Calcium in PDB 4r5j: Crystal Structure of the Dnak C-Terminus (Dnak-Sbd-A)

The structure of Crystal Structure of the Dnak C-Terminus (Dnak-Sbd-A), PDB code: 4r5j was solved by J.I.Leu, P.Zhang, M.E.Murphy, R.Marmorstein, D.L.George, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.25 / 2.36
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.658, 69.412, 75.771, 102.12, 104.20, 92.96
R / Rfree (%)	21.5 / 25.8

The binding sites of Calcium atom in the Crystal Structure of the Dnak C-Terminus (Dnak-Sbd-A) (pdb code 4r5j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of the Dnak C-Terminus (Dnak-Sbd-A), PDB code: 4r5j:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of the Dnak C-Terminus (Dnak-Sbd-A)


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 the Dnak C-Terminus (Dnak-Sbd-A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:67.5 occ:1.00 O A:HOH1028 2.6 52.0 1.0 ND1 A:HIS386 3.2 61.2 1.0 N A:ILE387 3.2 55.3 1.0 CA A:HIS386 3.3 50.2 1.0 CB A:HIS386 3.5 53.0 1.0 C C:THR403 3.6 31.4 1.0 O C:GLU402 3.6 37.6 1.0 CA C:THR403 3.7 30.4 1.0 N C:MET404 3.8 43.1 1.0 CG A:HIS386 3.8 65.5 1.0 C A:HIS386 3.8 54.0 1.0 O A:ILE387 3.8 43.7 1.0 CG2 A:ILE387 3.9 50.9 1.0 O C:THR403 4.0 37.9 1.0 C C:GLU402 4.1 31.6 1.0 CA C:MET404 4.1 37.5 1.0 N C:THR403 4.2 37.2 1.0 CG C:GLU402 4.2 42.0 1.0 CA A:ILE387 4.3 53.5 1.0 CE1 A:HIS386 4.3 61.4 1.0 N A:HIS386 4.5 54.5 1.0 C A:ILE387 4.5 46.8 1.0 CB A:ILE387 4.7 49.2 1.0 CD C:GLU402 4.8 44.6 1.0 O A:HIS385 4.8 59.1 1.0 CB C:GLU402 4.9 32.9 1.0 OE2 C:GLU402 5.0 52.7 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of the Dnak C-Terminus (Dnak-Sbd-A)


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 the Dnak C-Terminus (Dnak-Sbd-A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:64.2 occ:1.00 N B:ILE387 3.3 48.9 1.0 ND1 B:HIS386 3.3 56.2 1.0 CA B:HIS386 3.6 46.8 1.0 CB B:HIS386 3.6 48.6 1.0 O B:ILE387 3.7 38.9 1.0 CG2 B:ILE387 3.8 46.6 1.0 CG B:HIS386 3.9 62.0 1.0 C B:HIS386 4.0 52.3 1.0 CA B:ILE387 4.3 45.4 1.0 C B:ILE387 4.4 41.4 1.0 CE1 B:HIS386 4.5 50.0 1.0 CB B:ILE387 4.7 48.6 1.0 N B:HIS386 4.8 53.4 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of the Dnak C-Terminus (Dnak-Sbd-A)


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 the Dnak C-Terminus (Dnak-Sbd-A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca901 b:49.8 occ:1.00 ND1 C:HIS386 3.3 55.5 1.0 N C:ILE387 3.5 34.0 1.0 CA C:HIS386 3.6 47.3 1.0 C A:THR403 3.7 35.2 1.0 CB C:HIS386 3.7 43.0 1.0 O A:GLU402 3.8 39.7 1.0 CA A:THR403 3.9 38.2 1.0 N A:MET404 3.9 36.1 1.0 CG C:HIS386 3.9 52.0 1.0 O C:ILE387 4.0 36.4 1.0 CG2 C:ILE387 4.0 37.7 1.0 O A:THR403 4.1 35.2 1.0 C C:HIS386 4.1 47.4 1.0 C A:GLU402 4.2 33.4 1.0 CG A:GLU402 4.2 34.7 1.0 CA A:MET404 4.3 42.4 1.0 N A:THR403 4.3 30.4 1.0 CE1 C:HIS386 4.5 52.8 1.0 CA C:ILE387 4.6 36.7 1.0 C C:ILE387 4.7 36.8 1.0 CD A:GLU402 4.8 41.9 1.0 N C:HIS386 4.8 49.8 1.0 O A:HOH1001 4.8 31.3 1.0 CB C:ILE387 4.9 43.5 1.0 OE2 A:GLU402 4.9 47.6 1.0 CB A:GLU402 5.0 30.3 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of the Dnak C-Terminus (Dnak-Sbd-A)


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 the Dnak C-Terminus (Dnak-Sbd-A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca903 b:76.2 occ:1.00 NE2 C:HIS422 2.5 43.2 1.0 O A:HOH1012 2.6 47.8 1.0 O A:LEU411 3.0 38.9 1.0 OG1 C:THR420 3.2 41.1 1.0 CE1 C:HIS422 3.4 41.3 1.0 CD2 C:HIS422 3.5 45.1 1.0 C A:LEU411 3.9 37.1 1.0 CB A:HIS422 4.0 38.1 1.0 ND1 A:HIS422 4.0 42.7 1.0 CA A:LEU411 4.1 29.2 1.0 O A:HOH1022 4.2 46.6 1.0 CG2 C:THR416 4.2 28.8 1.0 CG A:HIS422 4.3 49.4 1.0 O A:SER423 4.4 46.1 1.0 OE1 A:GLN424 4.5 41.1 1.0 CB C:THR420 4.6 38.3 1.0 ND1 C:HIS422 4.6 36.7 1.0 O A:THR410 4.6 39.8 1.0 CG C:HIS422 4.7 44.6 1.0 CB A:LEU411 4.7 32.9 1.0 N A:SER423 4.8 40.0 1.0 CG A:LEU411 4.8 43.1 1.0 O A:HOH1017 4.9 43.8 1.0 C A:SER423 4.9 41.1 1.0 CB A:GLN424 4.9 24.5 1.0 CA A:HIS422 4.9 42.2 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of the Dnak C-Terminus (Dnak-Sbd-A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Dnak C-Terminus (Dnak-Sbd-A) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca902 b:55.1 occ:1.00 O D:HOH1018 2.1 49.7 1.0 N D:ILE387 3.3 40.3 1.0 CA D:HIS386 3.4 50.3 1.0 ND1 D:HIS386 3.5 61.9 1.0 CB D:HIS386 3.7 55.0 1.0 CG2 D:ILE387 3.8 41.9 1.0 C D:HIS386 3.9 44.6 1.0 O D:ILE387 3.9 42.8 1.0 CG D:HIS386 4.0 65.5 1.0 CA D:ILE387 4.4 40.7 1.0 N D:HIS386 4.6 56.1 1.0 CB D:ILE387 4.6 42.2 1.0 C D:ILE387 4.6 37.9 1.0 CE1 D:HIS386 4.6 64.8 1.0

J.I.Leu, P.Zhang, M.E.Murphy, R.Marmorstein, D.L.George. Structural Basis For the Inhibition of HSP70 and Dnak Chaperones By Small-Molecule Targeting of A C-Terminal Allosteric Pocket. Acs Chem.Biol. 2014.
ISSN: ESSN 1554-8937
PubMed: 25148104
DOI: 10.1021/CB500236Y