Calcium in PDB 7w4z: Crystal Structure of Fragmin Domain-1 in Complex with Actin (Amppnp- Form)

The structure of Crystal Structure of Fragmin Domain-1 in Complex with Actin (Amppnp- Form), PDB code: 7w4z was solved by S.Takeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.35 / 1.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.09, 91.07, 114.85, 90, 90, 90
R / Rfree (%)	14.3 / 15.8

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

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Fragmin Domain-1 in Complex with Actin (Amppnp- Form) (pdb code 7w4z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Fragmin Domain-1 in Complex with Actin (Amppnp- Form), PDB code: 7w4z:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Fragmin Domain-1 in Complex with Actin (Amppnp- Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Fragmin Domain-1 in Complex with Actin (Amppnp- Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:11.4 occ:0.80 O B:HOH485 2.0 13.7 0.2 O B:PRO122 2.3 14.1 1.0 O B:HOH485 2.3 16.8 0.8 OD2 B:ASP115 2.4 11.0 0.2 O A:HOH840 2.4 17.3 1.0 OE1 A:GLU167 2.4 12.8 0.8 OD2 B:ASP115 2.4 11.2 0.8 O B:GLY120 2.5 14.0 1.0 OD1 B:ASP115 2.5 11.1 0.8 OD1 B:ASP115 2.7 11.6 0.2 CG B:ASP115 2.8 10.1 0.8 CG B:ASP115 2.9 11.1 0.2 OE1 A:GLU167 3.4 12.2 0.2 C B:GLY120 3.4 14.0 1.0 C B:PRO122 3.5 12.9 1.0 CD A:GLU167 3.5 12.8 0.8 CA B:GLY120 4.0 13.4 1.0 CD A:GLU167 4.0 12.1 0.2 OE2 A:GLU167 4.0 13.3 0.8 O A:HOH652 4.1 16.4 1.0 N B:PRO122 4.1 12.7 1.0 C B:LEU121 4.2 12.4 1.0 OE2 A:GLU167 4.3 10.9 0.2 O A:HOH532 4.3 28.7 1.0 CA B:PRO122 4.3 12.8 1.0 CB B:ASP115 4.4 11.2 0.2 CB B:ASP115 4.4 10.2 0.8 N B:LEU121 4.4 13.1 1.0 O A:HOH516 4.4 19.4 1.0 O B:HOH348 4.5 18.7 1.0 O B:HOH513 4.5 37.5 1.0 N B:VAL123 4.5 11.4 1.0 O B:LEU121 4.5 13.7 1.0 CA B:VAL123 4.7 11.0 1.0 CD B:PRO122 4.7 11.8 1.0 O B:HOH359 4.7 16.4 1.0 O B:HOH438 4.8 25.9 1.0 CA B:LEU121 4.8 13.4 1.0 CG A:GLU167 4.8 12.2 0.8 NE2 B:GLN124 4.8 11.5 1.0 CB B:PRO122 4.8 12.4 1.0 CB A:GLU167 4.9 12.4 0.8 CB A:GLU167 4.9 11.6 0.2

Calcium binding site 2 out of 2 in the Crystal Structure of Fragmin Domain-1 in Complex with Actin (Amppnp- Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Fragmin Domain-1 in Complex with Actin (Amppnp- Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:10.4 occ:1.00 OD1 B:ASP70 2.3 11.3 1.0 O B:VAL152 2.4 11.9 1.0 O B:HOH409 2.4 11.6 1.0 O B:GLY69 2.4 10.6 1.0 O B:HOH466 2.4 12.7 1.0 OE2 B:GLU103 2.4 10.8 1.0 OE1 B:GLU103 2.5 10.1 1.0 CD B:GLU103 2.8 9.5 1.0 C B:GLY69 3.4 9.9 1.0 C B:VAL152 3.5 11.8 1.0 CG B:ASP70 3.5 10.1 1.0 N B:VAL152 3.9 12.1 1.0 CA B:ASP70 4.0 9.5 1.0 N B:ASP70 4.1 10.3 1.0 CA B:VAL152 4.2 11.5 1.0 O B:HOH330 4.3 10.7 1.0 CA B:GLY69 4.3 11.1 1.0 CG2 B:VAL152 4.3 12.9 1.0 C B:GLY151 4.3 13.6 1.0 CG B:GLU103 4.3 10.1 1.0 CB B:ASP70 4.4 10.3 1.0 O B:HOH382 4.4 17.4 1.0 OD2 B:ASP70 4.4 10.6 1.0 O B:HOH436 4.6 15.6 1.0 CA B:GLY151 4.6 13.0 1.0 N B:GLU153 4.6 11.8 1.0 OG1 B:THR100 4.6 11.1 1.0 C B:GLU153 4.7 11.6 1.0 N B:THR154 4.7 11.4 1.0 O B:HOH326 4.7 26.5 1.0 OG1 B:THR99 4.8 10.1 1.0 O B:HOH344 4.8 11.3 1.0 CA B:GLU153 4.9 13.1 1.0 CA B:THR99 4.9 10.8 1.0 N B:THR100 4.9 10.1 1.0 CB B:VAL152 4.9 12.6 1.0 O B:GLY151 5.0 18.0 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