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

Calcium binding site 1 out of 4 in 3u8i

Go back to Calcium Binding Sites List in 3u8i
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:Ca201

b:9.8
occ:1.00
 O A:TYR112 2.3 10.6 1.0
O A:GLY25 2.3 9.4 1.0
O A:HOH401 2.3 10.8 1.0
OD1 A:ASN114 2.4 12.1 1.0
O A:HOH403 2.4 14.9 1.0
O A:PHE23 2.4 10.0 1.0
HB3 A:TYR112 3.3 11.4 1.0
C A:PHE23 3.3 9.1 1.0
CG A:ASN114 3.4 12.6 1.0
C A:TYR112 3.5 9.8 1.0
C A:GLY25 3.5 8.6 1.0
HA A:PHE23 3.6 10.9 1.0
HA A:CYS26 3.7 12.0 1.0
HD21 A:ASN114 3.7 17.6 1.0
HB3 A:PHE23 3.9 11.4 1.0
ND2 A:ASN114 4.0 14.7 1.0
CA A:PHE23 4.0 9.1 1.0
H A:TYR112 4.0 12.9 1.0
C A:TYR24 4.1 8.7 1.0
O A:TYR24 4.1 8.9 1.0
HD2 A:TYR112 4.1 13.4 1.0
CB A:TYR112 4.2 9.5 1.0
N A:GLY25 4.2 8.8 1.0
HA A:SER113 4.2 14.6 0.7
CA A:TYR112 4.3 11.0 1.0
N A:TYR24 4.3 8.6 1.0
HA A:ASN114 4.3 14.7 1.0
HA A:SER113 4.3 15.8 0.3
N A:CYS26 4.4 9.1 1.0
CA A:CYS26 4.4 10.0 1.0
N A:ASN114 4.4 11.9 1.0
N A:TYR112 4.4 10.7 1.0
O A:HOH136 4.5 12.8 1.0
CA A:GLY25 4.5 8.9 1.0
H A:ASN114 4.5 14.3 1.0
H A:GLY25 4.5 10.5 1.0
N A:SER113 4.5 11.6 1.0
CB A:PHE23 4.5 9.5 1.0
O A:HOH145 4.5 14.4 1.0
C A:SER113 4.6 11.6 1.0
CA A:SER113 4.7 12.2 0.7
CB A:ASN114 4.7 13.2 1.0
CA A:TYR24 4.7 9.1 1.0
CA A:SER113 4.7 13.1 0.3
CA A:ASN114 4.7 12.3 1.0
C A:CYS26 4.8 9.8 1.0
HB2 A:TYR112 4.8 11.4 1.0
O A:CYS28 4.8 12.8 1.0
HA A:TYR24 4.8 10.9 1.0
HD22 A:ASN114 4.8 17.6 1.0
CD2 A:TYR112 4.9 11.2 1.0
HA2 A:GLY25 4.9 10.7 1.0
O A:VAL30 4.9 15.7 1.0
H A:TYR24 4.9 10.3 1.0
HD1 A:PHE23 5.0 15.3 1.0
O A:CYS26 5.0 12.5 1.0
SG A:CYS117 5.0 13.4 1.0

Calcium binding site 2 out of 4 in 3u8i

Go back to Calcium Binding Sites List in 3u8i
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:Ca202

