Calcium in PDB 7yl6: Cell Surface Protein Ywfg Protein Complexed with Alpha-1,2-Mannobiose

The structure of Cell Surface Protein Ywfg Protein Complexed with Alpha-1,2-Mannobiose, PDB code: 7yl6 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)	41.51 / 2.95
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	43.454, 276.634, 321.75, 90, 90, 90
R / Rfree (%)	21.1 / 26.8

The binding sites of Calcium atom in the Cell Surface Protein Ywfg Protein Complexed with Alpha-1,2-Mannobiose (pdb code 7yl6). 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 Complexed with Alpha-1,2-Mannobiose, PDB code: 7yl6:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cell Surface Protein Ywfg Protein Complexed with Alpha-1,2-Mannobiose


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 Complexed with Alpha-1,2-Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:64.3 occ:1.00 OD1 A:ASN156 2.1 67.5 1.0 OD2 A:ASP152 2.2 40.9 1.0 OD1 A:ASP152 2.3 75.4 1.0 O A:TYR154 2.5 59.1 1.0 OD2 A:ASP166 2.5 53.9 1.0 CG A:ASP152 2.6 48.1 1.0 CG A:ASN156 3.2 60.1 1.0 CG A:ASP166 3.4 59.9 1.0 C A:TYR154 3.7 64.0 1.0 OD1 A:ASP166 3.7 57.1 1.0 N A:ASN156 3.8 61.3 1.0 CB A:ASN156 3.9 54.5 1.0 CB A:ASP152 4.1 47.8 1.0 CA A:GLY136 4.1 62.0 1.0 ND2 A:ASN156 4.3 64.6 1.0 CA A:ASN156 4.4 64.7 1.0 C A:TYR155 4.5 58.2 1.0 NZ A:LYS150 4.5 53.7 1.0 N A:TYR155 4.5 61.2 1.0 CA A:TYR155 4.5 63.1 1.0 CA A:TYR154 4.6 59.0 1.0 O A:GLY136 4.7 86.3 1.0 CB A:TYR154 4.7 56.7 1.0 CB A:ASP166 4.8 59.4 1.0 N A:TYR154 4.9 58.1 1.0 C A:GLY136 4.9 62.8 1.0 CD2 A:TYR154 4.9 64.4 1.0 O A:GLY135 4.9 72.9 1.0 CA A:ASP152 5.0 50.1 1.0

Calcium binding site 2 out of 2 in the Cell Surface Protein Ywfg Protein Complexed with Alpha-1,2-Mannobiose


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 Complexed with Alpha-1,2-Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:54.4 occ:1.00 OD2 B:ASP152 2.1 48.4 1.0 OD1 B:ASN156 2.2 75.1 1.0 OD2 B:ASP166 2.4 46.0 1.0 OD1 B:ASP152 2.4 66.0 1.0 O B:TYR154 2.4 61.2 1.0 CG B:ASP152 2.5 50.3 1.0 CG B:ASP166 3.3 51.5 1.0 CG B:ASN156 3.4 61.4 1.0 OD1 B:ASP166 3.6 57.1 1.0 C B:TYR154 3.7 61.8 1.0 N B:ASN156 3.9 64.4 1.0 CA B:GLY136 4.0 57.6 1.0 CB B:ASP152 4.1 45.5 1.0 CB B:ASN156 4.1 54.3 1.0 NZ B:LYS150 4.3 46.9 1.0 ND2 B:ASN156 4.4 60.9 1.0 N B:TYR155 4.5 58.6 1.0 CA B:TYR155 4.5 61.9 1.0 C B:TYR155 4.5 69.8 1.0 CA B:ASN156 4.6 57.2 1.0 O B:GLY136 4.6 61.8 1.0 CA B:TYR154 4.7 69.5 1.0 CB B:TYR154 4.7 65.9 1.0 CB B:ASP166 4.7 49.6 1.0 O B:GLY135 4.8 70.9 1.0 C B:GLY136 4.8 55.8 1.0 N B:GLY136 4.8 59.1 1.0 N B:TYR154 4.9 74.8 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