Zinc in PDB 6dkd: Yeast DDI2 Cyanamide Hydratase

The structure of Yeast DDI2 Cyanamide Hydratase, PDB code: 6dkd 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)	39.77 / 3.00
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	264.643, 264.643, 119.304, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 22.1

The binding sites of Zinc atom in the Yeast DDI2 Cyanamide Hydratase (pdb code 6dkd). 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: 6dkd:
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:85.5 occ:0.62 O A:HOH413 2.0 87.0 0.6 OD2 A:ASP89 2.1 96.1 1.0 NE2 A:HIS55 2.2 62.2 1.0 NE2 A:HIS88 2.2 62.8 1.0 CG A:ASP89 3.0 75.2 1.0 CE1 A:HIS55 3.0 61.4 1.0 CD2 A:HIS88 3.1 60.6 1.0 CE1 A:HIS88 3.1 62.0 1.0 HE1 A:HIS55 3.2 73.7 1.0 CD2 A:HIS55 3.3 61.2 1.0 HD2 A:HIS88 3.3 72.7 1.0 HG22 A:THR157 3.3 64.0 1.0 HE1 A:HIS88 3.3 74.4 1.0 OD1 A:ASP89 3.5 78.3 1.0 HD2 A:HIS55 3.5 73.5 1.0 HD21 A:ASN161 3.5 70.9 1.0 HB A:THR157 3.7 64.0 1.0 CG2 A:THR157 4.0 53.4 1.0 HZ2 A:TRP186 4.0 71.7 1.0 HG21 A:THR157 4.0 64.0 1.0 ND1 A:HIS88 4.2 60.5 1.0 HB2 A:ASP89 4.2 81.8 1.0 ND1 A:HIS55 4.2 62.0 1.0 CG A:HIS88 4.2 58.9 1.0 CB A:ASP89 4.3 68.1 1.0 CG A:HIS55 4.3 64.4 1.0 CB A:THR157 4.3 53.3 1.0 HE1 A:PHE190 4.4 72.0 1.0 ND2 A:ASN161 4.4 59.1 1.0 OD1 A:ASN137 4.6 93.3 1.0 HG11 A:VAL59 4.7 99.7 1.0 CE1 A:PHE190 4.7 60.0 1.0 HB3 A:ASP89 4.8 81.8 1.0 HG23 A:THR157 4.8 64.0 1.0 HD22 A:ASN161 4.8 70.9 1.0 CZ2 A:TRP186 4.9 59.7 1.0 HD1 A:HIS55 4.9 74.5 1.0 HD1 A:HIS88 4.9 72.6 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:Zn301 b:85.6 occ:0.62 O B:HOH415 2.0 0.4 0.6 OD2 B:ASP89 2.1 0.5 1.0 NE2 B:HIS88 2.2 64.4 1.0 NE2 B:HIS55 2.2 64.5 1.0 CG B:ASP89 3.1 89.7 1.0 CD2 B:HIS88 3.1 63.3 1.0 CE1 B:HIS55 3.1 63.0 1.0 CE1 B:HIS88 3.2 62.1 1.0 HE1 B:HIS55 3.2 75.6 1.0 HD2 B:HIS88 3.2 76.0 1.0 CD2 B:HIS55 3.2 62.5 1.0 HG22 B:THR157 3.2 71.8 1.0 HD21 B:ASN161 3.4 77.3 1.0 HE1 B:HIS88 3.4 74.6 1.0 HD2 B:HIS55 3.4 75.0 1.0 OD1 B:ASP89 3.5 96.5 1.0 HB B:THR157 3.5 70.1 1.0 HG21 B:THR157 3.6 71.8 1.0 CG2 B:THR157 3.8 59.8 1.0 HZ2 