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Fluorine in PDB 2y3i: The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride

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

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:
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, PDB code: 2y3i 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 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.419, 103.877, 203.094, 90.00, 90.00, 90.00
R / Rfree (%) 26.3 / 30.3

Other elements in 2y3i:

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

Aluminium (Al) 2 atoms
Magnesium (Mg) 2 atoms
Chlorine (Cl) 2 atoms

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 (pdb code 2y3i). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 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, PDB code: 2y3i:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 2y3i

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Fluorine binding site 1 out of 8 in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1419

b:28.2
occ:1.00
 F1 A:ALF1419 0.0 28.2 1.0
AL A:ALF1419 1.8 28.5 1.0
F2 A:ALF1419 2.5 29.3 1.0
F3 A:ALF1419 2.5 30.4 1.0
O3B A:LA81418 2.5 27.1 1.0
N A:GLY373 2.7 24.7 1.0
O2 A:3PG1420 2.7 31.9 1.0
NH2 A:ARG38 2.8 33.5 1.0
O1B A:LA81418 3.2 27.7 1.0
PB A:LA81418 3.3 27.1 1.0
C1 A:3PG1420 3.3 30.7 1.0
O1 A:3PG1420 3.3 31.0 1.0
CA A:GLY372 3.5 25.4 1.0
C A:GLY372 3.5 25.1 1.0
F4 A:ALF1419 3.5 29.1 1.0
CA A:GLY373 3.6 24.9 1.0
CZ A:ARG38 3.7 33.1 1.0
O2B A:LA81418 3.8 25.9 1.0
MG A:MG1416 3.8 20.9 1.0
NH1 A:ARG38 3.9 33.5 1.0
N A:GLY395 4.2 30.5 1.0
N A:ASP374 4.5 25.1 1.0
O1A A:LA81418 4.5 27.0 1.0
C A:GLY373 4.6 24.9 1.0
C2 A:3PG1420 4.6 29.9 1.0
CA A:GLY395 4.6 30.6 1.0
O A:GLY372 4.7 25.3 1.0
O3A A:LA81418 4.7 27.0 1.0
OD1 A:ASP374 4.8 25.7 1.0
NZ A:LYS215 4.8 28.7 1.0
O A:THR393 4.9 30.1 1.0
NE A:ARG38 4.9 32.6 1.0
N A:GLY372 4.9 26.0 1.0

Fluorine binding site 2 out of 8 in 2y3i

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Fluorine binding site 2 out of 8 in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1419

b:29.3
occ:1.00
 F2 A:ALF1419 0.0 29.3 1.0
AL A:ALF1419 1.8 28.5 1.0
F4 A:ALF1419 2.4 29.1 1.0
F1 A:ALF1419 2.5 28.2 1.0
O1B A:LA81418 2.7 27.7 1.0
N A:GLY396 2.7 31.1 1.0
O2 A:3PG1420 2.8 31.9 1.0
CA A:GLY395 3.3 30.6 1.0
N A:GLY395 3.3 30.5 1.0
C A:GLY395 3.4 30.9 1.0
F3 A:ALF1419 3.6 30.4 1.0
CA A:GLY396 3.8 31.7 1.0
PB A:LA81418 3.8 27.1 1.0
O3B A:LA81418 4.0 27.1 1.0
NZ A:LYS219 4.0 27.3 1.0
C1 A:3PG1420 4.0 30.7 1.0
OD1 A:ASN336 4.2 24.5 1.0
O2B A:LA81418 4.3 25.9 1.0
CA A:GLY372 4.3 25.4 1.0
ND2 A:ASN336 4.4 23.8 1.0
NH2 A:ARG38 4.6 33.5 1.0
C A:GLY394 4.6 30.7 1.0
O A:GLY395 4.6 31.4 1.0
NZ A:LYS215 4.6 28.7 1.0
CG A:ASN336 4.7 24.2 1.0
O1 A:3PG1420 4.7 31.0 1.0
N A:GLY373 4.7 24.7 1.0
N A:ALA397 4.9 32.7 1.0
C A:GLY396 4.9 32.4 1.0

Fluorine binding site 3 out of 8 in 2y3i

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Fluorine binding site 3 out of 8 in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1419

b:30.4
occ:1.00
 F3 A:ALF1419 0.0 30.4 1.0
AL A:ALF1419 1.8 28.5 1.0
MG A:MG1416 1.8 20.9 1.0
O3B A:LA81418 2.3 27.1 1.0
O1A A:LA81418 2.5 27.0 1.0
F1 A:ALF1419 2.5 28.2 1.0
F4 A:ALF1419 2.6 29.1 1.0
NZ A:LYS215 2.7 28.7 1.0
O2 A:3PG1420 2.9 31.9 1.0
O1 A:3PG1420 3.0 31.0 1.0
O1B A:LA81418 3.1 27.7 1.0
PB A:LA81418 3.2 27.1 1.0
C1 A:3PG1420 3.3 30.7 1.0
F2 A:ALF1419 3.6 29.3 1.0
CE A:LYS215 3.6 28.9 1.0
OD1 A:ASP374 3.6 25.7 1.0
PA A:LA81418 3.9 26.6 1.0
O3A A:LA81418 4.0 27.0 1.0
O2B A:LA81418 4.5 25.9 1.0
N A:GLY373 4.5 24.7 1.0
CD A:LYS215 4.6 29.0 1.0
O2A A:LA81418 4.7 26.7 1.0
C2 A:3PG1420 4.8 29.9 1.0
O4P A:3PG1420 4.8 29.2 1.0
CG A:ASP374 4.9 25.5 1.0
NH1 A:ARG38 4.9 33.5 1.0
NH2 A:ARG38 4.9 33.5 1.0
O5' A:LA81418 4.9 28.1 1.0
CA A:GLY373 4.9 24.9 1.0
ND2 A:ASN25 4.9 35.6 1.0
N A:ASP374 5.0 25.1 1.0

Fluorine binding site 4 out of 8 in 2y3i

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Fluorine binding site 4 out of 8 in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1419

b:29.1
occ:1.00
 F4 A:ALF1419 0.0 29.1 1.0
AL A:ALF1419 1.8 28.5 1.0
F2 A:ALF1419 2.4 29.3 1.0
NZ A:LYS215 2.4 28.7 1.0
F3 A:ALF1419 2.6 30.4 1.0
O1B A:LA81418 2.8 27.7 1.0
O2 A:3PG1420 2.9 31.9 1.0
CE A:LYS215 3.3 28.9 1.0
F1 A:ALF1419 3.5 28.2 1.0
CD A:LYS215 3.6 29.0 1.0
NZ A:LYS219 3.7 27.3 1.0
O4P A:3PG1420 3.7 29.2 1.0
O1A A:LA81418 3.8 27.0 1.0
C1 A:3PG1420 3.9 30.7 1.0
PB A:LA81418 4.0 27.1 1.0
O3B A:LA81418 4.1 27.1 1.0
MG A:MG1416 4.1 20.9 1.0
CE A:LYS219 4.2 27.5 1.0
O1 A:3PG1420 4.4 31.0 1.0
N A:GLY396 4.4 31.1 1.0
CG A:LYS215 4.6 29.0 1.0
PA A:LA81418 4.6 26.6 1.0
O2A A:LA81418 4.6 26.7 1.0
O3A A:LA81418 4.7 27.0 1.0
CA A:GLY396 4.9 31.7 1.0
C2 A:3PG1420 5.0 29.9 1.0

Fluorine binding site 5 out of 8 in 2y3i

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Fluorine binding site 5 out of 8 in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1417

b:31.0
occ:1.00
 F1 D:ALF1417 0.0 31.0 1.0
AL D:ALF1417 1.8 30.6 1.0
O2 D:3PG1420 2.5 32.8 1.0
F3 D:ALF1417 2.5 32.4 1.0
F2 D:ALF1417 2.5 31.2 1.0
NH2 D:ARG38 2.8 34.3 1.0
O1B D:LA81416 2.8 27.2 1.0
N D:GLY373 2.8 31.8 1.0
O1 D:3PG1420 2.9 33.0 1.0
C1 D:3PG1420 3.0 32.5 1.0
O3B D:LA81416 3.0 26.8 1.0
PB D:LA81416 3.4 27.1 1.0
F4 D:ALF1417 3.6 30.2 1.0
CA D:GLY372 3.6 32.1 1.0
MG D:MG1418 3.7 18.2 1.0
C D:GLY372 3.7 31.8 1.0
CA D:GLY373 3.7 32.0 1.0
CZ D:ARG38 3.7 34.0 1.0
NH1 D:ARG38 3.9 33.8 1.0
O2B D:LA81416 4.0 27.3 1.0
N D:GLY395 4.1 34.0 1.0
O D:HOH2005 4.2 21.2 1.0
C2 D:3PG1420 4.4 32.2 1.0
O1A D:LA81416 4.5 29.4 1.0
CA D:GLY395 4.5 34.3 1.0
N D:ASP374 4.7 32.4 1.0
NZ D:LYS215 4.8 27.0 1.0
C D:GLY373 4.8 31.7 1.0
O D:THR393 4.8 33.8 1.0
O D:GLY372 4.9 31.4 1.0
O3A D:LA81416 4.9 27.7 1.0
NE D:ARG38 4.9 33.4 1.0
N D:GLY396 4.9 34.5 1.0
N D:GLY372 4.9 32.4 1.0
OD1 D:ASP374 4.9 36.4 1.0

