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Calcium 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:

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 3u8d). 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: 3u8d:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3u8d

Go back to Calcium Binding Sites List in 3u8d
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:Ca202

b:12.2
occ:1.00
 O A:HIS27 2.3 12.1 1.0
O29 A:U8D201 2.3 17.2 1.0
O A:GLY29 2.4 14.1 1.0
O A:GLY31 2.5 17.0 1.0
OD2 A:ASP48 2.5 13.8 1.0
O22 A:U8D201 2.6 12.0 1.0
OD1 A:ASP48 2.6 14.0 1.0
CG A:ASP48 2.9 16.1 1.0
H A:GLY31 3.4 15.5 1.0
C21 A:U8D201 3.5 12.6 1.0
C A:HIS27 3.5 12.9 1.0
C A:GLY29 3.6 11.5 1.0
C A:GLY31 3.6 15.5 1.0
N23 A:U8D201 3.6 14.8 1.0
P26 A:U8D201 3.7 15.4 1.0
N A:GLY31 3.8 12.8 1.0
HA A:CYS28 3.9 14.5 1.0
N A:GLY29 4.0 13.5 1.0
H A:GLY29 4.0 16.2 1.0
O27 A:U8D201 4.1 17.5 1.0
HA A:HIS27 4.2 14.8 1.0
HA A:VAL30 4.2 17.8 1.0
C A:CYS28 4.2 11.6 1.0
HB3 A:CYS44 4.2 14.6 1.0
C30 A:U8D201 4.2 14.3 1.0
CA A:GLY31 4.3 13.9 1.0
HB3 A:HIS27 4.3 13.2 1.0
HA3 A:GLY32 4.3 19.1 1.0
CA A:CYS28 4.4 12.1 1.0
CB A:ASP48 4.4 14.1 1.0
C A:VAL30 4.4 16.4 1.0
N A:CYS28 4.4 10.3 1.0
CA A:GLY29 4.4 11.3 1.0
CA A:HIS27 4.4 12.2 1.0
N A:VAL30 4.5 14.9 1.0
O A:HOH348 4.5 16.9 1.0
C25 A:U8D201 4.6 11.3 1.0
CA A:VAL30 4.6 14.8 1.0
N A:GLY32 4.7 18.0 1.0
O A:CYS44 4.7 11.4 1.0
HA2 A:GLY31 4.7 16.7 1.0
HB3 A:ASP48 4.7 17.0 1.0
O A:HOH343 4.7 18.3 1.0
O A:CYS28 4.8 13.4 1.0
HB2 A:ASP48 4.8 17.0 1.0
CA A:GLY32 4.8 15.9 1.0
HA2 A:GLY32 4.9 19.1 1.0
C11 A:U8D201 4.9 13.6 1.0
CB A:HIS27 4.9 10.9 1.0
HA A:ASP48 4.9 16.1 1.0
HA2 A:GLY29 4.9 13.6 1.0

Calcium binding site 2 out of 4 in 3u8d

Go back to Calcium Binding Sites List in 3u8d
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:Ca203