B:TRP186 4.0 71.8 1.0 CB B:THR157 4.2 58.4 1.0 CG B:HIS88 4.2 49.9 1.0 ND1 B:HIS88 4.2 64.5 1.0 HB2 B:ASP89 4.2 86.7 1.0 ND1 B:HIS55 4.2 64.8 1.0 ND2 B:ASN161 4.2 64.4 1.0 CB B:ASP89 4.3 72.3 1.0 CG B:HIS55 4.3 62.7 1.0 HE1 B:PHE190 4.4 60.6 1.0 OD1 B:ASN137 4.5 78.4 1.0 HG23 B:THR157 4.7 71.8 1.0 HG22 B:VAL59 4.7 81.6 1.0 HG21 B:VAL59 4.7 81.6 1.0 HD22 B:ASN161 4.7 77.3 1.0 CE1 B:PHE190 4.8 50.5 1.0 CZ2 B:TRP186 4.8 59.9 1.0 HB3 B:ASP89 4.8 86.7 1.0 HA B:THR157 4.8 70.3 1.0 HH2 B:TRP186 4.9 69.7 1.0 OD1 B:ASN161 4.9 57.0 1.0 HD1 B:HIS55 4.9 77.8 1.0 HD1 B:HIS88 5.0 77.4 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:79.8 occ:0.62 O C:HOH429 2.0 84.2 0.6 OD2 C:ASP89 2.1 85.9 1.0 NE2 C:HIS88 2.2 43.5 1.0 NE2 C:HIS55 2.2 46.3 1.0 CG C:ASP89 3.0 68.5 1.0 CE1 C:HIS55 3.1 43.3 1.0 CD2 C:HIS88 3.1 46.0 1.0 CE1 C:HIS88 3.2 44.1 1.0 HE1 C:HIS55 3.2 52.0 1.0 HD2 C:HIS88 3.2 55.2 1.0 CD2 C:HIS55 3.2 43.1 1.0 HD21 C:ASN161 3.3 53.1 1.0 HG22 C:THR157 3.3 53.2 1.0 OD1 C:ASP89 3.4 76.4 1.0 HE1 C:HIS88 3.4 53.0 1.0 HD2 C:HIS55 3.4 51.8 1.0 HB C:THR157 3.6 53.7 1.0 HZ2 C:TRP186 3.9 57.1 1.0 CG2 C:THR157 4.1 44.3 1.0 ND2 C:ASN161 4.1 44.3 1.0 ND1 C:HIS55 4.2 41.6 1.0 CG C:HIS88 4.2 44.4 1.0 ND1 C:HIS88 4.2 43.5 1.0 CG C:HIS55 4.3 45.6 1.0 HB2 C:ASP89 4.3 70.2 1.0 CB C:ASP89 4.3 58.5 1.0 HG21 C:THR157 4.3 53.2 1.0 CB C:THR157 4.3 44.8 1.0 HG21 C:VAL59 4.4 67.2 1.0 HE1 C:PHE190 4.5 42.6 1.0 OD1 C:ASN137 4.5 79.5 1.0 HD22 C:ASN161 4.6 53.1 1.0 CZ2 C:TRP186 4.7 47.6 1.0 CE1 C:PHE190 4.8 35.5 1.0 HB3 C:ASP89 4.8 70.2 1.0 HH2 C:TRP186 4.8 52.6 1.0 OD1 C:ASN161 4.8 44.0 1.0 HA C:THR157 4.8 49.9 1.0 HG23 C:THR157 4.9 53.2 1.0 HD1 C:HIS55 4.9 49.9 1.0 CG C:ASN161 4.9 40.5 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:Zn301 b:73.3 occ:0.62 O D:HOH430 2.0 72.0 0.6 OD2 D:ASP89 2.1 82.4 1.0 NE2 D:HIS55 2.2 48.2 1.0 NE2 D:HIS88 2.2 50.0 1.0 CG D:ASP89 3.0 68.3 1.0 CD2 D:HIS88 3.0 48.2 1.0 CE1 D:HIS55 3.1 46.4 1.0 HD2 D:HIS88 3.2 57.9 1.0 CD2 D:HIS55 3.2 46.1 1.0 HG22 D:THR157 3.2 63.5 1.0 HE1 D:HIS55 3.2 55.7 1.0 CE1 D:HIS88 3.2 46.8 