b:13.2
occ:0.70
 O A:GLY29 2.3 16.2 1.0
O A:HIS27 2.3 11.2 1.0
O A:GLY31 2.4 16.8 1.0
OD2 A:ASP48 2.4 12.8 0.7
O A:HOH425 2.4 29.8 1.0
O A:HOH443 2.8 25.9 1.0
CG A:ASP48 3.2 12.2 0.7
OD1 A:ASP48 3.2 13.0 0.6
C A:HIS27 3.4 9.8 1.0
C A:GLY29 3.5 13.3 1.0
C A:GLY31 3.5 16.7 1.0
HA A:HIS27 3.6 11.5 1.0
H A:GLY31 3.8 19.3 1.0
N A:GLY31 3.9 16.1 1.0
N A:GLY29 4.0 11.7 1.0
H A:GLY29 4.0 14.0 1.0
CA A:HIS27 4.0 9.6 1.0
HB3 A:HIS27 4.1 12.2 1.0
HA A:VAL30 4.2 18.4 1.0
C A:VAL30 4.2 15.1 1.0
C A:CYS28 4.2 11.1 1.0
HA2 A:GLY32 4.2 19.6 1.0
CA A:GLY31 4.2 16.4 1.0
HA A:CYS28 4.3 12.1 1.0
CA A:GLY29 4.3 12.9 1.0
N A:CYS28 4.3 9.3 1.0
O A:HOH189 4.4 17.3 1.0
N A:VAL30 4.4 13.6 1.0
HA3 A:GLY31 4.5 19.7 1.0
CA A:VAL30 4.5 15.3 1.0
CA A:CYS28 4.5 10.1 1.0
N A:GLY32 4.5 16.4 1.0
CB A:ASP48 4.6 11.7 1.0
HA2 A:GLY29 4.6 15.5 1.0
CB A:HIS27 4.6 10.2 1.0
O2 A:OLD47 4.7 17.1 1.0
HB3 A:CYS44 4.7 11.8 1.0
O A:CYS28 4.7 12.8 1.0
CA A:GLY32 4.7 16.3 1.0
HA3 A:GLY32 4.7 19.6 1.0
O A:VAL30 4.8 15.7 1.0
O A:HOH143 4.8 37.7 1.0
O A:HOH243 4.8 31.0 1.0
HD1 A:HIS27 4.8 14.3 1.0
HB3 A:ASP48 4.8 14.1 1.0
O A:HOH184 4.8 37.6 1.0
C9 A:OLD47 4.9 16.1 1.0
HB2 A:ASP48 4.9 14.1 1.0
HHA A:OLD47 4.9 17.5 1.0

Calcium binding site 3 out of 4 in 3u8i

Go back to Calcium Binding Sites List in 3u8i
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:Ca201

b:9.8
occ:1.00
 O B:TYR112 2.3 10.8 1.0
O B:GLY25 2.3 9.6 1.0
O B:HOH402 2.3 11.1 1.0
OD1 B:ASN114 2.4 12.0 1.0
O B:HOH404 2.4 14.6 1.0
O B:PHE23 2.4 9.5 1.0
HB3 B:TYR112 3.3 12.6 1.0
C B:PHE23 3.3 8.9 1.0
CG B:ASN114 3.4 12.7 1.0
C B:TYR112 3.5 10.2 1.0
C B:GLY25 3.5 8.4 1.0
HA B:PHE23 3.7 11.0 1.0
HD21 B:ASN114 3.7 17.6 1.0
HA B:CYS26 3.7 12.4 1.0
HB3 B:PHE23 3.9 11.4 1.0
ND2 B:ASN114 4.0 14.6 1.0
CA B:PHE23 4.0 9.2 1.0
H B:TYR112 4.0 13.3 1.0
C B:TYR24 4.1 8.4 1.0
O B:TYR24 4.1 9.0 1.0
HD2 B:TYR112 4.1 13.1 1.0
CB B:TYR112 4.2 10.5 1.0
N B:GLY25 4.2 8.9 1.0
HA B:SER113 4.2 14.1 0.7
CA B:TYR112 4.2 10.8 1.0
N B:TYR24 4.3 8.7 1.0
HA B:SER113 4.3 15.4 0.3
N B:CYS26 4.3 9.3 1.0
HA B:ASN114 4.3 14.5 1.0
CA B:CYS26 4.4 10.4 1.0
N B:ASN114 4.4 11.5 1.0
CA B:GLY25 4.4 9.1 1.0
O B:HOH138 4.4 12.8 1.0
N B:TYR112 4.4 11.1 1.0
H B:ASN114 4.4 13.8 1.0
H B:GLY25 4.5 10.7 1.0
N B:SER113 4.5 11.2 1.0
CB B:PHE23 4.5 9.5 1.0
O B:HOH148 4.5 14.9 1.0
C B:SER113 4.6 12.0 1.0
CA B:SER113 4.6 11.7 0.7
CA B:SER113 4.7 12.9 0.3
CA B:TYR24 4.7 9.1 1.0
CB B:ASN114 4.7 12.9 1.0
CA B:ASN114 4.7 12.1 1.0
C B:CYS26 4.8 9.5 1.0
HB2 B:TYR112 4.8 12.6 1.0
O B:CYS28 4.8 13.2 1.0
HD22 B:ASN114 4.8 17.6 1.0
HA B:TYR24 4.8 10.9 1.0
HA2 B:GLY25 4.9 11.0 1.0
CD2 B:TYR112 4.9 10.9 1.0
O B:VAL30 4.9 15.0 1.0
H B:TYR24 5.0 10.5 1.0
O B:CYS26 5.0 12.3 1.0
SG B:CYS117 5.0 13.7 1.0
HD1 B:PHE23 5.0 14.4 1.0

