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Fluorine in PDB 3lvr: The Crystal Structure of ASAP3 in Complex with ARF6 in Transition State Soaked with Calcium

Protein crystallography data

The structure of The Crystal Structure of ASAP3 in Complex with ARF6 in Transition State Soaked with Calcium, PDB code: 3lvr was solved by S.A.Ismail, I.R.Vetter, B.Sot, A.Wittinghofer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.46 / 3.38
Space group P 62
Cell size a, b, c (Å), α, β, γ (°) 146.450, 146.450, 49.620, 90.00, 90.00, 120.00
R / Rfree (%) 20.7 / 28.1

Other elements in 3lvr:

The structure of The Crystal Structure of ASAP3 in Complex with ARF6 in Transition State Soaked with Calcium also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Aluminium (Al) 1 atom
Zinc (Zn) 1 atom
Calcium (Ca) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Crystal Structure of ASAP3 in Complex with ARF6 in Transition State Soaked with Calcium (pdb code 3lvr). 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 Crystal Structure of ASAP3 in Complex with ARF6 in Transition State Soaked with Calcium, PDB code: 3lvr:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3lvr

Go back to Fluorine Binding Sites List in 3lvr
Fluorine binding site 1 out of 3 in the The Crystal Structure of ASAP3 in Complex with ARF6 in Transition State Soaked with Calcium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Crystal Structure of ASAP3 in Complex with ARF6 in Transition State Soaked with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F738

b:80.5
occ:1.00
F1 E:AF3738 0.0 80.5 1.0
AL E:AF3738 1.7 80.9 1.0
O E:HOH230 2.4 78.0 1.0
NZ E:LYS26 2.5 74.1 1.0
N E:GLY66 2.6 83.7 1.0
O3B E:GDP737 2.8 80.0 1.0
F3 E:AF3738 2.9 82.2 1.0
F2 E:AF3738 3.0 79.9 1.0
CA E:GLY65 3.2 86.7 1.0
C E:GLY65 3.3 85.5 1.0
OE1 E:GLN67 3.4 84.4 1.0
MG E:MG736 3.5 90.9 1.0
CA E:GLY66 3.6 82.8 1.0
O1B E:GDP737 3.6 80.6 1.0
CA E:ASP22 3.6 80.1 1.0
CE E:LYS26 3.7 72.4 1.0
PB E:GDP737 3.7 80.2 1.0
C E:GLY66 4.1 83.6 1.0
O2B E:GDP737 4.1 80.5 1.0
N E:ALA23 4.2 80.2 1.0
O E:LEU21 4.3 77.3 1.0
N E:ASP22 4.3 79.4 1.0
CB E:ASP22 4.3 82.5 1.0
C E:ASP22 4.4 79.9 1.0
N E:GLY65 4.5 88.2 1.0
O E:VAL64 4.5 85.3 1.0
N E:GLN67 4.5 85.2 1.0
O E:GLY65 4.5 86.8 1.0
CD E:GLN67 4.5 86.5 1.0
C E:LEU21 4.6 78.1 1.0
OG1 E:THR44 4.7 87.6 1.0
NH2 E:ARG469 4.7 93.0 1.0
O E:GLY66 4.8 83.3 1.0
CD E:LYS26 4.9 72.8 1.0
C E:VAL64 4.9 87.4 1.0
O E:THR44 4.9 90.0 1.0
O E:GLY20 4.9 78.7 1.0

