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Fluorine in PDB 6sc0: Thermolysin in Complex with Fragment J22

Enzymatic activity of Thermolysin in Complex with Fragment J22

All present enzymatic activity of Thermolysin in Complex with Fragment J22:
3.4.24.27;

Protein crystallography data

The structure of Thermolysin in Complex with Fragment J22, PDB code: 6sc0 was solved by F.Magari, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.29 / 1.53
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.572, 92.572, 129.113, 90.00, 90.00, 120.00
R / Rfree (%) 14.5 / 16.6

Other elements in 6sc0:

The structure of Thermolysin in Complex with Fragment J22 also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Calcium (Ca) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Thermolysin in Complex with Fragment J22 (pdb code 6sc0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Thermolysin in Complex with Fragment J22, PDB code: 6sc0:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6sc0

Go back to Fluorine Binding Sites List in 6sc0
Fluorine binding site 1 out of 3 in the Thermolysin in Complex with Fragment J22


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Thermolysin in Complex with Fragment J22 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F409

b:35.1
occ:1.00
F E:L5Q409 0.0 35.1 1.0
C6 E:L5Q409 1.3 36.0 1.0
F1 E:L5Q409 2.1 37.3 1.0
F2 E:L5Q409 2.1 38.2 1.0
C5 E:L5Q409 2.4 31.5 1.0
N1 E:L5Q409 2.8 28.2 1.0
O1 E:L5Q409 2.9 23.7 1.0
HD23 E:LEU202 3.0 25.5 1.0
HD21 E:LEU202 3.1 25.5 1.0
C4 E:L5Q409 3.1 26.9 1.0
CD2 E:LEU202 3.3 21.3 1.0
HD22 E:LEU202 3.4 25.5 1.0
HH22 E:ARG203 3.4 19.2 1.0
HG22 E:VAL139 3.5 19.4 1.0
HG22 E:ILE188 4.1 21.2 1.0
NH2 E:ARG203 4.1 16.0 1.0
HG13 E:VAL139 4.1 18.1 1.0
HH12 E:ARG203 4.3 21.0 1.0
C3 E:L5Q409 4.4 30.6 1.0
CG2 E:VAL139 4.5 16.1 1.0
HH21 E:ARG203 4.5 19.2 1.0
HG21 E:ILE188 4.5 21.2 1.0
HD23 E:LEU133 4.5 23.6 1.0
HA E:VAL139 4.6 16.1 1.0
HG11 E:VAL139 4.7 18.1 1.0
HG21 E:VAL139 4.7 19.4 1.0
CG2 E:ILE188 4.7 17.6 1.0
CG1 E:VAL139 4.8 15.1 1.0
CG E:LEU202 4.8 30.3 1.0
HZ E:PHE130 4.8 24.8 1.0
OD1 E:ASN112 4.8 20.2 1.0
NH1 E:ARG203 4.9 17.5 1.0
N E:L5Q409 4.9 32.2 1.0
CZ E:ARG203 4.9 16.1 1.0
OE2 E:GLU143 4.9 21.2 1.0
HG23 E:ILE188 5.0 21.2 1.0

Fluorine binding site 2 out of 3 in 6sc0

Go back to Fluorine Binding Sites List in 6sc0
Fluorine binding site 2 out of 3 in the Thermolysin in Complex with Fragment J22


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Thermolysin in Complex with Fragment J22 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F409

