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Fluorine in PDB 8s88: Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine

Enzymatic activity of Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine

All present enzymatic activity of Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine:
1.1.1.27;

Protein crystallography data

The structure of Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine, PDB code: 8s88 was solved by M.Van Gysel, J.Wouters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.67 / 2.07
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.53, 413.96, 85.3, 90, 109.57, 90
R / Rfree (%) 21.3 / 26.4

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine (pdb code 8s88). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 15 binding sites of Fluorine where determined in the Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine, PDB code: 8s88:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 15 in 8s88

Go back to Fluorine Binding Sites List in 8s88
Fluorine binding site 1 out of 15 in the Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine


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 L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:53.6
occ:0.63
 F15 A:SFX401 0.0 53.6 0.6
C12 A:SFX401 1.4 51.9 0.6
F13 A:SFX401 2.2 50.6 0.6
F14 A:SFX401 2.2 53.8 0.6
C9 A:SFX401 2.4 50.1 0.6
OE2 A:GLU286 2.4 42.2 1.0
CE A:MET276 3.0 39.7 1.0
C8 A:SFX401 3.1 46.3 0.6
CD A:GLU286 3.3 46.1 1.0
C10 A:SFX401 3.4 50.7 0.6
CD A:LYS278 3.5 38.8 1.0
CG A:GLU286 3.5 46.4 1.0
SD A:MET276 3.7 39.7 1.0
O A:HOH506 3.7 53.4 1.0
CH2 A:TRP148 4.3 42.9 1.0
CB A:LYS278 4.3 44.7 1.0
C7 A:SFX401 4.4 52.1 0.6
CB A:GLU286 4.4 41.4 1.0
CG A:LYS278 4.5 41.7 1.0
OE1 A:GLU286 4.5 49.7 1.0
CE A:LYS278 4.6 50.6 1.0
C11 A:SFX401 4.6 49.3 0.6
NZ A:LYS278 4.8 51.8 1.0
CG A:MET276 4.8 47.4 1.0
C6 A:SFX401 5.0 49.9 0.6
CZ3 A:TRP148 5.0 44.1 1.0

Fluorine binding site 2 out of 15 in 8s88

Go back to Fluorine Binding Sites List in 8s88
Fluorine binding site 2 out of 15 in the Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine


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 L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:50.6
occ:0.63
 F13 A:SFX401 0.0 50.6 0.6
C12 A:SFX401 1.4 51.9 0.6
F14 A:SFX401 2.2 53.8 0.6
F15 A:SFX401 2.2 53.6 0.6
O A:HOH506 2.3 53.4 1.0
C9 A:SFX401 2.4 50.1 0.6
C10 A:SFX401 2.8 50.7 0.6
OE2 A:GLU286 3.3 42.2 1.0
C8 A:SFX401 3.7 46.3 0.6
NZ A:LYS278 4.2 51.8 1.0
C11 A:SFX401 4.2 49.3 0.6
CD A:LYS278 4.2 38.8 1.0
CD A:GLU286 4.3 46.1 1.0
CE A:LYS278 4.6 50.6 1.0
C7 A:SFX401 4.8 52.1 0.6
CG A:GLU286 4.8 46.4 1.0

Fluorine binding site 3 out of 15 in 8s88

Go back to Fluorine Binding Sites List in 8s88
Fluorine binding site 3 out of 15 in the Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine


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 L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:53.8
occ:0.63
 F14 A:SFX401 0.0 53.8 0.6
C12 A:SFX401 1.4 51.9 0.6
F13 A:SFX401 2.2 50.6 0.6
F15 A:SFX401 2.2 53.6 0.6
C9 A:SFX401 2.4 50.1 0.6
O A:HOH506 2.7 53.4 1.0
C8 A:SFX401 2.8 46.3 0.6
C10 A:SFX401 3.5 50.7 0.6
CD A:LYS278 3.7 38.8 1.0
CE A:MET276 3.8 39.7 1.0
C7 A:SFX401 4.2 52.1 0.6
NZ A:LYS278 4.2 51.8 1.0
OE2 A:GLU286 4.5 42.2 1.0
CE A:LYS278 4.6 50.6 1.0
C11 A:SFX401 4.7 49.3 0.6
CB A:LYS278 4.9 44.7 1.0
CG A:LYS278 4.9 41.7 1.0
SD A:MET276 4.9 39.7 1.0
C6 A:SFX401 4.9 49.9 0.6

