Calcium in PDB 9lsc: Crystal Structure of MRFP1 with A Grafted Calcium-Binding Sequence and Two Bound Calcium Ions in A Calcium-Free Solution

The structure of Crystal Structure of MRFP1 with A Grafted Calcium-Binding Sequence and Two Bound Calcium Ions in A Calcium-Free Solution, PDB code: 9lsc 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)	37.56 / 1.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.69, 79.07, 65.68, 90, 91.07, 90
R / Rfree (%)	19.3 / 20.8

The binding sites of Calcium atom in the Crystal Structure of MRFP1 with A Grafted Calcium-Binding Sequence and Two Bound Calcium Ions in A Calcium-Free Solution (pdb code 9lsc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of MRFP1 with A Grafted Calcium-Binding Sequence and Two Bound Calcium Ions in A Calcium-Free Solution, PDB code: 9lsc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of MRFP1 with A Grafted Calcium-Binding Sequence and Two Bound Calcium Ions 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 Two Bound Calcium Ions in A Calcium-Free Solution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:18.8 occ:1.00 OD1 A:ASP154 2.0 16.8 1.0 OD1 A:ASP158 2.0 15.6 1.0 O A:GLU160 2.1 15.4 1.0 OD1 A:ASP156 2.1 16.2 1.0 OE2 A:GLU162 2.1 14.9 1.0 OE1 A:GLU162 2.2 14.3 1.0 CD A:GLU162 2.5 14.7 1.0 CG A:ASP158 2.9 15.4 1.0 CG A:ASP154 3.1 17.8 1.0 CG A:ASP156 3.1 16.6 1.0 C A:GLU160 3.2 15.5 1.0 OD2 A:ASP158 3.3 15.3 1.0 CA A:CA302 3.5 20.2 1.0 OD2 A:ASP156 3.6 16.0 1.0 N A:GLU160 3.7 15.7 1.0 CA A:ASP154 3.9 15.2 1.0 CA A:GLU160 3.9 15.2 1.0 OD2 A:ASP154 3.9 19.9 1.0 CB A:ASP154 4.0 17.0 1.0 CG A:GLU162 4.0 16.0 1.0 N A:ASP158 4.0 16.6 1.0 N A:ASP156 4.0 18.2 1.0 N A:GLY155 4.1 16.9 1.0 CB A:ASP158 4.3 15.8 1.0 CB A:GLU160 4.3 16.4 1.0 N A:ALA161 4.3 15.8 1.0 N A:GLY159 4.4 17.6 1.0 CB A:ASP156 4.4 17.9 1.0 C A:ASP154 4.4 17.5 1.0 N A:GLY157 4.5 18.4 1.0 C A:ALA161 4.5 15.7 1.0 CA A:ASP158 4.5 15.8 1.0 O A:HOH566 4.5 17.7 1.0 CA A:ASP156 4.5 19.4 1.0 N A:GLU162 4.5 15.7 1.0 CA A:ALA161 4.6 16.6 1.0 C A:ASP156 4.6 18.8 1.0 C A:GLY159 4.7 18.4 1.0 C A:ASP158 4.7 17.1 1.0 CB A:GLU162 4.9 16.2 1.0 O A:ALA161 4.9 16.7 1.0 O A:HOH533 4.9 16.8 1.0 C A:GLY155 5.0 18.9 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of MRFP1 with A Grafted Calcium-Binding Sequence and Two Bound Calcium Ions 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 Two Bound Calcium Ions in A Calcium-Free Solution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:20.2 occ:1.00 O A:HOH533 2.1 16.8 1.0 OD2 A:ASP156 2.1 16.0 1.0 OD2 A:ASP158 2.1 15.3 1.0 OE2 A:GLU162 2.1 14.9 1.0 O A:HOH566 2.1 17.7 1.0 CG A:ASP156 3.0 16.6 1.0 CD A:GLU162 3.1 14.7 1.0 CG A:ASP158 3.2 15.4 1.0 OD1 A:ASP156 3.3 16.2 1.0 CA A:CA301 3.5 18.8 1.0 OD1 A:ASP158 3.6 15.6 1.0 CG A:GLU162 3.8 16.0 1.0 OE1 A:GLU162 4.0 14.3 1.0 O A:HOH460 4.2 17.4 1.0 O A:HOH426 4.3 17.6 1.0 CB A:ASP156 4.4 17.9 1.0 CB A:ASP158 4.5 15.8 1.0 O A:GLU160 4.8 15.