b:37.3
occ:1.00
F1 E:L5Q409 0.0 37.3 1.0
C6 E:L5Q409 1.3 36.0 1.0
F E:L5Q409 2.1 35.1 1.0
F2 E:L5Q409 2.1 38.2 1.0
C5 E:L5Q409 2.4 31.5 1.0
HD23 E:LEU133 3.0 23.6 1.0
N1 E:L5Q409 3.0 28.2 1.0
HB3 E:ALA113 3.2 16.8 1.0
HG13 E:VAL139 3.3 18.1 1.0
HD22 E:LEU133 3.4 23.6 1.0
H E:ALA113 3.4 16.1 1.0
HG11 E:VAL139 3.4 18.1 1.0
CD2 E:LEU133 3.5 19.6 1.0
OD1 E:ASN112 3.7 20.2 1.0
HG22 E:VAL139 3.7 19.4 1.0
HD21 E:LEU133 3.8 23.6 1.0
CG1 E:VAL139 3.8 15.1 1.0
N E:ALA113 4.0 13.4 1.0
CB E:ALA113 4.0 14.0 1.0
C4 E:L5Q409 4.0 26.9 1.0
HA E:ASN112 4.1 16.7 1.0
OE2 E:GLU143 4.2 21.2 1.0
O E:ALA113 4.2 14.9 1.0
HB2 E:ALA113 4.2 16.8 1.0
HD21 E:LEU202 4.3 25.5 1.0
HG21 E:VAL139 4.3 19.4 1.0
O1 E:L5Q409 4.4 23.7 1.0
CG2 E:VAL139 4.4 16.1 1.0
HD22 E:LEU202 4.4 25.5 1.0
CA E:ALA113 4.5 15.1 1.0
HB3 E:LEU133 4.5 17.2 1.0
HG12 E:VAL139 4.5 18.1 1.0
HD23 E:LEU202 4.7 25.5 1.0
CD2 E:LEU202 4.7 21.3 1.0
C E:ALA113 4.7 12.6 1.0
CB E:VAL139 4.7 13.8 1.0
C E:ASN112 4.7 14.4 1.0
HZ E:PHE130 4.8 24.8 1.0
HB1 E:ALA113 4.8 16.8 1.0
CA E:ASN112 4.8 13.9 1.0
CG E:ASN112 4.8 20.4 1.0
HA E:VAL139 4.9 16.1 1.0
CG E:LEU133 4.9 18.4 1.0

Fluorine binding site 3 out of 3 in 6sc0

Go back to Fluorine Binding Sites List in 6sc0
Fluorine binding site 3 out of 3 in the Thermolysin in Complex with Fragment J22


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Thermolysin in Complex with Fragment J22 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F409

b:38.2
occ:1.00
F2 E:L5Q409 0.0 38.2 1.0
C6 E:L5Q409 1.3 36.0 1.0
F1 E:L5Q409 2.1 37.3 1.0
F E:L5Q409 2.1 35.1 1.0
C5 E:L5Q409 2.4 31.5 1.0
HG13 E:VAL139 2.5 18.1 1.0
OE2 E:GLU143 3.2 21.2 1.0
HG22 E:VAL139 3.3 19.4 1.0
HA E:VAL139 3.4 16.1 1.0
CG1 E:VAL139 3.4 15.1 1.0
HG11 E:VAL139 3.6 18.1 1.0
N1 E:L5Q409 3.7 28.2 1.0
HB3 E:ALA113 3.7 16.8 1.0
HB3 E:HIS142 3.8 15.6 1.0
HG2 E:GLU143 3.8 20.0 1.0
HD2 E:HIS142 3.9 14.5 1.0
CD2 E:HIS142 4.0 12.1 1.0
CB E:VAL139 4.0 13.8 1.0
CG2 E:VAL139 4.1 16.1 1.0
HG12 E:VAL139 4.1 18.1 1.0
CA E:VAL139 4.1 13.4 1.0
CD E:GLU143 4.1 16.5 1.0
CG E:HIS142 4.1 13.3 1.0
O1 E:L5Q409 4.2 23.7 1.0
O E:VAL139 4.2 13.8 1.0
C4 E:L5Q409 4.4 26.9 1.0
O2 E:BCT410 4.4 16.9 0.8
HG21 E:VAL139 4.4 19.4 1.0
CB E:HIS142 4.5 13.0 1.0
CG E:GLU143 4.5 16.6 1.0
NE2 E:HIS142 4.5 15.7 1.0
HH22 E:ARG203 4.5 19.2 1.0
C E:VAL139 4.6 12.7 1.0
O E:ALA113 4.6 14.9 1.0
HD23 E:LEU133 4.6 23.6 1.0
CB E:ALA113 4.7 14.0 1.0
ND1 E:HIS142 4.8 12.9 1.0
HG3 E:GLU143 4.8 20.0 1.0
H E:ALA113 4.8 16.1 1.0
HG23 E:VAL139 4.8 19.4 1.0
HB2 E:HIS142 4.8 15.6 1.0
C E:BCT410 4.9 17.2 0.8
CE1 E:HIS142 4.9 14.9 1.0
HB E:VAL139 5.0 16.6 1.0

Reference:

F.Magari, A.Heine, G.Klebe. Thermolysin in Complex with Fragment J22 To Be Published.
Page generated: Fri Aug 2 01:41:34 2024

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