Zinc in PDB 3h7t: Crystal Structure of Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1)

The structure of Crystal Structure of Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1), PDB code: 3h7t was solved by A.M.Buckle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.64 / 2.00
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	133.159, 133.159, 83.706, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / 17.5

The binding sites of Zinc atom in the Crystal Structure of Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1) (pdb code 3h7t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1), PDB code: 3h7t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1)


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 Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn236 b:41.1 occ:1.00 OD1 A:ASP167 2.0 20.2 1.0 OD1 B:ASP167 2.0 29.1 1.0 CG A:ASP167 2.7 25.7 1.0 O A:HOH315 2.8 19.6 1.0 CG B:ASP167 2.8 26.5 1.0 OD2 A:ASP167 2.9 22.6 1.0 ZN A:ZN241 3.0 59.8 1.0 OD2 B:ASP167 3.0 22.4 1.0 O B:HOH263 4.0 42.3 1.0 CB A:ASP167 4.1 21.6 1.0 CB B:ASP167 4.2 21.4 1.0 N B:ASP167 4.3 21.3 1.0 N A:ASP167 4.4 22.1 1.0 CD B:ARG149 4.4 20.1 1.0 CA B:ASP167 4.5 21.4 1.0 CA A:ASP167 4.6 21.8 1.0 CD A:ARG149 4.8 21.6 1.0 C B:TYR166 4.9 22.1 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1)


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 Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn237 b:65.5 occ:1.00 O A:HOH295 2.3 46.1 1.0 OE2 A:GLU153 2.4 37.0 1.0 OE1 A:GLU153 2.7 36.9 1.0 CD A:GLU153 2.9 33.7 1.0 ZN A:ZN241 3.2 59.8 1.0 O B:HOH331 3.4 43.9 1.0 O A:HOH263 3.8 31.5 1.0 O B:HOH263 3.8 42.3 1.0 O B:HOH387 4.1 31.3 1.0 CG A:GLU153 4.3 26.9 1.0 O A:HOH300 4.4 46.2 1.0 O A:ILE165 4.6 22.5 1.0 OD1 B:ASP167 4.8 29.1 1.0 NZ A:LYS150 5.0 49.0 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1)


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 Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn238 b:39.2 occ:1.00 OD2 B:ASP223 1.9 30.2 1.0 ZN A:ZN242 2.0 73.9 1.0 O A:HOH332 2.1 19.2 1.0 NE2 A:HIS78 2.2 26.3 1.0 CG B:ASP223 2.7 26.9 1.0 OD1 B:ASP223 2.8 29.4 1.0 CD2 A:HIS78 3.0 28.5 1.0 CE1 A:HIS78 3.3 32.3 1.0 NE2 A:GLN83 4.0 34.4 1.0 CB B:ASP223 4.1 28.1 1.0 CG A:HIS78 4.2 27.5 1.0 CD1 B:TYR220 4.2 18.7 1.0 ND1 A:HIS78 4.3 30.3 1.0 ND2 A:ASN84 4.4 25.9 1.0 O B:TYR219 4.5 24.2 1.0 O B:HOH336 4.5 30.0 1.0 O B:HOH272 4.7 30.9 1.0 CE1 B:TYR220 4.7 19.4 1.0 CB A:ARG76 4.8 26.1 1.0 N B:ASP223 4.9 27.5 1.0 O A:ARG76 4.9 23.6 1.0 CA B:TYR220 4.9 22.4 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1)


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 Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn239 b:52.3 occ:1.00 O A:HOH384 2.0 29.2 1.0 OE2 A:GLU209 2.2 45.8 1.0 OE2 A:GLU178 2.6 38.2 1.0 OE1 A:GLU178 2.8 42.5 1.0 CD A:GLU209 2.9 40.2 1.0 OE1 A:GLU209 2.9 44.6 1.0 CD A:GLU178 3.0 35.6 1.0 O A:HOH294 3.6 35.7 1.0 OE2 A:GLU175 4.3 43.7 1.0 CG A:GLU178 4.3 35.2 1.0 OH A:TYR180 4.3 28.0 1.0 CG A:GLU175 4.3 34.3 1.0 CG A:GLU209 4.4 36.3 1.0 CD A:GLU175 4.7 40.8 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1)


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 Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn240 b:36.6 occ:1.00 OD2 A:ASP223 1.9 27.1 1.0 O A:HOH303 1.9 21.8 1.0 ZN A:ZN243 2.1 69.7 1.0 NE2 B:HIS78 2.1 24.2 1.0 CG A:ASP223 2.7 30.5 1.0 OD1 A:ASP223 2.9 28.3 1.0 CD2 B:HIS78 3.0 19.7 1.0 CE1 B:HIS78 3.2 23.0 1.0 CB A:ASP223 4.2 30.5 1.0 CG B:HIS78 4.2 24.4 1.0 ND1 B:HIS78 4.2 21.9 1.0 NE2 B:GLN83 4.2 33.2 1.0 CD1 A:TYR220 4.3 22.6 1.0 O A:HOH366 4.3 29.8 1.0 ND2 B:ASN84 4.4 24.6 1.0 O A:TYR219 4.5 22.2 1.0 O A:HOH340 4.5 29.4 1.0 CB B:ARG76 4.7 24.2 1.0 CE1 A:TYR220 4.7 23.2 1.0 O B:ARG76 4.8 20.7 1.0 N A:ASP223 4.9 30.4 1.0 CA A:TYR220 4.9 22.7 1.0 NE B:ARG76 5.0 25.2 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1)


