Sodium in PDB 5j4h: Structure of Humanised Rada-Mutant HUMRADA22F in Complex with Indole- 6-Carboxylic Acid

The structure of Structure of Humanised Rada-Mutant HUMRADA22F in Complex with Indole- 6-Carboxylic Acid, PDB code: 5j4h 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)	50.16 / 1.37
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.459, 61.122, 87.767, 90.00, 90.00, 90.00
R / Rfree (%)	13.2 / 17

The structure of Structure of Humanised Rada-Mutant HUMRADA22F in Complex with Indole- 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 Indole- 6-Carboxylic Acid (pdb code 5j4h). 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 Indole- 6-Carboxylic Acid, PDB code: 5j4h:
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 Indole- 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 Indole- 6-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:26.5 occ:1.00 O A:HOH715 2.4 36.4 1.0 O A:HOH580 2.4 25.6 1.0 OD1 A:ASN199 2.5 13.2 1.0 O A:HOH765 2.5 44.4 1.0 O A:HOH688 3.1 21.1 1.0 CG A:ASN199 3.5 11.1 1.0 HD21 A:ASN199 3.5 13.8 1.0 O A:HOH503 3.7 46.6 1.0 O A:HOH615 3.8 34.6 1.0 ND2 A:ASN199 3.9 11.5 1.0 O A:HOH762 4.2 44.3 1.0 O A:HOH609 4.2 42.0 1.0 HD2 A:ARG230 4.3 12.8 1.0 HB3 A:ASP198 4.3 18.9 1.0 HA A:ASN199 4.4 11.4 1.0 HB2 A:ASP198 4.5 18.9 1.0 OE1 A:GLU195 4.6 25.0 1.0 O A:HOH658 4.6 31.2 1.0 HD22 A:ASN199 4.7 13.8 1.0 CB A:ASN199 4.8 9.8 1.0 O A:GLU195 4.8 12.5 1.0 O A:ASP198 4.8 15.1 1.0 CB A:ASP198 4.9 15.7 1.0 C A:ASP198 4.9 12.4 1.0 N A:ASN199 4.9 10.0 1.0 CA A:ASN199 4.9 9.5 1.0

Sodium binding site 2 out of 2 in the Structure of Humanised Rada-Mutant HUMRADA22F in Complex with Indole- 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 Indole- 6-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:39.7 occ:1.00 O A:HOH666 2.2 17.6 1.0 O A:HOH549 2.2 20.6 1.0 O A:HOH557 2.3 20.1 1.0 O A:GLN131 2.4 10.6 1.0 OD1 A:ASN273 2.5 16.1 1.0 HD21 A:ASN273 2.8 18.8 1.0 CG A:ASN273 3.3 12.0 1.0 ND2 A:ASN273 3.4 15.6 1.0 C A:GLN131 3.4 7.1 1.0 HA A:ALA132 3.4 9.9 1.0 O A:HOH714 3.6 23.3 1.0 O A:HOH632 3.6 24.8 1.0 HD1 A:HIS269 3.7 14.9 1.0 HB3 A:GLN131 3.8 8.9 1.0 HG1 A:THR310 4.1 14.2 1.0 N A:ALA132 4.1 6.6 1.0 HD22 A:ASN273 4.2 18.8 1.0 CA A:ALA132 4.2 8.2 1.0 HA A:GLN131 4.3 9.0 1.0 CA A:GLN131 4.3 7.5 1.0 ND1 A:HIS269 4.4 12.4 1.0 CB A:GLN131 4.5 7.4 1.0 OG1 A:THR310 4.6 11.8 1.0 HB2 A:ALA132 4.6 10.5 1.0 CB A:ASN273 4.7 10.3 1.0 HB2 A:GLN131 4.8 8.9 1.0 HB3 A:ALA272 4.8 10.2 1.0 H A:ALA132 4.9 8.0 1.0 HE1 A:HIS269 4.9 14.0 1.0 HA A:ASN273 4.9 10.5 1.0 O A:HOH635 5.0 43.3 1.0 HG21 A:THR310 5.0 16.8 1.0 CB A:ALA132 5.0 8.7 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