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Fluorine in PDB 2wzc: The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Aluminium Tetrafluoride

Enzymatic activity of The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Aluminium Tetrafluoride

All present enzymatic activity of The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Aluminium Tetrafluoride:
2.7.2.3;

Protein crystallography data

The structure of The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Aluminium Tetrafluoride, PDB code: 2wzc was solved by M.W.Bowler, M.J.Cliff, J.P.M.Marston, N.J.Baxter, A.M.H.Hownslow, A.V.Varga, J.Szabo, M.Vas, G.M.Blackburn, J.P.Waltho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.220, 91.920, 108.140, 90.00, 90.00, 90.00
R / Rfree (%) 16.415 / 19.763

Other elements in 2wzc:

The structure of The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Aluminium Tetrafluoride also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Aluminium Tetrafluoride (pdb code 2wzc). 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 Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Aluminium Tetrafluoride, PDB code: 2wzc:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 2wzc

Go back to Fluorine Binding Sites List in 2wzc
Fluorine binding site 1 out of 4 in the The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and 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 Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1419

b:7.8
occ:1.00
 F1 A:ALF1419 0.0 7.8 1.0
AL A:ALF1419 1.8 9.2 1.0
MG A:MG1417 2.0 8.9 1.0
F3 A:ALF1419 2.5 9.6 1.0
F2 A:ALF1419 2.6 10.3 1.0
O3B A:ADP1420 2.6 8.8 1.0
O A:HOH2470 2.7 3.5 1.0
O2 A:3PG1421 2.7 9.5 1.0
O1B A:ADP1420 2.8 8.8 1.0
O1A A:ADP1420 2.8 8.3 1.0
NZ A:LYS215 2.8 6.0 1.0
O1 A:3PG1421 3.0 9.8 1.0
O A:HOH2464 3.0 7.5 1.0
PB A:ADP1420 3.1 8.3 1.0
C1 A:3PG1421 3.2 7.7 1.0
CE A:LYS215 3.5 6.6 1.0
F4 A:ALF1419 3.6 10.9 1.0
PA A:ADP1420 3.7 9.0 1.0
O3A A:ADP1420 3.8 8.5 1.0
CD A:LYS215 3.9 6.4 1.0
OD2 A:ASP374 4.0 6.6 1.0
O2A A:ADP1420 4.3 10.1 1.0
NZ A:LYS219 4.4 6.6 1.0
O2B A:ADP1420 4.5 8.8 1.0
O A:HOH2471 4.7 5.3 1.0
C2 A:3PG1421 4.7 8.9 1.0
N A:GLY373 4.7 4.7 1.0
O A:HOH2473 4.7 4.8 1.0
O A:HOH2467 4.9 11.4 1.0

Fluorine binding site 2 out of 4 in 2wzc

Go back to Fluorine Binding Sites List in 2wzc
Fluorine binding site 2 out of 4 in the The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and 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 Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1419

b:10.3
occ:1.00
 F2 A:ALF1419 0.0 10.3 1.0
AL A:ALF1419 1.8 9.2 1.0
F4 A:ALF1419 2.5 10.9 1.0
O2 A:3PG1421 2.5 9.5 1.0
F1 A:ALF1419 2.6 7.8 1.0
N A:GLY373 2.7 4.7 1.0
O3B A:ADP1420 2.7 8.8 1.0
NH2 A:ARG38 2.8 5.5 1.0
O1 A:3PG1421 2.8 9.8 1.0
C1 A:3PG1421 2.9 7.7 1.0
O A:HOH2470 3.1 3.5 1.0
O1B A:ADP1420 3.2 8.8 1.0
PB A:ADP1420 3.4 8.3 1.0
CA A:GLY372 3.5 5.3 1.0
F3 A:ALF1419 3.5 9.6 1.0
C A:GLY372 3.5 5.6 1.0
CZ A:ARG38 3.6 5.2 1.0
NH1 A:ARG38 3.7 5.5 1.0
CA A:GLY373 3.7 5.7 1.0
MG A:MG1417 3.7 8.9 1.0
O2B A:ADP1420 4.1 8.8 1.0
C2 A:3PG1421 4.2 8.9 1.0
O A:HOH2213 4.2 4.3 1.0
N A:ASP374 4.5 5.6 1.0
N A:GLY395 4.6 5.8 1.0
C A:GLY373 4.6 5.4 1.0
NE A:ARG38 4.7 5.7 1.0
CA A:GLY395 4.7 5.8 1.0
O A:GLY372 4.8 6.3 1.0
O3A A:ADP1420 4.8 8.5 1.0
N A:GLY372 4.9 6.3 1.0
NZ A:LYS215 4.9 6.0 1.0
O3 A:3PG1421 4.9 9.1 1.0
O1A A:ADP1420 5.0 8.3 1.0
O A:THR393 5.0 5.6 1.0

