Atomistry » Fluorine » PDB 2y1x-2z5z » 2y3i
Atomistry »
  Fluorine »
    PDB 2y1x-2z5z »
      2y3i »

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

Go back to Fluorine Binding Sites List in 2y3i
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

Go back to Fluorine Binding Sites List in 2y3i
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

Go back to Fluorine Binding Sites List in 2y3i
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

Go back to Fluorine Binding Sites List in 2y3i
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

Go back to Fluorine Binding Sites List in 2y3i
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

Go back to Fluorine Binding Sites List in 2y3i
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

Go back to Fluorine Binding Sites List in 2y3i
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

Go back to Fluorine Binding Sites List in 2y3i
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy