Sodium in PDB 5ao5: ENDO180 D1-4, Monoclinic Form

The structure of ENDO180 D1-4, Monoclinic Form, PDB code: 5ao5 was solved by P.Paracuellos, D.C.Briggs, F.Carafoli, T.Loncar, E.Hohenester, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.158 / 2.48
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	126.370, 92.370, 127.650, 90.00, 100.31, 90.00
R / Rfree (%)	19.36 / 24.42

The binding sites of Sodium atom in the ENDO180 D1-4, Monoclinic Form (pdb code 5ao5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the ENDO180 D1-4, Monoclinic Form, PDB code: 5ao5:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the ENDO180 D1-4, Monoclinic Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of ENDO180 D1-4, Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na901 b:62.7 occ:1.00 OE1 A:GLU333 2.3 57.6 1.0 OD1 A:ASN348 2.4 49.4 1.0 OD1 A:ASP328 2.4 55.5 1.0 O A:ASN348 2.5 44.5 1.0 O A:HOH2078 2.5 61.0 1.0 OE1 A:GLN326 2.5 61.5 1.0 HE22 A:GLN326 2.8 68.8 1.0 HG2 A:GLN347 3.2 92.7 1.0 H A:ASN348 3.2 64.4 1.0 CD A:GLN326 3.3 58.5 1.0 CD A:GLU333 3.3 54.8 1.0 NE2 A:GLN326 3.4 57.3 1.0 CG A:ASP328 3.4 55.6 1.0 CG A:ASN348 3.4 49.6 1.0 H A:ASP328 3.4 63.1 1.0 HD21 A:ASN329 3.5 68.3 1.0 C A:ASN348 3.6 50.0 1.0 OE2 A:GLU333 3.8 62.7 1.0 OD2 A:ASP328 3.8 64.8 1.0 N A:ASN348 3.9 53.7 1.0 HD3 A:ARG349 4.0 0.1 1.0 HD22 A:ASN348 4.1 57.3 1.0 CG A:GLN347 4.1 77.2 1.0 CA A:ASN348 4.2 53.7 1.0 HE21 A:GLN326 4.2 68.8 1.0 ND2 A:ASN348 4.2 47.7 1.0 HB3 A:GLU333 4.2 68.9 1.0 N A:ASP328 4.2 52.6 1.0 HG3 A:GLN347 4.3 92.7 1.0 ND2 A:ASN329 4.3 56.9 1.0 HB2 A:GLU333 4.4 68.9 1.0 O A:ASP328 4.4 52.0 1.0 HA A:ARG349 4.4 63.4 1.0 CB A:ASN348 4.4 46.0 1.0 HB2 A:ASN329 4.5 66.3 1.0 CG A:GLU333 4.5 47.6 1.0 HA A:PRO327 4.6 54.2 1.0 HD22 A:ASN329 4.6 68.3 1.0 CB A:GLU333 4.6 57.4 1.0 C A:ASP328 4.6 49.7 1.0 CB A:ASP328 4.7 48.2 1.0 N A:ARG349 4.7 47.6 1.0 CA A:ASP328 4.8 51.4 1.0 CG A:GLN326 4.8 63.9 1.0 HE A:ARG349 4.8 0.5 1.0 OE1 A:GLN347 4.8 68.2 1.0 CD A:GLN347 4.9 65.0 1.0 CD A:ARG349 4.9 86.8 1.0 HA A:GLN347 4.9 60.0 1.0 HB3 A:ASN348 5.0 55.1 1.0 C A:GLN347 5.0 50.3 1.0

