Sodium in PDB 7w52: Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin

The structure of Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin, PDB code: 7w52 was solved by S.Takeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.67 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.987, 96.26, 426.923, 90, 90, 90
R / Rfree (%)	21 / 24.6

The structure of Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin also contains other interesting chemical elements:

Calcium

(Ca)

12 atoms

The binding sites of Sodium atom in the Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin (pdb code 7w52). 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 Fragmin Domain-1 (15-160) in Complex with Actin, PDB code: 7w52:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin


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 Fragmin Domain-1 (15-160) in Complex with Actin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:50.2 occ:1.00 O A:VAL30 2.3 32.2 1.0 O A:HOH748 2.3 55.5 1.0 O A:HOH682 2.5 45.6 1.0 O A:HOH538 2.8 45.6 1.0 O A:HOH709 3.3 53.9 1.0 C A:VAL30 3.3 27.8 1.0 CB A:PHE31 3.9 37.4 1.0 CA A:PHE31 4.0 35.1 1.0 N A:VAL30 4.1 33.3 1.0 N A:PHE31 4.1 30.5 1.0 OD1 A:ASP56 4.2 67.7 1.0 O A:HOH710 4.3 52.5 1.0 CA A:VAL30 4.3 34.6 1.0 OE1 A:GLU93 4.7 51.8 1.0 CB A:VAL30 4.9 29.6 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin


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 Fragmin Domain-1 (15-160) in Complex with Actin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na403 b:46.5 occ:1.00 O C:VAL30 2.1 35.9 1.0 O C:HOH611 2.4 42.2 1.0 O C:HOH713 2.4 45.6 1.0 O C:HOH724 2.5 48.4 1.0 O C:HOH768 2.5 59.0 1.0 C C:VAL30 3.3 29.4 1.0 N C:VAL30 4.0 29.3 1.0 OD2 C:ASP56 4.0 57.9 1.0 CA C:VAL30 4.1 31.9 1.0 N C:PHE31 4.2 34.7 1.0 CA C:PHE31 4.3 40.7 1.0 CB C:PHE31 4.4 38.3 1.0 CB C:VAL30 4.5 38.4 1.0 OD1 C:ASP56 4.6 59.0 1.0 CG C:ASP56 4.8 53.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin


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 Fragmin Domain-1 (15-160) in Complex with Actin within 5.0Å range: probe atom residue distance (Å) B Occ E:Na403 b:35.9 occ:1.00 O E:VAL30 2.2 40.0 1.0 O E:HOH674 2.4 55.4 1.0 O E:HOH535 2.4 42.7 1.0 O E:HOH515 2.5 42.3 1.0 O E:HOH508 2.5 51.5 1.0 O E:HOH633 2.6 45.9 1.0 C E:VAL30 3.3 36.6 1.0 N E:VAL30 4.0 34.6 1.0 OD2 E:ASP56 4.0 53.4 1.0 N E:PHE31 4.2 34.4 1.0 CA E:VAL30 4.2 38.4 1.0 CA E:PHE31 4.3 40.6 1.0 CB E:PHE31 4.3 35.0 1.0 OE1 E:GLU93 4.6 45.0 1.0 CB E:VAL30 4.7 44.0 1.0 OE2 E:GLU93 4.8 48.8 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Fragmin Domain-1 (15-160) in Complex with Actin


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 Fragmin Domain-1 (15-160) in Complex with Actin within 5.0Å range: probe atom residue distance (Å) B Occ G:Na403 b:58.1 occ:1.00 O G:HOH502 2.3 56.8 1.0 O G:HOH676 2.4 63.1 1.0 O G:VAL30 2.4 34.5 1.0 O G:HOH649 2.5 44.1 1.0 O G:HOH510 2.5 44.0 1.0 O G:HOH588 3.0 51.8 1.0 O G:HOH672 3.2 54.8 1.0 C G:VAL30 3.4 37.1 1.0 OD2 G:ASP56 3.8 79.0 1.0 CB G:PHE31 3.9 34.9 1.0 N G:VAL30 4.0 33.7 1.0 CA G:PHE31 4.1 37.4 1.0 N G:PHE31 4.1 37.9 1.0 CA G:VAL30 4.3 33.9 1.0 OE1 G:GLU93 4.5 56.7 1.0 OE2 G:GLU93 4.5 56.1 1.0 CG G:ASP56 4.6 73.6 1.0 OD1 G:ASP56 4.7 71.7 1.0 CD G:GLU93 4.9 48.8 1.0 CG G:PHE31 5.0 41.1 1.0 CB G:VAL30 5.0 33.5 1.0

Y.Kanematsu, A.Narita, T.Oda, R.Koike, M.Ota, Y.Takano, K.Moritsugu, I.Fujiwara, K.Tanaka, H.Komatsu, T.Nagae, N.Watanabe, M.Iwasa, Y.Maeda, S.Takeda. Structures and Mechanisms of Actin Atp Hydrolysis. Proc.Natl.Acad.Sci.Usa V. 119 41119 2022.
ISSN: ESSN 1091-6490
PubMed: 36252034
DOI: 10.1073/PNAS.2122641119