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Fluorine in PDB 5qc1: Crystal Structure of Human Cathepsin-S with Bound Ligand

Enzymatic activity of Crystal Structure of Human Cathepsin-S with Bound Ligand

All present enzymatic activity of Crystal Structure of Human Cathepsin-S with Bound Ligand:
3.4.22.27;

Protein crystallography data

The structure of Crystal Structure of Human Cathepsin-S with Bound Ligand, PDB code: 5qc1 was solved by S.D.Bembenek, M.K.Ameriks, T.Mirzadegan, H.Yang, C.Shao, S.K.Burley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.66 / 2.08
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.709, 37.032, 106.236, 90.00, 108.12, 90.00
R / Rfree (%) 19.9 / 27.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Cathepsin-S with Bound Ligand (pdb code 5qc1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Human Cathepsin-S with Bound Ligand, PDB code: 5qc1:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5qc1

Go back to Fluorine Binding Sites List in 5qc1
Fluorine binding site 1 out of 8 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:24.3
occ:1.00
 F13 A:B9S901 0.0 24.3 1.0
C2 A:B9S901 1.3 21.4 1.0
C3 A:B9S901 2.3 20.7 1.0
C1 A:B9S901 2.3 17.1 1.0
CD A:LYS64 3.1 24.2 1.0
CG A:LYS64 3.3 17.4 1.0
CE A:LYS64 3.3 34.2 1.0
O A:GLY68 3.4 14.5 1.0
CB A:LYS64 3.5 20.4 1.0
C4 A:B9S901 3.6 13.3 1.0
C6 A:B9S901 3.6 15.7 1.0
O A:HOH1180 3.6 29.5 1.0
N A:LYS64 3.7 13.3 1.0
O A:GLY62 3.7 16.9 1.0
C A:GLY68 3.9 15.1 1.0
O A:HOH1015 4.1 20.8 1.0
O A:ASN67 4.1 18.9 1.0
C5 A:B9S901 4.1 18.7 1.0
C A:ASN63 4.2 18.1 1.0
CA A:LYS64 4.2 15.0 1.0
O A:HOH1190 4.3 33.1 1.0
CA A:ASN63 4.4 17.2 1.0
CA A:GLY68 4.5 13.3 1.0
N A:GLY69 4.5 17.1 1.0
C A:ASN67 4.6 23.1 1.0
N A:GLY68 4.7 18.1 1.0
C A:GLY62 4.7 13.3 1.0
CA A:GLY69 4.8 14.2 1.0
NZ A:LYS64 4.8 30.1 1.0
O A:ASN63 5.0 19.7 1.0

Fluorine binding site 2 out of 8 in 5qc1

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Fluorine binding site 2 out of 8 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:16.4
occ:1.00
 F36 A:B9S901 0.0 16.4 1.0
C34 A:B9S901 1.3 15.1 1.0
F40 A:B9S901 2.1 14.8 1.0
F38 A:B9S901 2.1 16.4 1.0
C27 A:B9S901 2.4 10.9 1.0
C26 A:B9S901 2.7 10.8 1.0
SD A:MET71 2.8 9.8 1.0
CE A:MET71 3.2 8.8 1.0
CA A:GLY165 3.2 12.6 1.0
N A:GLY165 3.6 11.6 1.0
CA A:GLY137 3.7 10.7 1.0
C21 A:B9S901 3.7 14.7 1.0
O A:VAL136 4.0 10.9 1.0
C A:HIS164 4.0 9.3 1.0
O A:HIS164 4.0 11.9 1.0
N A:GLY137 4.1 16.4 1.0
C25 A:B9S901 4.1 14.5 1.0
C A:VAL136 4.3 10.8 1.0
C19 A:B9S901 4.3 16.3 1.0
C A:GLY165 4.6 15.5 1.0
CG A:MET71 4.6 14.9 1.0
CA A:TRP26 4.7 10.6 1.0
CB A:TRP26 4.7 11.4 1.0
C23 A:B9S901 4.8 11.5 1.0
N A:VAL166 4.9 8.9 1.0
C24 A:B9S901 5.0 16.8 1.0
O A:GLY69 5.0 22.7 1.0

