.0 O B:HOH424 3.4 68.8 1.0 OD1 B:ASP89 3.4 60.5 1.0 HD2 B:HIS55 3.5 57.9 1.0 HE1 B:HIS88 3.6 57.1 1.0 HZ2 B:TRP186 3.9 59.4 1.0 CG2 B:THR157 4.0 37.7 1.0 ND2 B:ASN161 4.1 48.2 1.0 CG B:HIS88 4.2 43.3 1.0 ND1 B:HIS55 4.2 50.0 1.0 HE1 B:PHE190 4.2 49.6 1.0 HB2 B:ASP89 4.2 66.7 1.0 ND1 B:HIS88 4.3 41.2 1.0 CG B:HIS55 4.3 50.0 1.0 HG21 B:VAL59 4.3 61.4 1.0 CB B:ASP89 4.3 55.6 1.0 CB B:THR157 4.4 41.9 1.0 CE1 B:PHE190 4.5 41.4 1.0 HD22 B:ASN161 4.6 57.9 1.0 HD2 B:HIS137 4.7 54.4 1.0 CZ2 B:TRP186 4.7 49.5 1.0 OD1 B:ASN161 4.8 49.0 1.0 HA B:THR157 4.8 55.1 1.0 NE2 B:HIS137 4.8 45.5 1.0 HH2 B:TRP186 4.8 60.2 1.0 HB3 B:ASP89 4.9 66.7 1.0 CG B:ASN161 4.9 49.6 1.0 HD1 B:HIS55 4.9 60.0 1.0

Zinc binding site 3 out of 9 in the Yeast DDI2 Cyanamide Hydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast DDI2 Cyanamide Hydratase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:64.4 occ:0.60 O C:HOH430 2.0 53.4 0.6 OD2 C:ASP89 2.1 51.1 1.0 NE2 C:HIS55 2.2 49.5 1.0 NE2 C:HIS88 2.2 37.1 1.0 CG C:ASP89 3.0 41.9 1.0 CE1 C:HIS55 3.0 45.8 1.0 CD2 C:HIS88 3.0 40.1 1.0 HD2 C:HIS88 3.1 48.2 1.0 HE1 C:HIS55 3.1 55.0 1.0 O C:HOH417 3.1 44.6 1.0 HD21 C:ASN161 3.2 48.5 1.0 OD1 C:ASP89 3.2 48.3 1.0 CD2 C:HIS55 3.3 40.9 1.0 CE1 C:HIS88 3.3 38.8 1.0 HD2 C:HIS55 3.5 49.1 1.0 HE1 C:HIS88 3.5 46.5 1.0 HZ2 C:TRP186 3.9 40.5 1.0 CG2 C:THR157 3.9 33.6 1.0 ND2 C:ASN161 4.0 40.4 1.0 ND1 C:HIS55 4.1 40.5 1.0 CG C:HIS88 4.2 38.9 1.0 CG C:HIS55 4.3 41.3 1.0 ND1 C:HIS88 4.3 34.4 1.0 CB C:ASP89 4.3 39.1 1.0 CB C:THR157 4.3 37.5 1.0 HE1 C:PHE190 4.3 34.3 1.0 HB2 C:ASP89 4.4 46.9 1.0 HG21 C:VAL59 4.5 37.3 1.0 HD22 C:ASN161 4.5 48.5 1.0 CE1 C:PHE190 4.7 28.6 1.0 OD1 C:ASN161 4.7 32.4 1.0 HD2 C:HIS137 4.7 48.2 1.0 CZ2 C:TRP186 4.7 33.8 1.0 NE2 C:HIS137 4.8 46.5 1.0 HA C:THR157 4.8 50.6 1.0 HH2 C:TRP186 4.8 47.7 1.0 CG C:ASN161 4.9 38.3 1.0 HD1 C:HIS55 4.9 48.6 1.0 HB3 C:ASP89 4.9 46.9 1.0

