Calcium in PDB 8w1m: T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp

The structure of T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp, PDB code: 8w1m was solved by D.J.Miller, C.Kalodimos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.10 / 2.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.761, 179.939, 66.587, 90, 90, 90
R / Rfree (%)	22.5 / 25.9

The structure of T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Calcium atom in the T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp (pdb code 8w1m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp, PDB code: 8w1m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:53.8 occ:1.00 OE2 A:GLU184 2.2 64.4 1.0 O A:LYS181 2.5 63.1 1.0 O A:ASN183 2.5 58.4 1.0 CD A:GLU184 3.1 57.4 1.0 C A:ASN183 3.3 63.5 1.0 N A:ASN183 3.6 57.1 1.0 CG A:GLU184 3.6 58.5 1.0 C A:LYS181 3.7 64.5 1.0 CA A:ASN183 4.0 60.5 1.0 C A:GLY182 4.1 55.9 1.0 N A:GLU184 4.1 63.8 1.0 OE1 A:GLU184 4.2 58.4 1.0 CA A:GLU184 4.3 60.2 1.0 CB A:LYS181 4.4 66.1 1.0 CA A:GLY182 4.5 54.5 1.0 N A:GLY182 4.5 61.0 1.0 CB A:GLU184 4.6 55.2 1.0 O A:GLY182 4.6 57.7 1.0 CA A:LYS181 4.6 61.6 1.0 CB A:ASN183 4.7 57.8 1.0

Calcium binding site 2 out of 5 in the T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:71.2 occ:1.00 OD2 A:ASP329 2.4 65.7 1.0 OD1 A:ASP329 2.7 68.6 1.0 CG A:ASP329 2.9 63.1 1.0 CB A:ASP329 4.4 59.4 1.0 O A:ASN183 4.6 58.4 1.0 OG1 A:THR185 4.6 50.8 1.0 O A:GLN327 4.8 64.8 1.0

Calcium binding site 3 out of 5 in the T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:70.6 occ:1.00 O A:ALA326 2.3 67.8 1.0 C A:ALA326 3.5 60.8 1.0 CA A:GLN327 4.0 59.2 1.0 OD1 A:ASP329 4.1 68.6 1.0 N A:GLN327 4.2 62.2 1.0 C A:GLN327 4.4 58.6 1.0 O A:ILE328 4.4 61.3 1.0 CA A:ALA326 4.5 63.8 1.0 NZ A:LYS353 4.6 65.4 1.0 O A:GLN327 4.6 64.8 1.0 CB A:ALA326 4.9 60.7 1.0 CE A:LYS353 4.9 64.3 1.0

Calcium binding site 4 out of 5 in the T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:56.2 occ:1.00 O A:ASP329 2.3 54.8 1.0 OD2 B:ASP382 2.3 55.8 1.0 OE1 A:GLU330 2.5 63.0 1.0 OD1 B:ASP382 2.6 51.5 1.0 CG B:ASP382 2.8 50.5 1.0 C A:ASP329 3.5 56.1 1.0 CD A:GLU330 3.6 53.9 1.0 NZ B:LYS23 4.1 56.4 1.0 CA A:GLU330 4.1 48.0 1.0 CB A:GLU330 4.2 50.4 1.0 CB B:ASP382 4.2 52.0 1.0 N A:GLU330 4.3 57.0 1.0 O A:HOH504 4.3 50.0 1.0 OE2 A:GLU330 4.4 58.7 1.0 CG A:GLU330 4.5 48.9 1.0 CA A:ASP329 4.6 56.0 1.0 OE1 A:GLU184 4.8 58.4 1.0 O B:ASP382 5.0 65.8 1.0

Calcium binding site 5 out of 5 in the T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:98.2 occ:1.00 OE1 B:GLU330 2.8 74.0 1.0 O A:GLY21 3.0 87.5 1.0 OD2 A:ASP382 3.3 80.9 1.0 OE2 B:GLU330 3.4 86.9 1.0 CD B:GLU330 3.5 81.1 1.0 OD1 A:ASP382 3.6 87.2 1.0 CG A:ASP382 3.8 80.3 1.0 C A:GLY21 4.1 81.3 1.0 O B:ASP329 4.3 52.0 1.0 CA A:GLY21 4.7 79.5 1.0 CG B:GLU330 4.8 69.9 1.0

D.J.Miller, C.Kalodimos. T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp To Be Published.