Calcium in PDB 3m6g: Crystal Structure of Actin in Complex with Lobophorolide

The structure of Crystal Structure of Actin in Complex with Lobophorolide, PDB code: 3m6g was solved by J.S.Allingham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.932, 86.419, 100.868, 90.00, 94.91, 90.00
R / Rfree (%)	18.3 / 22.7

The structure of Crystal Structure of Actin in Complex with Lobophorolide also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Actin in Complex with Lobophorolide (pdb code 3m6g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Actin in Complex with Lobophorolide, PDB code: 3m6g:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Actin in Complex with Lobophorolide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Actin in Complex with Lobophorolide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca372 b:53.1 occ:1.00 O A:HOH539 2.4 39.8 1.0 O A:HOH434 2.5 21.2 1.0 O A:HOH452 2.5 33.2 1.0 O A:HOH559 2.6 31.5 1.0 OE2 A:GLU205 2.6 28.3 1.0 CD A:GLU205 3.5 27.6 1.0 O A:HOH690 3.6 39.5 1.0 OE1 A:GLU205 3.8 25.4 1.0 O A:HOH457 3.9 28.2 1.0 O A:SER199 4.4 28.2 1.0 CG A:GLU205 4.7 26.5 1.0 O A:HOH465 4.7 32.5 1.0 CG2 A:THR202 4.7 26.7 1.0 OG A:SER199 4.9 32.4 1.0 O A:HOH558 4.9 42.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Actin in Complex with Lobophorolide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Actin in Complex with Lobophorolide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca373 b:44.4 occ:1.00 O A:HOH627 2.3 48.4 1.0 O A:VAL30 2.4 18.4 1.0 O A:HOH628 2.5 41.9 1.0 O A:HOH626 2.5 33.6 1.0 O A:HOH491 2.5 43.3 1.0 O A:HOH505 2.8 33.9 1.0 C A:VAL30 3.6 18.6 1.0 OD2 A:ASP56 4.0 33.6 1.0 N A:VAL30 4.2 17.2 1.0 CA A:VAL30 4.4 17.4 1.0 OD1 A:ASP56 4.5 33.1 1.0 N A:PHE31 4.5 18.3 1.0 CA A:PHE31 4.6 19.3 1.0 CB A:PHE31 4.6 18.9 1.0 CB A:VAL30 4.6 17.7 1.0 CG A:ASP56 4.7 32.0 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Actin in Complex with Lobophorolide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Actin in Complex with Lobophorolide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca372 b:41.1 occ:1.00 O B:HOH655 2.3 36.7 1.0 O B:TRP356 2.5 17.4 1.0 O B:HOH699 2.5 36.1 1.0 OE2 B:GLU361 2.6 31.8 1.0 O B:HOH721 2.6 33.7 1.0 O B:GLN354 2.6 23.3 1.0 OE1 B:GLU361 2.8 29.0 1.0 CD B:GLU361 3.1 29.6 1.0 C B:TRP356 3.6 17.9 1.0 C B:GLN354 3.8 23.2 1.0 C B:MET355 4.2 18.6 1.0 N B:TRP356 4.4 18.0 1.0 O B:MET355 4.4 17.2 1.0 N B:ILE357 4.4 17.9 1.0 CA B:ILE357 4.4 17.7 1.0 CA B:MET355 4.5 20.1 1.0 CG B:GLU361 4.6 26.0 1.0 N B:MET355 4.6 21.5 1.0 CA B:TRP356 4.6 18.1 1.0 O B:HOH656 4.7 37.4 1.0 CA B:GLN354 4.8 24.4 1.0 N B:THR358 4.8 18.1 1.0 CG2 B:THR358 4.8 18.2 1.0 O B:HOH409 5.0 49.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Actin in Complex with Lobophorolide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Actin in Complex with Lobophorolide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca373 b:64.1 occ:1.00 O B:HOH664 2.3 31.7 1.0 O B:HOH567 2.5 39.2 1.0 O B:HOH418 2.5 35.3 1.0 O B:VAL30 2.5 16.9 1.0 O B:HOH694 2.8 31.6 1.0 O B:HOH506 2.9 46.1 1.0 C B:VAL30 3.7 17.5 1.0 CB B:VAL30 4.2 16.6 1.0 CA B:VAL30 4.4 16.4 1.0 N B:VAL30 4.4 15.9 1.0 OD2 B:ASP56 4.5 34.8 1.0 N B:PHE31 4.7 17.7 1.0 CA B:PHE31 4.9 18.5 1.0 CG1 B:VAL30 4.9 15.8 1.0 OD1 B:ASP56 4.9 34.0 1.0 O B:HOH598 5.0 52.9 1.0

J.C.Blain, Y.F.Mok, J.Kubanek, J.S.Allingham. Two Molecules of Lobophorolide Cooperate to Stabilize An Actin Dimer Using Both Their "Ring" and "Tail" Region. Chem.Biol. V. 17 802 2010.
ISSN: ISSN 1074-5521
PubMed: 20797609
DOI: 10.1016/J.CHEMBIOL.2010.06.010