Zinc in PDB 8oqh: Structure of the Cytosolic Domain of Lysosome-Associated TMEM55B

All present enzymatic activity of Structure of the Cytosolic Domain of Lysosome-Associated TMEM55B:
3.1.3.78;

The structure of Structure of the Cytosolic Domain of Lysosome-Associated TMEM55B, PDB code: 8oqh was solved by D.Waschbusch, A.R.Khan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.22 / 1.76
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	29.412, 84.445, 32.177, 90, 98.32, 90
R / Rfree (%)	19.4 / 22.4

The binding sites of Zinc atom in the Structure of the Cytosolic Domain of Lysosome-Associated TMEM55B (pdb code 8oqh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the Cytosolic Domain of Lysosome-Associated TMEM55B, PDB code: 8oqh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the Cytosolic Domain of Lysosome-Associated TMEM55B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Cytosolic Domain of Lysosome-Associated TMEM55B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:27.6 occ:1.00 SG A:CYS111 2.2 29.1 1.0 SG A:CYS94 2.2 29.5 1.0 SG A:CYS114 2.3 27.1 1.0 SG A:CYS91 2.3 24.4 1.0 HB3 A:CYS111 3.0 31.0 1.0 H A:CYS114 3.0 33.7 1.0 H A:CYS94 3.0 35.4 1.0 CB A:CYS111 3.0 25.6 1.0 HB2 A:CYS111 3.1 31.0 1.0 HB3 A:CYS91 3.1 36.1 1.0 CB A:CYS91 3.2 29.9 1.0 HB2 A:CYS91 3.2 36.1 1.0 HB3 A:CYS94 3.3 38.9 1.0 CB A:CYS114 3.3 24.9 1.0 CB A:CYS94 3.4 32.2 1.0 HB A:VAL93 3.6 30.1 1.0 HB2 A:SER96 3.7 37.0 1.0 N A:CYS114 3.7 27.9 1.0 N A:CYS94 3.7 29.3 1.0 HB A:VAL113 3.7 33.0 1.0 H A:SER96 4.0 38.1 1.0 CA A:CYS94 4.1 35.6 1.0 CA A:CYS114 4.1 29.2 1.0 HB2 A:CYS94 4.1 38.9 1.0 H A:VAL93 4.3 31.5 1.0 H A:GLN95 4.3 37.0 1.0 H A:GLU116 4.4 31.4 1.0 HG A:SER96 4.4 43.8 1.0 O A:HOH613 4.5 29.6 1.0 CA A:CYS111 4.5 24.0 1.0 H A:VAL113 4.5 36.0 1.0 CB A:SER96 4.5 30.6 1.0 CB A:VAL93 4.6 24.9 1.0 HG12 A:VAL113 4.6 40.9 1.0 HB2 A:GLU116 4.6 33.8 1.0 CA A:CYS91 4.6 27.3 1.0 C A:CYS94 4.6 34.6 1.0 CB A:VAL113 4.6 27.3 1.0 N A:GLN95 4.7 30.7 1.0 N A:SER96 4.8 31.6 1.0 C A:VAL93 4.8 31.4 1.0 HD11 A:ILE98 4.8 39.9 1.0 OG A:SER96 4.8 36.3 1.0 C A:VAL113 4.8 31.6 1.0 H A:ASN115 4.8 30.5 1.0 HA A:CYS114 4.8 35.2 1.0 HG12 A:VAL93 4.8 38.0 1.0 HA A:CYS111 4.9 29.1 1.0 C A:CYS114 4.9 28.1 1.0 HA A:CYS94 4.9 42.9 1.0 HA A:CYS91 4.9 33.0 1.0 N A:VAL93 5.0 26.0 1.0 C A:CYS111 5.0 28.2 1.0

