Sodium in PDB 7nx0: Extracellular Tg and Egf-Like Domains of Alk

All present enzymatic activity of Extracellular Tg and Egf-Like Domains of Alk:
2.7.10.1;

The structure of Extracellular Tg and Egf-Like Domains of Alk, PDB code: 7nx0 was solved by S.De Munck, S.N.Savvides, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.26 / 1.95
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	129.11, 129.11, 109.75, 90, 90, 120
R / Rfree (%)	16.9 / 19.6

The binding sites of Sodium atom in the Extracellular Tg and Egf-Like Domains of Alk (pdb code 7nx0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Extracellular Tg and Egf-Like Domains of Alk, PDB code: 7nx0:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Extracellular Tg and Egf-Like Domains of Alk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Extracellular Tg and Egf-Like Domains of Alk within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:119.6 occ:1.00 O B:HOH693 2.6 46.5 1.0 O C:HOH685 2.6 51.0 1.0 O C:HOH722 2.7 42.5 1.0 O C:LEU136 2.9 41.7 1.0 HA C:LEU136 3.2 55.5 1.0 HB2 B:SER71 3.3 49.3 1.0 HZ1 C:LYS130 3.3 52.6 1.0 O C:HIS135 3.4 41.6 1.0 O B:HOH539 3.5 48.8 1.0 HD12 C:LEU136 3.5 65.0 1.0 HZ2 C:LYS130 3.5 52.6 1.0 C C:LEU136 3.7 42.6 1.0 O C:HOH557 3.7 53.8 1.0 HB3 B:SER71 3.8 49.3 1.0 O C:HOH561 3.8 85.0 1.0 O B:HOH550 3.9 39.1 1.0 NZ C:LYS130 3.9 43.8 1.0 CA C:LEU136 3.9 46.2 1.0 CB B:SER71 4.0 41.1 1.0 HG B:SER71 4.2 51.0 1.0 HZ3 C:LYS130 4.4 52.6 1.0 C C:HIS135 4.4 43.2 1.0 O B:HOH680 4.4 57.5 1.0 CD1 C:LEU136 4.5 54.2 1.0 OG B:SER71 4.6 42.5 1.0 N C:LEU136 4.7 43.8 1.0 HA C:SER137 4.7 52.7 1.0 HE2 C:LYS130 4.7 48.8 1.0 N C:SER137 4.8 42.8 1.0 HD13 C:LEU136 4.8 65.0 1.0 HG C:LEU136 4.9 62.4 1.0 H B:THR72 4.9 42.8 1.0 CE C:LYS130 4.9 40.6 1.0 HD11 C:LEU136 5.0 65.0 1.0 O B:HOH645 5.0 41.5 1.0

Sodium binding site 2 out of 4 in the Extracellular Tg and Egf-Like Domains of Alk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Extracellular Tg and Egf-Like Domains of Alk within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:79.1 occ:1.00 NA B:NA401 3.1 137.3 1.0 HB3 C:PRO169 3.2 55.5 1.0 HB2 C:PRO169 3.4 55.5 1.0 CB C:PRO169 3.7 46.2 1.0 HG2 C:PRO169 3.9 56.4 1.0 CG C:PRO169 4.2 46.9 1.0 HG3 C:PRO169 4.4 56.4 1.0 O B:HOH503 4.5 45.6 1.0 OE2 B:GLU165 4.8 48.6 1.0

Sodium binding site 3 out of 4 in the Extracellular Tg and Egf-Like Domains of Alk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Extracellular Tg and Egf-Like Domains of Alk within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:137.3 occ:1.00 HG3 C:PRO169 3.0 56.4 1.0 NA C:NA402 3.1 79.1 1.0 HB3 C:PRO169 3.2 55.5 1.0 O B:HOH503 3.3 45.6 1.0 HA3 B:GLY77 3.5 45.9 1.0 HB2 B:SER76 3.5 50.9 1.0 HG2 C:PRO169 3.5 56.4 1.0 CG C:PRO169 3.6 46.9 1.0 O B:SER76 3.6 37.6 1.0 CB C:PRO169 3.8 46.2 1.0 C B:SER76 3.9 38.2 1.0 HB3 B:SER76 4.0 50.9 1.0 HE22 C:GLN176 4.0 70.0 1.0 O B:HOH533 4.1 44.9 1.0 CB B:SER76 4.1 42.4 1.0 CA B:GLY77 4.2 38.2 1.0 OE2 B:GLU165 4.2 48.6 1.0 HB2 C:PRO169 4.3 55.5 1.0 N B:GLY77 4.3 37.5 1.0 NE2 C:GLN176 4.5 58.4 1.0 O B:HOH634 4.5 42.3 1.0 HA2 B:GLY77 4.5 45.9 1.0 O C:HOH728 4.6 127.9 1.0 HE21 C:GLN176 4.6 70.0 1.0 CA B:SER76 4.6 41.0 1.0 H B:SER76 4.6 48.5 1.0 O B:HOH632 4.7 45.4 1.0 H B:GLY77 4.9 45.0 1.0 HA C:PRO169 4.9 53.2 1.0 CD C:PRO169 5.0 44.7 1.0

Sodium binding site 4 out of 4 in the Extracellular Tg and Egf-Like Domains of Alk


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Extracellular Tg and Egf-Like Domains of Alk within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:106.0 occ:1.00 O B:HOH589 2.7 61.1 1.0 HG2 B:GLN298 2.7 63.5 1.0 O B:HOH700 3.0 55.0 1.0 HZ2 B:TRP304 3.5 58.5 1.0 OE1 B:GLN298 3.5 58.0 1.0 HD3 B:ARG78 3.5 63.1 1.0 CG B:GLN298 3.6 52.9 1.0 HH11 B:ARG78 3.6 70.6 1.0 HB3 B:GLN298 3.7 58.9 1.0 HD2 B:ARG78 3.9 63.1 1.0 CD B:GLN298 4.0 56.1 1.0 HA B:GLN298 4.0 54.2 1.0 CB B:GLN298 4.1 49.0 1.0 CZ2 B:TRP304 4.1 48.8 1.0 CD B:ARG78 4.1 52.6 1.0 NH1 B:ARG78 4.1 58.8 1.0 HE1 B:TRP304 4.1 53.0 1.0 HB2 B:ALA312 4.2 46.5 1.0 O B:HOH578 4.2 79.9 1.0 H B:GLY299 4.3 53.5 1.0 O B:HOH562 4.3 41.4 1.0 HG3 B:GLN298 4.3 63.5 1.0 HH12 B:ARG78 4.5 70.6 1.0 NE1 B:TRP304 4.6 44.1 1.0 CA B:GLN298 4.6 45.1 1.0 NE B:ARG78 4.6 55.8 1.0 CE2 B:TRP304 4.7 46.8 1.0 CZ B:ARG78 4.7 57.8 1.0 N B:GLY299 5.0 44.6 1.0 HB2 B:GLN298 5.0 58.9 1.0

S.De Munck, M.Provost, M.Kurikawa, I.Omori, J.Mukohyama, J.Felix, Y.Bloch, O.Abdel-Wahab, J.F.Bazan, A.Yoshimi, S.N.Savvides. Structural Basis of Cytokine-Mediated Activation of Alk Family Receptors. Nature 2021.
ISSN: ESSN 1476-4687
PubMed: 34646012
DOI: 10.1038/S41586-021-03959-5