1.0 HD2 D:HIS55 3.4 55.3 1.0 OD1 D:ASP89 3.4 73.3 1.0 HE1 D:HIS88 3.5 56.1 1.0 HD21 D:ASN161 3.5 65.3 1.0 HG21 D:THR157 3.6 63.5 1.0 HB D:THR157 3.6 62.6 1.0 CG2 D:THR157 3.8 53.0 1.0 HD21 D:ASN137 3.9 88.1 1.0 HZ2 D:TRP186 4.0 63.5 1.0 HB2 D:ASP89 4.1 65.0 1.0 ND1 D:HIS55 4.2 47.2 1.0 CG D:HIS88 4.2 46.1 1.0 CB D:THR157 4.2 52.2 1.0 CB D:ASP89 4.2 54.2 1.0 ND1 D:HIS88 4.2 44.4 1.0 CG D:HIS55 4.3 47.4 1.0 ND2 D:ASN161 4.3 54.5 1.0 HG21 D:VAL59 4.4 60.4 1.0 ND2 D:ASN137 4.6 73.4 1.0 HE1 D:PHE190 4.6 74.2 1.0 HD22 D:ASN137 4.6 88.1 1.0 HG23 D:THR157 4.6 63.5 1.0 HB3 D:ASP89 4.8 65.0 1.0 HH2 D:TRP186 4.8 63.6 1.0 HA D:THR157 4.8 59.3 1.0 CZ2 D:TRP186 4.8 52.9 1.0 OD1 D:ASN161 4.8 45.0 1.0 HD22 D:ASN161 4.9 65.3 1.0 CE1 D:PHE190 4.9 61.8 1.0 HD1 D:HIS55 4.9 56.7 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:71.4 occ:0.62 O E:HOH430 2.0 70.4 0.6 OD2 E:ASP89 2.1 81.0 1.0 NE2 E:HIS55 2.2 45.1 1.0 NE2 E:HIS88 2.2 40.4 1.0 CE1 E:HIS55 3.0 46.2 1.0 CG E:ASP89 3.1 63.4 1.0 CD2 E:HIS88 3.1 40.1 1.0 HE1 E:HIS55 3.1 55.4 1.0 HD2 E:HIS88 3.2 48.2 1.0 HD21 E:ASN161 3.2 52.3 1.0 CE1 E:HIS88 3.2 40.8 1.0 CD2 E:HIS55 3.2 45.5 1.0 HG22 E:THR157 3.3 51.4 1.0 OD1 E:ASP89 3.4 71.2 1.0 HE1 E:HIS88 3.5 48.9 1.0 HB E:THR157 3.5 51.0 1.0 HD2 E:HIS55 3.5 54.6 1.0 HD21 E:ASN137 3.8 79.5 1.0 HG21 E:THR157 3.9 51.4 1.0 CG2 E:THR157 3.9 42.8 1.0 HZ2 E:TRP186 3.9 56.3 1.0 ND2 E:ASN161 4.1 43.6 1.0 ND1 E:HIS55 4.1 48.6 1.0 HE1 E:PHE190 4.2 52.5 1.0 CB E:THR157 4.2 42.5 1.0 CG E:HIS88 4.2 39.8 1.0 ND1 E:HIS88 4.3 40.9 1.0 CG E:HIS55 4.3 48.2 1.0 CB E:ASP89 4.4 48.3 1.0 HB2 E:ASP89 4.4 58.0 1.0 HG21 E:VAL59 4.4 53.1 1.0 ND2 E:ASN137 4.5 66.3 1.0 HD22 E:ASN137 4.5 79.5 1.0 HD22 E:ASN161 4.6 52.3 1.0 CE1 E:PHE190 4.6 43.8 1.0 OD1 E:ASN161 4.7 39.7 1.0 HA E:THR157 4.7 51.4 1.0 CZ2 E:TRP186 4.8 46.9 1.0 HH2 E:TRP186 4.8 62.0 1.0 HG23 E:THR157 4.8 51.4 1.0 HB3 E:ASP89 4.8 58.0 1.0 HD1 E:HIS55 4.9 58.3 1.0 CG E:ASN161 4.9 38.5 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:Zn301 b:86.1 occ:0.62 O F:HOH413 2.0 88.1 0.6 OD2 F:ASP89 2.1 99.8 1.0 