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Zinc in PDB 2hh5: Crystal Structure of Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide

Enzymatic activity of Crystal Structure of Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide

All present enzymatic activity of Crystal Structure of Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide:
3.4.22.27;

Protein crystallography data

The structure of Crystal Structure of Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide, PDB code: 2hh5 was solved by G.Spraggon, M.Hornsby, S.A.Lesley, D.C.Tully, J.L.Harris, D.S.Karenewsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.20 / 1.80
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 109.542, 109.542, 98.529, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 22

Other elements in 2hh5:

The structure of Crystal Structure of Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide (pdb code 2hh5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide, PDB code: 2hh5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2hh5

Go back to Zinc Binding Sites List in 2hh5
Zinc binding site 1 out of 6 in the Crystal Structure of Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide


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 Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:21.5
occ:1.00
 ND1 B:HIS164 2.0 19.2 1.0
N1 B:GNQ501 2.1 20.9 1.0
CL B:CL801 2.2 24.4 1.0
SG B:CYS25 2.3 20.4 1.0
C8 B:GNQ501 2.9 21.4 1.0
CE1 B:HIS164 2.9 21.5 1.0
C7 B:GNQ501 2.9 18.6 1.0
CB B:CYS25 3.0 21.1 1.0
CG B:HIS164 3.1 19.5 1.0
C9 B:GNQ501 3.3 22.5 1.0
C4 B:GNQ501 3.3 17.0 1.0
CB B:HIS164 3.6 20.6 1.0
CA B:HIS164 3.7 20.3 1.0
N2 B:GNQ501 3.7 21.9 1.0
C6 B:GNQ501 4.0 17.4 1.0
NE2 B:HIS164 4.0 19.7 1.0
O B:ASN163 4.1 20.5 1.0
CD2 B:HIS164 4.2 20.3 1.0
N B:GLY165 4.3 19.2 1.0
CA B:CYS25 4.4 20.1 1.0
C B:GNQ501 4.5 23.0 1.0
C B:HIS164 4.5 21.0 1.0
C3 B:GNQ501 4.6 21.5 1.0
N B:CYS25 4.6 20.4 1.0
C10 B:GNQ501 4.7 20.5 1.0
NE2 B:GLN19 4.7 23.3 1.0
N B:HIS164 4.7 19.5 1.0
O B:GNQ501 4.8 22.6 1.0
C B:ASN163 4.8 19.1 1.0
CZ2 B:TRP186 4.9 22.7 1.0
OE1 B:GLN19 4.9 23.3 1.0
NE1 B:TRP186 4.9 21.5 1.0

Zinc binding site 2 out of 6 in 2hh5

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Zinc binding site 2 out of 6 in the Crystal Structure of Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide


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 Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:30.8
occ:1.00
 NE2 B:HIS142 1.9 23.1 1.0
OD2 B:ASP139 2.0 29.0 1.0
O B:HOH882 2.1 31.4 1.0
O B:HOH933 2.2 22.1 1.0
CG B:ASP139 2.6 24.4 1.0
OD1 B:ASP139 2.6 22.0 1.0
CE1 B:HIS142 2.8 27.3 1.0
CD2 B:HIS142 3.0 23.0 1.0
ND1 B:HIS142 3.9 20.8 1.0
O B:SER157 4.0 28.3 1.0
CB B:ASP139 4.0 23.2 1.0
OG1 B:THR159 4.0 32.9 1.0
CG B:HIS142 4.0 22.6 1.0
N B:THR159 4.1 27.9 1.0
CA B:CYS158 4.3 26.9 1.0
O B:ARG141 4.3 23.8 1.0
NH1 A:ARG141 4.4 24.6 1.0
C B:CYS158 4.6 27.9 1.0
CB B:ARG141 4.6 21.6 1.0
C B:SER157 4.8 26.8 1.0
C B:ARG141 4.8 22.1 1.0
CG2 B:THR159 4.8 30.2 1.0
N B:ARG141 4.8 22.4 1.0
CB B:THR159 4.8 31.0 1.0
SG B:CYS158 4.9 25.1 1.0
N B:CYS158 4.9 27.7 1.0
CA B:ARG141 5.0 22.1 1.0

Zinc binding site 3 out of 6 in 2hh5

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Zinc binding site 3 out of 6 in the Crystal Structure of Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide


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 Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:34.0
occ:1.00
 OE2 B:GLU193 2.0 28.7 1.0
OE2 B:GLU15 2.0 29.3 1.0
ND1 B:HIS188 2.1 29.0 1.0
CD B:GLU15 2.8 27.7 1.0
CD B:GLU193 2.9 30.5 1.0
CG B:HIS188 3.0 28.4 1.0
OE1 B:GLU15 3.0 23.5 1.0
CB B:HIS188 3.1 25.9 1.0
OE1 B:GLU193 3.1 32.4 1.0
CE1 B:HIS188 3.2 35.0 1.0
O B:HOH836 4.0 37.5 1.0
O B:HOH817 4.1 27.8 1.0
CD2 B:HIS188 4.1 32.7 1.0
NE2 B:HIS188 4.2 31.2 1.0
CG B:GLU193 4.3 28.7 1.0
CG B:GLU15 4.3 26.5 1.0
CA B:HIS188 4.7 24.0 1.0

