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Sodium 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
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3u8i

Go back to Sodium Binding Sites List in 3u8i
Sodium 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 Sodium with other atoms in the Na 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:Na204

b:11.5
occ:1.00
 HG3 A:PRO36 2.9 15.4 1.0
HG2 A:ARG42 3.0 13.1 1.0
HG11 A:VAL45 3.1 13.3 1.0
O A:HOH294 3.1 15.7 1.0
O A:HOH413 3.1 19.3 1.0
O A:HOH168 3.2 26.1 1.0
HG21 A:VAL45 3.3 12.7 1.0
HD2 A:ARG42 3.3 14.0 1.0
HG3 A:PRO122 3.3 20.2 1.0
HG2 A:PRO122 3.4 20.2 1.0
HB3 A:PRO122 3.6 19.3 1.0
HB A:VAL45 3.6 12.8 1.0
HB3 A:ARG42 3.7 12.5 1.0
CG A:ARG42 3.7 10.9 1.0
CG A:PRO122 3.7 16.9 1.0
CG A:PRO36 3.8 12.8 1.0
HA A:ARG42 3.8 11.3 1.0
CD A:ARG42 3.9 11.6 1.0
HG2 A:PRO36 3.9 15.4 1.0
CG1 A:VAL45 3.9 11.1 1.0
HD3 A:ARG42 4.0 14.0 1.0
CB A:PRO122 4.1 16.1 1.0
CB A:VAL45 4.1 10.7 1.0
CG2 A:VAL45 4.1 10.6 1.0
CB A:ARG42 4.1 10.4 1.0
HB2 A:PRO122 4.2 19.3 1.0
HG12 A:VAL45 4.3 13.3 1.0
O A:HOH269 4.4 32.3 1.0
CA A:ARG42 4.5 9.4 1.0
HG23 A:VAL45 4.5 12.7 1.0
HG3 A:ARG42 4.6 13.1 1.0
HG13 A:VAL45 4.6 13.3 1.0
HD3 A:PRO36 4.6 14.5 1.0
CD A:PRO36 4.7 12.1 1.0
HB3 A:PRO36 4.8 13.6 1.0
HG22 A:VAL45 4.8 12.7 1.0
CB A:PRO36 4.8 11.4 1.0
HD2 A:PRO36 4.8 14.5 1.0
O A:HOH276 4.8 38.9 1.0
O A:HOH408 4.9 15.4 1.0
O A:ARG42 4.9 10.8 1.0
HB2 A:PRO36 4.9 13.6 1.0

Sodium binding site 2 out of 4 in 3u8i

Go back to Sodium Binding Sites List in 3u8i
Sodium 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 Sodium with other atoms in the Na 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:Na125

b:15.3
occ:1.00
 HG3 A:LYS67 3.0 14.8 1.0
HG A:SER65 3.1 17.5 1.0
OG A:SER65 3.1 14.6 1.0
HA A:TYR66 3.2 12.1 1.0
O A:HOH171 3.3 28.5 1.0
HE3 A:LYS67 3.4 21.9 1.0
HB2 A:SER65 3.4 14.4 1.0
HD3 A:ARG84 3.5 22.0 1.0
HH11 A:ARG84 3.5 26.9 1.0
CB A:SER65 3.7 12.0 1.0
C A:SER65 3.8 10.4 1.0
CA A:TYR66 3.8 10.0 1.0
O A:SER65 3.8 10.7 1.0
N A:TYR66 3.8 9.7 1.0
C A:TYR66 3.9 9.5 1.0
CG A:LYS67 3.9 12.3 1.0
NH1 A:ARG84 3.9 22.4 1.0
HH12 A:ARG84 4.2 26.9 1.0
HG2 A:LYS67 4.2 14.8 1.0
CE A:LYS67 4.2 18.3 1.0
O A:TYR66 4.3 10.6 1.0
N A:LYS67 4.3 10.1 1.0
H A:TYR66 4.3 11.6 1.0
CD A:ARG84 4.3 18.3 1.0
CA A:SER65 4.4 10.7 1.0
H A:LYS67 4.4 12.1 1.0
CD A:LYS67 4.5 15.2 1.0
HD2 A:LYS67 4.5 18.2 1.0
CZ A:ARG84 4.5 23.9 1.0
HD2 A:ARG84 4.5 22.0 1.0
HB3 A:SER65 4.6 14.4 1.0
HE2 A:LYS67 4.6 21.9 1.0
NE A:ARG84 4.7 24.0 1.0
OE1 A:GLN80 4.9 12.9 1.0
CB A:LYS67 4.9 11.1 1.0

