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Fluorine in PDB 6v5t: Crystal Structure of Human Prethrombin-2 with Tryptophans Replaced By 5-F-Tryptophan

Enzymatic activity of Crystal Structure of Human Prethrombin-2 with Tryptophans Replaced By 5-F-Tryptophan

All present enzymatic activity of Crystal Structure of Human Prethrombin-2 with Tryptophans Replaced By 5-F-Tryptophan:
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure of Human Prethrombin-2 with Tryptophans Replaced By 5-F-Tryptophan, PDB code: 6v5t 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) 38.96 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.545, 58.887, 52.455, 90.00, 98.42, 90.00
R / Rfree (%) 17.7 / 23

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Prethrombin-2 with Tryptophans Replaced By 5-F-Tryptophan (pdb code 6v5t). 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 Prethrombin-2 with Tryptophans Replaced By 5-F-Tryptophan, PDB code: 6v5t:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 6v5t

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Fluorine binding site 1 out of 9 in the Crystal Structure of Human Prethrombin-2 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 Prethrombin-2 with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F29

b:34.5
occ:1.00
 F E:FTR29 0.0 34.5 1.0
CZ3 E:FTR29 1.4 25.1 1.0
CH2 E:FTR29 2.4 23.5 1.0
CE3 E:FTR29 2.4 22.8 1.0
CG E:ARG4 3.2 27.0 1.0
C E:GLY2 3.3 24.4 1.0
CA E:GLY2 3.3 25.0 1.0
N E:LEU3 3.6 28.0 1.0
CZ2 E:FTR29 3.6 24.1 1.0
CD2 E:FTR29 3.6 23.2 1.0
N E:GLY2 3.7 27.6 1.0
O E:PRO120 3.7 24.2 1.0
O E:GLY2 3.8 21.8 1.0
N E:ARG4 3.8 26.7 1.0
C E:LEU3 3.8 25.4 1.0
CG E:PRO28 3.8 25.5 1.0
CD2 E:HIS119 3.9 28.3 1.0
O E:LEU3 4.0 28.3 1.0
CA E:ARG4 4.0 28.1 1.0
CE2 E:FTR29 4.1 23.5 1.0
CB E:ARG4 4.2 28.0 1.0
CA E:LEU3 4.3 27.2 1.0
CD E:PRO28 4.3 25.3 1.0
CD E:ARG4 4.3 25.7 1.0
C E:PRO120 4.5 25.4 1.0
CG E:HIS119 4.7 28.1 1.0
O E:HIS119 4.7 23.1 1.0
CD1 E:FTR207 4.7 25.7 1.0
CB E:FTR207 4.8 23.3 1.0
CA E:VAL121 4.8 24.8 1.0
CB E:HIS119 4.8 28.3 1.0
NE2 E:HIS119 4.9 30.5 1.0
N E:VAL121 4.9 24.6 1.0
C E:HIS119 4.9 26.2 1.0
C E:CYS1 5.0 30.5 1.0
CG E:FTR29 5.0 21.2 1.0

Fluorine binding site 2 out of 9 in 6v5t

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Fluorine binding site 2 out of 9 in the Crystal Structure of Human Prethrombin-2 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 Prethrombin-2 with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F51

