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Calcium in PDB 3u8b: 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: 3u8b 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) 24.45 / 2.30
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 74.683, 74.683, 89.159, 90.00, 90.00, 120.00
R / Rfree (%) 20.7 / 25.7

Other elements in 3u8b:

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) 2 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 3u8b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 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: 3u8b:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3u8b

Go back to Calcium Binding Sites List in 3u8b
Calcium binding site 1 out of 2 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:46.3
occ:1.00
 O A:HOH152 2.2 41.5 1.0
O A:TYR112 2.3 50.2 1.0
OD1 A:ASN114 2.4 52.0 1.0
O A:HOH134 2.4 48.7 1.0
O A:GLY25 2.4 54.3 1.0
O A:PHE23 2.5 53.2 1.0
CG A:ASN114 3.4 54.0 1.0
C A:PHE23 3.4 49.7 1.0
HB3 A:TYR112 3.4 64.7 1.0
C A:TYR112 3.5 47.8 1.0
C A:GLY25 3.6 52.3 1.0
HD22 A:ASN114 3.7 60.5 1.0
HA A:PHE23 3.8 62.2 1.0
HA A:CYS26 3.8 59.4 1.0
H A:TYR112 3.9 59.2 1.0
ND2 A:ASN114 4.0 50.4 1.0
HB3 A:PHE23 4.0 62.0 1.0
O A:TYR24 4.0 42.0 1.0
C A:TYR24 4.1 54.5 1.0
CA A:PHE23 4.1 51.9 1.0
H A:ASN114 4.2 57.4 1.0
CA A:TYR112 4.2 52.3 1.0
N A:GLY25 4.2 49.8 1.0
N A:ASN114 4.2 47.8 1.0
CB A:TYR112 4.2 53.9 1.0
HD2 A:TYR112 4.3 66.8 1.0
O A:HOH153 4.3 45.1 1.0
HA A:SER113 4.3 65.3 1.0
O A:HOH151 4.3 49.8 1.0
N A:TYR24 4.3 47.2 1.0
HA A:ASN114 4.3 64.7 1.0
N A:TYR112 4.3 49.3 1.0
N A:CYS26 4.4 48.9 1.0
N A:SER113 4.4 51.0 1.0
CA A:GLY25 4.4 52.2 1.0
C A:SER113 4.5 51.2 1.0
CA A:CYS26 4.5 49.5 1.0
H A:GLY25 4.5 59.7 1.0
CB A:PHE23 4.6 51.7 1.0
CB A:ASN114 4.6 56.5 1.0
CA A:SER113 4.6 54.5 1.0
CA A:ASN114 4.6 53.9 1.0
O A:CYS28 4.7 46.3 1.0
CA A:TYR24 4.7 51.8 1.0
HD21 A:ASN114 4.8 60.5 1.0
C A:CYS26 4.8 48.7 1.0
HB2 A:TYR112 4.8 64.7 1.0
HA A:TYR24 4.8 62.2 1.0
HA2 A:GLY25 4.9 62.7 1.0
H A:TYR24 5.0 56.7 1.0

Calcium binding site 2 out of 2 in 3u8b

Go back to Calcium Binding Sites List in 3u8b
Calcium binding site 2 out of 2 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:44.5
occ:0.63
 OD2 A:ASP48 2.2 59.7 1.0
O A:GLY29 2.3 48.3 1.0
O A:HIS27 2.3 49.6 1.0
O A:GLY31 2.4 52.7 1.0
OD1 A:ASP48 2.4 55.8 1.0
CG A:ASP48 2.7 56.9 1.0
C A:GLY29 3.5 47.5 1.0
C A:HIS27 3.5 47.1 1.0
C A:GLY31 3.6 51.6 1.0
H A:GLY31 3.8 58.2 1.0
N A:GLY31 3.8 48.5 1.0
N A:GLY29 4.0 42.3 1.0
C A:VAL30 4.1 54.4 1.0
HA A:HIS27 4.1 60.2 1.0
H A:GLY29 4.1 50.8 1.0
HA A:VAL30 4.1 65.5 1.0
HA A:CYS28 4.2 53.4 1.0
CA A:GLY31 4.2 50.8 1.0
CB A:ASP48 4.2 53.2 1.0
HA3 A:GLY32 4.2 67.1 1.0
HB3 A:HIS27 4.2 57.8 1.0
C A:CYS28 4.2 45.4 1.0
CA A:GLY29 4.3 45.0 1.0
CA A:HIS27 4.4 50.2 1.0
N A:VAL30 4.4 46.5 1.0
N A:CYS28 4.4 44.5 1.0
CA A:VAL30 4.4 54.5 1.0
O A:HOH141 4.5 48.9 1.0
HB3 A:ASP48 4.5 63.8 1.0
CA A:CYS28 4.5 44.5 1.0
HA2 A:GLY31 4.5 61.0 1.0
O A:HOH138 4.6 43.9 1.0
HB3 A:CYS44 4.6 55.8 1.0
HB2 A:ASP48 4.6 63.8 1.0
O A:VAL30 4.6 60.3 1.0
O A:CYS28 4.6 46.3 1.0
O A:HOH133 4.6 48.5 1.0
N A:GLY32 4.6 49.3 1.0
HA2 A:GLY29 4.7 54.0 1.0
CB A:HIS27 4.8 48.2 1.0
CA A:GLY32 4.9 56.0 1.0
O A:CYS44 5.0 40.0 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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