Fluorine binding site 3 out of 4 in 2wzc

Go back to Fluorine Binding Sites List in 2wzc
Fluorine binding site 3 out of 4 in the The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and 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 Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1419

b:9.6
occ:1.00
 F3 A:ALF1419 0.0 9.6 1.0
AL A:ALF1419 1.8 9.2 1.0
F4 A:ALF1419 2.5 10.9 1.0
F1 A:ALF1419 2.5 7.8 1.0
O2 A:3PG1421 2.6 9.5 1.0
O A:HOH2471 2.6 5.3 1.0
O3B A:ADP1420 2.7 8.8 1.0
NZ A:LYS219 2.7 6.6 1.0
CE A:LYS219 3.3 7.2 1.0
NZ A:LYS215 3.3 6.0 1.0
CD A:LYS215 3.4 6.4 1.0
F2 A:ALF1419 3.5 10.3 1.0
C1 A:3PG1421 3.8 7.7 1.0
N A:GLY396 3.9 6.0 1.0
CE A:LYS215 3.9 6.6 1.0
PB A:ADP1420 4.0 8.3 1.0
O2A A:ADP1420 4.1 10.1 1.0
O1A A:ADP1420 4.2 8.3 1.0
O3P A:3PG1421 4.3 10.1 1.0
PA A:ADP1420 4.3 9.0 1.0
O1 A:3PG1421 4.3 9.8 1.0
MG A:MG1417 4.4 8.9 1.0
CA A:GLY396 4.4 5.9 1.0
O3A A:ADP1420 4.4 8.5 1.0
O A:HOH2217 4.5 13.4 1.0
O1B A:ADP1420 4.6 8.8 1.0
O A:HOH2213 4.6 4.3 1.0
CG A:LYS215 4.7 7.0 1.0
CD A:LYS219 4.7 8.4 1.0
C2 A:3PG1421 4.9 8.9 1.0
C A:GLY395 4.9 5.4 1.0
ND2 A:ASN336 4.9 5.8 1.0
C3 A:3PG1421 4.9 8.4 1.0
OD1 A:ASN336 4.9 7.9 1.0

Fluorine binding site 4 out of 4 in 2wzc

Go back to Fluorine Binding Sites List in 2wzc
Fluorine binding site 4 out of 4 in the The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and 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 Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Aluminium Tetrafluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1419

b:10.9
occ:1.00
 F4 A:ALF1419 0.0 10.9 1.0
AL A:ALF1419 1.8 9.2 1.0
F2 A:ALF1419 2.5 10.3 1.0
F3 A:ALF1419 2.5 9.6 1.0
O2 A:3PG1421 2.6 9.5 1.0
O A:HOH2213 2.6 4.3 1.0
N A:GLY396 2.7 6.0 1.0
O3B A:ADP1420 2.7 8.8 1.0
CA A:GLY395 3.0 5.8 1.0
N A:GLY395 3.1 5.8 1.0
C A:GLY395 3.3 5.4 1.0
F1 A:ALF1419 3.6 7.8 1.0
C1 A:3PG1421 3.6 7.7 1.0
CA A:GLY396 3.8 5.9 1.0
O A:HOH2471 3.9 5.3 1.0
CA A:GLY372 4.0 5.3 1.0
NH2 A:ARG38 4.0 5.5 1.0
PB A:ADP1420 4.1 8.3 1.0
NZ A:LYS219 4.1 6.6 1.0
ND2 A:ASN336 4.1 5.8 1.0
O1 A:3PG1421 4.3 9.8 1.0
C A:GLY394 4.4 5.7 1.0
C2 A:3PG1421 4.5 8.9 1.0
O A:GLY395 4.5 6.2 1.0
N A:ALA397 4.6 5.4 1.0
N A:GLY373 4.6 4.7 1.0
O1B A:ADP1420 4.7 8.8 1.0
O2B A:ADP1420 4.7 8.8 1.0
C A:GLY396 4.8 6.1 1.0
CE A:LYS219 4.8 7.2 1.0
CG A:ASN336 4.9 6.2 1.0
C A:GLY372 4.9 5.6 1.0
OD1 A:ASN336 4.9 7.9 1.0
O A:GLY166 4.9 5.2 1.0
CA A:GLY394 5.0 5.5 1.0

Reference:

M.J.Cliff, M.W.Bowler, J.Szabo, J.P.M.Marston, A.V.Varga, A.M.H.Hownslow, N.J.Baxter, G.M.Blackburn, M.Vas, J.P.Waltho. Transition State Analogue Structures of Human Phosphoglycerate Kinase Establish the Importance of Charge Balance in Catalysis. J.Am.Chem.Soc. V. 132 6507 2010.
ISSN: ISSN 0002-7863
PubMed: 20397725
DOI: 10.1021/JA100974T
Page generated: Wed Jul 31 16:31:32 2024

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