b:40.4
occ:1.00
 F E:FTR51 0.0 40.4 1.0
CZ3 E:FTR51 1.3 32.2 1.0
CE3 E:FTR51 2.3 30.0 1.0
CH2 E:FTR51 2.4 33.2 1.0
CD1 E:TYR89 3.0 26.9 1.0
CE1 E:TYR89 3.2 26.3 1.0
N E:LYS107 3.4 26.8 1.0
CB E:LEU105 3.5 24.1 1.0
CD2 E:FTR51 3.6 28.9 1.0
CZ2 E:FTR51 3.6 33.1 1.0
C E:MET106 3.7 26.3 1.0
C E:LEU105 3.7 25.8 1.0
CB E:LYS107 3.7 29.9 1.0
N E:MET106 3.8 24.3 1.0
O E:LEU105 3.8 26.9 1.0
CA E:LYS107 3.9 27.0 1.0
CG1 E:VAL241 3.9 25.0 1.0
CA E:MET106 4.0 24.3 1.0
CE2 E:FTR51 4.1 29.7 1.0
CG E:TYR89 4.1 24.6 1.0
O E:MET106 4.2 25.9 1.0
CA E:LEU105 4.2 24.2 1.0
O E:LYS87 4.4 31.8 1.0
CZ E:TYR89 4.5 26.2 1.0
CG E:LEU105 4.6 22.7 1.0
CB E:TYR89 4.6 26.6 1.0
CD1 E:LEU105 4.8 23.0 1.0
CG E:LYS107 4.8 32.3 1.0
CG E:FTR51 5.0 27.5 1.0
CD2 E:LEU105 5.0 23.9 1.0

Fluorine binding site 3 out of 9 in 6v5t

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Fluorine binding site 3 out of 9 in the Crystal Structure of Human Prethrombin-2 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 Prethrombin-2 with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F60

b:66.0
occ:1.00
 F E:FTR60D 0.0 66.0 1.0
CZ3 E:FTR60D 1.4 48.2 1.0
CE3 E:FTR60D 2.4 45.0 1.0
CH2 E:FTR60D 2.4 46.2 1.0
O1 E:GOL301 3.4 57.2 1.0
CD2 E:FTR60D 3.6 35.8 1.0
CZ2 E:FTR60D 3.6 44.5 1.0
CG2 E:THR147 3.9 63.1 1.0
CE2 E:FTR60D 4.1 36.2 1.0
NZ E:LYS60F 4.6 44.8 1.0
CZ2 E:FTR148 4.6 88.6 1.0
C1 E:GOL301 4.7 61.5 1.0
CE E:LYS60F 4.9 41.2 1.0
CH2 E:FTR148 4.9 91.3 1.0
CG E:FTR60D 4.9 32.7 1.0
O2 E:GOL301 4.9 60.9 1.0
C2 E:GOL301 5.0 62.2 1.0

Fluorine binding site 4 out of 9 in 6v5t

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Fluorine binding site 4 out of 9 in the Crystal Structure of Human Prethrombin-2 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 Prethrombin-2 with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F96

b:41.9
occ:1.00
 F E:FTR96 0.0 41.9 1.0
CZ3 E:FTR96 1.3 30.5 1.0
CH2 E:FTR96 2.4 30.3 1.0
CE3 E:FTR96 2.4 29.3 1.0
CG E:PRO60C 3.4 24.2 1.0
CZ2 E:FTR96 3.6 29.9 1.0
CD2 E:FTR96 3.6 28.1 1.0
CG E:ARG97 4.0 39.6 1.0
CE2 E:FTR96 4.1 28.2 1.0
CD E:PRO60C 4.2 24.4 1.0
CA E:ARG97 4.2 40.6 1.0
CB E:PRO60C 4.5 25.5 1.0
CB E:ARG97 4.6 40.2 1.0
N E:ARG97 4.8 35.9 1.0
N E:PRO60C 4.8 24.6 1.0
O E:FTR96 4.9 39.2 1.0
O E:ARG97 4.9 53.7 1.0
C E:FTR96 5.0 33.9 1.0
CG E:FTR96 5.0 28.3 1.0

