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Fluorine in PDB 6v64: Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan

Enzymatic activity of Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan

All present enzymatic activity of Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan:
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan, PDB code: 6v64 was solved by E.A.Ruben, Z.Chen, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.16 / 2.29
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.869, 86.599, 50.516, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 27.7

Other elements in 6v64:

The structure of Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan (pdb code 6v64). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan, PDB code: 6v64:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 6v64

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Fluorine binding site 1 out of 9 in the Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan


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 Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F29

b:37.2
occ:1.00
 F B:FTR29 0.0 37.2 1.0
CZ3 B:FTR29 1.4 36.1 1.0
CE3 B:FTR29 2.4 35.5 1.0
CH2 B:FTR29 2.4 33.8 1.0
C A:GLY2 3.4 39.1 1.0
CG A:ARG4 3.5 41.2 1.0
CA A:GLY2 3.6 39.7 1.0
N A:LEU3 3.6 42.4 1.0
CD2 B:FTR29 3.6 33.6 1.0
O B:PRO120 3.6 36.8 1.0
CZ2 B:FTR29 3.7 32.7 1.0
O A:GLY2 3.7 37.4 1.0
C A:LEU3 3.8 43.3 1.0
N A:ARG4 3.9 41.6 1.0
N A:GLY2 3.9 43.3 1.0
CE2 B:FTR29 4.1 32.0 1.0
CG B:PRO28 4.1 41.6 1.0
O A:LEU3 4.2 46.9 1.0
CD2 B:HIS119 4.2 38.7 1.0
CA A:ARG4 4.2 42.9 1.0
CA A:LEU3 4.2 42.6 1.0
CB A:ARG4 4.5 42.0 1.0
C B:PRO120 4.5 35.7 1.0
O B:HIS119 4.5 36.5 1.0
CD A:ARG4 4.5 39.5 1.0
CB B:HIS119 4.5 38.1 1.0
CD B:PRO28 4.5 40.3 1.0
CB B:FTR207 4.7 28.1 1.0
CD1 B:FTR207 4.7 29.8 1.0
CA B:VAL121 4.7 33.8 1.0
CG B:HIS119 4.7 39.4 1.0
N B:VAL121 4.8 34.8 1.0
C B:HIS119 4.9 36.8 1.0
CG B:FTR29 4.9 32.9 1.0
CG B:FTR207 5.0 28.1 1.0

Fluorine binding site 2 out of 9 in 6v64

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Fluorine binding site 2 out of 9 in the Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan


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 Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F51

b:40.0
occ:1.00
 F B:FTR51 0.0 40.0 1.0
CZ3 B:FTR51 1.4 41.0 1.0
CE3 B:FTR51 2.3 39.7 1.0
CH2 B:FTR51 2.4 43.4 1.0
N B:LYS107 3.4 39.6 1.0
CB B:LEU105 3.4 36.6 1.0
CD2 B:TYR89 3.5 44.9 1.0
C B:MET106 3.5 38.1 1.0
CB B:LYS107 3.6 45.0 1.0
C B:LEU105 3.6 33.8 1.0
CD2 B:FTR51 3.6 40.3 1.0
CZ2 B:FTR51 3.7 44.3 1.0
O B:LEU105 3.7 34.4 1.0
N B:MET106 3.8 34.3 1.0
CA B:LYS107 3.8 42.2 1.0
O B:MET106 3.9 38.0 1.0
CA B:MET106 3.9 37.3 1.0
CE2 B:TYR89 4.0 47.9 1.0
CE2 B:FTR51 4.1 42.3 1.0
CA B:LEU105 4.1 34.2 1.0
O B:LYS87 4.3 46.6 1.0
CG1 B:VAL241 4.3 46.6 1.0
CG B:LEU105 4.5 37.3 1.0
CG B:TYR89 4.6 44.5 1.0
CD2 B:LEU105 4.6 37.2 1.0
CG B:LYS107 4.7 48.0 1.0
CB B:TYR89 4.8 41.7 1.0
CD1 B:LEU105 4.9 39.4 1.0
CG B:FTR51 4.9 40.2 1.0

Fluorine binding site 3 out of 9 in 6v64

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Fluorine binding site 3 out of 9 in the Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan


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 Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F60

b:37.4
occ:1.00
 F B:FTR60D 0.0 37.4 1.0
CZ3 B:FTR60D 1.4 36.3 1.0
CH2 B:FTR60D 2.3 36.8 1.0
CE3 B:FTR60D 2.4 36.0 1.0
C3 B:0G6301 3.5 32.3 1.0
CZ2 B:FTR60D 3.6 37.6 1.0
CD2 B:FTR60D 3.7 36.7 1.0
CD2 B:HIS57 3.9 31.6 1.0
O1 B:0G6301 4.0 32.3 1.0
CE2 B:FTR60D 4.1 37.8 1.0
NE2 B:HIS57 4.2 30.8 1.0
O B:HOH405 4.2 41.4 1.0
CB1 B:0G6301 4.3 29.9 1.0
CE B:LYS60F 4.4 41.4 1.0
C1 B:0G6301 4.4 30.3 1.0
C2 B:0G6301 4.7 32.8 1.0
NZ B:LYS60F 4.7 41.9 1.0
O2 B:0G6301 4.8 33.4 1.0
N2 B:0G6301 4.8 30.5 1.0
CG1 B:0G6301 4.9 31.4 1.0
O B:HIS57 4.9 33.4 1.0
CA2 B:0G6301 5.0 32.2 1.0