Fluorine binding site 4 out of 15 in 8s88

Go back to Fluorine Binding Sites List in 8s88
Fluorine binding site 4 out of 15 in the Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine


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 L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:52.7
occ:0.64
 F15 B:SFX401 0.0 52.7 0.6
C12 B:SFX401 1.4 52.0 0.6
OE2 B:GLU286 2.2 42.7 1.0
F13 B:SFX401 2.2 57.3 0.6
F14 B:SFX401 2.2 48.5 0.6
C9 B:SFX401 2.4 49.1 0.6
CD B:GLU286 2.9 41.0 1.0
CG B:GLU286 3.0 40.8 1.0
CE B:MET276 3.2 34.1 1.0
C8 B:SFX401 3.2 46.8 0.6
C10 B:SFX401 3.3 52.0 0.6
CH2 B:TRP148 3.6 43.3 1.0
SD B:MET276 3.8 39.3 1.0
OE1 B:GLU286 4.0 41.6 1.0
O B:HOH572 4.2 51.4 1.0
CD B:LYS278 4.3 38.1 1.0
CB B:GLU286 4.4 41.2 1.0
CZ3 B:TRP148 4.4 41.0 1.0
C7 B:SFX401 4.4 49.0 0.6
C11 B:SFX401 4.5 47.8 0.6
CZ2 B:TRP148 4.5 39.6 1.0
CG B:MET276 4.7 42.6 1.0
C6 B:SFX401 5.0 47.6 0.6

Fluorine binding site 5 out of 15 in 8s88

Go back to Fluorine Binding Sites List in 8s88
Fluorine binding site 5 out of 15 in the Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine


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 L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:57.3
occ:0.64
 F13 B:SFX401 0.0 57.3 0.6
C12 B:SFX401 1.4 52.0 0.6
F15 B:SFX401 2.2 52.7 0.6
F14 B:SFX401 2.2 48.5 0.6
OE2 B:GLU286 2.3 42.7 1.0
C9 B:SFX401 2.3 49.1 0.6
C10 B:SFX401 2.6 52.0 0.6
O B:HOH572 2.8 51.4 1.0
CD B:GLU286 3.5 41.0 1.0
C8 B:SFX401 3.6 46.8 0.6
C11 B:SFX401 4.0 47.8 0.6
CG B:GLU286 4.3 40.8 1.0
OE1 B:GLU286 4.4 41.6 1.0
CH2 B:TRP148 4.6 43.3 1.0
C7 B:SFX401 4.7 49.0 0.6
C6 B:SFX401 4.9 47.6 0.6

Fluorine binding site 6 out of 15 in 8s88

Go back to Fluorine Binding Sites List in 8s88
Fluorine binding site 6 out of 15 in the Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine


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 L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:48.5
occ:0.64
 F14 B:SFX401 0.0 48.5 0.6
C12 B:SFX401 1.4 52.0 0.6
F15 B:SFX401 2.2 52.7 0.6
F13 B:SFX401 2.2 57.3 0.6
C9 B:SFX401 2.4 49.1 0.6
C8 B:SFX401 2.8 46.8 0.6
C10 B:SFX401 3.6 52.0 0.6
OE2 B:GLU286 3.8 42.7 1.0
C7 B:SFX401 4.2 49.0 0.6
CE B:MET276 4.3 34.1 1.0
CD B:LYS278 4.4 38.1 1.0
CE B:LYS278 4.5 44.5 1.0
NZ B:LYS278 4.6 42.1 1.0
CD B:GLU286 4.7 41.0 1.0
C11 B:SFX401 4.7 47.8 0.6
CG B:GLU286 4.8 40.8 1.0
C6 B:SFX401 5.0 47.6 0.6

Fluorine binding site 7 out of 15 in 8s88

Go back to Fluorine Binding Sites List in 8s88
Fluorine binding site 7 out of 15 in the Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine


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 L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:62.1
occ:0.70
 F15 C:SFX401 0.0 62.1 0.7
C12 C:SFX401 1.4 60.5 0.7
F14 C:SFX401 2.2 66.0 0.7
F13 C:SFX401 2.2 60.0 0.7
C9 C:SFX401 2.4 58.0 0.7
C8 C:SFX401 2.9 52.0 0.7
C10 C:SFX401 3.6 55.0 0.7
OE1 D:GLU13 4.0 74.6 1.0
N D:GLU13 4.1 50.9 1.0
C7 C:SFX401 4.3 49.5 0.7
CB D:GLU13 4.4 62.3 1.0
O D:VAL11 4.6 39.2 1.0
CA D:ALA12 4.7 48.0 1.0
C11 C:SFX401 4.8 54.2 0.7
C D:ALA12 4.8 49.2 1.0
CA D:GLU13 4.8 57.7 1.0
CD D:GLU13 5.0 78.9 1.0

Fluorine binding site 8 out of 15 in 8s88

Go back to Fluorine Binding Sites List in 8s88
Fluorine binding site 8 out of 15 in the Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine


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 L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:60.0
occ:0.70
 F13 C:SFX401 0.0 60.0 0.7
C12 C:SFX401 1.4 60.5 0.7
F14 C:SFX401 2.2 66.0 0.7
F15 C:SFX401 2.2 62.1 0.7
C9 C:SFX401 2.4 58.0 0.7
O D:VAL11 3.2 39.2 1.0
C10 C:SFX401 3.2 55.0 0.7
C8 C:SFX401 3.2 52.0 0.7
C D:VAL11 4.1 45.3 1.0
NZ C:LYS155 4.2 52.7 1.0
CA D:ALA12 4.4 48.0 1.0
C11 C:SFX401 4.4 54.2 0.7
C7 C:SFX401 4.4 49.5 0.7
N D:GLU13 4.6 50.9 1.0
CE C:LYS155 4.7 50.7 1.0
N D:ALA12 4.7 44.1 1.0
C D:ALA12 4.7 49.2 1.0
C6 C:SFX401 5.0 50.5 0.7

Fluorine binding site 9 out of 15 in 8s88

Go back to Fluorine Binding Sites List in 8s88
Fluorine binding site 9 out of 15 in the Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine


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 L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:66.0
occ:0.70
 F14 C:SFX401 0.0 66.0 0.7
C12 C:SFX401 1.4 60.5 0.7
F15 C:SFX401 2.2 62.1 0.7
F13 C:SFX401 2.2 60.0 0.7
C9 C:SFX401 2.4 58.0 0.7
C10 C:SFX401 2.7 55.0 0.7
C8 C:SFX401 3.6 52.0 0.7
C11 C:SFX401 4.1 54.2 0.7
O C:HOH634 4.3 57.6 1.0
OE1 D:GLU13 4.7 74.6 1.0
C7 C:SFX401 4.7 49.5 0.7
C6 C:SFX401 4.9 50.5 0.7

Fluorine binding site 10 out of 15 in 8s88

Go back to Fluorine Binding Sites List in 8s88
Fluorine binding site 10 out of 15 in the Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F401

b:58.0
occ:0.68
 F15 F:SFX401 0.0 58.0 0.7
C12 F:SFX401 1.4 61.3 0.7
F14 F:SFX401 2.2 60.6 0.7
F13 F:SFX401 2.2 67.0 0.7
C9 F:SFX401 2.4 59.0 0.7
C10 F:SFX401 3.2 61.5 0.7
C8 F:SFX401 3.3 56.8 0.7
NZ F:LYS155 3.3 53.5 1.0
O I:PRO10 3.6 41.7 1.0
O F:HOH553 4.1 49.3 1.0
C11 F:SFX401 4.4 52.3 0.7
C7 F:SFX401 4.5 53.9 0.7
CE F:LYS155 4.5 41.5 1.0
O I:VAL11 4.6 50.9 1.0
C I:PRO10 4.7 45.7 1.0
CA I:VAL11 4.8 40.8 1.0
C6 F:SFX401 4.9 53.1 0.7

Reference:

M.Van Gysel, J.Wouters. Crystal Structure of Human L-Lactate Dehydrogenase B Protein in Complex with Nadh, Oxamate and Fluoxetine To Be Published.
Page generated: Wed Jul 16 07:18:25 2025

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