Zinc binding site 4 out of 9 in the Yeast DDI2 Cyanamide Hydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast DDI2 Cyanamide Hydratase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:62.1 occ:0.60 O D:HOH430 2.0 49.4 0.6 OD2 D:ASP89 2.1 60.3 1.0 NE2 D:HIS55 2.2 47.2 1.0 NE2 D:HIS88 2.2 33.6 1.0 CD2 D:HIS88 3.0 33.2 1.0 CG D:ASP89 3.0 55.1 1.0 HD2 D:HIS88 3.0 39.9 1.0 CE1 D:HIS55 3.0 46.1 1.0 HE1 D:HIS55 3.1 55.4 1.0 CD2 D:HIS55 3.2 45.9 1.0 HD21 D:ASN161 3.3 52.4 1.0 OD1 D:ASP89 3.3 56.8 1.0 CE1 D:HIS88 3.3 41.2 1.0 O D:HOH407 3.4 52.9 1.0 HD2 D:HIS55 3.5 55.0 1.0 HE1 D:HIS88 3.6 49.5 1.0 HZ2 D:TRP186 4.0 49.6 1.0 CG2 D:THR157 4.0 42.0 1.0 ND2 D:ASN161 4.1 43.7 1.0 ND1 D:HIS55 4.2 48.5 1.0 CG D:HIS88 4.2 38.1 1.0 CG D:HIS55 4.3 45.8 1.0 ND1 D:HIS88 4.3 34.0 1.0 CB D:ASP89 4.3 46.4 1.0 HB2 D:ASP89 4.3 55.7 1.0 HE1 D:PHE190 4.3 54.8 1.0 CB D:THR157 4.4 41.6 1.0 HG23 D:VAL59 4.4 51.1 1.0 HD22 D:ASN161 4.6 52.4 1.0 CE1 D:PHE190 4.7 45.7 1.0 HD2 D:HIS137 4.7 52.4 1.0 NE2 D:HIS137 4.7 44.3 1.0 CZ2 D:TRP186 4.8 41.4 1.0 HA D:THR157 4.8 51.2 1.0 OD1 D:ASN161 4.8 41.6 1.0 HH2 D:TRP186 4.8 48.6 1.0 HB3 D:ASP89 4.9 55.7 1.0 HD1 D:HIS55 4.9 58.2 1.0 CG D:ASN161 4.9 39.9 1.0

Zinc binding site 5 out of 9 in the Yeast DDI2 Cyanamide Hydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Yeast DDI2 Cyanamide Hydratase within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:66.9 occ:0.60 O E:HOH435 2.0 55.8 0.6 OD2 E:ASP89 2.1 56.9 1.0 NE2 E:HIS88 2.2 35.8 1.0 NE2 E:HIS55 2.2 42.1 1.0 CD2 E:HIS88 3.0 39.0 1.0 CG E:ASP89 3.0 46.2 1.0 HD2 E:HIS88 3.0 46.8 1.0 CE1 E:HIS55 3.1 38.3 1.0 HE1 E:HIS55 3.2 46.0 1.0 CD2 E:HIS55 3.2 38.3 1.0 HD21 E:ASN161 3.2 45.6 1.0 OD1 E:ASP89 3.3 49.8 1.0 O E:HOH425 3.3 40.8 1.0 CE1 E:HIS88 3.3 40.4 1.0 HD2 E:HIS55 3.5 46.0 1.0 HE1 E:HIS88 3.6 48.4 1.0 CG2 E:THR157 3.9 36.7 1.0 HZ2 E:TRP186 4.0 36.7 1.0 ND2 E:ASN161 4.1 38.0 1.0 CG E:HIS88 4.2 34.4 1.0 ND1 E:HIS55 4.2 37.8 1.0 CG E:HIS55 4.3 42.9 1.0 ND1 E:HIS88 4.3 36.1 1.0 HE1 E:PHE190 4.3 43.8 1.0 CB E:ASP89 4.3 39.7 1.0 CB E:THR157 4.3 36.0 1.0 HG23 E:VAL59 4.3 46.7 1.0 HB2 E:ASP89 4.3 47.7 1.0 HD22 E:ASN161 4.6 45.6 1.0 CE1 E:PHE190 4.7 36.5 1.0 NE2 E:HIS137 4.7 38.8 1.0 HA E:THR157 4.7 48.7 1.0 OD1 E:ASN161 4.8 34.8 1.0 CZ2 E:TRP186 4.8 30.6 1.0 HD2 E:HIS137 4.8 46.2 1.0 HB3 E:ASP89 4.9 47.7 1.0 HH2 E:TRP186 4.9 44.1 1.0 CG E:ASN161 4.9 39.7 1.0 HD1 E:HIS55 4.9 45.3 1.0