Fluorine binding site 6 out of 8 in 2y3i

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Fluorine binding site 6 out of 8 in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1417

b:31.2
occ:1.00
 F2 D:ALF1417 0.0 31.2 1.0
AL D:ALF1417 1.8 30.6 1.0
O1B D:LA81416 2.4 27.2 1.0
F4 D:ALF1417 2.5 30.2 1.0
N D:GLY396 2.5 34.5 1.0
F1 D:ALF1417 2.5 31.0 1.0
O2 D:3PG1420 2.9 32.8 1.0
CA D:GLY395 3.0 34.3 1.0
O D:HOH2005 3.0 21.2 1.0
N D:GLY395 3.0 34.0 1.0
C D:GLY395 3.2 34.1 1.0
F3 D:ALF1417 3.6 32.4 1.0
CA D:GLY396 3.6 34.7 1.0
OD1 D:ASN336 3.9 33.0 1.0
PB D:LA81416 3.9 27.1 1.0
C1 D:3PG1420 4.1 32.5 1.0
CA D:GLY372 4.2 32.1 1.0
NZ D:LYS219 4.2 33.8 1.0
ND2 D:ASN336 4.3 32.2 1.0
C D:GLY394 4.3 33.4 1.0
O2B D:LA81416 4.4 27.3 1.0
O D:GLY395 4.4 33.3 1.0
O3B D:LA81416 4.4 26.8 1.0
CG D:ASN336 4.4 31.8 1.0
O1 D:3PG1420 4.6 33.0 1.0
NH2 D:ARG38 4.6 34.3 1.0
N D:ALA397 4.7 33.8 1.0
C D:GLY396 4.8 34.0 1.0
N D:GLY373 4.8 31.8 1.0
NZ D:LYS215 5.0 27.0 1.0
CA D:GLY394 5.0 33.3 1.0

Fluorine binding site 7 out of 8 in 2y3i

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Fluorine binding site 7 out of 8 in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1417

b:32.4
occ:1.00
 F3 D:ALF1417 0.0 32.4 1.0
AL D:ALF1417 1.8 30.6 1.0
MG D:MG1418 2.0 18.2 1.0
O1A D:LA81416 2.5 29.4 1.0
F1 D:ALF1417 2.5 31.0 1.0
F4 D:ALF1417 2.6 30.2 1.0
O3B D:LA81416 2.6 26.8 1.0
NZ D:LYS215 2.6 27.0 1.0
O1B D:LA81416 2.9 27.2 1.0
O1 D:3PG1420 3.0 33.0 1.0
O2 D:3PG1420 3.0 32.8 1.0
PB D:LA81416 3.2 27.1 1.0
C1 D:3PG1420 3.3 32.5 1.0
CE D:LYS215 3.5 26.5 1.0
F2 D:ALF1417 3.6 31.2 1.0
PA D:LA81416 3.9 29.2 1.0
OD1 D:ASP374 3.9 36.4 1.0
O3A D:LA81416 4.1 27.7 1.0
CD D:LYS215 4.4 26.7 1.0
O2B D:LA81416 4.6 27.3 1.0
N D:GLY373 4.6 31.8 1.0
O2A D:LA81416 4.6 29.6 1.0
C2 D:3PG1420 4.7 32.2 1.0
O4P D:3PG1420 4.8 31.0 1.0
NH2 D:ARG38 4.9 34.3 1.0
O5' D:LA81416 4.9 30.4 1.0

Fluorine binding site 8 out of 8 in 2y3i

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Fluorine binding site 8 out of 8 in the The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of The Structure of the Fully Closed Conformation of Human Pgk in Complex with L-Adp, 3PG and the Tsa Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1417

b:30.2
occ:1.00
 F4 D:ALF1417 0.0 30.2 1.0
AL D:ALF1417 1.8 30.6 1.0
O1B D:LA81416 2.5 27.2 1.0
F2 D:ALF1417 2.5 31.2 1.0
F3 D:ALF1417 2.6 32.4 1.0
NZ D:LYS215 2.9 27.0 1.0
NZ D:LYS219 3.3 33.8 1.0
O2 D:3PG1420 3.3 32.8 1.0
F1 D:ALF1417 3.6 31.0 1.0
O1A D:LA81416 3.6 29.4 1.0
CE D:LYS215 3.7 26.5 1.0
CD D:LYS215 3.7 26.7 1.0
PB D:LA81416 3.7 27.1 1.0
CE D:LYS219 3.8 33.9 1.0
O3B D:LA81416 4.1 26.8 1.0
N D:GLY396 4.2 34.5 1.0
O3A D:LA81416 4.2 27.7 1.0
PA D:LA81416 4.3 29.2 1.0
O2A D:LA81416 4.3 29.6 1.0
C1 D:3PG1420 4.3 32.5 1.0
MG D:MG1418 4.3 18.2 1.0
O4P D:3PG1420 4.4 31.0 1.0
CG D:LYS215 4.6 27.2 1.0
CA D:GLY396 4.6 34.7 1.0
ND2 D:ASN336 4.7 32.2 1.0
O1 D:3PG1420 4.7 33.0 1.0
O D:HOH2005 4.7 21.2 1.0
O2B D:LA81416 4.9 27.3 1.0
CD D:LYS219 5.0 33.6 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: Wed Jul 31 16:48:42 2024

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