Sodium in PDB 5j4k: Structure of Humanised Rada-Mutant HUMRADA22F in Complex with 1- Indane-6-Carboxylic Acid

The structure of Structure of Humanised Rada-Mutant HUMRADA22F in Complex with 1- Indane-6-Carboxylic Acid, PDB code: 5j4k was solved by G.Fischer, M.Marsh, T.Moschetti, T.Sharpe, D.Scott, M.Morgan, H.Ng, J.Skidmore, A.Venkitaraman, C.Abell, T.L.Blundell, M.Hyvonen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.20 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.440, 61.214, 87.742, 90.00, 90.00, 90.00
R / Rfree (%)	12.9 / 16.4

The structure of Structure of Humanised Rada-Mutant HUMRADA22F in Complex with 1- Indane-6-Carboxylic Acid also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Structure of Humanised Rada-Mutant HUMRADA22F in Complex with 1- Indane-6-Carboxylic Acid (pdb code 5j4k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Humanised Rada-Mutant HUMRADA22F in Complex with 1- Indane-6-Carboxylic Acid, PDB code: 5j4k:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Humanised Rada-Mutant HUMRADA22F in Complex with 1- Indane-6-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Humanised Rada-Mutant HUMRADA22F in Complex with 1- Indane-6-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:23.7 occ:1.00 O A:HOH737 2.4 42.9 1.0 O A:HOH680 2.4 34.5 1.0 O A:HOH729 2.4 41.7 1.0 O A:HOH606 2.5 25.6 1.0 OD1 A:ASN199 2.5 15.0 1.0 O A:HOH695 2.8 40.6 1.0 O A:HOH674 3.0 24.0 1.0 CG A:ASN199 3.5 12.4 1.0 HD22 A:ASN199 3.5 15.3 1.0 O A:HOH616 3.9 39.4 1.0 ND2 A:ASN199 3.9 12.8 1.0 O A:HOH731 4.1 41.4 1.0 HD2 A:ARG230 4.1 13.2 1.0 O A:HOH508 4.1 38.7 1.0 HB3 A:ASP198 4.3 22.7 1.0 HA A:ASN199 4.4 12.5 1.0 O A:HOH512 4.5 45.7 1.0 O A:HOH644 4.5 32.5 1.0 OE1 A:GLU195 4.6 27.3 1.0 HB2 A:ASP198 4.7 22.7 1.0 HD21 A:ASN199 4.7 15.3 1.0 CB A:ASN199 4.8 11.8 1.0 O A:ASP198 4.9 16.9 1.0 O A:GLU195 4.9 13.4 1.0 HE A:ARG230 4.9 14.9 1.0 CA A:ASN199 5.0 10.4 1.0 CB A:ASP198 5.0 18.9 1.0 C A:ASP198 5.0 14.1 1.0 N A:ASN199 5.0 11.5 1.0

Sodium binding site 2 out of 2 in the Structure of Humanised Rada-Mutant HUMRADA22F in Complex with 1- Indane-6-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Humanised Rada-Mutant HUMRADA22F in Complex with 1- Indane-6-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:34.3 occ:1.00 O A:HOH589 2.1 19.3 1.0 O A:HOH539 2.2 23.0 1.0 O A:HOH563 2.3 22.6 1.0 O A:GLN131 2.4 12.3 1.0 OD1 A:ASN273 2.5 19.5 1.0 HD22 A:ASN273 2.8 22.7 1.0 CG A:ASN273 3.3 15.5 1.0 ND2 A:ASN273 3.4 18.9 1.0 HA A:ALA132 3.4 11.7 1.0 C A:GLN131 3.4 9.1 1.0 O A:HOH690 3.6 28.6 1.0 O A:HOH605 3.6 26.1 1.0 HB3 A:GLN131 3.9 10.9 1.0 N A:ALA132 4.1 8.8 1.0 CA A:ALA132 4.2 9.8 1.0 HD21 A:ASN273 4.2 22.7 1.0 HG1 A:THR310 4.2 16.2 1.0 HA A:GLN131 4.3 10.9 1.0 ND1 A:HIS269 4.4 14.8 1.0 CA A:GLN131 4.4 9.1 1.0 OG1 A:THR310 4.6 13.5 1.0 CB A:GLN131 4.6 9.1 1.0 HB2 A:ALA132 4.7 12.4 1.0 CB A:ASN273 4.8 11.6 1.0 HB3 A:ALA272 4.8 12.3 1.0 HB2 A:GLN131 4.9 10.9 1.0 H A:ALA132 4.9 10.6 1.0 HE1 A:HIS269 4.9 17.4 1.0 HG21 A:THR310 4.9 18.2 1.0 HB3 A:HIS269 5.0 14.6 1.0 HA A:ASN273 5.0 11.6 1.0 CB A:ALA132 5.0 10.3 1.0

T.Moschetti, T.Sharpe, G.Fischer, M.E.Marsh, H.K.Ng, M.Morgan, D.E.Scott, T.L.Blundell, A.R Venkitaraman, J.Skidmore, C.Abell, M.Hyvonen. Engineering Archeal Surrogate Systems For the Development of Protein-Protein Interaction Inhibitors Against Human RAD51. J.Mol.Biol. V. 428 4589 2016.
ISSN: ESSN 1089-8638
PubMed: 27725183
DOI: 10.1016/J.JMB.2016.10.009