b:18.0
occ:1.00
 O A:HOH307 2.3 19.3 1.0
O A:TYR112 2.4 15.2 1.0
OD1 A:ASN114 2.4 14.2 1.0
O A:HOH310 2.5 12.4 1.0
O A:GLY25 2.5 14.3 1.0
O A:PHE23 2.6 11.6 1.0
C A:PHE23 3.4 16.3 1.0
HB3 A:TYR112 3.5 15.3 1.0
C A:TYR112 3.6 15.2 1.0
C A:GLY25 3.6 13.1 1.0
CG A:ASN114 3.6 14.6 1.0
HA A:CYS26 3.7 16.0 1.0
HA A:PHE23 3.7 18.7 1.0
HB3 A:PHE23 4.0 18.2 1.0
CA A:PHE23 4.1 15.6 1.0
HD22 A:ASN114 4.1 18.4 1.0
H A:ASN114 4.1 17.8 1.0
C A:TYR24 4.1 13.9 1.0
O A:TYR24 4.1 13.3 1.0
HD2 A:TYR112 4.1 20.8 1.0
HA A:SER113 4.2 20.6 0.9
N A:TYR24 4.2 12.5 1.0
H A:TYR112 4.2 16.9 1.0
N A:ASN114 4.2 14.8 1.0
O A:HOH312 4.2 14.7 1.0
N A:GLY25 4.3 13.6 1.0
ND2 A:ASN114 4.3 15.3 1.0
CB A:TYR112 4.3 12.7 1.0
CA A:TYR112 4.3 16.4 1.0
O B:HOH324 4.3 15.8 1.0
HA A:ASN114 4.3 23.9 1.0
N A:CYS26 4.4 11.9 1.0
CA A:CYS26 4.4 13.3 1.0
N A:TYR112 4.5 14.1 1.0
CA A:GLY25 4.5 14.4 1.0
N A:SER113 4.6 14.8 1.0
H A:GLY25 4.6 16.4 1.0
CB A:PHE23 4.6 15.1 1.0
C A:SER113 4.6 17.1 1.0
CA A:TYR24 4.7 12.4 1.0
CA A:SER113 4.7 17.1 0.1
CA A:SER113 4.7 17.1 0.9
CB A:ASN114 4.7 19.1 1.0
CA A:ASN114 4.7 19.8 1.0
HA A:TYR24 4.8 15.0 1.0
O A:CYS28 4.8 13.4 1.0
C A:CYS26 4.8 15.1 1.0
H A:TYR24 4.8 15.1 1.0
O A:HOH343 4.8 18.3 1.0
HB2 A:TYR112 4.9 15.3 1.0
CD2 A:TYR112 4.9 17.2 1.0
HA2 A:GLY25 4.9 17.3 1.0
HB2 A:ASN114 5.0 23.0 1.0

Calcium binding site 3 out of 4 in 3u8d

Go back to Calcium Binding Sites List in 3u8d
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:Ca202

b:13.4
occ:1.00
 O29 B:U8D201 2.2 13.6 1.0
O B:GLY29 2.3 12.2 1.0
O B:HIS27 2.3 15.0 1.0
O B:GLY31 2.5 15.3 1.0
OD1 B:ASP48 2.5 17.4 1.0
OD2 B:ASP48 2.5 17.1 1.0
O22 B:U8D201 2.6 11.1 1.0
CG B:ASP48 2.8 17.1 1.0
C B:GLY29 3.5 11.6 1.0
H B:GLY31 3.5 17.6 1.0
C B:HIS27 3.5 13.9 1.0
C21 B:U8D201 3.6 12.4 1.0
C B:GLY31 3.6 18.7 1.0
P26 B:U8D201 3.7 17.4 1.0
N B:GLY31 3.8 14.6 1.0
N23 B:U8D201 3.8 10.0 1.0
O27 B:U8D201 4.0 16.3 1.0
HA B:VAL30 4.0 14.8 1.0
HA B:CYS28 4.0 13.9 1.0
N B:GLY29 4.1 13.5 1.0
H B:GLY29 4.1 16.3 1.0
HB3 B:CYS44 4.1 16.1 1.0
HA B:HIS27 4.2 17.7 1.0
HB3 B:HIS27 4.2 16.3 1.0
C B:CYS28 4.3 15.6 1.0
C30 B:U8D201 4.3 12.9 1.0
HA3 B:GLY32 4.3 19.1 1.0
CA B:GLY31 4.3 17.3 1.0
C B:VAL30 4.4 13.1 1.0
CB B:ASP48 4.4 15.1 1.0
N B:VAL30 4.4 12.1 1.0
C25 B:U8D201 4.4 13.4 1.0
CA B:GLY29 4.4 11.8 1.0
CA B:HIS27 4.4 14.7 1.0
CA B:VAL30 4.4 12.3 1.0
N B:CYS28 4.5 13.6 1.0
CA B:CYS28 4.5 11.5 1.0
O B:HOH420 4.6 19.8 1.0
O B:HOH351 4.6 24.2 1.0
N B:GLY32 4.6 17.8 1.0
O B:CYS44 4.7 15.0 1.0
HB3 B:ASP48 4.7 18.1 1.0
HB2 B:ASP48 4.8 18.1 1.0
HA2 B:GLY32 4.8 19.1 1.0
CA B:GLY32 4.8 15.9 1.0
O B:HOH376 4.8 21.5 1.0
O B:CYS28 4.9 11.9 1.0
O B:HOH327 4.9 14.4 1.0
CB B:HIS27 4.9 13.5 1.0
C11 B:U8D201 4.9 9.7 1.0
HA B:ASP48 4.9 18.8 1.0
HA2 B:GLY31 5.0 20.8 1.0
HA3 B:GLY31 5.0 20.8 1.0
HA2 B:GLY29 5.0 14.2 1.0

