Atomistry » Fluorine » PDB 6v34-6viw » 6v64
Atomistry »
  Fluorine »
    PDB 6v34-6viw »
      6v64 »

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

Go back to Fluorine Binding Sites List in 6v64
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

Go back to Fluorine Binding Sites List in 6v64
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

Go back to Fluorine Binding Sites List in 6v64
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

Go back to Fluorine Binding Sites List in 6v64
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

Go back to Fluorine Binding Sites List in 6v64
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

Go back to Fluorine Binding Sites List in 6v64
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

Go back to Fluorine Binding Sites List in 6v64
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

Go back to Fluorine Binding Sites List in 6v64
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

Go back to Fluorine Binding Sites List in 6v64
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: Fri Aug 2 02:53:09 2024

Last articles

Cl in 2XQK
Cl in 2XPV
Cl in 2XQH
Cl in 2XQI
Cl in 2XQJ
Cl in 2XQ0
Cl in 2XQG
Cl in 2XPW
Cl in 2XQF
Cl in 2XNT
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy