Zinc in PDB 5yox: Hd Domain-Containing Protein YGK1(YGL101W)

The structure of Hd Domain-Containing Protein YGK1(YGL101W), PDB code: 5yox was solved by J.Yang, F.Wang, Z.Gao, K.Zhou, Q.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.77 / 2.61
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.633, 142.178, 112.266, 90.00, 89.99, 90.00
R / Rfree (%)	20.7 / 24.5

The binding sites of Zinc atom in the Hd Domain-Containing Protein YGK1(YGL101W) (pdb code 5yox). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Hd Domain-Containing Protein YGK1(YGL101W), PDB code: 5yox:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Hd Domain-Containing Protein YGK1(YGL101W)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hd Domain-Containing Protein YGK1(YGL101W) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:42.9 occ:0.47 OD1 A:ASP159 2.0 60.1 1.0 OD2 A:ASP159 2.0 60.5 1.0 NE2 A:HIS61 2.0 48.0 1.0 OD2 A:ASP90 2.1 57.6 1.0 NE2 A:HIS89 2.1 50.1 1.0 CG A:ASP159 2.2 53.7 1.0 CD2 A:HIS61 2.9 48.9 1.0 CE1 A:HIS89 3.0 46.9 1.0 CE1 A:HIS61 3.1 50.9 1.0 CD2 A:HIS89 3.2 50.2 1.0 CG A:ASP90 3.3 56.0 1.0 CB A:ASP159 3.8 45.4 1.0 OD1 A:ASP90 3.9 50.8 1.0 CG A:HIS61 4.1 43.6 1.0 ND1 A:HIS61 4.1 42.6 1.0 ND1 A:HIS89 4.1 46.2 1.0 CG A:HIS89 4.3 50.1 1.0 CG A:MSE65 4.4 52.1 1.0 CB A:ASP90 4.4 53.1 1.0 CA A:ASP159 4.7 44.7 1.0 OH A:TYR144 4.9 54.1 1.0

Zinc binding site 2 out of 8 in the Hd Domain-Containing Protein YGK1(YGL101W)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hd Domain-Containing Protein YGK1(YGL101W) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:59.1 occ:0.69 NE2 B:HIS61 2.0 41.9 1.0 OD1 B:ASP159 2.1 40.3 1.0 NE2 B:HIS89 2.1 30.2 1.0 OD2 B:ASP90 2.1 31.7 1.0 CE1 B:HIS61 2.4 44.8 1.0 CG B:ASP159 2.9 43.7 1.0 CE1 B:HIS89 2.9 42.7 1.0 CG B:ASP90 3.0 45.1 1.0 CD2 B:HIS89 3.2 42.0 1.0 CD2 B:HIS61 3.3 46.9 1.0 NH1 B:ARG43 3.5 53.0 1.0 OD1 B:ASP90 3.5 41.6 1.0 OD2 B:ASP159 3.5 48.1 1.0 ND1 B:HIS61 3.7 39.8 1.0 NH2 B:ARG43 3.7 44.0 1.0 CB B:ASP159 3.8 37.9 1.0 CZ B:ARG43 3.9 51.5 1.0 ND1 B:HIS89 4.1 36.9 1.0 CG B:HIS61 4.1 42.4 1.0 CB B:ASP90 4.2 39.8 1.0 CG B:HIS89 4.3 39.3 1.0 OH B:TYR144 4.4 41.8 1.0 CA B:ASP159 4.6 40.5 1.0 SE B:MSE65 4.9 66.0 1.0 CG B:MSE65 5.0 44.7 1.0