Zinc binding site 2 out of 4 in the Structure of the Cytosolic Domain of Lysosome-Associated TMEM55B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Cytosolic Domain of Lysosome-Associated TMEM55B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:28.2 occ:1.00 SG A:CYS132 2.2 28.2 1.0 SG A:CYS149 2.2 29.0 1.0 SG A:CYS134 2.3 28.2 1.0 SG A:CYS154 2.3 27.9 1.0 HB3 A:CYS134 2.7 39.3 1.0 HB2 A:CYS149 2.9 34.5 1.0 CB A:CYS149 3.0 28.6 1.0 HB3 A:CYS149 3.1 34.5 1.0 CB A:CYS134 3.1 32.6 1.0 HB3 A:CYS132 3.1 30.3 1.0 HB3 A:CYS154 3.2 38.9 1.0 CB A:CYS132 3.2 25.1 1.0 CB A:CYS154 3.2 32.2 1.0 H A:CYS134 3.3 33.2 1.0 HB2 A:CYS154 3.3 38.9 1.0 HB2 A:CYS132 3.4 30.3 1.0 HB2 A:SER136 3.5 45.2 1.0 HB2 A:CYS134 3.8 39.3 1.0 HB2 A:ARG151 3.8 49.5 1.0 HB2 A:ARG156 3.8 41.2 1.0 N A:CYS134 4.0 27.4 1.0 CA A:CYS134 4.1 23.6 1.0 HG3 A:ARG151 4.2 50.6 1.0 H A:SER136 4.2 27.6 1.0 H A:ARG156 4.2 36.9 1.0 HG2 A:ARG151 4.4 50.6 1.0 HG3 A:ARG156 4.4 46.3 1.0 CB A:SER136 4.4 37.4 1.0 HD11 A:LEU138 4.5 39.7 1.0 CA A:CYS149 4.5 31.6 1.0 H A:ARG151 4.5 45.4 1.0 CG A:ARG151 4.6 42.0 1.0 CA A:CYS132 4.6 26.4 1.0 CB A:ARG151 4.6 41.0 1.0 CA A:CYS154 4.7 31.5 1.0 HD11 A:ILE158 4.7 53.6 1.0 H A:LYS155 4.7 44.8 1.0 HE2 A:TYR153 4.7 57.1 1.0 CB A:ARG156 4.7 34.1 1.0 HG A:SER136 4.7 47.0 1.0 HA A:CYS149 4.8 38.2 1.0 HD21 A:LEU138 4.8 41.4 1.0 OG A:SER136 4.8 39.0 1.0 HA A:CYS134 4.8 28.6 1.0 C A:CYS134 4.9 26.1 1.0 HB3 A:SER136 4.9 45.2 1.0 HD2 A:ARG156 4.9 54.6 1.0 HD2 A:PRO133 4.9 32.5 1.0 HA A:CYS132 4.9 31.9 1.0 C A:CYS132 5.0 26.9 1.0 HA A:CYS154 5.0 38.0 1.0

Zinc binding site 3 out of 4 in the Structure of the Cytosolic Domain of Lysosome-Associated TMEM55B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Cytosolic Domain of Lysosome-Associated TMEM55B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:27.7 occ:1.00 SG B:CYS149 2.3 29.8 1.0 SG B:CYS132 2.3 30.1 1.0 SG B:CYS154 2.3 29.4 1.0 SG B:CYS134 2.3 27.3 1.0 HB3 B:CYS134 2.8 33.1 1.0 HB2 B:CYS149 2.9 34.6 1.0 CB B:CYS149 3.0 28.6 1.0 HB3 B:CYS149 3.0 34.6 1.0 HB3 B:CYS154 3.1 34.6 1.0 CB B:CYS134 3.1 27.4 1.0 HB3 B:CYS132 3.1 33.8 1.0 CB B:CYS154 3.2 28.7 1.0 CB B:CYS132 3.2 28.0 1.0 HB2 B:CYS154 3.3 34.6 1.0 H B:CYS134 3.3 35.0 1.0 HB2 B:CYS132 3.5 33.8 1.0 HB2 B:SER136 3.7 35.5 1.0 HB2 B:ARG151 3.7 37.6 1.0 HB2 B:CYS134 3.8 33.1 1.0 HG3 B:ARG151 3.9 49.4 1.0 HH11 B:ARG156 4.0 42.7 1.0 N B:CYS134 4.0 29.0 1.0 HD2 B:ARG156 4.0 37.3 1.0 HB2 B:ARG156 4.1 38.4 1.0 CA B:CYS134 4.1 27.7 1.0 H B:ARG156 4.2 37.2 1.0 H B:SER136 4.3 28.5 1.0 HG B:SER136 4.5 48.1 1.0 CA B:CYS149 4.5 37.3 1.0 H B:ARG151 4.5 37.4 1.0 HD11 B:LEU138 4.5 42.4 1.0 CB B:SER136 4.6 29.4 1.0 CB B:ARG151 4.6 31.1 1.0 HD11 B:ILE158 4.6 45.9 1.0 CA B:CYS154 4.6 29.0 1.0 HD2 B:PRO133 4.6 32.0 1.0 CA B:CYS132 4.6 30.8 1.0 CG B:ARG151 4.7 41.0 1.0 HE1 B:TYR153 4.7 52.9 1.0 H B:LYS155 4.7 38.1 1.0 OG B:SER136 4.7 39.9 1.0 HA B:CYS149 4.8 45.0 1.0 NH1 B:ARG156 4.8 35.4 1.0 HA B:CYS134 4.9 33.4 1.0 H B:ASN135 4.9 31.0 1.0 C B:CYS134 4.9 24.6 1.0 CD B:ARG156 4.9 30.9 1.0 HG3 B:ARG156 4.9 35.9 1.0 C B:CYS132 5.0 32.5 1.0 HA B:CYS154 5.0 35.0 1.0 HA B:CYS132 5.0 37.1 1.0 HD21 B:LEU138 5.0 47.3 1.0

