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Bromine in PDB 3u8i: Functionally Selective Inhibition of Group Iia Phospholipase A2 Reveals A Role For Vimentin in Regulating Arachidonic Acid Metabolism

Enzymatic activity of Functionally Selective Inhibition of Group Iia Phospholipase A2 Reveals A Role For Vimentin in Regulating Arachidonic Acid Metabolism

All present enzymatic activity of Functionally Selective Inhibition of Group Iia Phospholipase A2 Reveals A Role For Vimentin in Regulating Arachidonic Acid Metabolism:
3.1.1.4;

Protein crystallography data

The structure of Functionally Selective Inhibition of Group Iia Phospholipase A2 Reveals A Role For Vimentin in Regulating Arachidonic Acid Metabolism, PDB code: 3u8i was solved by L.K.Lee, K.J.Bryant, R.Bouveret, P.-W.Lei, A.P.Duff, S.J.Harrop, E.P.Huang, R.P.Harvey, M.H.Gelb, P.P.Gray, P.M.Curmi, A.M.Cunningham, W.B.Church, K.F.Scott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.31 / 1.10
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 70.426, 70.426, 47.301, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 18.6

Other elements in 3u8i:

The structure of Functionally Selective Inhibition of Group Iia Phospholipase A2 Reveals A Role For Vimentin in Regulating Arachidonic Acid Metabolism also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Chlorine (Cl) 4 atoms
Sodium (Na) 4 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Functionally Selective Inhibition of Group Iia Phospholipase A2 Reveals A Role For Vimentin in Regulating Arachidonic Acid Metabolism (pdb code 3u8i). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Functionally Selective Inhibition of Group Iia Phospholipase A2 Reveals A Role For Vimentin in Regulating Arachidonic Acid Metabolism, PDB code: 3u8i:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 3u8i

Go back to Bromine Binding Sites List in 3u8i
Bromine binding site 1 out of 2 in the Functionally Selective Inhibition of Group Iia Phospholipase A2 Reveals A Role For Vimentin in Regulating Arachidonic Acid Metabolism


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Functionally Selective Inhibition of Group Iia Phospholipase A2 Reveals A Role For Vimentin in Regulating Arachidonic Acid Metabolism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br47

b:13.5
occ:0.43
BR A:OLD47 0.0 13.5 0.4
CZ A:OLD47 1.9 14.2 1.0
CE3 A:OLD47 2.8 15.8 1.0
HE3 A:OLD47 2.9 18.9 1.0
CE2 A:OLD47 2.9 14.2 1.0
HE2 A:OLD47 3.0 17.1 1.0
HA2 A:GLY22 3.1 12.5 1.0
HD2 A:HIS6 3.2 14.2 1.0
O A:HOH205 3.3 19.3 1.0
HE2 A:HIS6 3.4 16.4 1.0
HB2 A:TYR21 3.5 11.8 1.0
HB1 A:ALA17 3.6 15.4 1.0
HD13 A:ILE9 3.8 12.7 1.0
CD2 A:HIS6 3.8 11.8 1.0
CA A:GLY22 3.8 10.4 1.0
N A:GLY22 3.8 9.0 1.0
O A:ALA17 3.8 11.9 1.0
HD12 A:ILE9 3.8 12.7 1.0
HB3 A:TYR21 3.8 11.8 1.0
NE2 A:HIS6 3.8 13.7 1.0
HA3 A:GLY22 3.9 12.5 1.0
HD11 A:ILE9 4.0 12.7 1.0
C A:TYR21 4.0 9.5 1.0
HD11 A:LEU2 4.0 18.0 1.0
CD1 A:ILE9 4.1 10.5 1.0
CB A:TYR21 4.1 9.8 1.0
H A:GLY22 4.1 10.8 1.0
CD1 A:OLD47 4.1 15.2 1.0
HA A:ALA18 4.2 13.9 1.0
CD3 A:OLD47 4.2 13.4 1.0
O A:TYR21 4.3 11.7 1.0
HE2 A:PHE5 4.3 13.3 1.0
C A:ALA17 4.4 11.1 1.0
CB A:ALA17 4.5 12.8 1.0
HD2 A:PHE5 4.5 12.3 1.0
CA A:TYR21 4.6 9.6 1.0
HD12 A:LEU2 4.6 18.0 1.0
CE2 A:PHE5 4.7 11.1 1.0
HB3 A:ALA17 4.7 15.4 1.0
CG1 A:OLD47 4.7 13.7 1.0
CD2 A:PHE5 4.7 10.2 1.0
CD1 A:LEU2 4.8 15.0 1.0
H A:TYR21 4.8 11.0 1.0
HD1 A:OLD47 4.9 18.3 1.0
HD3 A:OLD47 5.0 16.1 1.0
HA2 A:GLY29 5.0 15.5 1.0

