Sodium in PDB 4l73: CA2+-Bound Mthk Rck Domain at 2.5 Angstrom

The structure of CA2+-Bound Mthk Rck Domain at 2.5 Angstrom, PDB code: 4l73 was solved by F.J.Smith, B.S.Rothberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.51 / 2.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	67.960, 67.960, 159.891, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 22.6

The structure of CA2+-Bound Mthk Rck Domain at 2.5 Angstrom also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	5 atoms

The binding sites of Sodium atom in the CA2+-Bound Mthk Rck Domain at 2.5 Angstrom (pdb code 4l73). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the CA2+-Bound Mthk Rck Domain at 2.5 Angstrom, PDB code: 4l73:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the CA2+-Bound Mthk Rck Domain at 2.5 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of CA2+-Bound Mthk Rck Domain at 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:26.4 occ:1.00 O A:HOH509 2.2 40.8 1.0 O B:HOH502 2.2 44.0 1.0 O A:ASP287 2.2 53.3 1.0 OD1 A:ASP287 2.4 65.3 1.0 C A:ASP287 3.2 52.3 1.0 NH2 B:ARG308 3.3 86.2 1.0 CG A:ASP287 3.6 63.0 1.0 CA A:ASP287 3.8 53.5 1.0 O A:HOH513 4.1 26.8 1.0 CB A:ASP287 4.2 57.2 1.0 NA A:NA405 4.3 27.5 1.0 N A:VAL288 4.4 49.9 1.0 CZ B:ARG308 4.6 87.2 1.0 OD2 A:ASP287 4.6 68.0 1.0 CA A:VAL288 4.7 50.5 1.0

Sodium binding site 2 out of 8 in the CA2+-Bound Mthk Rck Domain at 2.5 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of CA2+-Bound Mthk Rck Domain at 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:27.5 occ:1.00 O A:HOH513 2.0 26.8 1.0 OD2 A:ASP287 2.4 68.0 1.0 O A:HOH511 2.4 38.2 1.0 O B:HOH506 2.4 45.3 1.0 OD1 A:ASP287 2.6 65.3 1.0 CG A:ASP287 2.8 63.0 1.0 O A:HOH537 3.6 62.6 1.0 NA B:NA406 3.7 52.5 1.0 NA A:NA404 4.3 26.4 1.0 CB A:ASP287 4.3 57.2 1.0 O B:HOH502 4.4 44.0 1.0 O B:HOH519 4.6 38.5 0.5 NA A:NA408 4.8 63.3 1.0 O B:HOH540 4.8 60.1 1.0 CD1 B:LEU281 4.9 56.1 1.0 OD2 A:ASP284 4.9 74.9 1.0 O A:HOH509 4.9 40.8 1.0 OD1 B:ASP284 5.0 58.0 1.0

Sodium binding site 3 out of 8 in the CA2+-Bound Mthk Rck Domain at 2.5 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of CA2+-Bound Mthk Rck Domain at 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:55.5 occ:1.00 O A:HOH530 2.3 51.6 1.0 O A:SER137 2.4 63.1 1.0 O A:HOH521 2.5 37.8 1.0 O A:GLY156 2.6 61.2 1.0 C A:SER137 3.5 63.2 1.0 C A:GLY156 3.7 59.4 1.0 N A:GLY136 4.2 68.1 1.0 N A:SER137 4.2 66.6 1.0 C A:GLY136 4.2 72.8 1.0 CA A:GLU138 4.3 65.0 1.0 N A:GLU138 4.3 63.8 1.0 CA A:GLY156 4.4 60.2 1.0 N A:VAL139 4.5 49.4 1.0 O A:GLY136 4.5 80.0 1.0 CA A:SER137 4.5 64.6 1.0 CA A:GLY136 4.6 72.0 1.0 N A:ALA157 4.6 57.2 1.0 CA A:ALA157 4.8 57.8 1.0 C A:GLU138 4.9 59.7 1.0 O A:LEU134 4.9 55.1 1.0

Sodium binding site 4 out of 8 in the CA2+-Bound Mthk Rck Domain at 2.5 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of CA2+-Bound Mthk Rck Domain at 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:75.5 occ:1.00 O A:HOH542 2.4 60.3 1.0 O A:ARG176 2.6 82.2 1.0 OD2 A:ASP202 2.7 83.7 1.0 NH2 A:ARG116 3.7 0.1 1.0 CG A:ASP202 3.7 80.7 1.0 C A:ARG176 3.8 78.5 1.0 OD1 A:ASP202 4.1 85.0 1.0 OG A:SER204 4.5 76.5 1.0 CA A:ARG176 4.6 77.1 1.0 N A:GLY177 4.7 74.9 1.0 CA A:GLY177 4.8 73.9 1.0 CZ A:ARG116 4.9 99.5 1.0