Calcium binding site 4 out of 4 in 3u8i

Go back to Calcium Binding Sites List in 3u8i
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:Ca202

b:13.4
occ:0.71
 O B:GLY29 2.3 15.8 1.0
O B:HIS27 2.3 11.0 1.0
OD2 B:ASP48 2.4 15.8 1.0
O B:GLY31 2.4 16.8 1.0
O B:HOH428 2.4 32.2 1.0
O B:HOH442 2.8 25.9 1.0
CG B:ASP48 3.2 14.4 1.0
OD1 B:ASP48 3.2 17.8 1.0
C B:HIS27 3.4 10.1 1.0
C B:GLY29 3.5 13.2 1.0
C B:GLY31 3.5 17.0 1.0
HA B:HIS27 3.6 11.4 1.0
H B:GLY31 3.8 19.3 1.0
N B:GLY31 3.8 16.1 1.0
N B:GLY29 4.0 11.9 1.0
H B:GLY29 4.0 14.3 1.0
CA B:HIS27 4.0 9.5 1.0
HB3 B:HIS27 4.2 11.6 1.0
HA B:VAL30 4.2 17.1 1.0
C B:VAL30 4.2 14.5 1.0
C B:CYS28 4.2 11.0 1.0
CA B:GLY31 4.2 17.3 1.0
HA2 B:GLY32 4.2 21.2 1.0
HA B:CYS28 4.2 12.0 1.0
CA B:GLY29 4.3 12.7 1.0
N B:CYS28 4.3 9.2 1.0
O B:HOH174 4.4 17.0 1.0
N B:VAL30 4.4 13.3 1.0
HA3 B:GLY31 4.5 20.7 1.0
CA B:VAL30 4.5 14.2 1.0
CA B:CYS28 4.5 10.0 1.0
N B:GLY32 4.5 16.9 1.0
HA2 B:GLY29 4.6 15.2 1.0
CB B:ASP48 4.6 12.2 1.0
CB B:HIS27 4.7 9.6 1.0
O2 B:OLD47 4.7 17.0 1.0
HB3 B:CYS44 4.7 12.4 1.0
O B:HOH385 4.7 37.9 1.0
O B:CYS28 4.7 13.2 1.0
CA B:GLY32 4.7 17.6 1.0
HA3 B:GLY32 4.7 21.2 1.0
O B:HOH339 4.8 41.0 1.0
O B:HOH222 4.8 31.5 1.0
O B:VAL30 4.8 15.0 1.0
HD1 B:HIS27 4.8 14.4 1.0
HB3 B:ASP48 4.8 14.6 1.0
C9 B:OLD47 4.9 16.5 1.0
HB2 B:ASP48 4.9 14.6 1.0
HH B:OLD47 4.9 17.6 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: Sat Jul 13 20:05:03 2024

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