Calcium in PDB 9lsf: Crystal Structure of MRFP1 with A Grafted Calcium-Binding Sequence and One Bound Calcium Ion in A Calcium-Free Solution

The structure of Crystal Structure of MRFP1 with A Grafted Calcium-Binding Sequence and One Bound Calcium Ion in A Calcium-Free Solution, PDB code: 9lsf was solved by R.Uehara, Y.Kamiya, S.Maeda, K.Okamoto, S.Toya, R.Chiba, H.Amesaka, K.Takano, H.Matsumura, S.-I.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.08 / 1.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.25, 86.01, 109.95, 90, 90, 90
R / Rfree (%)	17.5 / 19.8

The binding sites of Calcium atom in the Crystal Structure of MRFP1 with A Grafted Calcium-Binding Sequence and One Bound Calcium Ion in A Calcium-Free Solution (pdb code 9lsf). 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 MRFP1 with A Grafted Calcium-Binding Sequence and One Bound Calcium Ion in A Calcium-Free Solution, PDB code: 9lsf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of MRFP1 with A Grafted Calcium-Binding Sequence and One Bound Calcium Ion in A Calcium-Free Solution


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 MRFP1 with A Grafted Calcium-Binding Sequence and One Bound Calcium Ion in A Calcium-Free Solution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:22.9 occ:1.00 OD1 A:ASP156 2.2 28.2 1.0 O A:GLU160 2.3 22.2 1.0 OE1 A:GLU162 2.3 25.1 1.0 OD1 A:ASP158 2.4 26.3 1.0 OD1 A:ASP154 2.4 24.7 1.0 O A:HOH418 2.7 34.2 1.0 OE2 A:GLU162 2.9 27.7 1.0 CD A:GLU162 3.0 24.2 1.0 CG A:ASP158 3.3 31.3 1.0 CG A:ASP156 3.3 34.9 1.0 C A:GLU160 3.4 22.3 1.0 CG A:ASP154 3.5 25.9 1.0 OD2 A:ASP158 3.8 30.5 1.0 OD2 A:ASP156 3.9 37.8 1.0 N A:GLU160 3.9 23.0 1.0 CA A:GLU160 4.1 24.6 1.0 N A:ASP156 4.2 26.9 1.0 CA A:ASP154 4.2 19.9 1.0 CB A:ASP154 4.2 19.7 1.0 CB A:GLU160 4.3 29.0 1.0 N A:ASP158 4.3 26.8 1.0 OD2 A:ASP154 4.3 27.9 1.0 N A:GLY155 4.4 21.2 1.0 CB A:ASP158 4.4 28.6 1.0 CG A:GLU162 4.5 18.6 1.0 CB A:ASP156 4.5 32.8 1.0 N A:ALA161 4.5 20.2 1.0 N A:GLY157 4.7 29.5 1.0 C A:ASP154 4.7 25.1 1.0 C A:ALA161 4.7 18.1 1.0 CA A:ASP156 4.7 27.8 1.0 CA A:ASP158 4.7 26.2 1.0 N A:GLY159 4.8 25.7 1.0 CA A:ALA161 4.8 18.9 1.0 N A:GLU162 4.8 16.9 1.0 C A:ASP156 4.8 32.4 1.0 C A:ASP158 4.9 30.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of MRFP1 with A Grafted Calcium-Binding Sequence and One Bound Calcium Ion in A Calcium-Free Solution


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 MRFP1 with A Grafted Calcium-Binding Sequence and One Bound Calcium Ion in A Calcium-Free Solution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:26.6 occ:1.00 OD1 B:ASP156 2.1 27.3 1.0 OE1 B:GLU162 2.1 31.9 1.0 OD1 B:ASP158 2.2 26.9 1.0 OD1 B:ASP154 2.3 24.1 1.0 O B:GLU160 2.3 21.3 1.0 OE2 B:GLU162 2.3 23.7 1.0 CD B:GLU162 2.5 21.3 1.0 CG B:ASP158 3.0 31.0 1.0 CG B:ASP156 3.1 32.5 1.0 OD2 B:ASP158 3.4 35.3 1.0 CG B:ASP154 3.4 24.8 1.0 O B:HOH401 3.4 34.8 1.0 C B:GLU160 3.4 21.6 1.0 OD2 B:ASP156 3.6 41.4 1.0 N B:GLU160 3.9 23.4 1.0 CG B:GLU162 4.0 31.6 1.0 N B:ASP156 4.0 30.1 1.0 CA B:GLU160 4.1 23.4 1.0 CA B:ASP154 4.2 21.8 1.0 CB B:ASP154 4.2 21.2 1.0 N B:ASP158 4.2 27.9 1.0 N B:GLY155 4.2 24.1 1.0 CB B:GLU160 4.2 27.6 1.0 OD2 B:ASP154 4.2 28.9 1.0 CB B:ASP156 4.3 29.3 1.0 CB B:ASP158 4.3 28.6 1.0 CA B:ASP156 4.5 30.6 1.0 N B:ALA161 4.5 20.4 1.0 N B:GLY157 4.6 29.8 1.0 C B:ASP156 4.6 31.3 1.0 C B:ASP154 4.7 26.3 1.0 CA B:ASP158 4.7 28.3 1.0 C B:ALA161 4.7 21.5 1.0 N B:GLU162 4.7 19.0 1.0 N B:GLY159 4.7 26.3 1.0 CA B:ALA161 4.8 20.4 1.0 C B:ASP158 4.8 28.4 1.0 CB B:GLU162 4.9 23.1 1.0 C B:GLY159 5.0 25.6 1.0

R.Uehara, Y.Kamiya, S.Maeda, K.Okamoto, S.Toya, R.Chiba, H.Amesaka, K.Takano, H.Matsumura, S.I.Tanaka. Enhanced Secretion Through Type 1 Secretion System By Grafting A Calcium-Binding Sequence to Modify the Folding of Cargo Proteins Protein Sci. V. 34 2025.
ISSN: ESSN 1469-896X
DOI: 10.1002/PRO.70165