NE2 F:HIS55 2.2 50.9 1.0 NE2 F:HIS88 2.2 56.8 1.0 CG F:ASP89 3.0 83.7 1.0 CE1 F:HIS55 3.1 50.3 1.0 CD2 F:HIS88 3.1 55.6 1.0 CE1 F:HIS88 3.2 56.4 1.0 HE1 F:HIS55 3.2 60.3 1.0 CD2 F:HIS55 3.2 49.9 1.0 HD2 F:HIS88 3.3 66.7 1.0 HG22 F:THR157 3.4 64.9 1.0 HE1 F:HIS88 3.4 67.6 1.0 HD2 F:HIS55 3.4 59.9 1.0 OD1 F:ASP89 3.5 92.8 1.0 HD21 F:ASN161 3.5 64.4 1.0 HB F:THR157 3.5 64.8 1.0 HG21 F:THR157 3.8 64.9 1.0 HZ2 F:TRP186 3.9 55.7 1.0 CG2 F:THR157 3.9 54.1 1.0 ND1 F:HIS55 4.2 53.0 1.0 CB F:THR157 4.2 54.0 1.0 HB2 F:ASP89 4.2 78.6 1.0 HG21 F:VAL59 4.2 56.4 1.0 ND1 F:HIS88 4.3 54.9 1.0 CG F:HIS88 4.3 54.0 1.0 CB F:ASP89 4.3 65.5 1.0 CG F:HIS55 4.3 52.1 1.0 ND2 F:ASN161 4.3 53.7 1.0 HE1 F:PHE190 4.5 66.7 1.0 HH2 F:TRP186 4.6 55.4 1.0 CZ2 F:TRP186 4.7 46.4 1.0 HA F:THR157 4.8 61.6 1.0 CE1 F:PHE190 4.8 55.5 1.0 OD1 F:ASN137 4.8 70.7 1.0 HB3 F:ASP89 4.8 78.6 1.0 OD1 F:ASN161 4.8 49.6 1.0 HG23 F:THR157 4.8 64.9 1.0 HD22 F:ASN161 4.9 64.4 1.0 HD1 F:HIS55 5.0 63.6 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:Zn302 b:99.9 occ:0.62 O G:HOH411 2.0 0.2 0.6 OD2 G:ASP89 2.1 0.6 1.0 NE2 G:HIS88 2.2 65.9 1.0 NE2 G:HIS55 2.2 82.1 1.0 CG G:ASP89 3.0 97.8 1.0 CD2 G:HIS88 3.0 64.8 1.0 CD2 G:HIS55 3.1 83.0 1.0 CE1 G:HIS55 3.1 81.5 1.0 HD2 G:HIS88 3.2 77.7 1.0 CE1 G:HIS88 3.2 67.3 1.0 HD2 G:HIS55 3.3 99.7 1.0 HD21 G:ASN161 3.3 92.3 1.0 HE1 G:HIS55 3.4 97.8 1.0 OD1 G:ASP89 3.4 99.6 1.0 HG22 G:THR157 3.4 82.4 1.0 HE1 G:HIS88 3.5 80.8 1.0 HB G:THR157 3.6 82.3 1.0 HG21 G:THR157 3.8 82.4 1.0 HD21 G:ASN137 3.8 0.8 1.0 CG2 G:THR157 4.0 68.7 1.0 HZ2 G:TRP186 4.0 97.1 1.0 ND2 G:ASN161 4.1 76.9 1.0 CG G:HIS88 4.2 63.0 1.0 ND1 G:HIS55 4.2 83.7 1.0 CG G:HIS55 4.2 83.9 1.0 ND1 G:HIS88 4.2 66.5 1.0 HE1 G:PHE190 4.3 90.6 1.0 HB2 G:ASP89 4.3 0.8 1.0 CB G:ASP89 4.3 85.7 1.0 CB G:THR157 4.3 68.6 1.0 ND2 G:ASN137 4.5 84.0 1.0 HD22 G:ASN137 4.5 0.8 1.0 HD22 G:ASN161 4.6 92.3 1.0 HG21 G:VAL59 4.6 83.5 1.0 CE1 G:PHE190 4.7 75.5 1.0 HB3 G:ASP89 4.8 0.8 1.0 HA G:THR157 4.8 79.0 1.0 HG23 G:THR157 4.9 82.4 1.0 CZ2 G:TRP186 4.9 81.0 1.0 OD1 G:ASN161 4.9 84.8 1.0 