Zinc binding site 6 out of 9 in the Yeast DDI2 Cyanamide Hydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Yeast DDI2 Cyanamide Hydratase within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn302 b:64.9 occ:0.60 O F:HOH425 2.0 57.5 0.6 OD2 F:ASP89 2.1 64.3 1.0 NE2 F:HIS55 2.2 46.4 1.0 NE2 F:HIS88 2.2 45.0 1.0 CD2 F:HIS88 3.0 44.0 1.0 CG F:ASP89 3.0 55.8 1.0 CE1 F:HIS55 3.0 45.7 1.0 HD2 F:HIS88 3.0 52.8 1.0 HE1 F:HIS55 3.1 54.8 1.0 CD2 F:HIS55 3.3 46.4 1.0 HD21 F:ASN161 3.3 52.5 1.0 CE1 F:HIS88 3.3 46.0 1.0 OD1 F:ASP89 3.3 55.6 1.0 HD2 F:HIS55 3.5 55.7 1.0 O F:HOH416 3.6 52.6 1.0 HE1 F:HIS88 3.6 55.2 1.0 HZ2 F:TRP186 4.0 48.1 1.0 CG2 F:THR157 4.0 45.4 1.0 ND2 F:ASN161 4.1 43.8 1.0 ND1 F:HIS55 4.2 46.2 1.0 CG F:HIS88 4.2 45.2 1.0 HG21 F:VAL59 4.2 53.6 1.0 ND1 F:HIS88 4.3 42.0 1.0 HE1 F:PHE190 4.3 56.4 1.0 CG F:HIS55 4.3 45.2 1.0 CB F:THR157 4.3 45.6 1.0 CB F:ASP89 4.3 49.1 1.0 HB2 F:ASP89 4.3 59.0 1.0 HD22 F:ASN161 4.6 52.5 1.0 CE1 F:PHE190 4.7 47.0 1.0 HA F:THR157 4.7 54.8 1.0 OD1 F:ASN161 4.7 47.5 1.0 CZ2 F:TRP186 4.8 40.1 1.0 HD2 F:HIS137 4.8 57.0 1.0 NE2 F:HIS137 4.8 46.1 1.0 HB3 F:ASP89 4.9 59.0 1.0 CG F:ASN161 4.9 45.4 1.0 HD1 F:HIS55 4.9 55.5 1.0 HH2 F:TRP186 5.0 43.7 1.0

Zinc binding site 7 out of 9 in the Yeast DDI2 Cyanamide Hydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Yeast DDI2 Cyanamide Hydratase within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn301 b:96.5 occ:0.60 HE2 G:HIS55 1.5 81.3 1.0 O G:HOH422 2.0 0.3 0.6 OD2 G:ASP89 2.1 0.2 1.0 NE2 G:HIS88 2.2 0.9 1.0 NE2 G:HIS55 2.2 67.8 1.0 CD2 G:HIS88 3.0 0.7 1.0 CE1 G:HIS55 3.0 68.1 1.0 CG G:ASP89 3.0 95.1 1.0 HD2 G:HIS88 3.0 1.0 1.0 HE1 G:HIS55 3.1 81.7 1.0 HD21 G:ASN161 3.2 72.1 1.0 CD2 G:HIS55 3.3 66.7 1.0 CE1 G:HIS88 3.3 0.8 1.0 O G:HOH414 3.3 68.7 1.0 OD1 G:ASP89 3.3 0.3 1.0 HD2 G:HIS55 3.5 80.1 1.0 HE1 G:HIS88 3.6 0.6 1.0 CG2 G:THR157 3.9 52.0 1.0 HZ2 G:TRP186 4.0 86.8 1.0 ND2 G:ASN161 4.0 60.1 1.0 ND1 G:HIS55 4.1 70.4 1.0 CG G:HIS88 4.2 94.2 1.0 HE1 G:PHE190 4.2 72.8 1.0 CB G:THR157 4.2 54.3 1.0 CG G:HIS55 4.3 66.9 1.0 ND1 G:HIS88 4.3 0.1 1.0 HG23 G:VAL59 4.3 75.0 1.0 CB G:ASP89 4.4 78.8 1.0 HB2 G:ASP89 4.4 94.6 1.0 HD22 G:ASN161 4.5 72.1 1.0 CE1 G:PHE190 4.6 60.7 1.0 HA G:THR157 4.6 67.5 1.0 OD1 G:ASN161 4.8 67.8 1.0 HD2 G:HIS137 4.8 71.4 1.0 CZ2 G:TRP186 4.8 72.4 1.0 CG G:ASN161 4.9 66.3 1.0 HD1 G:HIS55 4.9 84.5 1.0 HB3 G:ASP89 4.9 94.6 1.0 NE2 G:HIS137 5.0 61.2 1.0