Sodium binding site 3 out of 4 in 3u8i

Go back to Sodium Binding Sites List in 3u8i
Sodium 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 Sodium with other atoms in the Na 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:Na204

b:11.5
occ:1.00
 HG3 B:PRO36 3.0 15.9 1.0
HG2 B:ARG42 3.0 12.4 1.0
HG11 B:VAL45 3.1 13.4 1.0
O B:HOH290 3.1 15.3 1.0
O B:HOH211 3.1 17.1 1.0
O B:HOH218 3.1 26.4 1.0
HG21 B:VAL45 3.3 11.9 1.0
HD2 B:ARG42 3.3 14.3 1.0
HG3 B:PRO122 3.4 21.2 1.0
HG2 B:PRO122 3.4 21.2 1.0
HB3 B:PRO122 3.6 21.0 1.0
HB B:VAL45 3.7 12.6 1.0
CG B:ARG42 3.7 10.3 1.0
HB3 B:ARG42 3.8 12.6 1.0
CG B:PRO122 3.8 17.7 1.0
CG B:PRO36 3.8 13.2 1.0
HA B:ARG42 3.8 11.7 1.0
HG2 B:PRO36 3.8 15.9 1.0
CD B:ARG42 3.9 11.9 1.0
CG1 B:VAL45 3.9 11.2 1.0
HD3 B:ARG42 4.0 14.3 1.0
CB B:PRO122 4.1 17.5 1.0
O B:HOH329 4.1 25.3 1.0
CB B:VAL45 4.1 10.5 1.0
CG2 B:VAL45 4.1 9.9 1.0
CB B:ARG42 4.2 10.5 1.0
HB2 B:PRO122 4.3 21.0 1.0
HG12 B:VAL45 4.3 13.4 1.0
O B:HOH331 4.4 31.1 1.0
CA B:ARG42 4.5 9.8 1.0
HG23 B:VAL45 4.5 11.9 1.0
HG3 B:ARG42 4.6 12.4 1.0
HD3 B:PRO36 4.6 14.7 1.0
HG13 B:VAL45 4.6 13.4 1.0
CD B:PRO36 4.7 12.3 1.0
HG22 B:VAL45 4.8 11.9 1.0
HB3 B:PRO36 4.8 14.2 1.0
HD2 B:PRO36 4.8 14.7 1.0
CB B:PRO36 4.8 11.8 1.0
O B:HOH275 4.8 34.7 1.0
O B:HOH407 4.9 15.9 1.0
O B:ARG42 4.9 11.0 1.0
HB2 B:PRO36 5.0 14.2 1.0

Sodium binding site 4 out of 4 in 3u8i

Go back to Sodium Binding Sites List in 3u8i
Sodium 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 Sodium with other atoms in the Na 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:Na126

b:14.9
occ:1.00
 HG3 B:LYS67 3.0 14.5 1.0
HG B:SER65 3.1 16.7 1.0
OG B:SER65 3.1 13.9 1.0
HA B:TYR66 3.2 11.4 1.0
O B:HOH172 3.2 15.9 1.0
O B:HOH150 3.3 25.8 1.0
HE3 B:LYS67 3.4 21.4 1.0
HB2 B:SER65 3.4 14.5 1.0
HD3 B:ARG84 3.4 21.8 1.0
HH11 B:ARG84 3.6 25.2 1.0
CB B:SER65 3.7 12.1 1.0
C B:SER65 3.8 10.1 1.0
CA B:TYR66 3.8 9.5 1.0
O B:SER65 3.8 11.0 1.0
N B:TYR66 3.8 10.1 1.0
C B:TYR66 3.9 9.3 1.0
CG B:LYS67 3.9 12.1 1.0
NH1 B:ARG84 4.0 21.0 1.0
CE B:LYS67 4.2 17.9 1.0
HH12 B:ARG84 4.2 25.2 1.0
O B:TYR66 4.3 10.2 1.0
HG2 B:LYS67 4.3 14.5 1.0
H B:TYR66 4.3 12.1 1.0
N B:LYS67 4.3 9.8 1.0
CD B:ARG84 4.3 18.1 1.0
HD2 B:LYS67 4.4 18.6 1.0
CA B:SER65 4.4 10.7 1.0
H B:LYS67 4.4 11.8 1.0
CD B:LYS67 4.4 15.5 1.0
HD2 B:ARG84 4.5 21.8 1.0
CZ B:ARG84 4.5 23.8 1.0
HB3 B:SER65 4.6 14.5 1.0
HE2 B:LYS67 4.6 21.4 1.0
NE B:ARG84 4.7 24.1 1.0
OE1 B:GLN80 4.9 12.9 1.0
CB B:LYS67 5.0 10.8 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: Mon Oct 7 13:26:06 2024

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