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Fluorine in PDB 5qbx: 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: 5qbx 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) 28.61 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 34.502, 59.579, 56.590, 100.32, 95.76, 101.20
R / Rfree (%) 18.8 / 22.7

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 6 in 5qbx

Go back to Fluorine Binding Sites List in 5qbx
Fluorine binding site 1 out of 6 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:29.9
occ:1.00
 F17 A:B8V901 0.0 29.9 1.0
C13 A:B8V901 1.3 30.8 1.0
F19 A:B8V901 2.2 29.0 1.0
F21 A:B8V901 2.2 30.6 1.0
C4 A:B8V901 2.4 32.5 1.0
C5 A:B8V901 2.7 32.9 1.0
SD A:MET71 3.0 27.7 1.0
CA A:GLY165 3.2 24.9 1.0
CE A:MET71 3.3 27.5 1.0
N A:GLY165 3.5 24.1 1.0
CA A:GLY137 3.6 24.2 1.0
C3 A:B8V901 3.7 33.8 1.0
O A:VAL136 3.8 23.9 1.0
C A:HIS164 3.9 24.6 1.0
O A:HIS164 3.9 25.4 1.0
N A:GLY137 4.1 22.6 1.0
C6 A:B8V901 4.1 34.4 1.0
C A:VAL136 4.2 23.8 1.0
S23 A:B8V901 4.5 36.3 1.0
C A:GLY165 4.6 25.8 1.0
C2 A:B8V901 4.8 31.9 1.0
CG A:MET71 4.8 28.2 1.0
N A:HIS164 4.9 27.8 1.0
CA A:HIS164 4.9 26.8 1.0
C A:GLY137 4.9 22.8 1.0
N A:VAL166 5.0 25.6 1.0
C1 A:B8V901 5.0 33.6 1.0

Fluorine binding site 2 out of 6 in 5qbx

Go back to Fluorine Binding Sites List in 5qbx
Fluorine binding site 2 out of 6 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:29.0
occ:1.00
 F19 A:B8V901 0.0 29.0 1.0
C13 A:B8V901 1.4 30.8 1.0
F17 A:B8V901 2.2 29.9 1.0
F21 A:B8V901 2.2 30.6 1.0
C4 A:B8V901 2.4 32.5 1.0
O A:GLY69 3.1 29.9 1.0
C3 A:B8V901 3.1 33.8 1.0
O A:HOH1044 3.2 34.6 1.0
S23 A:B8V901 3.3 36.3 1.0
C5 A:B8V901 3.4 32.9 1.0
SD A:MET71 3.9 27.7 1.0
CB A:TRP26 3.9 24.8 1.0
N A:GLY165 4.0 24.1 1.0
CA A:GLY165 4.1 24.9 1.0
C A:GLY69 4.3 28.9 1.0
CA A:TRP26 4.4 24.8 1.0
C2 A:B8V901 4.4 31.9 1.0
C25 A:B8V901 4.5 36.7 1.0
C A:HIS164 4.5 24.6 1.0
C6 A:B8V901 4.6 34.4 1.0
N A:TRP26 4.6 25.2 1.0
C23 A:B8V901 4.7 37.1 1.0
OG A:SER25 4.7 23.6 1.0
CA A:PHE70 4.8 26.8 1.0
CE A:MET71 4.9 27.5 1.0
O A:HOH1111 4.9 31.6 1.0
CA A:HIS164 5.0 26.8 1.0
N A:HIS164 5.0 27.8 1.0
CG A:TRP26 5.0 25.7 1.0
N A:PHE70 5.0 27.7 1.0

Fluorine binding site 3 out of 6 in 5qbx

Go back to Fluorine Binding Sites List in 5qbx
Fluorine binding site 3 out of 6 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:30.6
occ:1.00
 F21 A:B8V901 0.0 30.6 1.0
C13 A:B8V901 1.4 30.8 1.0
F17 A:B8V901 2.2 29.9 1.0
F19 A:B8V901 2.2 29.0 1.0
C4 A:B8V901 2.4 32.5 1.0
S23 A:B8V901 2.9 36.3 1.0
C3 A:B8V901 2.9 33.8 1.0
N A:HIS164 3.1 27.8 1.0
C A:HIS164 3.2 24.6 1.0
N A:GLY165 3.3 24.1 1.0
O A:HIS164 3.5 25.4 1.0
C A:ASN163 3.5 29.6 1.0
CA A:HIS164 3.5 26.8 1.0
C5 A:B8V901 3.6 32.9 1.0
CA A:GLY165 3.9 24.9 1.0
CA A:ASN163 3.9 30.4 1.0
O A:ASN163 4.1 29.1 1.0
N A:ASN163 4.1 31.2 1.0
CA A:GLY137 4.2 24.2 1.0
C2 A:B8V901 4.3 31.9 1.0
CG2 A:VAL162 4.3 30.1 1.0
O A:HOH1044 4.5 34.6 1.0
C A:VAL162 4.6 31.6 1.0
CB A:VAL162 4.6 31.1 1.0
O A:HOH1111 4.7 31.6 1.0
C23 A:B8V901 4.7 37.1 1.0
C6 A:B8V901 4.7 34.4 1.0
N A:VAL138 4.9 25.5 1.0
O A:VAL162 4.9 30.8 1.0
OG A:SER25 5.0 23.6 1.0
CB A:HIS164 5.0 27.6 1.0
O A:VAL138 5.0 23.4 1.0