Bromine binding site 2 out of 2 in 3u8i

Go back to Bromine Binding Sites List in 3u8i
Bromine binding site 2 out of 2 in the Functionally Selective Inhibition of Group Iia Phospholipase A2 Reveals A Role For Vimentin in Regulating Arachidonic Acid Metabolism


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Functionally Selective Inhibition of Group Iia Phospholipase A2 Reveals A Role For Vimentin in Regulating Arachidonic Acid Metabolism within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br47

b:14.0
occ:0.46
BR B:OLD47 0.0 14.0 0.5
CZ B:OLD47 1.9 15.2 1.0
CE3 B:OLD47 2.8 16.2 1.0
HE3 B:OLD47 2.9 19.4 1.0
CE2 B:OLD47 2.9 14.6 1.0
HE2 B:OLD47 3.0 17.5 1.0
HA2 B:GLY22 3.1 12.0 1.0
HD2 B:HIS6 3.2 15.4 1.0
O B:HOH198 3.3 19.4 1.0
HE2 B:HIS6 3.4 16.1 1.0
HB2 B:TYR21 3.5 12.1 1.0
HB1 B:ALA17 3.6 15.9 1.0
HD13 B:ILE9 3.7 12.1 1.0
CA B:GLY22 3.8 10.0 1.0
CD2 B:HIS6 3.8 12.8 1.0
N B:GLY22 3.8 8.9 1.0
HD12 B:ILE9 3.8 12.1 1.0
O B:ALA17 3.8 11.4 1.0
HB3 B:TYR21 3.9 12.1 1.0
NE2 B:HIS6 3.9 13.4 1.0
HA3 B:GLY22 3.9 12.0 1.0
HD11 B:ILE9 4.0 12.1 1.0
C B:TYR21 4.0 9.5 1.0
CD1 B:ILE9 4.0 10.1 1.0
H B:GLY22 4.1 10.7 1.0
HD11 B:LEU2 4.1 17.7 1.0
CB B:TYR21 4.1 10.1 1.0
CD1 B:OLD47 4.1 15.9 1.0
HA B:ALA18 4.2 14.7 1.0
CD3 B:OLD47 4.2 14.0 1.0
O B:TYR21 4.3 12.0 1.0
HE2 B:PHE5 4.3 13.2 1.0
C B:ALA17 4.4 10.7 1.0
CB B:ALA17 4.5 13.3 1.0
HD2 B:PHE5 4.5 12.1 1.0
CA B:TYR21 4.6 9.2 1.0
CE2 B:PHE5 4.7 11.0 1.0
HD12 B:LEU2 4.7 17.7 1.0
HB3 B:ALA17 4.7 15.9 1.0
CG1 B:OLD47 4.7 14.9 1.0
CD2 B:PHE5 4.7 10.1 1.0
H B:TYR21 4.8 10.8 1.0
CD1 B:LEU2 4.8 14.7 1.0
HD1 B:OLD47 4.9 19.1 1.0
HD3 B:OLD47 5.0 16.8 1.0

Reference:

L.K.Lee, K.J.Bryant, R.Bouveret, P.W.Lei, A.P.Duff, S.J.Harrop, E.P.Huang, R.P.Harvey, M.H.Gelb, P.P.Gray, P.M.Curmi, A.M.Cunningham, W.B.Church, K.F.Scott. Selective Inhibition of Human Group Iia-Secreted Phospholipase A2 (Hgiia) Signaling Reveals Arachidonic Acid Metabolism Is Associated with Colocalization of Hgiia to Vimentin in Rheumatoid Synoviocytes. J.Biol.Chem. V. 288 15269 2013.
ISSN: ISSN 0021-9258
PubMed: 23482564
DOI: 10.1074/JBC.M112.397893
Page generated: Sat Dec 12 02:16:02 2020

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