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Fluorine in PDB 2ybe: The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution

Enzymatic activity of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution

All present enzymatic activity of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution:
2.7.2.3;

Protein crystallography data

The structure of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution, PDB code: 2ybe was solved by M.W.Bowler, L.Chaloin, C.Lionne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.202, 91.030, 108.807, 90.00, 90.00, 90.00
R / Rfree (%) 19.316 / 24.329

Other elements in 2ybe:

The structure of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Aluminium (Al) 1 atom
Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution (pdb code 2ybe). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution, PDB code: 2ybe:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 2ybe

Go back to Fluorine Binding Sites List in 2ybe
Fluorine binding site 1 out of 4 in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1420

b:22.1
occ:1.00
 F1 A:ALF1420 0.0 22.1 1.0
AL A:ALF1420 1.8 23.6 1.0
F2 A:ALF1420 2.5 24.2 1.0
O1B A:LA81419 2.5 26.4 1.0
F3 A:ALF1420 2.5 21.6 1.0
O2 A:3PG1421 2.7 22.0 1.0
N A:GLY373 2.8 28.3 1.0
NH2 A:ARG38 2.8 26.3 1.0
C1 A:3PG1421 3.0 18.9 1.0
O1 A:3PG1421 3.0 18.8 1.0
O A:HOH2115 3.1 19.5 1.0
O3B A:LA81419 3.1 27.6 1.0
PB A:LA81419 3.4 25.3 1.0
CA A:GLY372 3.5 29.1 1.0
F4 A:ALF1420 3.6 25.7 1.0
MG A:MG1417 3.6 31.6 1.0
CZ A:ARG38 3.6 25.6 1.0
C A:GLY372 3.6 28.6 1.0
NH1 A:ARG38 3.7 23.7 1.0
CA A:GLY373 3.7 31.2 1.0
O2B A:LA81419 4.1 29.6 1.0
C2 A:3PG1421 4.2 15.1 1.0
O A:HOH2047 4.3 19.2 1.0
N A:ASP374 4.5 32.1 1.0
N A:GLY395 4.6 25.9 1.0
O3A A:LA81419 4.6 27.1 1.0
NZ A:LYS215 4.6 26.0 1.0
CA A:GLY395 4.7 23.8 1.0
C A:GLY373 4.7 31.9 1.0
O1A A:LA81419 4.8 22.2 1.0
NE A:ARG38 4.8 24.4 1.0
O A:GLY372 4.8 27.9 1.0
O A:HOH2112 4.8 21.9 1.0
N A:GLY372 4.9 29.0 1.0
ND2 A:ASN336 5.0 26.2 1.0

Fluorine binding site 2 out of 4 in 2ybe

Go back to Fluorine Binding Sites List in 2ybe
Fluorine binding site 2 out of 4 in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1420

b:24.2
occ:1.00
 F2 A:ALF1420 0.0 24.2 1.0
AL A:ALF1420 1.8 23.6 1.0
F1 A:ALF1420 2.5 22.1 1.0
F4 A:ALF1420 2.5 25.7 1.0
O1B A:LA81419 2.5 26.4 1.0
N A:GLY396 2.7 26.1 1.0
O A:HOH2047 2.7 19.2 1.0
O2 A:3PG1421 2.7 22.0 1.0
CA A:GLY395 3.1 23.8 1.0
N A:GLY395 3.2 25.9 1.0
C A:GLY395 3.4 26.7 1.0
F3 A:ALF1420 3.5 21.6 1.0
C1 A:3PG1421 3.7 18.9 1.0
CA A:GLY396 3.8 27.7 1.0
O A:HOH2114 4.0 20.8 1.0
ND2 A:ASN336 4.0 26.2 1.0
NZ A:LYS219 4.0 29.8 1.0
NH2 A:ARG38 4.1 26.3 1.0
CA A:GLY372 4.1 29.1 1.0
PB A:LA81419 4.2 25.3 1.0
C A:GLY394 4.4 25.8 1.0
O1 A:3PG1421 4.5 18.8 1.0
C2 A:3PG1421 4.5 15.1 1.0
O A:GLY395 4.6 24.0 1.0
N A:ALA397 4.7 25.8 1.0
O2B A:LA81419 4.7 29.6 1.0
N A:GLY373 4.7 28.3 1.0
CE A:LYS219 4.8 31.2 1.0
O3B A:LA81419 4.8 27.6 1.0
CG A:ASN336 4.8 30.3 1.0
C A:GLY396 4.8 27.3 1.0
O3A A:LA81419 4.9 27.1 1.0
OD1 A:ASN336 4.9 33.1 1.0
O A:GLY166 5.0 20.7 1.0