Sodium binding site 5 out of 8 in the CA2+-Bound Mthk Rck Domain at 2.5 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of CA2+-Bound Mthk Rck Domain at 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:63.3 occ:1.00 O A:HOH537 2.4 62.6 1.0 OD2 A:ASP284 2.6 74.9 1.0 OD2 B:ASP287 2.6 73.5 1.0 OD1 A:ASP284 2.7 70.9 1.0 CG A:ASP284 3.0 68.0 1.0 OD1 B:ASP287 3.2 72.1 1.0 OD2 A:ASP287 3.3 68.0 1.0 CG B:ASP287 3.3 69.2 1.0 NA B:NA406 3.3 52.5 1.0 O A:HOH511 3.4 38.2 1.0 CG A:ASP287 4.3 63.0 1.0 CB A:ASP284 4.5 58.9 1.0 CB A:ASP287 4.6 57.2 1.0 CB B:ASP287 4.8 59.8 1.0 NA A:NA405 4.8 27.5 1.0 O B:HOH506 5.0 45.3 1.0

Sodium binding site 6 out of 8 in the CA2+-Bound Mthk Rck Domain at 2.5 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of CA2+-Bound Mthk Rck Domain at 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:67.9 occ:1.00 O B:HOH533 2.3 40.2 1.0 O B:HOH517 2.5 52.9 1.0 O B:HOH503 2.6 44.9 1.0 O B:SER137 2.7 55.8 1.0 O B:GLY156 3.1 65.6 1.0 C B:SER137 3.6 56.0 1.0 CA B:GLU138 4.2 54.4 1.0 C B:GLY156 4.3 61.2 1.0 C B:GLY136 4.3 72.1 1.0 N B:GLU138 4.3 54.5 1.0 N B:GLY136 4.3 72.8 1.0 N B:SER137 4.4 65.4 1.0 O B:GLY136 4.4 76.5 1.0 CA B:GLY136 4.6 75.9 1.0 CA B:SER137 4.6 60.1 1.0 N B:VAL139 4.8 40.6 1.0 CA B:GLY156 4.9 63.3 1.0

Sodium binding site 7 out of 8 in the CA2+-Bound Mthk Rck Domain at 2.5 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of CA2+-Bound Mthk Rck Domain at 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:63.3 occ:1.00 O B:HOH513 2.3 47.0 1.0 O B:ARG176 2.6 68.3 1.0 OD2 B:ASP202 2.6 57.3 1.0 O B:HOH522 2.9 48.9 1.0 O B:HOH527 3.3 46.2 1.0 NH2 B:ARG116 3.5 72.8 1.0 CG B:ASP202 3.7 54.0 1.0 C B:ARG176 3.7 64.2 1.0 O B:ALA178 3.8 51.0 1.0 OD1 B:ASP202 4.1 51.1 1.0 CB B:VAL205 4.5 46.7 1.0 CZ B:ARG116 4.5 71.0 1.0 CA B:ARG176 4.5 59.9 1.0 NH1 B:ARG116 4.6 68.5 1.0 CG2 B:VAL205 4.6 42.5 1.0 O B:VAL175 4.7 46.0 1.0 N B:GLY177 4.7 60.9 1.0 CA B:GLY177 4.8 59.7 1.0 OG B:SER204 4.9 67.1 1.0 N B:ALA178 4.9 44.9 1.0 CA B:VAL205 4.9 48.0 1.0 CB B:ASP202 5.0 52.8 1.0 C B:ALA178 5.0 45.2 1.0

Sodium binding site 8 out of 8 in the CA2+-Bound Mthk Rck Domain at 2.5 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of CA2+-Bound Mthk Rck Domain at 2.5 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:52.5 occ:1.00 OD2 B:ASP287 2.3 73.5 1.0 O B:HOH506 2.4 45.3 1.0 O A:HOH511 2.6 38.2 1.0 OD2 B:ASP284 2.6 59.5 1.0 O A:HOH537 2.9 62.6 1.0 OD1 B:ASP284 3.3 58.0 1.0 CG B:ASP284 3.3 57.1 1.0 NA A:NA408 3.3 63.3 1.0 CG B:ASP287 3.6 69.2 1.0 NA A:NA405 3.7 27.5 1.0 OD2 A:ASP287 4.0 68.0 1.0 O B:HOH519 4.1 38.5 0.5 CB B:ASP287 4.2 59.8 1.0 OD1 B:ASP287 4.5 72.1 1.0 O B:HOH521 4.8 45.8 1.0 CB B:ASP284 4.8 53.9 1.0 O A:HOH513 5.0 26.8 1.0

F.J.Smith, V.P.Pau, G.Cingolani, B.S.Rothberg. Structural Basis of Allosteric Interactions Among Ca(2+)-Binding Sites in A K(+) Channel Rck Domain. Nat Commun V. 4 2621 2013.
ISSN: ESSN 2041-1723
PubMed: 24126388
DOI: 10.1038/NCOMMS3621