Calcium binding site 4 out of 4 in 3u8d

Go back to Calcium Binding Sites List in 3u8d
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:Ca203

b:19.1
occ:1.00
 O B:TYR112 2.3 14.4 1.0
O B:HOH343 2.4 11.6 1.0
O B:HOH310 2.4 13.5 1.0
O B:GLY25 2.5 11.7 1.0
OD1 B:ASN114 2.5 15.2 1.0
O B:PHE23 2.6 14.5 1.0
C B:PHE23 3.4 14.5 1.0
HB3 B:TYR112 3.5 19.1 1.0
C B:TYR112 3.5 15.5 1.0
C B:GLY25 3.6 15.1 1.0
CG B:ASN114 3.6 17.3 1.0
HA B:PHE23 3.7 17.3 1.0
HA B:CYS26 3.8 14.3 1.0
HB3 B:PHE23 4.0 15.4 1.0
CA B:PHE23 4.1 14.4 1.0
H B:ASN114 4.1 16.5 1.0
HD22 B:ASN114 4.1 23.2 1.0
O B:TYR24 4.2 17.6 1.0
HA B:SER113 4.2 18.7 0.8
C B:TYR24 4.2 17.0 1.0
N B:ASN114 4.2 13.7 1.0
HD2 B:TYR112 4.3 16.8 1.0
ND2 B:ASN114 4.3 19.3 1.0
CB B:TYR112 4.3 15.8 1.0
HA B:ASN114 4.3 19.8 1.0
N B:GLY25 4.3 12.3 1.0
CA B:TYR112 4.3 17.7 1.0
N B:TYR24 4.4 15.7 1.0
O B:HOH319 4.4 19.6 1.0
N B:CYS26 4.4 13.1 1.0
H B:TYR112 4.4 17.9 1.0
O A:HOH355 4.4 18.8 1.0
CA B:CYS26 4.5 11.9 1.0
N B:SER113 4.5 15.2 1.0
N B:TYR112 4.5 14.8 1.0
CA B:GLY25 4.5 16.3 1.0
C B:SER113 4.5 15.0 1.0
CB B:PHE23 4.6 12.8 1.0
O B:HOH420 4.6 19.8 1.0
CA B:SER113 4.6 15.5 0.8
CA B:SER113 4.6 15.5 0.2
H B:GLY25 4.7 14.8 1.0
CA B:ASN114 4.7 16.5 1.0
CB B:ASN114 4.7 21.6 1.0
O B:CYS28 4.7 11.9 1.0
CA B:TYR24 4.8 14.2 1.0
C B:CYS26 4.9 12.7 1.0
HB2 B:TYR112 4.9 19.1 1.0
HA B:TYR24 4.9 17.1 1.0
HA2 B:GLY25 5.0 19.6 1.0
HB2 B:ASN114 5.0 26.0 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 20:02:42 2024

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