Sodium in PDB 6d1u: Crystal Structure of the Human Clr:RAMP1 Extracellular Domain Heterodimer in Complex with Adrenomedullin 2/Intermedin

The structure of Crystal Structure of the Human Clr:RAMP1 Extracellular Domain Heterodimer in Complex with Adrenomedullin 2/Intermedin, PDB code: 6d1u was solved by A.Pioszak, A.Roehrkasse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.64 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	172.295, 106.041, 136.911, 90.00, 122.53, 90.00
R / Rfree (%)	19.4 / 22.3

The binding sites of Sodium atom in the Crystal Structure of the Human Clr:RAMP1 Extracellular Domain Heterodimer in Complex with Adrenomedullin 2/Intermedin (pdb code 6d1u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Human Clr:RAMP1 Extracellular Domain Heterodimer in Complex with Adrenomedullin 2/Intermedin, PDB code: 6d1u:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Human Clr:RAMP1 Extracellular Domain Heterodimer in Complex with Adrenomedullin 2/Intermedin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Human Clr:RAMP1 Extracellular Domain Heterodimer in Complex with Adrenomedullin 2/Intermedin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2202 b:61.1 occ:1.00 O A:HOH2469 2.3 66.2 1.0 OD1 A:ASN2066 2.3 50.2 1.0 O A:HOH2525 2.4 57.2 1.0 O A:HOH2502 2.4 42.1 1.0 O A:HOH2309 2.5 51.5 1.0 O A:HOH2393 2.6 43.9 1.0 CG A:ASN2066 3.5 40.1 1.0 O A:HOH2555 3.5 58.1 1.0 O A:GLY2109 3.8 36.1 1.0 CB A:ASN2066 4.2 37.3 1.0 N A:ASN2066 4.3 31.4 1.0 O A:HOH2535 4.4 40.6 1.0 ND2 A:ASN2066 4.5 41.6 1.0 OD1 A:ASN2110 4.5 44.1 1.0 O A:HOH2516 4.6 53.5 1.0 O A:TYR2064 4.8 35.7 1.0 CA A:ASN2066 4.9 35.7 1.0 C A:GLY2109 4.9 35.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Human Clr:RAMP1 Extracellular Domain Heterodimer in Complex with Adrenomedullin 2/Intermedin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Human Clr:RAMP1 Extracellular Domain Heterodimer in Complex with Adrenomedullin 2/Intermedin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na2202 b:42.2 occ:1.00 OD1 C:ASN2066 2.3 40.4 1.0 O C:HOH2348 2.4 34.5 1.0 O C:GLN2059 2.4 39.2 1.0 O C:HOH2322 2.5 36.9 1.0 O C:HOH2387 2.5 39.6 1.0 O C:HOH2410 2.6 46.4 1.0 CG C:ASN2066 3.4 39.3 1.0 C C:GLN2059 3.6 41.0 1.0 O C:GLY2109 3.9 44.6 1.0 N C:GLN2059 4.0 41.1 1.0 N C:GLU2061 4.2 40.8 1.0 CB C:ASN2066 4.2 40.8 1.0 N C:ASN2066 4.3 39.3 1.0 CA C:GLN2059 4.3 42.2 1.0 ND2 C:ASN2066 4.4 36.8 1.0 O C:TYR2064 4.5 38.4 1.0 N C:ALA2060 4.6 41.5 1.0 CA C:ALA2060 4.7 42.4 1.0 CB C:GLN2059 4.7 40.8 1.0 N C:GLY2062 4.8 42.2 1.0 O C:HOH2345 4.8 39.1 1.0 C C:ALA2060 4.9 41.8 1.0 O C:HOH2395 4.9 49.8 1.0 OD1 C:ASN2110 4.9 47.9 1.0 CA C:ASN2066 4.9 38.2 1.0 CA C:GLU2061 5.0 42.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Human Clr:RAMP1 Extracellular Domain Heterodimer in Complex with Adrenomedullin 2/Intermedin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Human Clr:RAMP1 Extracellular Domain Heterodimer in Complex with Adrenomedullin 2/Intermedin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na2203 b:52.3 occ:1.00 O C:HOH2411 2.2 51.5 1.0 O C:HOH2332 2.3 40.8 1.0 O C:HOH2408 2.4 44.6 1.0 O C:GLU2061 2.4 38.4 1.0 O C:GLY2062 2.6 44.7 1.0 O C:ASP2108 2.6 44.5 1.0 C C:GLU2061 3.1 40.8 1.0 C C:ASP2108 3.2 43.8 1.0 C C:GLY2062 3.4 41.8 1.0 NA C:NA2204 3.5 60.2 1.0 CA C:ASP2108 3.7 47.2 1.0 N C:GLY2062 3.8 42.2 1.0 O C:HOH2326 3.8 54.7 1.0 CA C:GLY2062 3.9 41.2 1.0 CA C:GLU2061 4.1 42.5 1.0 N C:GLY2109 4.1 40.1 1.0 CB C:GLU2061 4.2 46.4 1.0 N C:VAL2063 4.4 39.4 1.0 O C:GLN2107 4.5 44.8 1.0 CB C:ASP2108 4.5 48.9 1.0 CA C:GLY2109 4.6 40.0 1.0 CA C:VAL2063 4.8 39.7 1.0 N C:ASP2108 4.8 47.5 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Human Clr:RAMP1 Extracellular Domain Heterodimer in Complex with Adrenomedullin 2/Intermedin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Human Clr:RAMP1 Extracellular Domain Heterodimer in Complex with Adrenomedullin 2/Intermedin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na2204 b:60.2 occ:1.00 O C:HOH2326 2.3 54.7 1.0 O C:HOH2411 2.5 51.5 1.0 O C:HOH2408 2.6 44.6 1.0 NA C:NA2203 3.5 52.3 1.0 O C:GLU2061 3.9 38.4 1.0 O C:HOH2332 4.8 40.8 1.0

A.M.Roehrkasse, J.M.Booe, S.M.Lee, M.L.Warner, A.A.Pioszak. Structure-Function Analyses Reveal A Triple Beta-Turn Receptor-Bound Conformation of Adrenomedullin 2/Intermedin and Enable Peptide Antagonist Design. J. Biol. Chem. V. 293 15840 2018.
ISSN: ESSN 1083-351X
PubMed: 30139742
DOI: 10.1074/JBC.RA118.005062