Fluorine binding site 3 out of 8 in 5qc1

Go back to Fluorine Binding Sites List in 5qc1
Fluorine binding site 3 out of 8 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:16.4
occ:1.00
 F38 A:B9S901 0.0 16.4 1.0
C34 A:B9S901 1.3 15.1 1.0
F40 A:B9S901 2.1 14.8 1.0
F36 A:B9S901 2.1 16.4 1.0
C27 A:B9S901 2.4 10.9 1.0
C19 A:B9S901 3.0 16.3 1.0
C21 A:B9S901 3.0 14.7 1.0
O A:GLY69 3.3 22.7 1.0
N17 A:B9S901 3.3 10.9 1.0
CB A:TRP26 3.5 11.4 1.0
C26 A:B9S901 3.5 10.8 1.0
O A:HOH1120 3.5 18.4 1.0
N A:GLY165 3.8 11.6 1.0
SD A:MET71 3.8 9.8 1.0
CA A:GLY165 4.0 12.6 1.0
CA A:TRP26 4.0 10.6 1.0
C23 A:B9S901 4.3 11.5 1.0
N A:TRP26 4.4 12.4 1.0
C A:HIS164 4.4 9.3 1.0
C A:GLY69 4.4 15.9 1.0
CG A:TRP26 4.7 14.6 1.0
C25 A:B9S901 4.7 14.5 1.0
C15 A:B9S901 4.7 16.8 1.0
OG A:SER25 4.8 10.4 1.0
CE A:MET71 4.9 8.8 1.0
N A:HIS164 4.9 9.1 1.0
O A:HIS164 4.9 11.9 1.0
CA A:HIS164 4.9 11.1 1.0
CA A:PHE70 5.0 16.2 1.0

Fluorine binding site 4 out of 8 in 5qc1

Go back to Fluorine Binding Sites List in 5qc1
Fluorine binding site 4 out of 8 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:14.8
occ:1.00
 F40 A:B9S901 0.0 14.8 1.0
C34 A:B9S901 1.3 15.1 1.0
F38 A:B9S901 2.1 16.4 1.0
F36 A:B9S901 2.1 16.4 1.0
C27 A:B9S901 2.4 10.9 1.0
C A:HIS164 3.0 9.3 1.0
C21 A:B9S901 3.0 14.7 1.0
C19 A:B9S901 3.1 16.3 1.0
N A:GLY165 3.1 11.6 1.0
N A:HIS164 3.1 9.1 1.0
O A:HIS164 3.3 11.9 1.0
C26 A:B9S901 3.4 10.8 1.0
CA A:HIS164 3.5 11.1 1.0
CA A:GLY165 3.6 12.6 1.0
C A:ASN163 3.6 17.6 1.0
CA A:GLY137 3.9 10.7 1.0
CA A:ASN163 4.1 13.0 1.0
O A:ASN163 4.1 14.8 1.0
N17 A:B9S901 4.2 10.9 1.0
N A:ASN163 4.2 12.8 1.0
C23 A:B9S901 4.3 11.5 1.0
CG2 A:VAL162 4.5 12.7 1.0
O A:HOH1120 4.5 18.4 1.0
C25 A:B9S901 4.6 14.5 1.0
C A:VAL162 4.7 14.6 1.0
CB A:VAL162 4.7 14.1 1.0
SD A:MET71 4.8 9.8 1.0
N A:VAL138 4.9 13.3 1.0
C A:GLY137 4.9 10.9 1.0
N A:GLY137 4.9 16.4 1.0
C24 A:B9S901 5.0 16.8 1.0
CB A:HIS164 5.0 10.8 1.0

Fluorine binding site 5 out of 8 in 5qc1

Go back to Fluorine Binding Sites List in 5qc1
Fluorine binding site 5 out of 8 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:20.5
occ:1.00
 F13 B:B9S901 0.0 20.5 1.0
C2 B:B9S901 1.3 20.8 1.0
C1 B:B9S901 2.3 16.5 1.0
C3 B:B9S901 2.3 18.1 1.0
CD B:LYS64 3.1 19.2 1.0
CG B:LYS64 3.1 19.2 1.0
CE B:LYS64 3.2 25.2 1.0
CB B:LYS64 3.5 10.0 1.0
O B:GLY68 3.5 15.3 1.0
C6 B:B9S901 3.6 21.0 1.0
C4 B:B9S901 3.6 15.4 1.0
N B:LYS64 3.6 16.3 1.0
O B:GLY62 3.7 12.9 1.0
C B:GLY68 3.9 17.3 1.0
C5 B:B9S901 4.1 14.5 1.0
C B:ASN63 4.1 18.7 1.0
CA B:LYS64 4.2 18.4 1.0
CA B:ASN63 4.3 17.2 1.0
O B:ASN67 4.3 15.9 1.0
N B:GLY69 4.4 14.9 1.0
CA B:GLY68 4.5 18.4 1.0
NZ B:LYS64 4.6 30.7 1.0
C B:GLY62 4.7 16.1 1.0
O B:HOH1206 4.7 23.4 1.0
CA B:GLY69 4.7 14.3 1.0
C B:ASN67 4.8 14.8 1.0
N B:GLY68 4.9 16.0 1.0
O B:ASN63 4.9 17.4 1.0
N B:ASN63 4.9 18.5 1.0

