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Calcium in PDB 3u8h: 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: 3u8h 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) 24.48 / 2.30
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 74.792, 74.792, 49.926, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 22.5

Other elements in 3u8h:

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:

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Functionally Selective Inhibition of Group Iia Phospholipase A2 Reveals A Role For Vimentin in Regulating Arachidonic Acid Metabolism (pdb code 3u8h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Functionally Selective Inhibition of Group Iia Phospholipase A2 Reveals A Role For Vimentin in Regulating Arachidonic Acid Metabolism, PDB code: 3u8h:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3u8h

Go back to Calcium Binding Sites List in 3u8h
Calcium 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 Calcium with other atoms in the Ca 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:Ca126

b:39.6
occ:1.00
 O A:GLY25 2.3 32.9 1.0
O A:TYR112 2.3 36.2 1.0
OD1 A:ASN114 2.3 41.6 1.0
O A:HOH136 2.4 24.5 1.0
O A:HOH152 2.4 3.2 0.6
O A:PHE23 2.4 32.2 1.0
C A:PHE23 3.4 30.8 1.0
C A:GLY25 3.4 33.0 1.0
CG A:ASN114 3.5 42.4 1.0
C A:TYR112 3.5 35.1 1.0
O A:TYR24 4.0 30.7 1.0
C A:TYR24 4.0 30.8 1.0
CA A:PHE23 4.0 30.7 1.0
N A:GLY25 4.1 31.9 1.0
ND2 A:ASN114 4.1 43.9 1.0
CB A:TYR112 4.2 34.1 1.0
CA A:TYR112 4.2 33.7 1.0
N A:TYR24 4.3 30.2 1.0
N A:CYS26 4.3 32.9 1.0
CA A:GLY25 4.4 32.6 1.0
N A:TYR112 4.4 31.6 1.0
CA A:CYS26 4.4 35.0 1.0
N A:ASN114 4.4 37.8 1.0
O A:HOH173 4.5 33.0 1.0
CB A:PHE23 4.5 31.7 1.0
O A:HOH179 4.5 24.8 1.0
N A:SER113 4.6 35.9 1.0
C A:SER113 4.6 36.2 1.0
O A:CYS28 4.6 34.3 1.0
CA A:TYR24 4.6 30.5 1.0
CB A:ASN114 4.7 40.6 1.0
CA A:ASN114 4.7 39.4 1.0
C A:CYS26 4.7 34.5 1.0
CA A:SER113 4.8 36.2 1.0
O A:HOH133 4.8 2.0 1.0
CD2 A:TYR112 5.0 34.0 1.0

Calcium binding site 2 out of 4 in 3u8h

Go back to Calcium Binding Sites List in 3u8h
Calcium 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 Calcium with other atoms in the Ca 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:Ca127

b:33.4
occ:1.00
 O A:GLY29 2.3 32.2 1.0
O3 A:BHP125 2.3 37.9 1.0
O A:GLY31 2.3 36.2 1.0
O1 A:BHP125 2.3 32.0 1.0
O A:HIS27 2.4 34.6 1.0
OD1 A:ASP48 2.5 29.9 1.0
OD2 A:ASP48 2.6 38.2 1.0
CG A:ASP48 2.9 35.2 1.0
C13 A:BHP125 3.2 32.8 1.0
C A:GLY31 3.4 37.5 1.0
C31 A:BHP125 3.5 42.4 1.0
C A:GLY29 3.5 32.1 1.0
C A:HIS27 3.6 33.4 1.0
N A:GLY29 3.7 31.6 1.0
C14 A:BHP125 3.9 35.2 1.0
N A:GLY31 3.9 36.6 1.0
N A:BHP125 3.9 31.1 1.0
C29 A:BHP125 4.1 36.0 1.0
CA A:GLY31 4.1 37.6 1.0
CA A:GLY29 4.2 31.9 1.0
C A:CYS28 4.2 32.2 1.0
C12 A:BHP125 4.3 29.0 1.0
O4T A:BHP125 4.3 43.3 1.0
C A:VAL30 4.3 35.4 1.0
C30 A:BHP125 4.4 39.0 1.0
CA A:CYS28 4.4 32.6 1.0
CB A:ASP48 4.4 34.6 1.0
N A:CYS28 4.4 33.4 1.0
CA A:HIS27 4.4 34.0 1.0
N A:VAL30 4.5 34.0 1.0
N A:GLY32 4.5 41.3 1.0
CA A:VAL30 4.7 35.1 1.0
O A:VAL30 4.7 36.2 1.0
CA A:GLY32 4.8 42.5 1.0
O A:CYS44 4.9 37.7 1.0
CB A:HIS27 4.9 35.0 1.0