Fluorine binding site 3 out of 4 in 2ybe

Go back to Fluorine Binding Sites List in 2ybe
Fluorine binding site 3 out of 4 in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1420

b:21.6
occ:1.00
 F3 A:ALF1420 0.0 21.6 1.0
AL A:ALF1420 1.8 23.6 1.0
MG A:MG1417 2.2 31.6 1.0
F4 A:ALF1420 2.5 25.7 1.0
F1 A:ALF1420 2.5 22.1 1.0
NZ A:LYS215 2.5 26.0 1.0
O2 A:3PG1421 2.6 22.0 1.0
O1B A:LA81419 2.7 26.4 1.0
O1A A:LA81419 2.7 22.2 1.0
O3B A:LA81419 2.9 27.6 1.0
O A:HOH2112 2.9 21.9 1.0
O A:HOH2115 2.9 19.5 1.0
O1 A:3PG1421 3.0 18.8 1.0
PB A:LA81419 3.1 25.3 1.0
C1 A:3PG1421 3.2 18.9 1.0
CE A:LYS215 3.4 27.3 1.0
F2 A:ALF1420 3.5 24.2 1.0
O3A A:LA81419 3.6 27.1 1.0
CD A:LYS215 3.7 29.0 1.0
PA A:LA81419 3.7 25.0 1.0
OD2 A:ASP374 4.2 30.3 1.0
NZ A:LYS219 4.4 29.8 1.0
O2A A:LA81419 4.5 29.4 1.0
O2B A:LA81419 4.6 29.6 1.0
O A:HOH2114 4.6 20.8 1.0
C2 A:3PG1421 4.7 15.1 1.0
O A:HOH2113 4.7 42.4 1.0
N A:GLY373 4.8 28.3 1.0
O A:HOH2116 4.8 28.0 1.0
O4P A:3PG1421 5.0 20.3 1.0
O1P A:3PG1421 5.0 14.5 1.0
O5' A:LA81419 5.0 28.3 1.0

Fluorine binding site 4 out of 4 in 2ybe

Go back to Fluorine Binding Sites List in 2ybe
Fluorine binding site 4 out of 4 in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride at 2.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1420

b:25.7
occ:1.00
 F4 A:ALF1420 0.0 25.7 1.0
AL A:ALF1420 1.8 23.6 1.0
F3 A:ALF1420 2.5 21.6 1.0
F2 A:ALF1420 2.5 24.2 1.0
O2 A:3PG1421 2.6 22.0 1.0
O A:HOH2114 2.7 20.8 1.0
NZ A:LYS219 2.8 29.8 1.0
O1B A:LA81419 2.8 26.4 1.0
CE A:LYS219 3.1 31.2 1.0
CD A:LYS215 3.2 29.0 1.0
NZ A:LYS215 3.2 26.0 1.0
F1 A:ALF1420 3.6 22.1 1.0
CE A:LYS215 3.8 27.3 1.0
C1 A:3PG1421 3.8 18.9 1.0
N A:GLY396 4.0 26.1 1.0
O3A A:LA81419 4.0 27.1 1.0
PB A:LA81419 4.0 25.3 1.0
O4P A:3PG1421 4.2 20.3 1.0
O1A A:LA81419 4.3 22.2 1.0
PA A:LA81419 4.5 25.0 1.0
O1 A:3PG1421 4.5 18.8 1.0
MG A:MG1417 4.5 31.6 1.0
CA A:GLY396 4.5 27.7 1.0
O A:HOH2048 4.6 27.9 1.0
O3B A:LA81419 4.6 27.6 1.0
CG A:LYS215 4.6 31.3 1.0
CD A:LYS219 4.7 34.4 1.0
O2A A:LA81419 4.7 29.4 1.0
O A:HOH2047 4.7 19.2 1.0
O A:HOH2110 4.8 41.6 1.0
ND2 A:ASN336 4.8 26.2 1.0
OD1 A:ASN336 4.9 33.1 1.0
C3 A:3PG1421 4.9 14.2 1.0
C2 A:3PG1421 4.9 15.1 1.0

Reference:

P.Lallemand, L.Chaloin, B.Roy, T.Barman, M.W.Bowler, C.Lionne. Interaction of Human 3-Phosphoglycerate Kinase with Its Two Substrates: Is Substrate Antagonism A Kinetic Advantage? J.Mol.Biol. V. 409 742 2011.
ISSN: ISSN 0022-2836
PubMed: 21549713
DOI: 10.1016/J.JMB.2011.04.048
Page generated: Mon Jul 14 14:59:35 2025

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