Calcium in PDB 2d1k: Ternary Complex of the WH2 Domain of Mim with Actin-Dnase I

All present enzymatic activity of Ternary Complex of the WH2 Domain of Mim with Actin-Dnase I:
3.1.21.1;

The structure of Ternary Complex of the WH2 Domain of Mim with Actin-Dnase I, PDB code: 2d1k was solved by D.Chereau, F.Kerff, R.Dominguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.40 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.093, 75.487, 228.991, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 28.4

The structure of Ternary Complex of the WH2 Domain of Mim with Actin-Dnase I also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Ternary Complex of the WH2 Domain of Mim with Actin-Dnase I (pdb code 2d1k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Ternary Complex of the WH2 Domain of Mim with Actin-Dnase I, PDB code: 2d1k:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Ternary Complex of the WH2 Domain of Mim with Actin-Dnase I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Complex of the WH2 Domain of Mim with Actin-Dnase I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1381 b:64.5 occ:1.00 O A:HOH1386 2.0 60.5 1.0 O A:HOH1385 2.0 39.4 1.0 O2G A:ATP1380 2.2 64.6 1.0 O1B A:ATP1380 2.3 61.6 1.0 PG A:ATP1380 3.2 63.0 1.0 O3G A:ATP1380 3.3 63.4 1.0 PB A:ATP1380 3.5 64.2 1.0 O3B A:ATP1380 3.7 62.9 1.0 CA A:GLY13 3.8 57.2 1.0 NE2 A:GLN137 3.9 56.7 1.0 O3A A:ATP1380 4.4 63.5 1.0 OD2 A:ASP154 4.4 79.2 1.0 O1A A:ATP1380 4.5 68.7 1.0 CD A:GLN137 4.5 57.5 1.0 OD1 A:ASP11 4.5 72.4 1.0 O1G A:ATP1380 4.6 63.0 1.0 NZ A:LYS18 4.7 50.3 1.0 N A:GLY13 4.7 57.4 1.0 O2B A:ATP1380 4.7 59.7 1.0 O A:ASN12 4.7 53.3 1.0 OD1 A:ASP154 4.7 78.9 1.0 N A:SER14 4.8 58.2 1.0 OE1 A:GLN137 4.8 59.4 1.0 C A:GLY13 4.9 58.3 1.0 OD2 A:ASP11 5.0 74.3 1.0

Calcium binding site 2 out of 2 in the Ternary Complex of the WH2 Domain of Mim with Actin-Dnase I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Complex of the WH2 Domain of Mim with Actin-Dnase I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1273 b:36.8 occ:1.00 O B:HOH1277 2.2 28.1 1.0 OD1 B:ASP201 2.3 34.5 1.0 O B:THR203 2.4 31.1 1.0 O B:THR207 2.5 38.5 1.0 OG1 B:THR203 2.5 32.3 1.0 O B:THR205 2.5 29.4 1.0 O B:HOH1281 2.6 29.0 1.0 OD2 B:ASP201 2.7 24.8 1.0 CG B:ASP201 2.9 30.9 1.0 C B:THR203 3.5 33.7 1.0 C B:THR207 3.6 36.1 1.0 C B:THR205 3.7 27.2 1.0 CB B:THR203 3.9 30.6 1.0 CA B:THR203 4.1 31.7 1.0 N B:THR207 4.2 30.3 1.0 N B:THR205 4.2 35.0 1.0 N B:THR203 4.3 33.1 1.0 C B:ALA204 4.4 34.0 1.0 CB B:ASP201 4.4 28.9 1.0 N B:ALA204 4.5 33.8 1.0 C B:SER206 4.5 31.9 1.0 N B:ASN208 4.5 36.6 1.0 CA B:THR207 4.5 32.8 1.0 CA B:THR205 4.6 33.0 1.0 CA B:SER206 4.6 27.8 1.0 N B:SER206 4.6 24.5 1.0 CA B:ASN208 4.6 39.0 1.0 CA B:ALA204 4.7 36.4 1.0 CE2 B:TYR253 4.7 36.5 1.0 OG1 B:THR207 4.8 30.6 1.0 CG2 B:THR203 4.8 30.5 1.0 O B:ALA204 4.9 39.4 1.0 OH B:TYR253 5.0 35.4 1.0

S.H.Lee, F.Kerff, D.Chereau, F.Ferron, A.Klug, R.Dominguez. Structural Basis For the Actin-Binding Function of Missing-in-Metastasis Structure V. 15 145 2007.
ISSN: ISSN 0969-2126
PubMed: 17292833
DOI: 10.1016/J.STR.2006.12.005