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Fluorine in PDB 2b4r: Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Plasmodium Falciparum at 2.25 Angstrom Resolution Reveals Intriguing Extra Electron Density in the Active Site

Enzymatic activity of Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Plasmodium Falciparum at 2.25 Angstrom Resolution Reveals Intriguing Extra Electron Density in the Active Site

All present enzymatic activity of Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Plasmodium Falciparum at 2.25 Angstrom Resolution Reveals Intriguing Extra Electron Density in the Active Site:
1.2.1.12;

Protein crystallography data

The structure of Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Plasmodium Falciparum at 2.25 Angstrom Resolution Reveals Intriguing Extra Electron Density in the Active Site, PDB code: 2b4r was solved by M.A.Robien, J.Bosch, W.G.J.Hol, Structural Genomics Of Pathogenicprotozoa Consortium (Sgpp), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.37 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.327, 104.585, 90.838, 90.00, 107.35, 90.00
R / Rfree (%) 18.3 / 24.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Plasmodium Falciparum at 2.25 Angstrom Resolution Reveals Intriguing Extra Electron Density in the Active Site (pdb code 2b4r). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Plasmodium Falciparum at 2.25 Angstrom Resolution Reveals Intriguing Extra Electron Density in the Active Site, PDB code: 2b4r:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 2b4r

Go back to Fluorine Binding Sites List in 2b4r
Fluorine binding site 1 out of 3 in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Plasmodium Falciparum at 2.25 Angstrom Resolution Reveals Intriguing Extra Electron Density in the Active Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Plasmodium Falciparum at 2.25 Angstrom Resolution Reveals Intriguing Extra Electron Density in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
O:F601

b:81.6
occ:1.00
 F O:AES601 0.0 81.6 1.0
S O:AES601 1.6 79.5 1.0
O1S O:AES601 2.4 82.9 1.0
O2S O:AES601 2.4 77.7 1.0
C1 O:AES601 2.7 77.8 1.0
C6 O:AES601 3.0 76.2 1.0
O2D O:NAD801 3.2 40.1 1.0
C2 O:AES601 4.0 75.0 1.0
C5 O:AES601 4.3 76.0 1.0
O O:HOH842 4.4 48.9 1.0
C2D O:NAD801 4.4 42.6 1.0
O O:HOH837 4.6 48.1 1.0
OD1 O:ASN185 4.7 81.5 1.0
CG O:ASN185 5.0 76.8 1.0

Fluorine binding site 2 out of 3 in 2b4r

Go back to Fluorine Binding Sites List in 2b4r
Fluorine binding site 2 out of 3 in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Plasmodium Falciparum at 2.25 Angstrom Resolution Reveals Intriguing Extra Electron Density in the Active Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Plasmodium Falciparum at 2.25 Angstrom Resolution Reveals Intriguing Extra Electron Density in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
P:F602

b:73.7
occ:1.00
 F P:AES602 0.0 73.7 1.0
S P:AES602 1.6 71.8 1.0
O1S P:AES602 2.4 75.4 1.0
O2S P:AES602 2.4 68.3 1.0
C1 P:AES602 2.7 68.4 1.0
C6 P:AES602 3.0 66.0 1.0
OD1 P:ASN185 3.8 83.1 1.0
O2D P:NAD701 4.0 41.5 1.0
C2 P:AES602 4.0 65.4 1.0
CG P:ASN185 4.2 76.1 1.0
O P:HOH720 4.3 40.8 1.0
C5 P:AES602 4.4 66.7 1.0
ND2 P:ASN185 4.6 73.7 1.0
NH1 P:ARG237 4.8 81.2 1.0

Fluorine binding site 3 out of 3 in 2b4r

Go back to Fluorine Binding Sites List in 2b4r
Fluorine binding site 3 out of 3 in the Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Plasmodium Falciparum at 2.25 Angstrom Resolution Reveals Intriguing Extra Electron Density in the Active Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Plasmodium Falciparum at 2.25 Angstrom Resolution Reveals Intriguing Extra Electron Density in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
R:F603

b:77.2
occ:1.00
 F R:AES603 0.0 77.2 1.0
S R:AES603 1.6 73.9 1.0
O1S R:AES603 2.4 79.8 1.0
O2S R:AES603 2.4 74.9 1.0
C1 R:AES603 2.7 70.1 1.0
C2 R:AES603 3.0 67.9 1.0
O2D R:NAD901 3.7 46.1 1.0
C6 R:AES603 4.0 67.0 1.0
C3 R:AES603 4.4 68.5 1.0
OD1 R:ASN185 4.4 70.5 1.0
O R:HOH923 4.4 39.6 1.0
CG R:ASN185 4.6 64.1 1.0
O R:HOH942 4.6 46.6 1.0
ND2 R:ASN185 4.7 60.9 1.0
C2D R:NAD901 4.8 39.8 1.0

Reference:

M.A.Robien, J.Bosch, F.S.Buckner, W.C.Van Voorhis, E.A.Worthey, P.Myler, C.Mehlin, E.E.Boni, O.Kalyuzhniy, L.Anderson, A.Lauricella, S.Gulde, J.R.Luft, G.Detitta, J.M.Caruthers, K.O.Hodgson, M.Soltis, F.Zucker, C.L.Verlinde, E.A.Merritt, L.W.Schoenfeld, W.G.Hol. Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Plasmodium Falciparum at 2.25 A Resolution Reveals Intriguing Extra Electron Density in the Active Site Proteins V. 62 570 2006.
ISSN: ISSN 0887-3585
PubMed: 16345073
DOI: 10.1002/PROT.20801
Page generated: Wed Jul 31 13:49:12 2024

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