Fluorine binding site 2 out of 3 in 3lvr

Go back to Fluorine Binding Sites List in 3lvr
Fluorine binding site 2 out of 3 in the The Crystal Structure of ASAP3 in Complex with ARF6 in Transition State Soaked with Calcium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Crystal Structure of ASAP3 in Complex with ARF6 in Transition State Soaked with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F738

b:79.9
occ:1.00
F2 E:AF3738 0.0 79.9 1.0
AL E:AF3738 1.7 80.9 1.0
MG E:MG736 1.7 90.9 1.0
OG1 E:THR44 2.3 87.6 1.0
O E:HOH230 2.3 78.0 1.0
O3B E:GDP737 2.4 80.0 1.0
O E:HOH220 2.4 73.8 1.0
O2B E:GDP737 2.7 80.5 1.0
F3 E:AF3738 2.9 82.2 1.0
F1 E:AF3738 3.0 80.5 1.0
N E:THR44 3.0 91.3 1.0
PB E:GDP737 3.1 80.2 1.0
CB E:THR44 3.5 91.3 1.0
OG1 E:THR27 3.6 82.7 1.0
CA E:THR44 3.7 92.7 1.0
NH2 E:ARG469 3.8 93.0 1.0
NZ E:LYS26 4.0 74.1 1.0
O E:THR44 4.0 90.0 1.0
C E:PRO43 4.1 94.1 1.0
O1B E:GDP737 4.1 80.6 1.0
CA E:PRO43 4.2 93.3 1.0
CA E:GLY65 4.2 86.7 1.0
O3A E:GDP737 4.3 80.8 1.0
O2A E:GDP737 4.3 80.9 1.0
C E:THR44 4.3 92.8 1.0
CG2 E:THR44 4.4 93.8 1.0
OE1 E:GLN67 4.5 84.4 1.0
CB E:THR27 4.8 84.7 1.0
PA E:GDP737 4.8 80.6 1.0
O E:ILE42 4.9 96.9 1.0
CZ E:ARG469 5.0 91.0 1.0

Fluorine binding site 3 out of 3 in 3lvr

Go back to Fluorine Binding Sites List in 3lvr
Fluorine binding site 3 out of 3 in the The Crystal Structure of ASAP3 in Complex with ARF6 in Transition State Soaked with Calcium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Crystal Structure of ASAP3 in Complex with ARF6 in Transition State Soaked with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F738

b:82.2
occ:1.00
F3 E:AF3738 0.0 82.2 1.0
AL E:AF3738 1.7 80.9 1.0
NH2 E:ARG469 2.4 93.0 1.0
O3B E:GDP737 2.6 80.0 1.0
OE1 E:GLN67 2.6 84.4 1.0
O E:HOH230 2.7 78.0 1.0
F1 E:AF3738 2.9 80.5 1.0
F2 E:AF3738 2.9 79.9 1.0
CZ E:ARG469 3.6 91.0 1.0
CD E:GLN67 3.6 86.5 1.0
N E:ALA23 3.6 80.2 1.0
NE2 E:GLN67 3.8 88.2 1.0
CB E:ASP22 3.9 82.5 1.0
CB E:PRO43 3.9 94.0 1.0
CA E:PRO43 4.0 93.3 1.0
CA E:ASP22 4.0 80.1 1.0
NE E:ARG469 4.0 87.7 1.0
PB E:GDP737 4.1 80.2 1.0
N E:THR44 4.2 91.3 1.0
C E:ASP22 4.3 79.9 1.0
O E:HOH220 4.4 73.8 1.0
C E:PRO43 4.5 94.1 1.0
MG E:MG736 4.5 90.9 1.0
CA E:ALA23 4.5 81.0 1.0
NH1 E:ARG469 4.6 93.3 1.0
O2B E:GDP737 4.7 80.5 1.0
O1B E:GDP737 4.8 80.6 1.0
O3A E:GDP737 4.8 80.8 1.0
N E:GLY66 4.8 83.7 1.0
CG E:PRO43 4.9 96.8 1.0
CG E:GLN67 5.0 88.7 1.0
O E:THR44 5.0 90.0 1.0

Reference:

S.A.Ismail, I.R.Vetter, B.Sot, A.Wittinghofer. The Structure of An Arf-Arfgap Complex Reveals A CA2+ Regulatory Mechanism Cell(Cambridge,Mass.) V. 141 812 2010.
ISSN: ISSN 0092-8674
PubMed: 20510928
DOI: 10.1016/J.CELL.2010.03.051
Page generated: Sun Dec 13 11:50:39 2020

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