Sodium in PDB 4z79: Leiomodin-1 Actin-Binding Site 2 (ABS2)

The structure of Leiomodin-1 Actin-Binding Site 2 (ABS2), PDB code: 4z79 was solved by G.Rebowski, M.Boczkowska, R.Dominguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.18 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.019, 52.192, 75.890, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 17.7

The structure of Leiomodin-1 Actin-Binding Site 2 (ABS2) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Leiomodin-1 Actin-Binding Site 2 (ABS2) (pdb code 4z79). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Leiomodin-1 Actin-Binding Site 2 (ABS2), PDB code: 4z79:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Leiomodin-1 Actin-Binding Site 2 (ABS2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Leiomodin-1 Actin-Binding Site 2 (ABS2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:31.9 occ:1.00 O A:HOH770 2.6 30.5 1.0 HA A:ALA354 2.7 10.2 1.0 HG2 A:LYS326 3.3 13.8 1.0 CA A:ALA354 3.6 8.5 1.0 O A:GLU353 3.9 9.5 1.0 HA A:LYS326 4.1 11.0 1.0 O A:ALA354 4.2 8.8 1.0 CG A:LYS326 4.2 11.5 1.0 HB1 A:ALA354 4.2 11.3 1.0 HB2 A:ALA354 4.3 11.3 1.0 C A:ALA354 4.3 8.2 1.0 CB A:ALA354 4.3 9.4 1.0 N A:ALA354 4.4 8.3 1.0 HE3 A:LYS326 4.5 30.2 1.0 C A:GLU353 4.5 9.4 1.0 HG3 A:LYS326 4.6 13.8 1.0 HB3 A:LYS326 4.6 12.1 1.0 CB A:LYS326 4.8 10.1 1.0 CA A:LYS326 4.9 9.1 1.0 HD2 A:PHE357 4.9 11.3 1.0 O A:HOH684 5.0 16.8 1.0

Sodium binding site 2 out of 3 in the Leiomodin-1 Actin-Binding Site 2 (ABS2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Leiomodin-1 Actin-Binding Site 2 (ABS2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:23.9 occ:1.00 HZ3 A:LYS387 2.1 10.8 0.5 HD3 A:LYS387 2.7 13.7 0.5 O A:LEU383 2.7 7.0 1.0 O A:HOH690 2.7 8.7 1.0 HZ2 A:LYS387 2.8 10.8 0.5 NZ A:LYS387 2.8 9.0 0.5 HA A:ASN414 3.0 10.6 1.0 O A:LYS384 3.2 8.0 1.0 HD22 A:ASN414 3.2 8.7 1.0 O A:ASN386 3.2 8.2 1.0 HG2 A:LYS387 3.2 13.5 0.5 HA A:LYS384 3.3 7.6 1.0 O A:GLN413 3.3 11.1 1.0 CD A:LYS387 3.4 11.4 0.5 HB2 A:ASN414 3.4 9.5 1.0 C A:LYS384 3.4 6.4 1.0 HZ2 A:LYS387 3.5 14.4 0.5 HZ1 A:LYS387 3.5 10.8 0.5 HD2 A:LYS387 3.5 13.7 0.5 CE A:LYS387 3.6 13.4 0.5 ND2 A:ASN414 3.6 7.2 1.0 C A:LEU383 3.8 7.2 1.0 CA A:LYS384 3.8 6.3 1.0 CA A:ASN414 3.8 8.8 1.0 CB A:ASN414 3.9 7.9 1.0 HG3 A:LYS387 3.9 13.5 0.5 HE2 A:LYS387 4.0 16.0 0.5 C A:ASN386 4.0 6.2 1.0 CG A:LYS387 4.0 11.3 0.5 N A:ALA385 4.0 6.9 1.0 H A:ASN386 4.0 7.8 1.0 CG A:ASN414 4.1 8.3 1.0 N A:ASN386 4.1 6.5 1.0 C A:ALA385 4.1 8.4 1.0 HD21 A:ASN414 4.1 8.7 1.0 HA A:LYS387 4.2 9.3 0.5 N A:LYS384 4.2 6.0 1.0 HA A:LYS387 4.2 12.9 0.5 NZ A:LYS387 4.3 12.0 0.5 C A:GLN413 4.3 11.3 1.0 H A:ASN415 4.3 10.5 1.0 HE3 A:LYS387 4.4 16.0 0.5 HZ3 A:LYS387 4.4 14.4 0.5 CA A:ALA385 4.5 9.7 1.0 HA A:ALA385 4.5 11.7 1.0 H A:ALA385 4.5 8.3 1.0 O A:ALA385 4.5 9.6 1.0 N A:ASN414 4.5 7.8 1.0 CA A:ASN386 4.7 6.7 1.0 N A:LYS387 4.7 9.6 1.0 CG A:LYS387 4.7 12.4 0.5 OG1 A:THR416 4.8 9.9 1.0 HZ1 A:LYS387 4.8 14.4 0.5 HB3 A:ASN414 4.8 9.5 1.0 HD2 A:LYS387 4.8 16.9 0.5 CA A:LYS387 4.9 10.8 0.5 CA A:LYS387 4.9 7.7 0.5 CD A:LYS387 4.9 14.1 0.5 HG1 A:THR416 4.9 11.9 1.0 HG2 A:LYS387 4.9 14.9 0.5 HA A:LEU383 4.9 9.4 1.0 N A:ASN415 4.9 8.8 1.0 C A:ASN414 4.9 8.2 1.0

Sodium binding site 3 out of 3 in the Leiomodin-1 Actin-Binding Site 2 (ABS2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Leiomodin-1 Actin-Binding Site 2 (ABS2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na510 b:16.8 occ:1.00 HH21 A:ARG483 3.2 17.0 1.0 HH22 A:ARG483 3.3 17.0 1.0 NH2 A:ARG483 3.5 14.2 1.0 HD2 A:ARG483 4.4 19.2 1.0 CZ A:ARG483 4.7 13.5 1.0

M.Boczkowska, G.Rebowski, E.Kremneva, P.Lappalainen, R.Dominguez. How Leiomodin and Tropomodulin Use A Common Fold For Different Actin Assembly Functions. Nat Commun V. 6 8314 2015.
ISSN: ESSN 2041-1723
PubMed: 26370058
DOI: 10.1038/NCOMMS9314