Fluorine binding site 5 out of 9 in 6v5t

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Fluorine binding site 5 out of 9 in the Crystal Structure of Human Prethrombin-2 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 Prethrombin-2 with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F141

b:37.3
occ:1.00
 F E:FTR141 0.0 37.3 1.0
CZ3 E:FTR141 1.4 33.0 1.0
CH2 E:FTR141 2.4 31.1 1.0
CE3 E:FTR141 2.4 28.7 1.0
O E:HOH420 2.7 28.0 1.0
CG E:GLN30 3.1 25.1 1.0
O E:VAL31 3.2 23.5 1.0
CG E:MET32 3.4 28.8 1.0
C E:VAL31 3.4 27.1 1.0
CZ2 E:FTR141 3.6 29.2 1.0
N E:MET32 3.6 26.8 1.0
CD2 E:FTR141 3.6 28.7 1.0
OD2 E:ASP194 3.8 31.1 1.0
NE2 E:GLN30 3.9 26.4 1.0
N E:VAL31 4.0 27.5 1.0
CA E:MET32 4.0 26.8 1.0
CD E:GLN30 4.1 28.3 1.0
CE2 E:FTR141 4.1 31.1 1.0
CB E:GLN30 4.2 24.7 1.0
O E:HOH462 4.2 28.5 1.0
CA E:VAL31 4.2 25.6 1.0
CB E:MET32 4.2 26.4 1.0
C E:GLN30 4.3 27.4 1.0
CE E:MET32 4.5 30.4 1.0
O E:GLN30 4.7 28.1 1.0
CA E:GLN30 4.8 25.2 1.0
SD E:MET32 4.8 31.0 1.0
CD1 E:LEU155 4.9 29.2 1.0
CG E:FTR141 5.0 28.5 1.0

Fluorine binding site 6 out of 9 in 6v5t

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Fluorine binding site 6 out of 9 in the Crystal Structure of Human Prethrombin-2 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 Prethrombin-2 with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F148

b:89.1
occ:1.00
 F E:FTR148 0.0 89.1 1.0
CZ3 E:FTR148 1.4 89.0 1.0
CE3 E:FTR148 2.4 86.8 1.0
CH2 E:FTR148 2.4 91.3 1.0
CD2 E:FTR148 3.6 85.8 1.0
CZ2 E:FTR148 3.6 88.6 1.0
O E:HOH482 3.8 51.7 1.0
CZ2 E:FTR60D 3.8 44.5 1.0
CG E:GLU217 4.0 77.4 1.0
OE2 E:GLU217 4.1 79.1 1.0
CE2 E:FTR148 4.1 85.8 1.0
CH2 E:FTR60D 4.3 46.2 1.0
CD E:GLU217 4.6 79.3 1.0
CG E:FTR148 5.0 81.5 1.0
O2 E:GOL301 5.0 60.9 1.0

Fluorine binding site 7 out of 9 in 6v5t

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Fluorine binding site 7 out of 9 in the Crystal Structure of Human Prethrombin-2 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 Prethrombin-2 with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F207

b:37.7
occ:1.00
 F E:FTR207 0.0 37.7 1.0
CZ3 E:FTR207 1.3 28.1 1.0
CE3 E:FTR207 2.3 26.0 1.0
CH2 E:FTR207 2.4 27.7 1.0
CD1 E:LEU14F 3.1 40.1 1.0
CG2 E:VAL200 3.5 21.4 1.0
O E:VAL200 3.6 20.1 1.0
CB E:ARG137 3.6 23.3 1.0
CD2 E:FTR207 3.6 26.4 1.0
CZ2 E:FTR207 3.6 25.9 1.0
C E:VAL200 3.8 20.3 1.0
CA E:MET201 3.8 20.6 1.0
N E:LYS202 3.8 25.0 1.0
C E:MET201 3.8 23.9 1.0
N E:MET201 3.9 19.9 1.0
CD E:ARG137 4.0 25.9 1.0
CE2 E:FTR207 4.1 26.4 1.0
NE E:ARG137 4.1 27.3 1.0
NH1 E:ARG137 4.3 25.9 1.0
CZ E:ARG137 4.3 26.3 1.0
CB E:VAL200 4.3 19.8 1.0
CG E:ARG137 4.5 23.7 1.0
O E:MET201 4.5 23.5 1.0
N E:ARG137 4.6 23.4 1.0
CB E:LYS202 4.6 27.3 1.0
CG E:LEU14F 4.6 40.2 1.0
CA E:VAL200 4.7 21.2 1.0
CA E:LYS202 4.7 27.0 1.0
CA E:ARG137 4.7 23.6 1.0
O E:HOH425 4.7 35.5 1.0
CG E:FTR207 4.9 23.8 1.0
O E:HOH465 4.9 25.5 1.0
NH2 E:ARG137 5.0 27.8 1.0

