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Chlorine in PDB 3u8d: 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: 3u8d 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) 19.82 / 1.81
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 74.422, 74.422, 93.674, 90.00, 90.00, 120.00
R / Rfree (%) 12.1 / 18.9

Other elements in 3u8d:

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 Binding Sites:

The binding sites of Chlorine atom in the Functionally Selective Inhibition of Group Iia Phospholipase A2 Reveals A Role For Vimentin in Regulating Arachidonic Acid Metabolism (pdb code 3u8d). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Functionally Selective Inhibition of Group Iia Phospholipase A2 Reveals A Role For Vimentin in Regulating Arachidonic Acid Metabolism, PDB code: 3u8d:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3u8d

Go back to Chlorine Binding Sites List in 3u8d
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl204

b:21.1
occ:1.00
 HZ2 A:LYS108 2.9 28.4 1.0
HZ3 A:LYS108 3.0 28.4 1.0
HZ1 A:LYS108 3.1 28.4 1.0
O A:HOH421 3.2 25.2 1.0
NZ A:LYS108 3.2 23.6 1.0
O A:HOH332 3.5 14.3 1.0
O A:HOH434 4.4 27.8 1.0
CE A:LYS108 4.7 20.0 1.0
O A:HOH464 4.8 30.6 1.0
O A:HOH428 4.9 36.0 1.0

Chlorine binding site 2 out of 4 in 3u8d

Go back to Chlorine Binding Sites List in 3u8d
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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
A:Cl205

b:24.1
occ:1.00
 H A:ILE75 2.4 27.1 1.0
HG3 A:ARG74 2.9 34.0 1.0
HA A:ARG74 2.9 22.4 1.0
HE2 A:LYS92 3.0 21.4 1.0
O A:HOH424 3.2 20.1 1.0
N A:ILE75 3.3 22.5 1.0
HG21 A:THR96 3.5 17.2 1.0
HE3 A:LYS92 3.6 21.4 1.0
HZ3 A:LYS92 3.6 29.1 1.0
HB A:ILE75 3.6 20.4 1.0
CE A:LYS92 3.6 17.8 1.0
HG22 A:THR96 3.7 17.2 1.0
CA A:ARG74 3.8 18.7 1.0
CG A:ARG74 3.8 28.3 1.0
O A:ILE75 3.8 19.3 1.0
CG2 A:THR96 4.0 14.2 1.0
C A:ARG74 4.0 20.5 1.0
HG12 A:ILE75 4.0 17.8 1.0
NZ A:LYS92 4.1 24.2 1.0
HG2 A:ARG74 4.1 34.0 1.0
CA A:ILE75 4.2 17.4 1.0
CB A:ARG74 4.3 26.6 1.0
CB A:ILE75 4.3 17.0 1.0
HG23 A:THR96 4.4 17.2 1.0
HB2 A:ARG74 4.4 32.0 1.0
HZ2 A:LYS92 4.5 29.1 1.0
C A:ILE75 4.5 20.5 1.0
O A:SER73 4.5 19.6 1.0
HE A:ARG74 4.5 48.2 1.0
O A:HOH442 4.6 35.2 1.0
CG1 A:ILE75 4.7 14.8 1.0
HG3 A:LYS92 4.7 14.1 1.0
O A:HOH409 4.8 30.1 1.0
HZ1 A:LYS92 4.8 29.1 1.0
CD A:ARG74 4.9 27.4 1.0
NE A:ARG74 4.9 40.1 1.0
N A:ARG74 4.9 22.9 1.0
CD A:LYS92 5.0 13.5 1.0

Chlorine binding site 3 out of 4 in 3u8d

Go back to Chlorine Binding Sites List in 3u8d
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl204

b:20.1
occ:1.00
 HH11 B:ARG7 2.5 21.0 1.0
HD21 B:ASN4 2.6 22.9 1.0
HD3 B:ARG7 3.0 19.0 1.0
HE1 B:PHE68 3.1 22.2 1.0
HD2 B:ARG7 3.2 19.0 1.0
HA B:ASN4 3.2 17.1 1.0
NH1 B:ARG7 3.3 17.4 1.0
ND2 B:ASN4 3.4 19.1 1.0
CD B:ARG7 3.6 15.8 1.0
HD22 B:ASN4 3.6 22.9 1.0
CE1 B:PHE68 3.7 18.5 1.0
HH12 B:ARG7 3.7 21.0 1.0
HB2 B:ARG7 4.0 15.4 1.0
CA B:ASN4 4.2 14.2 1.0
HZ B:PHE68 4.3 24.0 1.0
CZ B:ARG7 4.3 19.9 1.0
CZ B:PHE68 4.3 20.0 1.0
CG B:ASN4 4.4 13.6 1.0
HB3 B:ASN4 4.4 19.2 1.0
HD1 B:PHE68 4.4 19.6 1.0
NE B:ARG7 4.4 16.1 1.0
CD1 B:PHE68 4.4 16.3 1.0
CB B:ASN4 4.5 16.0 1.0
CB B:ARG7 4.6 12.8 1.0
HB3 B:ARG7 4.6 15.4 1.0
CG B:ARG7 4.7 16.2 1.0
O B:ASN4 4.9 13.2 1.0
H B:PHE68 4.9 19.9 1.0
N B:ASN4 5.0 11.5 1.0

Chlorine binding site 4 out of 4 in 3u8d

Go back to Chlorine Binding Sites List in 3u8d
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl205

b:24.6
occ:0.50
 HG2 B:GLN86 2.6 32.4 1.0
O B:HOH335 3.1 25.9 1.0
HA B:GLN86 3.1 23.3 1.0
HB2 B:GLU89 3.4 18.1 1.0
HG3 B:GLU89 3.4 26.2 1.0
CG B:GLN86 3.5 26.9 1.0
HG3 B:GLN86 3.6 32.4 1.0
HB3 B:GLU89 4.0 18.1 1.0
CB B:GLU89 4.0 15.0 1.0
CA B:GLN86 4.0 19.4 1.0
HE21 B:GLN86 4.0 31.4 1.0
CG B:GLU89 4.1 21.8 1.0
CB B:GLN86 4.2 20.7 1.0
HB3 B:GLN86 4.4 24.9 1.0
HG2 B:GLU89 4.5 26.2 1.0
O B:GLN86 4.6 14.0 1.0
CD B:GLN86 4.6 27.8 1.0
NE2 B:GLN86 4.6 26.1 1.0
C B:GLN86 4.8 14.9 1.0
N B:GLN86 5.0 16.5 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: Fri Jul 11 11:08:11 2025

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