Calcium in PDB 7ebp: The Structural Analysis of A.Muciniphila Sulfatase

The structure of The Structural Analysis of A.Muciniphila Sulfatase, PDB code: 7ebp was solved by R.Bao, C.C.Li, X.Y.Tang, Y.B.Zhu, Y.J.Song, N.L.Zhao, Q.Huang, X.Y.Mou, G.H.Luo, T.G.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.29 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.342, 112.722, 165.011, 90, 90, 90
R / Rfree (%)	18.6 / 20.9

The binding sites of Calcium atom in the The Structural Analysis of A.Muciniphila Sulfatase (pdb code 7ebp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The Structural Analysis of A.Muciniphila Sulfatase, PDB code: 7ebp:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The Structural Analysis of A.Muciniphila Sulfatase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structural Analysis of A.Muciniphila Sulfatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:12.3 occ:1.00 HE22 A:GLN369 1.6 17.0 1.0 OD2 A:ASP368 2.2 18.9 1.0 SG A:CYS81 2.3 20.3 1.0 OD1 A:ASP40 2.3 28.6 1.0 OD1 A:ASP41 2.3 19.2 1.0 NE2 A:GLN369 2.3 14.2 1.0 HE21 A:GLN369 2.7 17.0 1.0 CG A:ASP368 2.8 18.8 1.0 OD1 A:ASP368 2.8 14.4 1.0 CG A:ASP40 3.0 44.0 1.0 CG A:ASP41 3.1 17.9 1.0 HA A:CYS81 3.1 14.9 1.0 HB3 A:CYS81 3.2 19.5 1.0 CB A:CYS81 3.2 16.2 1.0 OD2 A:ASP40 3.3 23.0 1.0 CD A:GLN369 3.3 22.8 1.0 OD2 A:ASP41 3.5 17.2 1.0 HD2 A:HIS206 3.5 23.8 1.0 HZ3 A:LYS381 3.6 21.1 1.0 CA A:CYS81 3.6 12.5 1.0 H A:ASP41 3.6 18.5 1.0 HH22 A:ARG85 3.6 24.4 1.0 OE1 A:GLN369 3.7 21.8 1.0 HE3 A:LYS381 3.7 22.3 1.0 N A:ASP41 3.8 15.4 1.0 HA A:ASP40 3.9 14.9 1.0 H A:CYS81 4.0 14.9 1.0 HD2 A:LYS381 4.0 19.2 1.0 N A:CYS81 4.0 12.4 1.0 HB2 A:CYS81 4.1 19.5 1.0 HA A:ASP41 4.2 19.4 1.0 NZ A:LYS381 4.2 17.6 1.0 CB A:ASP368 4.2 15.5 1.0 HZ2 A:LYS130 4.2 68.8 1.0 HZ2 A:LYS381 4.3 21.1 1.0 CB A:ASP40 4.3 38.7 1.0 CB A:ASP41 4.3 17.4 1.0 C A:ASP40 4.3 17.1 1.0 CE A:LYS381 4.3 18.6 1.0 CA A:ASP40 4.4 12.4 1.0 CA A:ASP41 4.4 16.2 1.0 HB2 A:ASP368 4.4 18.6 1.0 CD2 A:HIS206 4.4 19.9 1.0 HH12 A:ARG85 4.4 21.6 1.0 H A:GLN369 4.5 17.1 1.0 NH2 A:ARG85 4.5 20.3 1.0 HO3 A:GOL602 4.5 22.4 1.0 HG3 A:GLN369 4.6 18.8 1.0 CG A:GLN369 4.6 15.7 1.0 HZ3 A:LYS130 4.6 68.8 1.0 HB3 A:ASP368 4.7 18.6 1.0 HB2 A:ASP41 4.7 20.8 1.0 CD A:LYS381 4.7 16.0 1.0 HB3 A:ASP40 4.8 46.4 1.0 NZ A:LYS130 4.9 57.3 1.0 HB2 A:ASP40 4.9 46.4 1.0 C A:LEU80 4.9 16.4 1.0 C A:CYS81 5.0 19.0 1.0 HH21 A:ARG85 5.0 24.4 1.0 HB3 A:ASP41 5.0 20.8 1.0 O3 A:GOL602 5.0 18.7 1.0

