Calcium in PDB 8pz4: Structure of Alginate Transporter, Alge, Solved at Wavelength 2.755 A

The structure of Structure of Alginate Transporter, Alge, Solved at Wavelength 2.755 A, PDB code: 8pz4 was solved by R.Duman, K.El Omari, V.Mykhaylyk, C.Orr, A.Wagner, L.Vogeley, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.58 / 1.77
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	57.35, 74.69, 115.9, 90, 102.48, 90
R / Rfree (%)	18.8 / 23.4

The binding sites of Calcium atom in the Structure of Alginate Transporter, Alge, Solved at Wavelength 2.755 A (pdb code 8pz4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Alginate Transporter, Alge, Solved at Wavelength 2.755 A, PDB code: 8pz4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Alginate Transporter, Alge, Solved at Wavelength 2.755 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Alginate Transporter, Alge, Solved at Wavelength 2.755 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:36.2 occ:1.00 O A:ALA125 2.3 26.7 1.0 O A:HOH1250 2.4 31.3 1.0 O A:GLU133 2.4 17.6 1.0 O A:TYR130 2.5 20.2 1.0 OE1 A:GLU133 2.6 25.5 1.0 O A:THR128 2.7 23.2 1.0 C A:ALA125 3.4 23.9 1.0 C A:GLU133 3.5 21.1 1.0 C A:TYR130 3.6 25.3 1.0 CD A:GLU133 3.6 25.6 1.0 C A:THR128 3.7 25.5 1.0 OG1 A:THR128 3.8 27.1 1.0 CB A:GLU133 3.8 21.5 1.0 CB A:ALA125 3.9 26.2 1.0 CA A:ALA125 3.9 25.7 1.0 CA A:GLU133 4.0 20.8 1.0 N A:TYR130 4.1 21.5 1.0 N A:THR128 4.2 23.4 1.0 N A:GLU133 4.2 19.4 1.0 O A:HOH1157 4.3 33.4 1.0 CG A:GLU133 4.3 20.3 1.0 O A:HOH1229 4.4 38.1 1.0 CA A:TYR130 4.4 22.3 1.0 C A:ALA129 4.4 30.1 1.0 N A:PRO131 4.4 22.6 1.0 CA A:THR128 4.4 23.1 1.0 O A:HOH1136 4.4 22.3 1.0 N A:GLY126 4.5 24.9 1.0 OE2 A:GLU133 4.5 22.0 1.0 CA A:PRO131 4.5 24.0 1.0 N A:HIS134 4.6 16.4 1.0 N A:ALA129 4.6 23.9 1.0 CB A:THR128 4.7 27.4 1.0 C A:PRO131 4.8 21.8 1.0 CA A:ALA129 4.8 29.4 1.0 O A:ALA129 4.9 28.2 1.0 CA A:GLY126 4.9 28.9 1.0 CA A:HIS134 4.9 17.6 1.0 N A:LEU127 4.9 21.6 1.0 CB A:TYR130 4.9 23.0 1.0

Calcium binding site 2 out of 2 in the Structure of Alginate Transporter, Alge, Solved at Wavelength 2.755 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Alginate Transporter, Alge, Solved at Wavelength 2.755 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:76.0 occ:1.00 OD2 A:ASP46 2.1 54.5 1.0 O A:ALA50 2.1 61.8 1.0 O A:GLY52 2.3 59.4 1.0 OD1 A:ASP46 2.4 50.7 1.0 OD1 A:ASP44 2.4 46.2 1.0 CG A:ASP46 2.5 49.2 1.0 OD2 A:ASP44 3.0 46.9 1.0 CG A:ASP44 3.1 43.6 1.0 C A:ALA50 3.2 65.2 1.0 C A:GLY52 3.4 61.8 1.0 C A:PRO51 3.8 66.8 1.0 N A:ALA50 3.8 54.6 1.0 O A:PRO51 3.9 66.9 1.0 CA A:ALA50 4.0 59.0 1.0 CB A:ASP46 4.1 41.3 1.0 N A:GLY52 4.1 66.5 1.0 N A:PRO51 4.2 70.4 1.0 CA A:PRO51 4.3 68.7 1.0 N A:GLY53 4.3 60.2 1.0 CA A:GLY48 4.3 45.0 1.0 CA A:GLY53 4.3 56.6 1.0 CA A:GLY52 4.3 63.4 1.0 N A:GLY48 4.4 39.7 1.0 CB A:ALA50 4.4 57.1 1.0 CB A:ASP44 4.5 38.5 1.0 C A:GLY48 4.6 47.7 1.0 N A:THR49 4.6 46.6 1.0 N A:ASP46 4.8 38.4 1.0 CA A:ASP46 4.9 39.8 1.0 C A:GLY53 5.0 57.4 1.0

K.El Omari, R.Duman, V.Mykhaylyk, C.M.Orr, M.Latimer-Smith, G.Winter, V.Grama, F.Qu, K.Bountra, H.S.Kwong, M.Romano, R.I.Reis, L.Vogeley, L.Vecchia, C.D.Owen, S.Wittmann, M.Renner, M.Senda, N.Matsugaki, Y.Kawano, T.A.Bowden, I.Moraes, J.M.Grimes, E.J.Mancini, M.A.Walsh, C.R.Guzzo, R.J.Owens, E.Y.Jones, D.G.Brown, D.I.Stuart, K.Beis, A.Wagner. Experimental Phasing Opportunities For Macromolecular Crystallography at Very Long Wavelengths. Commun Chem V. 6 219 2023.
ISSN: ESSN 2399-3669
PubMed: 37828292
DOI: 10.1038/S42004-023-01014-0