Fluorine binding site 4 out of 6 in 5qbx

Go back to Fluorine Binding Sites List in 5qbx
Fluorine binding site 4 out of 6 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
B:F901

b:28.8
occ:1.00
 F17 B:B8V901 0.0 28.8 1.0
C13 B:B8V901 1.3 30.7 1.0
F19 B:B8V901 2.1 28.0 1.0
F21 B:B8V901 2.2 29.5 1.0
C4 B:B8V901 2.4 30.3 1.0
C5 B:B8V901 2.7 31.1 1.0
SD B:MET71 2.9 25.2 1.0
CE B:MET71 3.1 24.6 1.0
CA B:GLY165 3.2 26.4 1.0
N B:GLY165 3.6 24.9 1.0
CA B:GLY137 3.6 28.2 1.0
C3 B:B8V901 3.7 32.0 1.0
O B:VAL136 3.8 25.4 1.0
O B:HIS164 4.0 26.4 1.0
C B:HIS164 4.0 26.8 1.0
C6 B:B8V901 4.1 32.9 1.0
N B:GLY137 4.1 26.4 1.0
C B:VAL136 4.2 27.2 1.0
S23 B:B8V901 4.5 36.5 1.0
C B:GLY165 4.6 25.6 1.0
CG B:MET71 4.7 27.5 1.0
C2 B:B8V901 4.8 31.5 1.0
N B:VAL166 4.9 27.7 1.0
C1 B:B8V901 5.0 31.6 1.0
C B:GLY137 5.0 26.8 1.0

Fluorine binding site 5 out of 6 in 5qbx

Go back to Fluorine Binding Sites List in 5qbx
Fluorine binding site 5 out of 6 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:28.0
occ:1.00
 F19 B:B8V901 0.0 28.0 1.0
C13 B:B8V901 1.3 30.7 1.0
F17 B:B8V901 2.1 28.8 1.0
F21 B:B8V901 2.2 29.5 1.0
C4 B:B8V901 2.4 30.3 1.0
C3 B:B8V901 3.0 32.0 1.0
S23 B:B8V901 3.2 36.5 1.0
O B:GLY69 3.3 28.2 1.0
C5 B:B8V901 3.4 31.1 1.0
O B:HOH1119 3.5 21.1 1.0
SD B:MET71 3.8 25.2 1.0
N B:GLY165 3.9 24.9 1.0
CB B:TRP26 4.0 26.5 1.0
CA B:GLY165 4.0 26.4 1.0
C2 B:B8V901 4.3 31.5 1.0
C B:HIS164 4.4 26.8 1.0
C B:GLY69 4.4 28.1 1.0
CA B:TRP26 4.4 25.0 1.0
C25 B:B8V901 4.5 40.1 1.0
O B:HOH1103 4.5 23.4 1.0
C23 B:B8V901 4.5 36.2 1.0
C6 B:B8V901 4.6 32.9 1.0
N B:TRP26 4.7 23.9 1.0
OG B:SER25 4.7 21.6 1.0
CE B:MET71 4.8 24.6 1.0
O B:HIS164 4.9 26.4 1.0
N B:HIS164 4.9 26.8 1.0
CA B:PHE70 4.9 28.3 1.0
CA B:HIS164 4.9 26.1 1.0
C1 B:B8V901 5.0 31.6 1.0

Fluorine binding site 6 out of 6 in 5qbx

Go back to Fluorine Binding Sites List in 5qbx
Fluorine binding site 6 out of 6 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:29.5
occ:1.00
 F21 B:B8V901 0.0 29.5 1.0
C13 B:B8V901 1.4 30.7 1.0
F19 B:B8V901 2.2 28.0 1.0
F17 B:B8V901 2.2 28.8 1.0
C4 B:B8V901 2.4 30.3 1.0
C3 B:B8V901 2.9 32.0 1.0
S23 B:B8V901 3.0 36.5 1.0
C B:HIS164 3.1 26.8 1.0
N B:HIS164 3.1 26.8 1.0
N B:GLY165 3.3 24.9 1.0
O B:HIS164 3.3 26.4 1.0
C5 B:B8V901 3.5 31.1 1.0
CA B:HIS164 3.5 26.1 1.0
C B:ASN163 3.6 28.1 1.0
CA B:GLY165 3.8 26.4 1.0
CA B:GLY137 4.0 28.2 1.0
CA B:ASN163 4.1 28.0 1.0
N B:ASN163 4.1 28.3 1.0
CG2 B:VAL162 4.2 30.3 1.0
C2 B:B8V901 4.2 31.5 1.0
O B:ASN163 4.3 27.9 1.0
CB B:VAL162 4.5 30.2 1.0
C B:VAL162 4.6 28.6 1.0
O B:HOH1103 4.6 23.4 1.0
C6 B:B8V901 4.6 32.9 1.0
N B:VAL138 4.7 26.6 1.0
O B:HOH1119 4.7 21.1 1.0
C23 B:B8V901 4.8 36.2 1.0
O B:VAL138 4.9 26.7 1.0
C B:GLY137 4.9 26.8 1.0
SD B:MET71 5.0 25.2 1.0
C1 B:B8V901 5.0 31.6 1.0
O B:VAL162 5.0 30.8 1.0
CB B:HIS164 5.0 25.5 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 12:58:56 2024

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