Fluorine binding site 4 out of 9 in 6v64

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Fluorine binding site 4 out of 9 in the Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan


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 Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F96

b:43.5
occ:1.00
 F B:FTR96 0.0 43.5 1.0
CZ3 B:FTR96 1.3 41.5 1.0
CE3 B:FTR96 2.4 39.4 1.0
CH2 B:FTR96 2.4 42.8 1.0
CG B:PRO60C 3.5 34.4 1.0
CD2 B:FTR96 3.6 38.5 1.0
CZ2 B:FTR96 3.6 42.3 1.0
CA B:ARG97 4.1 42.3 1.0
CE2 B:FTR96 4.1 39.7 1.0
CD B:PRO60C 4.2 33.1 1.0
CG B:ARG97 4.2 41.1 1.0
O B:FTR96 4.5 42.7 1.0
N B:ARG97 4.7 41.1 1.0
CB B:ARG97 4.7 41.7 1.0
CB B:PRO60C 4.7 35.2 1.0
O B:ARG97 4.8 45.7 1.0
C B:FTR96 4.8 39.8 1.0
N B:PRO60C 4.9 34.4 1.0
CG B:FTR96 5.0 37.9 1.0
C B:ARG97 5.0 44.3 1.0

Fluorine binding site 5 out of 9 in 6v64

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Fluorine binding site 5 out of 9 in the Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan


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 Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F141

b:47.4
occ:1.00
 F B:FTR141 0.0 47.4 1.0
CZ3 B:FTR141 1.4 46.5 1.0
CE3 B:FTR141 2.4 44.4 1.0
CH2 B:FTR141 2.4 46.5 1.0
O B:HOH453 2.7 43.3 1.0
CG B:GLN30 3.0 35.5 1.0
O B:VAL31 3.2 33.2 1.0
C B:VAL31 3.2 33.9 1.0
CG B:MET32 3.3 44.4 1.0
N B:MET32 3.3 36.6 1.0
CD2 B:FTR141 3.6 44.4 1.0
CZ2 B:FTR141 3.7 47.8 1.0
N B:VAL31 3.7 32.7 1.0
CA B:MET32 3.8 37.5 1.0
CA B:VAL31 3.9 33.6 1.0
C B:GLN30 3.9 33.8 1.0
CB B:GLN30 4.0 35.4 1.0
CD B:GLN30 4.1 34.3 1.0
CB B:MET32 4.1 41.6 1.0
NE2 B:GLN30 4.1 33.4 1.0
CE2 B:FTR141 4.1 46.9 1.0
O B:GLN30 4.3 34.0 1.0
CA B:GLN30 4.5 33.6 1.0
CD1 B:LEU155 4.7 36.4 1.0
SD B:MET32 4.8 50.2 1.0
CE B:MET32 4.9 48.4 1.0
CG B:FTR141 5.0 44.1 1.0

Fluorine binding site 6 out of 9 in 6v64

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Fluorine binding site 6 out of 9 in the Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan


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 Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F148

b:66.9
occ:1.00
 F B:FTR148 0.0 66.9 1.0
CZ3 B:FTR148 1.4 65.7 1.0
CH2 B:FTR148 2.3 66.8 1.0
CE3 B:FTR148 2.3 65.3 1.0
O B:HOH496 3.1 49.5 1.0
CZ2 B:FTR148 3.6 68.2 1.0
CD2 B:FTR148 3.6 65.7 1.0
CE2 B:FTR148 4.0 67.3 1.0
CG B:FTR148 4.9 66.5 1.0

Fluorine binding site 7 out of 9 in 6v64

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Fluorine binding site 7 out of 9 in the Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan


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 Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F207