Zinc binding site 3 out of 8 in the Hd Domain-Containing Protein YGK1(YGL101W)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Hd Domain-Containing Protein YGK1(YGL101W) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn300 b:34.8 occ:0.47 OD1 C:ASP159 1.9 37.5 1.0 OD2 C:ASP159 2.1 36.5 1.0 OD2 C:ASP90 2.1 46.4 1.0 NE2 C:HIS61 2.1 42.8 1.0 NE2 C:HIS89 2.2 45.8 1.0 CG C:ASP159 2.2 37.0 1.0 CE1 C:HIS89 3.1 39.0 1.0 CE1 C:HIS61 3.1 44.3 1.0 CD2 C:HIS61 3.1 45.1 1.0 CD2 C:HIS89 3.2 41.6 1.0 CG C:ASP90 3.3 48.9 1.0 CB C:ASP159 3.6 39.6 1.0 O C:HOH416 3.7 43.2 1.0 OD1 C:ASP90 3.8 54.5 1.0 ND1 C:HIS89 4.2 35.8 1.0 ND1 C:HIS61 4.2 41.2 1.0 CG C:HIS61 4.3 41.9 1.0 CG C:HIS89 4.3 35.3 1.0 CB C:ASP90 4.5 47.3 1.0 OH C:TYR144 4.6 48.4 1.0 CA C:ASP159 4.7 51.0 1.0 CG C:MSE65 4.9 48.1 1.0

Zinc binding site 4 out of 8 in the Hd Domain-Containing Protein YGK1(YGL101W)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Hd Domain-Containing Protein YGK1(YGL101W) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn300 b:57.2 occ:0.39 NE2 D:HIS89 2.1 42.9 1.0 CG D:ASP159 2.3 52.4 1.0 NE2 D:HIS61 2.4 53.3 1.0 CB D:ASP159 2.4 47.7 1.0 OD2 D:ASP90 2.6 42.7 1.0 OD2 D:ASP159 2.6 68.0 1.0 OD1 D:ASP159 2.7 56.9 1.0 CD2 D:HIS89 2.8 53.2 1.0 CE1 D:HIS61 2.9 51.6 1.0 CE1 D:HIS89 3.1 47.8 1.0 CG D:ASP90 3.6 59.6 1.0 CD2 D:HIS61 3.6 52.4 1.0 CA D:ASP159 3.9 39.6 1.0 O D:HOH412 3.9 49.8 1.0 OD1 D:ASP90 3.9 63.6 1.0 CG D:HIS89 4.0 53.1 1.0 ND1 D:HIS89 4.1 51.7 1.0 ND1 D:HIS61 4.2 47.8 1.0 SE D:MSE65 4.4 64.0 1.0 O D:HOH409 4.5 48.9 1.0 C D:ASP159 4.5 40.6 1.0 CG D:HIS61 4.6 45.3 1.0 OH D:TYR144 4.6 56.4 1.0 CE D:MSE65 4.6 52.9 1.0 CB D:ASP90 4.8 61.1 1.0 O D:ASP159 4.8 44.1 1.0 N D:ASP159 5.0 40.9 1.0

Zinc binding site 5 out of 8 in the Hd Domain-Containing Protein YGK1(YGL101W)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Hd Domain-Containing Protein YGK1(YGL101W) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn300 b:40.7 occ:0.53 OD2 E:ASP159 2.0 22.9 1.0 NE2 E:HIS89 2.0 37.4 1.0 NE2 E:HIS61 2.0 45.5 1.0 OD2 E:ASP90 2.1 36.1 1.0 CD2 E:HIS61 2.8 46.9 1.0 CD2 E:HIS89 2.9 34.5 1.0 CE1 E:HIS89 3.0 32.6 1.0 CE1 E:HIS61 3.1 47.4 1.0 CG E:ASP159 3.2 39.9 1.0 CG E:ASP90 3.2 36.5 1.0 OD1 E:ASP90 3.7 37.9 1.0 OD1 E:ASP159 3.8 44.2 1.0 CG E:HIS61 4.0 45.3 1.0 CG E:HIS89 4.0 32.6 1.0 ND1 E:HIS61 4.1 43.4 1.0 ND1 E:HIS89 4.1 30.7 1.0 CB E:ASP159 4.4 36.6 1.0 CB E:ASP90 4.4 39.7 1.0 NH1 E:ARG43 4.8 46.2 1.0 CG E:MSE65 4.9 44.1 1.0

Zinc binding site 6 out of 8 in the Hd Domain-Containing Protein YGK1(YGL101W)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Hd Domain-Containing Protein YGK1(YGL101W) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn300 b:45.6 occ:0.52 CE1 F:HIS89 1.8 42.4 1.0 OD2 F:ASP90 2.0 48.2 1.0 NE2 F:HIS89 2.0 49.5 1.0 OD1 F:ASP159 2.0 46.7 1.0 OD2 F:ASP159 2.1 49.8 1.0 NE2 F:HIS61 2.1 40.9 1.0 CG F:ASP159 2.3 44.1 1.0 CE1 F:HIS61 2.9 46.8 1.0 ND1 F:HIS89 3.0 48.0 1.0 CG F:ASP90 3.1 55.8 1.0 CD2 F:HIS61 3.2 47.0 1.0 CD2 F:HIS89 3.3 49.5 1.0 OD1 F:ASP90 3.5 56.7 1.0 CB F:ASP159 3.8 40.3 1.0 CG F:HIS89 3.8 44.1 1.0 NH1 F:ARG43 3.9 55.4 1.0 NH2 F:ARG43 3.9 56.1 1.0 ND1 F:HIS61 4.1 43.3 1.0 CG F:HIS61 4.2 45.0 1.0 OH F:TYR144 4.2 43.0 1.0 CZ F:ARG43 4.4 56.2 1.0 CB F:ASP90 4.4 54.0 1.0 CA F:ASP159 4.8 38.5 1.0

Zinc binding site 7 out of 8 in the Hd Domain-Containing Protein YGK1(YGL101W)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Hd Domain-Containing Protein YGK1(YGL101W) within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn300 b:59.6 occ:0.43 OD2 G:ASP159 2.1 44.9 1.0 OD1 G:ASP159 2.1 59.2 1.0 OD1 G:ASP90 2.1 69.3 1.0 NE2 G:HIS61 2.1 60.4 1.0 OD2 G:ASP90 2.4 66.0 1.0 CG G:ASP159 2.4 55.5 1.0 CG G:ASP90 2.5 67.5 1.0 CD2 G:HIS61 2.9 55.6 1.0 CE1 G:HIS61 3.2 56.9 1.0 CB G:ASP90 3.9 63.5 1.0 CB G:ASP159 4.0 57.8 1.0 NE2 G:HIS89 4.0 52.9 1.0 CE G:MSE65 4.1 65.0 1.0 CG G:HIS61 4.1 47.5 1.0 ND1 G:HIS61 4.2 46.5 1.0 SE G:MSE65 4.3 87.6 1.0 CD2 G:HIS89 4.6 57.9 1.0 CD1 G:ILE58 4.8 53.0 1.0 CA G:ASP159 4.9 58.0 1.0

Zinc binding site 8 out of 8 in the Hd Domain-Containing Protein YGK1(YGL101W)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Hd Domain-Containing Protein YGK1(YGL101W) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn300 b:64.4 occ:0.34 NE2 H:HIS89 2.0 61.8 1.0 OD2 H:ASP159 2.1 70.4 1.0 NE2 H:HIS61 2.1 60.8 1.0 OD1 H:ASP159 2.1 71.8 1.0 OD2 H:ASP90 2.2 74.4 1.0 CG H:ASP159 2.2 66.2 1.0 CE1 H:HIS61 2.7 68.3 1.0 CD2 H:HIS89 2.8 65.4 1.0 CE1 H:HIS89 3.2 63.0 1.0 CD2 H:HIS61 3.4 70.9 1.0 CG H:ASP90 3.4 74.9 1.0 CB H:ASP159 3.4 60.1 1.0 OH H:TYR144 3.9 74.4 1.0 ND1 H:HIS61 3.9 63.8 1.0 OD1 H:ASP90 4.0 75.3 1.0 CG H:HIS89 4.0 63.0 1.0 ND1 H:HIS89 4.2 56.2 1.0 CG H:HIS61 4.3 62.9 1.0 CZ H:TYR144 4.4 66.8 1.0 CA H:ASP159 4.4 57.1 1.0 CB H:ASP90 4.6 70.5 1.0 CE1 H:TYR144 4.6 68.6 1.0 O H:ASP159 4.9 68.9 1.0

J.Yang, F.Wang, K.Zhou, Z.Gao, Q.Liu. Hd Domain-Containing Protein YGK1(YGL101W) To Be Published.