Calcium binding site 2 out of 2 in the The Structural Analysis of A.Muciniphila Sulfatase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structural Analysis of A.Muciniphila Sulfatase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:13.5 occ:1.00 OD1 B:ASP41 2.2 14.9 1.0 OD2 B:ASP368 2.2 19.9 1.0 OD1 B:ASP40 2.3 17.8 1.0 SG B:CYS81 2.3 19.3 1.0 NE2 B:GLN369 2.3 13.7 1.0 HE21 B:GLN369 2.7 16.5 1.0 CG B:ASP368 2.8 16.0 1.0 OD1 B:ASP368 2.8 13.5 1.0 CG B:ASP41 3.0 19.4 1.0 CG B:ASP40 3.0 29.5 1.0 HA B:CYS81 3.2 20.9 1.0 HB3 B:CYS81 3.2 24.1 1.0 CB B:CYS81 3.2 20.1 1.0 OD2 B:ASP40 3.3 22.6 1.0 CD B:GLN369 3.3 22.1 1.0 OD2 B:ASP41 3.4 18.2 1.0 H B:ASP41 3.5 21.7 1.0 HZ1 B:LYS381 3.5 23.2 1.0 HD2 B:HIS206 3.5 31.5 1.0 CA B:CYS81 3.6 17.4 1.0 OE1 B:GLN369 3.6 25.5 1.0 HE3 B:LYS381 3.7 24.5 1.0 HH12 B:ARG85 3.7 23.5 1.0 N B:ASP41 3.8 18.1 1.0 HA B:ASP40 3.9 16.8 1.0 H B:CYS81 4.0 18.2 1.0 N B:CYS81 4.0 15.2 1.0 HD2 B:LYS381 4.1 23.2 1.0 HB2 B:CYS81 4.1 24.1 1.0 HA B:ASP41 4.1 16.3 1.0 NZ B:LYS381 4.1 19.3 1.0 HZ3 B:LYS381 4.2 23.2 1.0 CB B:ASP41 4.2 13.6 1.0 CB B:ASP368 4.2 19.5 1.0 CB B:ASP40 4.3 24.5 1.0 CE B:LYS381 4.3 20.4 1.0 C B:ASP40 4.3 19.3 1.0 CA B:ASP41 4.3 13.6 1.0 HZ3 B:LYS130 4.3 68.8 1.0 CD2 B:HIS206 4.3 26.2 1.0 CA B:ASP40 4.4 14.0 1.0 HB2 B:ASP368 4.4 23.4 1.0 HH22 B:ARG85 4.4 19.8 1.0 H B:GLN369 4.5 17.1 1.0 HB2 B:ASP41 4.5 16.3 1.0 NH1 B:ARG85 4.6 19.6 1.0 HG3 B:GLN369 4.6 24.7 1.0 CG B:GLN369 4.6 20.6 1.0 HB3 B:ASP368 4.7 23.4 1.0 HB3 B:ASP40 4.7 29.4 1.0 CD B:LYS381 4.7 19.4 1.0 NE2 B:HIS206 4.7 26.9 1.0 HO3 B:GOL602 4.8 31.8 1.0 HZ1 B:LYS130 4.9 68.8 1.0 HB3 B:ASP41 4.9 16.3 1.0 HB2 B:ASP40 4.9 29.4 1.0 C B:LEU80 4.9 13.4 1.0

C.C.Li, X.Y.Tang, Y.B.Zhu, Y.J.Song, N.L.Zhao, Q.Huang, X.Y.Mou, G.H.Luo, T.G.Liu, A.P.Tong, H.Tang, R.Bao. Structural Analysis of the Sulfatase Amas From Akkermansia Muciniphila. Acta Crystallogr D Struct V. 77 1614 2021BIOL.
ISSN: ISSN 2059-7983
PubMed: 34866616
DOI: 10.1107/S2059798321010317