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Chlorine 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:

Bromine (Br) 2 atoms
Calcium (Ca) 4 atoms
Sodium (Na) 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 3u8i). 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: 3u8i:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3u8i

Go back to Chlorine Binding Sites List in 3u8i
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:Cl203

b:11.6
occ:1.00
 HD22 A:ASN4 2.5 13.9 1.0
HH11 A:ARG7 2.6 22.5 1.0
HA A:ASN4 3.0 11.0 1.0
HD2 A:ARG7 3.0 18.9 1.0
HD3 A:ARG7 3.2 18.9 1.0
HE1 A:PHE68 3.2 14.0 1.0
ND2 A:ASN4 3.3 11.6 1.0
NH1 A:ARG7 3.4 18.7 1.0
CD A:ARG7 3.6 15.7 1.0
HD21 A:ASN4 3.7 13.9 1.0
CE1 A:PHE68 3.7 11.6 1.0
HB2 A:ARG7 3.8 12.1 1.0
HH12 A:ARG7 3.8 22.5 1.0
CA A:ASN4 3.9 9.2 1.0
HB3 A:ASN4 3.9 10.7 1.0
CG A:ASN4 4.2 10.6 1.0
CB A:ASN4 4.2 8.9 1.0
HZ A:PHE68 4.3 14.0 1.0
CZ A:PHE68 4.3 11.7 1.0
CZ A:ARG7 4.4 17.4 1.0
CD1 A:PHE68 4.4 10.9 1.0
HD1 A:PHE68 4.4 13.1 1.0
CB A:ARG7 4.4 10.1 1.0
NE A:ARG7 4.5 17.0 1.0
HB3 A:ARG7 4.5 12.1 1.0
CG A:ARG7 4.7 12.1 1.0
O A:ASN4 4.7 9.5 1.0
N A:ASN4 4.8 9.6 1.0
C A:ASN4 4.8 8.7 1.0
HG12 A:VAL3 4.9 18.1 1.0

Chlorine binding site 2 out of 4 in 3u8i

Go back to Chlorine Binding Sites List in 3u8i
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:Cl126

b:21.8
occ:1.00
 HZ2 A:LYS108 2.3 29.1 1.0
HZ3 A:LYS108 2.7 29.1 1.0
NZ A:LYS108 2.9 24.2 1.0
HZ1 A:LYS108 3.3 29.1 1.0
HD2 A:LYS108 3.9 24.3 1.0
HD3 A:LYS108 3.9 24.3 1.0
O A:HOH223 4.0 31.4 1.0
CE A:LYS108 4.1 22.4 1.0
CD A:LYS108 4.2 20.2 1.0
HE3 A:LYS108 4.5 26.8 1.0
HE2 A:LYS108 4.8 26.8 1.0

Chlorine binding site 3 out of 4 in 3u8i

Go back to Chlorine Binding Sites List in 3u8i
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:Cl203

b:11.6
occ:1.00
 HD22 B:ASN4 2.5 14.3 1.0
HH11 B:ARG7 2.6 23.3 1.0
HA B:ASN4 3.0 11.4 1.0
HD2 B:ARG7 3.0 18.8 1.0
HD3 B:ARG7 3.2 18.8 1.0
HE1 B:PHE68 3.2 13.5 1.0
ND2 B:ASN4 3.3 11.9 1.0
NH1 B:ARG7 3.4 19.4 1.0
CD B:ARG7 3.6 15.7 1.0
HD21 B:ASN4 3.7 14.3 1.0
CE1 B:PHE68 3.7 11.2 1.0
HB2 B:ARG7 3.8 12.2 1.0
HH12 B:ARG7 3.8 23.3 1.0
CA B:ASN4 3.9 9.5 1.0
HB3 B:ASN4 3.9 10.8 1.0
CG B:ASN4 4.2 10.4 1.0
CB B:ASN4 4.2 9.0 1.0
HZ B:PHE68 4.3 13.9 1.0
CZ B:PHE68 4.3 11.6 1.0
CZ B:ARG7 4.4 17.5 1.0
HB3 B:ARG7 4.4 12.2 1.0
CB B:ARG7 4.4 10.2 1.0
CD1 B:PHE68 4.4 10.5 1.0
NE B:ARG7 4.5 15.8 1.0
HD1 B:PHE68 4.5 12.6 1.0
CG B:ARG7 4.6 11.7 1.0
O B:ASN4 4.7 9.4 1.0
N B:ASN4 4.8 9.3 1.0
C B:ASN4 4.8 8.7 1.0
HG12 B:VAL3 4.9 19.1 1.0

Chlorine binding site 4 out of 4 in 3u8i

Go back to Chlorine Binding Sites List in 3u8i
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:Cl125

b:22.0
occ:1.00
 HZ2 B:LYS108 2.4 28.3 1.0
HZ3 B:LYS108 2.7 28.3 1.0
NZ B:LYS108 2.9 23.6 1.0
HZ1 B:LYS108 3.4 28.3 1.0
HD3 B:LYS108 3.9 25.0 1.0
HD2 B:LYS108 3.9 25.0 1.0
O B:HOH224 4.0 32.2 1.0
CE B:LYS108 4.1 22.2 1.0
CD B:LYS108 4.2 20.9 1.0
HE3 B:LYS108 4.6 26.6 1.0
HE2 B:LYS108 4.8 26.6 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: Sun Jul 21 05:54:41 2024

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