b:30.5
occ:1.00
 F B:FTR207 0.0 30.5 1.0
CZ3 B:FTR207 1.3 27.3 1.0
CH2 B:FTR207 2.3 28.7 1.0
CE3 B:FTR207 2.4 27.0 1.0
O B:VAL200 3.3 26.6 1.0
CG2 B:VAL200 3.5 26.5 1.0
CD1 A:LEU14F 3.5 27.3 1.0
CB B:ARG137 3.6 28.4 1.0
CZ2 B:FTR207 3.6 29.3 1.0
CD2 B:FTR207 3.6 27.4 1.0
C B:VAL200 3.8 26.1 1.0
N B:LYS202 3.9 27.8 1.0
CA B:MET201 3.9 27.2 1.0
CE2 B:FTR207 4.1 28.5 1.0
C B:MET201 4.1 26.3 1.0
NE B:ARG137 4.1 31.5 1.0
N B:MET201 4.1 26.9 1.0
CD B:ARG137 4.2 30.3 1.0
CZ B:ARG137 4.2 32.7 1.0
N B:ARG137 4.3 27.0 1.0
NH1 B:ARG137 4.3 32.8 1.0
CB B:VAL200 4.5 26.1 1.0
CB B:LYS202 4.5 29.3 1.0
CG B:ARG137 4.5 29.3 1.0
O A:HOH201 4.6 36.5 1.0
CA B:ARG137 4.6 27.0 1.0
CA B:LYS202 4.7 29.1 1.0
CG A:LEU14F 4.7 27.6 1.0
CA B:VAL200 4.8 25.5 1.0
CD2 A:LEU14F 4.8 28.5 1.0
NH2 B:ARG137 4.8 33.2 1.0
O B:MET201 4.8 24.4 1.0
CG B:FTR207 5.0 28.1 1.0
C B:GLY136 5.0 26.9 1.0

Fluorine binding site 8 out of 9 in 6v64

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Fluorine binding site 8 out of 9 in the Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan


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 Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F215

b:35.5
occ:1.00
 F B:FTR215 0.0 35.5 1.0
CZ3 B:FTR215 1.4 33.7 1.0
CE3 B:FTR215 2.4 32.8 1.0
CH2 B:FTR215 2.4 32.4 1.0
O B:HOH407 2.6 33.4 1.0
OG1 B:THR172 3.3 35.1 1.0
OE1 B:GLU217 3.4 45.9 1.0
CD1 B:ILE174 3.5 39.7 1.0
CD2 B:FTR215 3.6 30.3 1.0
CZ2 B:FTR215 3.6 31.3 1.0
CB B:THR172 3.9 36.1 1.0
CD1 B:PHE227 3.9 31.8 1.0
CD B:GLU217 3.9 44.3 1.0
CB B:ILE174 4.0 39.1 1.0
CE1 B:PHE227 4.0 33.9 1.0
CG B:GLU217 4.0 41.1 1.0
CG2 B:THR172 4.0 35.0 1.0
CE2 B:FTR215 4.1 30.1 1.0
CG1 B:ILE174 4.2 39.8 1.0
CG2 B:ILE174 4.3 38.9 1.0
O B:HOH402 4.5 39.0 1.0
C B:GLY216 4.5 33.0 1.0
CA B:GLY216 4.5 30.7 1.0
O B:GLY216 4.7 34.0 1.0
CG B:PHE227 4.7 30.4 1.0
N B:GLU217 4.8 34.7 1.0
CZ B:PHE227 4.9 34.2 1.0
OE2 B:GLU217 4.9 47.2 1.0
O B:HOH452 4.9 32.7 1.0
CG B:FTR215 5.0 28.2 1.0

Fluorine binding site 9 out of 9 in 6v64

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Fluorine binding site 9 out of 9 in the Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Human Thrombin Bound to Ppack with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F237

b:37.6
occ:1.00
 F B:FTR237 0.0 37.6 1.0
CZ3 B:FTR237 1.4 36.3 1.0
CE3 B:FTR237 2.4 35.6 1.0
CH2 B:FTR237 2.4 38.0 1.0
CD1 B:LEU105 3.6 39.4 1.0
CG1 B:ILE103 3.6 27.4 1.0
CG2 B:ILE103 3.6 27.5 1.0
CD2 B:FTR237 3.6 37.0 1.0
CZ2 B:FTR237 3.6 39.2 1.0
CG B:LEU105 3.8 37.3 1.0
C B:ALA104 3.9 30.1 1.0
CA B:ALA104 3.9 30.2 1.0
N B:ALA104 4.0 28.9 1.0
CD1 B:ILE103 4.0 26.6 1.0
N B:LEU105 4.1 31.9 1.0
CG1 B:ILE238 4.1 33.0 1.0
C B:ILE103 4.1 28.4 1.0
CE2 B:FTR237 4.1 39.9 1.0
CB B:ILE103 4.1 27.0 1.0
O B:ALA104 4.2 29.5 1.0
O B:ILE103 4.3 29.9 1.0
CB B:LEU105 4.4 36.6 1.0
CD1 B:LEU53 4.4 30.6 1.0
O B:TYR89 4.6 34.7 1.0
CA B:ILE103 4.7 27.5 1.0
CA B:LEU105 4.8 34.2 1.0
CA B:ILE238 4.8 35.1 1.0
N B:HIS91 4.9 33.9 1.0
CG B:FTR237 5.0 38.3 1.0
CB B:ILE238 5.0 33.8 1.0

Reference:

E.A.Ruben, P.S.Gandhi, Z.Chen, S.K.Koester, G.T.Dekoster, C.Frieden, E.Di Cera. 19F uc(Nmr) Reveals the Conformational Properties of Free Thrombin and Its Zymogen Precursor Prethrombin-2. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32358061
DOI: 10.1074/JBC.RA120.013419
Page generated: Tue Jul 15 16:32:42 2025

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