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Fluorine in PDB 2wzb: The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Magnesium Trifluoride

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

All present enzymatic activity of The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Magnesium Trifluoride:
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 Magnesium Trifluoride, PDB code: 2wzb 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 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.430, 92.180, 109.000, 90.00, 90.00, 90.00
R / Rfree (%) 16.094 / 18.63

Other elements in 2wzb:

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

Magnesium (Mg) 2 atoms
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 Magnesium Trifluoride (pdb code 2wzb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Magnesium Trifluoride, PDB code: 2wzb:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 2wzb

Go back to Fluorine Binding Sites List in 2wzb
Fluorine binding site 1 out of 3 in the The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Magnesium Trifluoride


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 Magnesium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1421

b:8.1
occ:1.00
 F1 A:MGF1421 0.0 8.1 1.0
MG A:MGF1421 1.9 7.9 1.0
MG A:MG1417 2.0 8.6 1.0
NZ A:LYS215 2.7 4.6 1.0
O A:HOH2614 2.7 3.0 1.0
O1A A:ADP1419 2.8 7.2 1.0
O1B A:ADP1419 2.8 7.3 1.0
O3B A:ADP1419 2.9 7.2 1.0
O2 A:3PG1420 3.0 7.6 1.0
O A:HOH2608 3.0 6.2 1.0
O1 A:3PG1420 3.2 9.5 1.0
F3 A:MGF1421 3.3 8.2 1.0
PB A:ADP1419 3.3 7.3 1.0
CE A:LYS215 3.3 4.0 1.0
F2 A:MGF1421 3.4 8.1 1.0
C1 A:3PG1420 3.5 7.2 1.0
CD A:LYS215 3.6 5.1 1.0
PA A:ADP1419 3.7 7.2 1.0
O3A A:ADP1419 3.9 7.1 1.0
OD2 A:ASP374 4.1 5.5 1.0
O2A A:ADP1419 4.2 8.2 1.0
NZ A:LYS219 4.4 6.6 1.0
O A:HOH2617 4.7 3.1 1.0
O2B A:ADP1419 4.7 7.7 1.0
O A:HOH2611 4.7 9.7 1.0
O A:HOH2616 4.8 4.2 1.0
CG A:LYS215 4.8 5.2 1.0
N A:GLY373 4.9 4.5 1.0
C2 A:3PG1420 4.9 7.9 1.0
O3P A:3PG1420 4.9 8.3 1.0

Fluorine binding site 2 out of 3 in 2wzb

Go back to Fluorine Binding Sites List in 2wzb
Fluorine binding site 2 out of 3 in the The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Magnesium Trifluoride


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 Magnesium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1421

b:8.1
occ:1.00
 F2 A:MGF1421 0.0 8.1 1.0
MG A:MGF1421 1.9 7.9 1.0
N A:GLY373 2.7 4.5 1.0
NH2 A:ARG38 2.8 4.2 1.0
O2 A:3PG1420 2.8 7.6 1.0
O3B A:ADP1419 3.0 7.2 1.0
CA A:GLY372 3.2 3.8 1.0
C1 A:3PG1420 3.2 7.2 1.0
O1 A:3PG1420 3.3 9.5 1.0
F3 A:MGF1421 3.3 8.2 1.0
F1 A:MGF1421 3.4 8.1 1.0
C A:GLY372 3.4 4.4 1.0
O A:HOH2303 3.5 4.2 1.0
N A:GLY395 3.5 4.5 1.0
O1B A:ADP1419 3.5 7.3 1.0
CA A:GLY395 3.7 4.5 1.0
PB A:ADP1419 3.7 7.3 1.0
CZ A:ARG38 3.7 3.9 1.0
CA A:GLY373 3.8 4.4 1.0
O A:HOH2614 3.9 3.0 1.0
NH1 A:ARG38 4.0 5.1 1.0
O2B A:ADP1419 4.2 7.7 1.0
MG A:MG1417 4.4 8.6 1.0
C2 A:3PG1420 4.4 7.9 1.0
C A:GLY394 4.4 3.7 1.0
N A:GLY372 4.5 4.5 1.0
N A:GLY396 4.6 5.0 1.0
O A:THR393 4.6 4.4 1.0
O A:GLY372 4.7 5.2 1.0
C A:GLY395 4.7 4.4 1.0
NE A:ARG38 4.8 4.4 1.0
N A:ASP374 4.8 4.1 1.0
C A:GLY373 4.9 3.9 1.0
CA A:GLY394 4.9 4.0 1.0
ND2 A:ASN336 5.0 4.0 1.0

Fluorine binding site 3 out of 3 in 2wzb

Go back to Fluorine Binding Sites List in 2wzb
Fluorine binding site 3 out of 3 in the The Catalytically Active Fully Closed Conformation of Human Phosphoglycerate Kinase in Complex with Adp, 3PG and Magnesium Trifluoride


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 Magnesium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1421

b:8.2
occ:1.00
 F3 A:MGF1421 0.0 8.2 1.0
MG A:MGF1421 1.9 7.9 1.0
O A:HOH2617 2.7 3.1 1.0
N A:GLY396 2.7 5.0 1.0
O2 A:3PG1420 2.7 7.6 1.0
O3B A:ADP1419 2.8 7.2 1.0
NZ A:LYS219 2.8 6.6 1.0
CE A:LYS219 3.3 6.8 1.0
F1 A:MGF1421 3.3 8.1 1.0
F2 A:MGF1421 3.3 8.1 1.0
O A:HOH2303 3.5 4.2 1.0
CA A:GLY396 3.6 5.2 1.0
C A:GLY395 3.6 4.4 1.0
CA A:GLY395 3.7 4.5 1.0
C1 A:3PG1420 4.0 7.2 1.0
PB A:ADP1419 4.3 7.3 1.0
N A:GLY395 4.3 4.5 1.0
CD A:LYS215 4.3 5.1 1.0
O A:HOH2001 4.4 10.0 1.0
NZ A:LYS215 4.4 4.6 1.0
ND2 A:ASN336 4.6 4.0 1.0
OD1 A:ASN336 4.6 7.5 1.0
O1 A:3PG1420 4.6 9.5 1.0
O2A A:ADP1419 4.7 8.2 1.0
CD A:LYS219 4.8 7.8 1.0
C A:GLY396 4.8 4.8 1.0
O1B A:ADP1419 4.8 7.3 1.0
O A:GLY395 4.8 5.5 1.0
O3P A:3PG1420 4.8 8.3 1.0
NE2 A:HIS169 4.8 2.5 1.0
N A:ALA397 4.9 4.5 1.0
CE A:LYS215 5.0 4.0 1.0
O3A A:ADP1419 5.0 7.1 1.0
CG A:ASN336 5.0 3.9 1.0
C2 A:3PG1420 5.0 7.9 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: Sun Dec 13 11:41:19 2020

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