Calcium in PDB 7yl4: Cell Surface Protein Ywfg Protein (Apo Form)

The structure of Cell Surface Protein Ywfg Protein (Apo Form), PDB code: 7yl4 was solved by W.Tsuchiya, Z.Fujimoto, C.Suzuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.53 / 2.50
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	43.219, 272.93, 320.332, 90, 90, 90
R / Rfree (%)	24.6 / 28

The binding sites of Calcium atom in the Cell Surface Protein Ywfg Protein (Apo Form) (pdb code 7yl4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cell Surface Protein Ywfg Protein (Apo Form), PDB code: 7yl4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cell Surface Protein Ywfg Protein (Apo Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cell Surface Protein Ywfg Protein (Apo Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:75.0 occ:1.00 OD1 A:ASN156 2.1 54.6 1.0 OD2 A:ASP152 2.1 54.8 1.0 O A:TYR154 2.3 75.7 1.0 OD1 A:ASP152 2.5 82.2 1.0 CG A:ASP152 2.6 56.0 1.0 OD2 A:ASP166 2.7 58.4 1.0 CG A:ASN156 3.2 62.7 1.0 N A:ASN156 3.5 70.2 1.0 C A:TYR154 3.5 57.6 1.0 CB A:ASN156 3.6 67.0 1.0 CG A:ASP166 3.7 71.0 1.0 OD1 A:ASP166 4.0 70.6 1.0 CB A:ASP152 4.1 48.9 1.0 CA A:GLY136 4.1 64.9 1.0 CA A:ASN156 4.2 68.7 1.0 C A:TYR155 4.3 62.0 1.0 ND2 A:ASN156 4.3 72.1 1.0 CA A:TYR155 4.3 54.2 1.0 N A:TYR155 4.3 51.9 1.0 CA A:TYR154 4.5 52.4 1.0 O A:GLY135 4.6 47.9 1.0 O A:GLY136 4.6 71.1 1.0 CB A:TYR154 4.7 50.4 1.0 N A:GLY136 4.7 54.9 1.0 N A:TYR154 4.8 51.7 1.0 NZ A:LYS150 4.8 51.8 1.0 CD2 A:TYR154 4.8 49.6 1.0 C A:GLY136 4.9 70.6 1.0 C A:GLY135 4.9 51.9 1.0 O A:ASP117 5.0 47.3 1.0

Calcium binding site 2 out of 2 in the Cell Surface Protein Ywfg Protein (Apo Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cell Surface Protein Ywfg Protein (Apo Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:71.5 occ:1.00 OD2 B:ASP152 2.1 59.5 1.0 OD1 B:ASN156 2.2 62.0 1.0 OD2 B:ASP166 2.2 39.6 1.0 O B:TYR154 2.4 63.6 1.0 O B:HOH705 2.6 32.8 1.0 OD1 B:ASP152 2.7 70.2 1.0 CG B:ASP152 2.7 59.8 1.0 CG B:ASP166 3.2 46.7 1.0 CG B:ASN156 3.2 52.6 1.0 OD1 B:ASP166 3.5 40.1 1.0 C B:TYR154 3.5 58.5 1.0 N B:ASN156 3.7 60.3 1.0 CB B:ASN156 3.8 51.5 1.0 CB B:ASP152 4.2 56.1 1.0 C B:TYR155 4.2 64.2 1.0 CA B:TYR155 4.2 56.3 1.0 N B:TYR155 4.3 63.7 1.0 CA B:ASN156 4.3 49.9 1.0 CA B:GLY136 4.4 42.3 1.0 ND2 B:ASN156 4.4 51.4 1.0 NZ B:LYS150 4.5 39.8 1.0 CB B:ASP166 4.6 40.8 1.0 CA B:TYR154 4.6 59.2 1.0 N B:TYR154 4.7 70.5 1.0 CB B:TYR154 4.8 56.5 1.0 CE1 B:PHE175 4.9 58.9 1.0 CZ B:PHE175 5.0 59.3 1.0 CD2 B:TYR154 5.0 69.8 1.0

W.Tsuchiya, Z.Fujimoto, N.Inagaki, H.Nakagawa, M.Tanaka, H.Kimoto-Nira, T.Yamazaki, C.Suzuki. Cell-Surface Protein Ywfg of Lactococcus Lactis Binds to Alpha-1,2-Linked Mannose. Plos One V. 18 73955 2023.
ISSN: ESSN 1932-6203
PubMed: 36602978
DOI: 10.1371/JOURNAL.PONE.0273955