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of MRFP1 with A Grafted Calcium-Binding Sequence and Two Bound Calcium Ions 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 3 of Crystal Structure of MRFP1 with A Grafted Calcium-Binding Sequence and Two Bound Calcium Ions in A Calcium-Free Solution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:20.3 occ:1.00 OD2 B:ASP156 2.1 18.2 1.0 OE1 B:GLU162 2.1 15.0 1.0 O B:HOH515 2.1 17.3 1.0 OD2 B:ASP158 2.1 15.7 1.0 O B:HOH543 2.1 17.5 1.0 CG B:ASP156 3.0 16.2 1.0 CD B:GLU162 3.1 13.7 1.0 CG B:ASP158 3.2 17.2 1.0 OD1 B:ASP156 3.3 16.9 1.0 CA B:CA302 3.5 19.2 1.0 OD1 B:ASP158 3.6 15.9 1.0 CG B:GLU162 3.8 16.2 1.0 OE2 B:GLU162 4.0 16.0 1.0 O B:HOH489 4.1 31.5 1.0 O B:HOH449 4.2 18.8 1.0 O B:HOH437 4.3 17.5 1.0 CB B:ASP156 4.4 18.8 1.0 CB B:ASP158 4.5 15.9 1.0 O B:GLU160 4.8 14.7 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of MRFP1 with A Grafted Calcium-Binding Sequence and Two Bound Calcium Ions 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 4 of Crystal Structure of MRFP1 with A Grafted Calcium-Binding Sequence and Two Bound Calcium Ions in A Calcium-Free Solution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:19.2 occ:1.00 OD1 B:ASP154 2.0 17.4 1.0 OD1 B:ASP158 2.1 15.9 1.0 OD1 B:ASP156 2.1 16.9 1.0 O B:GLU160 2.1 14.7 1.0 OE1 B:GLU162 2.1 15.0 1.0 OE2 B:GLU162 2.2 16.0 1.0 CD B:GLU162 2.5 13.7 1.0 CG B:ASP158 3.0 17.2 1.0 CG B:ASP156 3.1 16.2 1.0 CG B:ASP154 3.1 16.4 1.0 C B:GLU160 3.2 14.6 1.0 OD2 B:ASP158 3.3 15.7 1.0 CA B:CA301 3.5 20.3 1.0 OD2 B:ASP156 3.5 18.2 1.0 N B:GLU160 3.7 16.8 1.0 CA B:ASP154 3.9 16.7 1.0 CA B:GLU160 3.9 16.3 1.0 OD2 B:ASP154 4.0 17.9 1.0 CB B:ASP154 4.0 16.9 1.0 N B:ASP156 4.0 17.8 1.0 CG B:GLU162 4.0 16.2 1.0 N B:ASP158 4.0 16.5 1.0 N B:GLY155 4.1 17.0 1.0 CB B:ASP158 4.3 15.9 1.0 CB B:GLU160 4.3 16.0 1.0 N B:ALA161 4.3 14.7 1.0 N B:GLY159 4.4 16.6 1.0 CB B:ASP156 4.4 18.8 1.0 C B:ASP154 4.4 16.8 1.0 N B:GLY157 4.5 19.1 1.0 O B:HOH515 4.5 17.3 1.0 C B:ALA161 4.5 16.4 1.0 CA B:ASP158 4.5 17.0 1.0 N B:GLU162 4.5 14.5 1.0 CA B:ASP156 4.5 19.5 1.0 CA B:ALA161 4.6 15.7 1.0 C B:ASP156 4.6 19.1 1.0 C B:GLY159 4.7 16.9 1.0 C B:ASP158 4.7 17.0 1.0 CB B:GLU162 4.9 15.6 1.0 O B:ALA161 4.9 16.1 1.0 C B:GLY155 5.0 19.5 1.0 O B:HOH543 5.0 17.5 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