Fluorine binding site 8 out of 9 in 6v5t

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Fluorine binding site 8 out of 9 in the Crystal Structure of Human Prethrombin-2 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 Prethrombin-2 with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F215

b:0.8
occ:1.00
 F E:FTR215 0.0 0.8 1.0
CZ3 E:FTR215 1.4 90.2 1.0
CH2 E:FTR215 2.4 90.9 1.0
CE3 E:FTR215 2.4 88.3 1.0
N E:GLY219 3.5 95.3 1.0
CZ2 E:FTR215 3.6 86.6 1.0
CD2 E:FTR215 3.6 86.5 1.0
CG1 E:ILE174 3.7 60.0 1.0
CA E:GLY219 3.8 97.5 1.0
OG1 E:THR172 4.0 60.3 1.0
CE2 E:FTR215 4.1 84.1 1.0
C E:GLU217 4.3 86.4 1.0
CB E:GLU217 4.4 79.4 1.0
CD1 E:PHE227 4.4 45.4 1.0
CE1 E:PHE227 4.5 48.6 1.0
CB E:ILE174 4.5 60.1 1.0
CA E:GLU217 4.7 79.6 1.0
N E:GLU217 4.7 78.0 1.0
CD1 E:ILE174 4.8 60.3 1.0
CB E:THR172 4.9 54.5 1.0
CG E:FTR215 5.0 83.4 1.0

Fluorine binding site 9 out of 9 in 6v5t

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Fluorine binding site 9 out of 9 in the Crystal Structure of Human Prethrombin-2 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 Prethrombin-2 with Tryptophans Replaced By 5-F-Tryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F237

b:35.0
occ:1.00
 F E:FTR237 0.0 35.0 1.0
CZ3 E:FTR237 1.4 30.4 1.0
CE3 E:FTR237 2.4 26.2 1.0
CH2 E:FTR237 2.4 27.8 1.0
CG1 E:ILE103 3.5 22.2 1.0
CG E:LEU105 3.6 22.7 1.0
CD2 E:FTR237 3.6 26.6 1.0
CZ2 E:FTR237 3.6 26.3 1.0
CD1 E:LEU105 3.7 23.0 1.0
C E:ALA104 3.7 24.6 1.0
CG2 E:ILE103 3.7 21.2 1.0
N E:ALA104 3.7 22.3 1.0
CA E:ALA104 3.8 22.9 1.0
N E:LEU105 3.8 22.9 1.0
CG1 E:ILE238 3.9 24.3 1.0
C E:ILE103 3.9 21.3 1.0
CB E:ILE103 4.1 20.3 1.0
CE2 E:FTR237 4.1 28.6 1.0
CD1 E:ILE103 4.1 21.6 1.0
O E:ALA104 4.1 22.2 1.0
O E:ILE103 4.2 23.3 1.0
CD1 E:LEU53 4.3 25.6 1.0
CB E:LEU105 4.3 24.1 1.0
CA E:ILE103 4.6 20.8 1.0
CA E:ILE238 4.6 24.1 1.0
CA E:LEU105 4.6 24.2 1.0
CD2 E:LEU105 4.7 23.9 1.0
O E:TYR89 4.8 31.7 1.0
CB E:ILE238 4.8 25.5 1.0
CD1 E:ILE238 5.0 24.3 1.0
CG E:FTR237 5.0 26.6 1.0
N E:ILE238 5.0 23.4 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 02:53:08 2024

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