Zinc binding site 4 out of 4 in the Structure of the Cytosolic Domain of Lysosome-Associated TMEM55B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Cytosolic Domain of Lysosome-Associated TMEM55B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:24.4 occ:1.00 SG B:CYS91 2.2 25.0 1.0 SG B:CYS114 2.3 26.8 1.0 SG B:CYS94 2.3 26.0 1.0 SG B:CYS111 2.3 26.3 1.0 HB3 B:CYS111 3.0 31.4 1.0 HB3 B:CYS114 3.1 32.6 1.0 H B:CYS94 3.1 38.7 1.0 CB B:CYS111 3.1 25.9 1.0 H B:CYS114 3.1 31.8 1.0 HB3 B:CYS94 3.2 36.0 1.0 HB2 B:CYS111 3.2 31.4 1.0 CB B:CYS91 3.2 24.1 1.0 HB2 B:CYS91 3.2 29.1 1.0 HB3 B:CYS91 3.2 29.1 1.0 CB B:CYS114 3.3 26.9 1.0 CB B:CYS94 3.3 29.8 1.0 N B:CYS94 3.7 32.0 1.0 HB B:VAL93 3.7 42.9 1.0 N B:CYS114 3.8 26.3 1.0 HB B:VAL113 3.9 33.9 1.0 HB2 B:SER96 3.9 39.2 1.0 H B:SER96 3.9 33.0 1.0 CA B:CYS94 4.0 30.5 1.0 HB2 B:CYS114 4.0 32.6 1.0 CA B:CYS114 4.1 24.5 1.0 HB2 B:CYS94 4.1 36.0 1.0 HG B:SER96 4.3 35.3 1.0 H B:GLN95 4.3 38.8 1.0 H B:VAL93 4.3 31.0 1.0 HG12 B:VAL93 4.4 42.8 1.0 H B:GLU116 4.5 36.6 1.0 CA B:CYS111 4.6 21.8 1.0 H B:VAL113 4.6 33.5 1.0 C B:CYS94 4.6 30.9 1.0 HD11 B:ILE98 4.6 30.4 1.0 N B:GLN95 4.6 32.2 1.0 CB B:VAL93 4.6 35.5 1.0 HB2 B:GLU116 4.6 33.6 1.0 O B:HOH602 4.7 24.7 1.0 CA B:CYS91 4.7 28.1 1.0 N B:SER96 4.7 27.3 1.0 CB B:SER96 4.7 32.4 1.0 C B:VAL93 4.8 28.9 1.0 OG B:SER96 4.8 29.2 1.0 HG12 B:VAL113 4.8 34.1 1.0 CB B:VAL113 4.8 28.0 1.0 C B:VAL113 4.8 31.5 1.0 C B:CYS114 4.8 27.1 1.0 HA B:CYS114 4.9 29.6 1.0 H B:ASN115 4.9 29.4 1.0 HA B:CYS94 4.9 36.8 1.0 HA B:CYS111 4.9 26.4 1.0 HA B:CYS91 5.0 34.0 1.0 N B:VAL93 5.0 25.7 1.0

D.Washcbusch, A.R.Khan. Structure of the Cytosolic Domain of Lysosome-Associated TMEM55B To Be Published.