HD1 G:HIS55 5.0 0.5 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:0.7 occ:0.62 OD2 H:ASP89 2.1 0.6 1.0 NE2 H:HIS55 2.2 0.8 1.0 NE2 H:HIS88 2.2 0.5 1.0 CG H:ASP89 3.0 0.2 1.0 CD2 H:HIS88 3.1 0.4 1.0 CD2 H:HIS55 3.1 0.9 1.0 HD2 H:HIS88 3.2 0.3 1.0 CE1 H:HIS55 3.2 1.0 1.0 CE1 H:HIS88 3.2 0.5 1.0 HD2 H:HIS55 3.3 0.1 1.0 HG22 H:THR157 3.3 0.9 1.0 HE1 H:HIS55 3.4 0.6 1.0 OD1 H:ASP89 3.4 0.5 1.0 HE1 H:HIS88 3.5 0.2 1.0 HG21 H:THR157 3.7 0.9 1.0 CG2 H:THR157 3.9 0.4 1.0 HD21 H:ASN137 3.9 0.0 1.0 HD21 H:ASN161 4.1 0.0 1.0 HB2 H:ASP89 4.2 0.1 1.0 CG H:HIS88 4.2 0.1 1.0 ND1 H:HIS88 4.3 0.8 1.0 HB H:THR157 4.3 0.3 1.0 CB H:ASP89 4.3 0.1 1.0 HZ2 H:TRP186 4.3 0.7 1.0 ND1 H:HIS55 4.3 0.5 1.0 CG H:HIS55 4.3 0.1 1.0 HG21 H:VAL59 4.5 0.5 1.0 ND2 H:ASN137 4.6 0.2 1.0 HH2 H:TRP186 4.6 0.2 1.0 HG23 H:THR157 4.7 0.9 1.0 CB H:THR157 4.7 0.2 1.0 HD22 H:ASN137 4.7 0.0 1.0 HB3 H:ASP89 4.8 0.1 1.0 HE1 H:PHE190 4.9 0.9 1.0 ND2 H:ASN161 4.9 0.0 1.0 CZ2 H:TRP186 5.0 0.4 1.0 HA H:THR157 5.0 0.8 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:0.7 occ:0.44 OD2 I:ASP89 2.1 0.6 1.0 NE2 I:HIS88 2.2 0.7 1.0 NE2 I:HIS55 2.2 0.4 1.0 CD2 I:HIS88 2.9 0.9 1.0 HD2 I:HIS88 2.9 0.5 1.0 HD21 I:ASN161 3.0 0.2 1.0 CG I:ASP89 3.1 0.1 1.0 CE1 I:HIS55 3.1 0.7 1.0 HG21 I:THR157 3.1 0.3 1.0 CD2 I:HIS55 3.1 0.5 1.0 HE1 I:HIS55 3.2 0.3 1.0 CE1 I:HIS88 3.3 0.2 1.0 HD2 I:HIS55 3.4 0.3 1.0 HG22 I:THR157 3.4 0.3 1.0 OD1 I:ASP89 3.4 1.0 1.0 CG2 I:THR157 3.6 0.6 1.0 HE1 I:HIS88 3.7 0.6 1.0 HB I:THR157 3.7 0.6 1.0 ND2 I:ASN161 3.9 0.7 1.0 ND1 I:HIS55 4.2 0.2 1.0 CG I:HIS88 4.2 0.8 1.0 CB I:THR157 4.2 0.8 1.0 CG I:HIS55 4.2 0.8 1.0 ND1 I:HIS88 4.3 0.8 1.0 HD22 I:ASN161 4.3 0.2 1.0 HG21 I:VAL59 4.3 0.8 1.0 CB I:ASP89 4.4 0.1 1.0 HB2 I:ASP89 4.4 0.6 1.0 HZ2 I:TRP186 4.5 0.7 1.0 HA I:THR157 4.5 0.9 1.0 HG23 I:THR157 4.5 0.3 1.0 HE2 I:PHE190 4.6 0.4 1.0 HD21 I:ASN137 4.7 1.0 1.0 OD1 I:ASN161 4.7 0.3 1.0 CG I:ASN161 4.8 0.4 1.0 HB3 I:ASP89 4.9 0.6 1.0 HD1 I:HIS55 4.9 0.2 1.0 CA I:THR157 5.0 0.2 1.0 HD22 I:ASN137 5.0 1.0 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