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 Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn241 b:59.8 occ:1.00 ZN A:ZN236 3.0 41.1 1.0 O A:HOH295 3.2 46.1 1.0 ZN A:ZN237 3.2 65.5 1.0 O B:HOH263 3.5 42.3 1.0 OD1 B:ASP167 3.8 29.1 1.0 OE1 A:GLU153 3.9 36.9 1.0 OD1 A:ASP167 4.2 20.2 1.0 OD2 B:ASP167 4.3 22.4 1.0 CD A:ARG149 4.4 21.6 1.0 CG B:ASP167 4.5 26.5 1.0 CG A:ARG149 4.5 22.0 1.0 CD A:GLU153 4.6 33.7 1.0 O A:HOH315 4.7 19.6 1.0 OE2 A:GLU153 4.8 37.0 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1)


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 Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn242 b:73.9 occ:1.00 ZN A:ZN238 2.0 39.2 1.0 O A:HOH332 3.3 19.2 1.0 OD2 B:ASP223 3.3 30.2 1.0 NE2 A:HIS78 3.4 26.3 1.0 O B:HOH336 3.5 30.0 1.0 OD1 B:ASP223 3.5 29.4 1.0 ND2 A:ASN84 3.6 25.9 1.0 CG B:ASP223 3.7 26.9 1.0 CB A:ARG76 3.9 26.1 1.0 CD2 A:HIS78 4.1 28.5 1.0 CD1 B:TYR220 4.3 18.7 1.0 CE1 B:TYR220 4.4 19.4 1.0 CG A:ARG76 4.4 24.4 1.0 CE1 A:HIS78 4.5 32.3 1.0 NE2 A:GLN83 4.5 34.4 1.0 O A:HOH359 4.6 26.3 1.0 O A:ARG76 4.6 23.6 1.0 CG A:ASN84 4.7 26.3 1.0 CG1 B:VAL75 4.8 28.5 1.0 NE A:ARG76 4.8 25.4 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1)


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 Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn243 b:69.7 occ:1.00 ZN A:ZN240 2.1 36.6 1.0 O A:HOH303 3.3 21.8 1.0 O A:HOH340 3.4 29.4 1.0 OD2 A:ASP223 3.5 27.1 1.0 NE2 B:HIS78 3.5 24.2 1.0 ND2 B:ASN84 3.5 24.6 1.0 OD1 A:ASP223 3.7 28.3 1.0 CB B:ARG76 3.7 24.2 1.0 CG A:ASP223 3.9 30.5 1.0 CD2 B:HIS78 4.2 19.7 1.0 CG B:ARG76 4.2 22.8 1.0 CE1 A:TYR220 4.4 23.2 1.0 O B:HOH339 4.4 20.1 1.0 CD1 A:TYR220 4.4 22.6 1.0 CE1 B:HIS78 4.5 23.0 1.0 O B:ARG76 4.5 20.7 1.0 NE2 B:GLN83 4.6 33.2 1.0 CG B:ASN84 4.6 26.6 1.0 NE B:ARG76 4.8 25.2 1.0 CG1 A:VAL75 5.0 24.9 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1)


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 Scabies Mite Inactivated Protease Paralogue S-D1 (Smipp-S-D1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn236 b:60.7 occ:1.00 OE2 B:GLU153 2.1 31.1 1.0 CD B:GLU153 2.8 29.4 1.0 O A:HOH315 2.9 19.6 1.0 OE1 B:GLU153 3.0 31.1 1.0 O B:HOH347 3.5 24.0 1.0 O A:HOH330 3.7 37.8 1.0 CG B:GLU153 4.3 26.7 1.0 O A:HOH351 4.4 39.8 1.0 O B:ILE165 4.5 23.8 1.0 OD1 A:ASP167 4.6 20.2 1.0 OD2 A:ASP167 4.8 22.6 1.0 CG A:ASP167 4.8 25.7 1.0

K.Fischer, C.G.Langendorf, J.A.Irving, S.Reynolds, C.Willis, S.Beckham, R.H.Law, S.Yang, T.A.Bashtannyk-Puhalovich, S.Mcgowan, J.C.Whisstock, R.N.Pike, D.J.Kemp, A.M.Buckle. Structural Mechanisms of Inactivation in Scabies Mite Serine Protease Paralogues. J.Mol.Biol. V. 390 635 2009.
ISSN: ISSN 0022-2836
PubMed: 19427318
DOI: 10.1016/J.JMB.2009.04.082