Zinc binding site 8 out of 9 in the Yeast DDI2 Cyanamide Hydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Yeast DDI2 Cyanamide Hydratase within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn500 b:94.6 occ:0.60 OD2 H:ASP89 2.1 0.4 1.0 NE2 H:HIS88 2.2 92.0 1.0 NE2 H:HIS55 2.2 81.1 1.0 HD2 H:HIS88 2.8 0.5 1.0 CD2 H:HIS88 2.8 90.5 1.0 CG H:ASP89 2.9 0.4 1.0 OD1 H:ASP89 3.0 0.1 1.0 CE1 H:HIS55 3.0 81.1 1.0 HE1 H:HIS55 3.1 97.3 1.0 CD2 H:HIS55 3.3 81.6 1.0 CE1 H:HIS88 3.4 91.3 1.0 HD21 H:ASN161 3.5 98.4 1.0 HD2 H:HIS55 3.5 97.9 1.0 HE1 H:HIS88 3.7 0.6 1.0 CG2 H:THR157 3.9 83.2 1.0 HZ2 H:TRP186 4.0 95.8 1.0 CG H:HIS88 4.1 93.5 1.0 ND1 H:HIS55 4.2 81.8 1.0 CB H:ASP89 4.3 0.3 1.0 ND1 H:HIS88 4.3 92.1 1.0 CG H:HIS55 4.3 83.4 1.0 ND2 H:ASN161 4.3 82.0 1.0 HB2 H:ASP89 4.4 0.6 1.0 CB H:THR157 4.4 85.0 1.0 HE1 H:PHE190 4.4 83.5 1.0 NE2 H:HIS137 4.4 0.8 1.0 HG22 H:VAL59 4.6 0.2 1.0 HD2 H:HIS137 4.6 0.9 1.0 HA H:THR157 4.7 0.2 1.0 HG23 H:VAL59 4.7 0.2 1.0 CD2 H:HIS137 4.7 0.5 1.0 HD22 H:ASN161 4.8 98.4 1.0 HB3 H:ASP89 4.8 0.6 1.0 CZ2 H:TRP186 4.8 79.8 1.0 CE1 H:PHE190 4.8 69.6 1.0 HH2 H:TRP186 4.8 97.4 1.0 HD1 H:HIS55 4.9 98.1 1.0

Zinc binding site 9 out of 9 in the Yeast DDI2 Cyanamide Hydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Yeast DDI2 Cyanamide Hydratase within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn500 b:1.0 occ:0.60 OD2 I:ASP89 2.1 0.8 1.0 NE2 I:HIS88 2.2 0.8 1.0 NE2 I:HIS55 2.2 0.3 1.0 HD2 I:HIS88 2.9 0.3 1.0 CD2 I:HIS88 2.9 0.1 1.0 HD21 I:ASN161 3.1 0.5 1.0 CE1 I:HIS55 3.1 0.5 1.0 CG I:ASP89 3.1 0.4 1.0 CD2 I:HIS55 3.2 0.2 1.0 HE1 I:HIS55 3.3 0.4 1.0 CE1 I:HIS88 3.4 0.1 1.0 HD2 I:HIS55 3.4 0.2 1.0 OD1 I:ASP89 3.4 0.3 1.0 HE1 I:HIS88 3.7 0.1 1.0 CG2 I:THR157 3.7 0.1 1.0 ND2 I:ASN161 3.9 0.8 1.0 ND1 I:HIS55 4.2 0.0 1.0 CG I:HIS88 4.2 0.1 1.0 CG I:HIS55 4.2 0.9 1.0 CB I:THR157 4.3 0.4 1.0 ND1 I:HIS88 4.3 0.4 1.0 HD22 I:ASN161 4.4 0.5 1.0 HG22 I:VAL59 4.4 0.5 1.0 CB I:ASP89 4.4 0.2 1.0 HB2 I:ASP89 4.4 0.2 1.0 HZ2 I:TRP186 4.4 0.1 1.0 HA I:THR157 4.5 0.8 1.0 HE2 I:PHE190 4.6 0.3 1.0 OD1 I:ASN161 4.7 0.3 1.0 CG I:ASN161 4.8 1.0 1.0 HD1 I:HIS55 4.9 0.4 1.0 HB3 I:ASP89 4.9 0.2 1.0 HG23 I:VAL59 4.9 0.5 1.0

J.Li, Y.Jia, A.Lin, M.Hanna, L.Chelico, W.Xiao, S.A.Moore. Structure of DDI2, A Highly Inducible Detoxifying Metalloenzyme Fromsaccharomyces Cerevisiae. J.Biol.Chem. V. 294 10674 2019.
ISSN: ESSN 1083-351X
PubMed: 31152065
DOI: 10.1074/JBC.RA118.006394