Sodium binding site 2 out of 4 in the ENDO180 D1-4, Monoclinic Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of ENDO180 D1-4, Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:50.0 occ:1.00 OD1 A:ASP493 2.3 45.3 1.0 O A:HOH2092 2.4 58.1 1.0 O A:ASP493 2.4 41.3 1.0 O A:HOH2090 2.4 45.3 1.0 OD1 A:ASN472 2.4 48.8 1.0 OE1 A:GLU470 2.5 44.8 1.0 H A:ASP493 3.1 50.3 1.0 CD A:GLU470 3.2 42.5 1.0 HB2 A:ASN473 3.3 66.1 1.0 OE2 A:GLU470 3.3 37.4 1.0 CG A:ASN472 3.3 51.0 1.0 H A:ASN472 3.4 54.6 1.0 C A:ASP493 3.4 45.2 1.0 CG A:ASP493 3.5 46.1 1.0 HD22 A:ASN472 3.5 61.1 1.0 O A:HOH2094 3.6 38.9 1.0 N A:ASP493 3.7 41.9 1.0 ND2 A:ASN472 3.8 50.9 1.0 HB3 A:ASN492 3.9 47.7 1.0 N A:ASN472 4.0 45.5 1.0 H A:ASN473 4.0 66.3 1.0 CA A:ASP493 4.0 41.6 1.0 N A:ASN473 4.1 55.3 1.0 HA A:SER494 4.2 65.8 1.0 CB A:ASN473 4.2 55.1 1.0 HA A:PRO471 4.3 51.6 1.0 OD2 A:ASP493 4.3 47.6 1.0 C A:ASN472 4.3 53.2 1.0 CB A:ASP493 4.4 45.9 1.0 N A:SER494 4.4 49.8 1.0 CA A:ASN472 4.5 52.0 1.0 CB A:ASN472 4.5 45.2 1.0 HA A:ASN473 4.5 77.6 1.0 CA A:ASN473 4.5 64.7 1.0 HD21 A:ASN472 4.5 61.1 1.0 OD1 A:ASN473 4.6 67.4 1.0 CG A:GLU470 4.7 40.5 1.0 HB3 A:GLU470 4.8 55.7 1.0 HA A:ASN492 4.8 49.6 1.0 CA A:SER494 4.8 54.8 1.0 CB A:ASN492 4.8 39.8 1.0 CG A:ASN473 4.8 66.5 1.0 C A:ASN492 4.8 44.6 1.0 HB3 A:ASN473 4.8 66.1 1.0 HB3 A:ASP493 4.9 55.0 1.0 HA A:GLU470 4.9 50.1 1.0 C A:PRO471 4.9 39.2 1.0 HA A:ASP493 4.9 50.0 1.0 O A:ASN472 5.0 53.2 1.0 HB3 A:SER494 5.0 66.7 1.0

Sodium binding site 3 out of 4 in the ENDO180 D1-4, Monoclinic Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of ENDO180 D1-4, Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na901 b:66.8 occ:1.00 OD1 B:ASP328 2.4 65.3 1.0 OD1 B:ASN348 2.4 48.3 1.0 OE1 B:GLU333 2.5 64.2 1.0 O B:HOH2053 2.5 77.3 1.0 O B:ASN348 2.5 66.6 1.0 OE1 B:GLN326 2.5 60.1 1.0 HE22 B:GLN326 2.7 80.0 1.0 H B:ASN348 3.2 77.9 1.0 NE2 B:GLN326 3.3 66.7 1.0 CD B:GLN326 3.3 63.3 1.0 CD B:GLU333 3.4 64.3 1.0 CG B:ASP328 3.4 64.2 1.0 H B:ASP328 3.5 75.8 1.0 CG B:ASN348 3.5 53.5 1.0 C B:ASN348 3.6 60.3 1.0 OE2 B:GLU333 3.6 64.4 1.0 OD2 B:ASP328 3.8 71.5 1.0 HB3 B:GLN347 3.8 70.6 1.0 N B:ASN348 3.9 64.9 1.0 HD3 B:ARG349 3.9 98.2 1.0 HE21 B:GLN326 4.1 80.0 1.0 CA B:ASN348 4.2 62.7 1.0 N B:ASP328 4.3 63.2 1.0 OD1 B:ASN329 4.3 64.6 1.0 HD22 B:ASN348 4.3 74.1 1.0 ND2 B:ASN348 4.4 61.7 1.0 HB3 B:GLU333 4.4 76.9 1.0 HA B:ARG349 4.5 78.3 1.0 CB B:ASN348 4.5 63.9 1.0 HA B:PRO327 4.5 71.6 1.0 O B:ASP328 4.6 58.8 1.0 HB2 B:ASN329 4.6 86.5 1.0 HB2 B:GLU333 4.6 76.9 1.0 HE B:ARG349 4.6 0.1 1.0 CG B:GLU333 4.7 65.0 1.0 CB B:ASP328 4.7 68.3 1.0 OE1 B:GLN347 4.7 68.1 1.0 CB B:GLN347 4.7 58.8 1.0 CG B:GLN326 4.8 60.8 1.0 C B:ASP328 4.8 56.8 1.0 N B:ARG349 4.8 67.6 1.0 CB B:GLU333 4.8 64.1 1.0 CD B:ARG349 4.8 81.9 1.0 CA B:ASP328 4.8 64.6 1.0 HA B:GLN347 4.9 63.6 1.0 C B:GLN347 4.9 55.9 1.0 HB3 B:ASN348 5.0 76.7 1.0