Calcium binding site 3 out of 4 in 3u8h

Go back to Calcium Binding Sites List in 3u8h
Calcium 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 Calcium with other atoms in the Ca 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:Ca126

b:37.9
occ:1.00
 O B:TYR112 2.3 37.3 1.0
OD1 B:ASN114 2.3 43.1 1.0
O B:HOH135 2.3 2.0 0.6
O B:GLY25 2.4 34.6 1.0
O B:HOH160 2.4 13.1 1.0
O B:PHE23 2.5 34.3 1.0
CG B:ASN114 3.4 45.0 1.0
C B:PHE23 3.5 32.4 1.0
C B:TYR112 3.5 35.7 1.0
C B:GLY25 3.6 33.7 1.0
ND2 B:ASN114 4.1 46.9 1.0
CA B:PHE23 4.1 33.0 1.0
C B:TYR24 4.2 31.6 1.0
N B:ASN114 4.2 39.3 1.0
O B:TYR24 4.2 30.9 1.0
N B:GLY25 4.3 32.3 1.0
CA B:TYR112 4.3 34.1 1.0
CB B:TYR112 4.3 33.3 1.0
CB B:PHE23 4.4 34.9 1.0
N B:TYR24 4.4 31.4 1.0
C B:SER113 4.4 37.8 1.0
N B:TYR112 4.5 33.2 1.0
N B:SER113 4.5 37.0 1.0
N B:CYS26 4.5 33.7 1.0
CA B:CYS26 4.5 36.4 1.0
CA B:GLY25 4.5 32.8 1.0
CA B:SER113 4.6 37.7 1.0
CB B:ASN114 4.6 42.4 1.0
O B:HOH149 4.6 2.0 1.0
CA B:ASN114 4.7 40.9 1.0
O B:CYS28 4.7 36.2 1.0
O B:HOH164 4.7 27.3 1.0
CA B:TYR24 4.8 31.5 1.0
C B:CYS26 4.9 36.7 1.0
CD2 B:TYR112 5.0 33.2 1.0

Calcium binding site 4 out of 4 in 3u8h

Go back to Calcium Binding Sites List in 3u8h
Calcium 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 Calcium with other atoms in the Ca 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:Ca127

b:36.0
occ:1.00
 O B:GLY31 2.2 41.6 1.0
O1 B:BHP125 2.3 27.8 1.0
O B:GLY29 2.3 37.5 1.0
O B:HIS27 2.3 37.5 1.0
O3 B:BHP125 2.4 37.4 1.0
OD1 B:ASP48 2.4 32.1 1.0
OD2 B:ASP48 2.6 37.6 1.0
CG B:ASP48 2.8 35.3 1.0
C13 B:BHP125 3.2 27.7 1.0
C B:GLY31 3.4 44.9 1.0
C B:GLY29 3.5 37.5 1.0
C31 B:BHP125 3.6 40.0 1.0
C B:HIS27 3.6 36.3 1.0
N B:GLY29 3.8 35.0 1.0
N B:GLY31 3.8 44.2 1.0
C14 B:BHP125 3.9 32.8 1.0
N B:BHP125 3.9 30.9 1.0
CA B:GLY31 4.0 45.6 1.0
C29 B:BHP125 4.1 33.1 1.0
C B:VAL30 4.2 42.8 1.0
C12 B:BHP125 4.2 25.3 1.0
CA B:GLY29 4.3 36.3 1.0
C B:CYS28 4.3 35.0 1.0
CB B:ASP48 4.3 34.2 1.0
O4T B:BHP125 4.4 42.9 1.0
CA B:CYS28 4.4 34.6 1.0
C30 B:BHP125 4.4 34.9 1.0
N B:CYS28 4.4 35.4 1.0
N B:GLY32 4.4 41.4 1.0
CA B:HIS27 4.5 36.8 1.0
N B:VAL30 4.5 39.4 1.0
O B:VAL30 4.6 42.7 1.0
CA B:VAL30 4.7 42.2 1.0
CA B:GLY32 4.8 41.9 1.0
O B:HOH164 4.8 27.3 1.0
CB B:HIS27 4.9 38.1 1.0
O B:CYS44 5.0 37.1 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 Jul 13 20:03:35 2024

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