Fluorine binding site 6 out of 8 in 5qc1

Go back to Fluorine Binding Sites List in 5qc1
Fluorine binding site 6 out of 8 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:16.9
occ:1.00
 F36 B:B9S901 0.0 16.9 1.0
C34 B:B9S901 1.3 17.5 1.0
F40 B:B9S901 2.1 15.0 1.0
F38 B:B9S901 2.1 14.1 1.0
C27 B:B9S901 2.4 13.0 1.0
C26 B:B9S901 2.7 11.9 1.0
SD B:MET71 2.8 10.2 1.0
CE B:MET71 3.0 10.4 1.0
CA B:GLY165 3.3 9.5 1.0
CA B:GLY137 3.6 7.6 1.0
C21 B:B9S901 3.7 10.8 1.0
N B:GLY165 3.7 8.2 1.0
O B:VAL136 3.8 9.9 1.0
N B:GLY137 3.9 11.1 1.0
C25 B:B9S901 4.1 14.4 1.0
C B:VAL136 4.1 9.9 1.0
C B:HIS164 4.2 11.2 1.0
O B:HIS164 4.3 9.3 1.0
C19 B:B9S901 4.3 12.5 1.0
CG B:MET71 4.6 12.4 1.0
CB B:TRP26 4.6 12.3 1.0
CA B:TRP26 4.6 12.8 1.0
C B:GLY165 4.7 12.3 1.0
C23 B:B9S901 4.8 14.9 1.0
O B:HOH1118 4.9 12.3 1.0
C24 B:B9S901 5.0 12.2 1.0

Fluorine binding site 7 out of 8 in 5qc1

Go back to Fluorine Binding Sites List in 5qc1
Fluorine binding site 7 out of 8 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:14.1
occ:1.00
 F38 B:B9S901 0.0 14.1 1.0
C34 B:B9S901 1.3 17.5 1.0
F36 B:B9S901 2.1 16.9 1.0
F40 B:B9S901 2.2 15.0 1.0
C27 B:B9S901 2.4 13.0 1.0
C19 B:B9S901 3.0 12.5 1.0
C21 B:B9S901 3.0 10.8 1.0
O B:GLY69 3.3 19.9 1.0
N17 B:B9S901 3.3 13.8 1.0
CB B:TRP26 3.4 12.3 1.0
C26 B:B9S901 3.5 11.9 1.0
SD B:MET71 3.8 10.2 1.0
N B:GLY165 3.8 8.2 1.0
CA B:TRP26 4.0 12.8 1.0
CA B:GLY165 4.0 9.5 1.0
O B:HOH1106 4.1 9.8 1.0
C23 B:B9S901 4.3 14.9 1.0
N B:TRP26 4.4 11.8 1.0
C B:GLY69 4.4 14.3 1.0
C B:HIS164 4.4 11.2 1.0
CG B:TRP26 4.6 13.7 1.0
C25 B:B9S901 4.7 14.4 1.0
C15 B:B9S901 4.7 13.8 1.0
CE B:MET71 4.8 10.4 1.0
N B:HIS164 4.9 13.7 1.0
CA B:PHE70 4.9 13.3 1.0
CA B:HIS164 5.0 12.7 1.0
OG B:SER25 5.0 9.1 1.0

Fluorine binding site 8 out of 8 in 5qc1

Go back to Fluorine Binding Sites List in 5qc1
Fluorine binding site 8 out of 8 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:15.0
occ:1.00
 F40 B:B9S901 0.0 15.0 1.0
C34 B:B9S901 1.3 17.5 1.0
F36 B:B9S901 2.1 16.9 1.0
F38 B:B9S901 2.2 14.1 1.0
C27 B:B9S901 2.3 13.0 1.0
C B:HIS164 3.1 11.2 1.0
C21 B:B9S901 3.1 10.8 1.0
N B:GLY165 3.1 8.2 1.0
C19 B:B9S901 3.2 12.5 1.0
N B:HIS164 3.2 13.7 1.0
C26 B:B9S901 3.3 11.9 1.0
O B:HIS164 3.3 9.3 1.0
CA B:GLY165 3.5 9.5 1.0
CA B:HIS164 3.6 12.7 1.0
CA B:GLY137 3.6 7.6 1.0
C B:ASN163 3.8 13.6 1.0
CA B:ASN163 4.3 14.3 1.0
N B:ASN163 4.3 10.3 1.0
N17 B:B9S901 4.3 13.8 1.0
C23 B:B9S901 4.3 14.9 1.0
CG2 B:VAL162 4.4 14.6 1.0
O B:ASN163 4.4 11.6 1.0
C25 B:B9S901 4.5 14.4 1.0
N B:GLY137 4.6 11.1 1.0
CB B:VAL162 4.7 18.2 1.0
C B:GLY137 4.7 12.9 1.0
N B:VAL138 4.7 9.8 1.0
C B:VAL162 4.7 12.6 1.0
SD B:MET71 4.8 10.2 1.0
O B:VAL136 4.8 9.9 1.0
O B:HOH1106 4.9 9.8 1.0
C24 B:B9S901 4.9 12.2 1.0
C B:GLY165 5.0 12.3 1.0

Reference:

S.D.Bembenek, M.K.Ameriks, T.Mirzadegan, H.Yang, C.Shao, S.K.Burley. Crystal Structure of Human Cathepsin-S with Bound Ligand To Be Published.
Page generated: Thu Aug 1 13:01:21 2024

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