Sodium binding site 4 out of 4 in the ENDO180 D1-4, Monoclinic Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of ENDO180 D1-4, Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:61.3 occ:1.00 OD1 B:ASP493 2.3 52.0 1.0 O B:HOH2067 2.4 53.8 1.0 OD1 B:ASN472 2.4 45.9 1.0 O B:ASP493 2.4 50.6 1.0 O B:HOH2066 2.4 48.3 1.0 OE1 B:GLU470 2.4 56.5 1.0 H B:ASP493 3.0 58.7 1.0 OE2 B:GLU470 3.1 45.5 1.0 CD B:GLU470 3.1 49.2 1.0 CG B:ASN472 3.2 48.2 1.0 HB2 B:ASN473 3.3 77.4 1.0 H B:ASN472 3.4 57.6 1.0 HD22 B:ASN472 3.4 59.6 1.0 C B:ASP493 3.4 55.1 1.0 CG B:ASP493 3.5 45.4 1.0 ND2 B:ASN472 3.6 49.6 1.0 O B:HOH2069 3.7 53.2 1.0 N B:ASP493 3.7 48.9 1.0 HB3 B:ASN492 3.9 71.0 1.0 N B:ASN472 4.0 48.0 1.0 H B:ASN473 4.0 70.1 1.0 CA B:ASP493 4.0 53.1 1.0 N B:ASN473 4.1 58.4 1.0 CB B:ASN473 4.2 64.5 1.0 HA B:SER494 4.3 65.5 1.0 HA B:PRO471 4.3 58.1 1.0 C B:ASN472 4.3 51.2 1.0 OD2 B:ASP493 4.4 51.8 1.0 CB B:ASP493 4.4 47.6 1.0 HD21 B:ASN472 4.4 59.6 1.0 CB B:ASN472 4.4 45.4 1.0 CA B:ASN472 4.5 52.6 1.0 N B:SER494 4.5 51.8 1.0 HA B:ASN473 4.5 90.4 1.0 CA B:ASN473 4.6 75.3 1.0 OD1 B:ASN473 4.6 78.6 1.0 CG B:GLU470 4.6 53.1 1.0 HA B:ASN492 4.7 57.2 1.0 HB3 B:GLU470 4.7 61.4 1.0 CB B:ASN492 4.8 59.1 1.0 C B:ASN492 4.8 55.1 1.0 CG B:ASN473 4.9 78.6 1.0 CA B:SER494 4.9 54.6 1.0 HB3 B:ASP493 4.9 57.1 1.0 HA B:GLU470 4.9 56.6 1.0 C B:PRO471 4.9 46.0 1.0 HB3 B:ASN473 4.9 77.4 1.0 HA B:ASP493 5.0 63.7 1.0 HB3 B:ASN472 5.0 54.5 1.0 HB2 B:ASN472 5.0 54.5 1.0

P.Paracuellos, D.C.Briggs, F.Carafoli, T.Loncar, E.Hohenester. Insights Into Collagen Uptake By C-Type Mannose Receptors From the Crystal Structure of ENDO180 Domains 1-4. Structure V. 23 2133 2015.
ISSN: ISSN 0969-2126
PubMed: 26481812
DOI: 10.1016/J.STR.2015.09.004