Zinc binding site 4 out of 6 in 2hh5

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Zinc binding site 4 out of 6 in the Crystal Structure of Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide


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 Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:22.8
occ:1.00
 ND1 A:HIS164 2.0 22.9 1.0
N1 A:GNQ401 2.1 21.2 1.0
SG A:CYS25 2.2 23.6 1.0
CL A:CL802 2.3 24.8 1.0
CE1 A:HIS164 2.9 21.5 1.0
C8 A:GNQ401 2.9 23.1 1.0
C7 A:GNQ401 2.9 23.9 1.0
CB A:CYS25 3.0 24.8 1.0
CG A:HIS164 3.1 20.6 1.0
C9 A:GNQ401 3.2 23.8 1.0
C4 A:GNQ401 3.4 20.6 1.0
CB A:HIS164 3.6 20.6 1.0
CA A:HIS164 3.6 21.8 1.0
N2 A:GNQ401 3.7 23.6 1.0
C6 A:GNQ401 4.0 22.1 1.0
NE2 A:HIS164 4.0 20.4 1.0
O A:ASN163 4.1 20.1 1.0
CD2 A:HIS164 4.2 20.3 1.0
N A:GLY165 4.2 21.0 1.0
CA A:CYS25 4.4 25.6 1.0
C A:HIS164 4.4 21.5 1.0
C A:GNQ401 4.4 22.8 1.0
N A:CYS25 4.6 25.0 1.0
C10 A:GNQ401 4.6 23.5 1.0
C3 A:GNQ401 4.7 22.2 1.0
NE2 A:GLN19 4.7 25.1 1.0
N A:HIS164 4.7 20.8 1.0
O A:GNQ401 4.8 20.6 1.0
C A:ASN163 4.8 21.7 1.0
CZ2 A:TRP186 4.9 21.3 1.0
NE1 A:TRP186 5.0 23.8 1.0

Zinc binding site 5 out of 6 in 2hh5

Go back to Zinc Binding Sites List in 2hh5
Zinc binding site 5 out of 6 in the Crystal Structure of Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide


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 Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:29.1
occ:1.00
 OD2 A:ASP139 1.9 25.7 1.0
NE2 A:HIS142 2.1 21.7 1.0
O A:HOH940 2.1 25.3 1.0
O A:HOH803 2.3 23.7 1.0
CG A:ASP139 2.6 23.2 1.0
OD1 A:ASP139 2.6 20.7 1.0
CD2 A:HIS142 3.0 20.2 1.0
CE1 A:HIS142 3.1 22.7 1.0
O A:SER157 3.9 27.9 1.0
CB A:ASP139 4.0 20.6 1.0
N A:THR159 4.1 26.3 1.0
ND1 A:HIS142 4.1 22.0 1.0
CA A:CYS158 4.1 25.9 1.0
CG A:HIS142 4.1 20.1 1.0
OG1 A:THR159 4.4 29.0 1.0
O A:ARG141 4.5 22.8 1.0
C A:CYS158 4.5 26.8 1.0
NH2 B:ARG141 4.5 32.2 1.0
C A:SER157 4.7 26.5 1.0
CG2 A:THR159 4.7 31.2 1.0
CB A:ARG141 4.7 22.6 1.0
N A:ARG141 4.8 20.2 1.0
N A:CYS158 4.8 26.6 1.0
C A:ARG141 4.8 20.8 1.0
SG A:CYS158 4.9 25.1 1.0
ND2 A:ASN163 4.9 18.5 1.0
CB A:THR159 5.0 27.1 1.0

Zinc binding site 6 out of 6 in 2hh5

Go back to Zinc Binding Sites List in 2hh5
Zinc binding site 6 out of 6 in the Crystal Structure of Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide


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 Cathepsin S in Complex with A Zinc Mediated Non-Covalent Arylaminoethyl Amide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:55.0
occ:1.00
 OD1 A:ASP3 1.9 46.6 1.0
O A:HOH926 2.4 36.8 1.0
O A:HOH864 2.4 34.6 1.0
CG A:ASP3 3.0 38.3 1.0
OD2 A:ASP3 3.4 40.6 1.0
O A:HOH850 3.8 35.9 1.0
O A:HOH885 3.8 32.7 1.0
OE2 A:GLU178 4.1 37.6 1.0
CB A:ASP3 4.2 34.9 1.0
O A:ASP3 4.7 34.3 1.0
CA A:ASP3 4.8 34.5 1.0

Reference:

D.C.Tully, H.Liu, A.K.Chatterjee, P.B.Alper, R.Epple, J.A.Williams, M.J.Roberts, D.H.Woodmansee, B.T.Masick, C.Tumanut, J.Li, G.Spraggon, M.Hornsby, J.Chang, T.Tuntland, T.Hollenbeck, P.Gordon, J.L.Harris, D.S.Karanewsky. Synthesis and Sar of Arylaminoethyl Amides As Noncovalent Inhibitors of Cathepsin S: P3 Cyclic Ethers. Bioorg.Med.Chem.Lett. V. 16 5112 2006.
ISSN: ISSN 0960-894X
PubMed: 16876402
DOI: 10.1016/J.BMCL.2006.07.033
Page generated: Wed Dec 16 03:30:10 2020

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