Calcium in PDB 5h6u: Structure of Alginate-Binding Protein ALGQ2 in Complex with An Alginate Pentasaccharide

The structure of Structure of Alginate-Binding Protein ALGQ2 in Complex with An Alginate Pentasaccharide, PDB code: 5h6u was solved by K.Uenishi, A.Kaneko, Y.Maruyama, B.Mikami, K.Murata, W.Hashimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.68 / 2.01
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.107, 59.179, 82.724, 84.62, 90.16, 87.99
R / Rfree (%)	20.1 / 26.1

The binding sites of Calcium atom in the Structure of Alginate-Binding Protein ALGQ2 in Complex with An Alginate Pentasaccharide (pdb code 5h6u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Alginate-Binding Protein ALGQ2 in Complex with An Alginate Pentasaccharide, PDB code: 5h6u:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of Alginate-Binding Protein ALGQ2 in Complex with An Alginate Pentasaccharide


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-Binding Protein ALGQ2 in Complex with An Alginate Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:29.2 occ:1.00 OD1 A:ASN173 2.2 27.9 1.0 OD1 A:ASP171 2.3 32.8 1.0 OD1 A:ASP179 2.3 24.3 1.0 O A:LYS177 2.3 26.8 1.0 OD1 A:ASN175 2.5 31.7 1.0 OE2 A:GLU180 2.5 26.6 1.0 OE1 A:GLU180 2.6 31.5 1.0 CD A:GLU180 2.9 28.6 1.0 CG A:ASN173 3.0 28.1 1.0 ND2 A:ASN173 3.3 34.3 1.0 CG A:ASP179 3.4 32.1 1.0 CG A:ASN175 3.4 30.4 1.0 C A:LYS177 3.5 33.2 1.0 CG A:ASP171 3.5 36.6 1.0 ND2 A:ASN175 3.8 29.4 1.0 OD2 A:ASP179 4.0 29.1 1.0 CA A:ASP171 4.0 30.7 1.0 N A:LYS177 4.0 37.0 1.0 N A:ASP179 4.0 30.7 1.0 CA A:LYS177 4.2 32.9 1.0 CB A:ASP171 4.2 29.3 1.0 N A:ASN175 4.3 33.9 1.0 CG A:GLU180 4.4 25.8 1.0 CB A:ASN173 4.4 26.4 1.0 OD2 A:ASP171 4.4 32.7 1.0 C A:ASP171 4.4 30.2 1.0 N A:ASN173 4.5 27.2 1.0 N A:ALA178 4.5 31.2 1.0 N A:GLY174 4.5 28.6 1.0 CB A:LYS177 4.5 33.0 1.0 O A:HOH666 4.6 25.9 1.0 N A:GLU180 4.6 27.4 1.0 CB A:ASP179 4.6 26.1 1.0 CA A:ALA178 4.7 31.5 1.0 CB A:ASN175 4.7 29.2 1.0 O A:ASP171 4.7 31.9 1.0 CA A:ASP179 4.8 31.2 1.0 CA A:ASN173 4.8 29.8 1.0 N A:GLY176 4.8 35.4 1.0 C A:ASN173 4.8 32.9 1.0 CA A:ASN175 4.9 33.6 1.0 C A:ALA178 4.9 31.1 1.0 C A:ASN175 4.9 36.5 1.0 C A:GLY176 5.0 33.6 1.0 N A:PRO172 5.0 32.0 1.0

Calcium binding site 2 out of 6 in the Structure of Alginate-Binding Protein ALGQ2 in Complex with An Alginate Pentasaccharide


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-Binding Protein ALGQ2 in Complex with An Alginate Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:41.6 occ:1.00 O B:HOH724 2.3 36.1 1.0 O A:HOH659 2.3 36.9 1.0 O B:ASP121 2.4 29.5 1.0 OD2 A:ASP440 2.4 35.4 1.0 O A:LYS436 2.6 38.8 1.0 C B:ASP121 3.5 30.8 1.0 CG A:ASP440 3.6 35.1 1.0 C A:LYS436 3.7 34.5 1.0 CG A:LYS436 3.9 35.2 1.0 CB B:ASP121 4.2 29.1 1.0 CA B:ASP121 4.2 29.6 1.0 OD1 A:ASP440 4.4 33.0 1.0 CA A:LYS436 4.5 30.6 1.0 O A:HOH750 4.5 32.0 1.0 CD1 A:TYR437 4.5 32.7 1.0 N B:GLY122 4.5 34.5 1.0 CB A:ASP440 4.6 26.7 1.0 N A:TYR437 4.7 30.0 1.0 CA A:TYR437 4.7 28.5 1.0 OD1 B:ASN123 4.7 30.7 1.0 CA B:GLY122 4.7 26.8 1.0 CB A:LYS436 4.7 34.8 1.0 ND2 B:ASN123 4.8 29.5 1.0 CD A:LYS436 4.8 43.9 1.0 CE1 A:TYR437 4.9 36.3 1.0 CG B:ASP121 4.9 32.1 1.0 CG B:ASN123 4.9 29.8 1.0

Calcium binding site 3 out of 6 in the Structure of Alginate-Binding Protein ALGQ2 in Complex with An Alginate Pentasaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Alginate-Binding Protein ALGQ2 in Complex with An Alginate Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:49.2 occ:1.00 O A:HOH768 2.4 29.0 1.0 O A:GLY133 2.4 27.2 1.0 O A:HOH784 2.5 31.8 1.0 O A:HOH658 3.0 31.9 1.0 O A:HOH843 3.0 30.7 1.0 C A:GLY133 3.6 21.7 1.0 N A:GLY133 4.2 25.7 1.0 CA A:VAL134 4.4 22.6 1.0 N A:VAL134 4.4 23.5 1.0 CA A:GLY133 4.5 23.8 1.0 O A:GLN310 4.7 22.9 1.0 CG A:ARG309 4.8 23.5 1.0 CB A:ARG309 4.8 26.8 1.0 O A:ARG309 4.9 26.2 1.0 CG2 A:VAL134 4.9 24.1 1.0

Calcium binding site 4 out of 6 in the Structure of Alginate-Binding Protein ALGQ2 in Complex with An Alginate Pentasaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Alginate-Binding Protein ALGQ2 in Complex with An Alginate Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:46.3 occ:1.00 OD1 B:ASP179 2.1 39.7 1.0 O B:LYS177 2.3 43.7 1.0 OD1 B:ASN173 2.4 50.2 1.0 OD1 B:ASN175 2.5 44.4 1.0 OD1 B:ASP171 2.5 44.2 1.0 OE2 B:GLU180 2.5 50.5 1.0 OE1 B:GLU180 2.8 42.0 1.0 CD B:GLU180 2.9 45.4 1.0 CG B:ASN173 3.1 46.6 1.0 CG B:ASP179 3.2 38.9 1.0 ND2 B:ASN173 3.2 42.5 1.0 CG B:ASN175 3.4 44.5 1.0 C B:LYS177 3.4 46.9 1.0 CG B:ASP171 3.6 48.9 1.0 ND2 B:ASN175 3.6 44.1 1.0 OD2 B:ASP179 3.7 41.8 1.0 N B:ASP179 3.8 41.7 1.0 N B:LYS177 4.0 45.6 1.0 CA B:LYS177 4.1 44.4 1.0 CG B:GLU180 4.2 37.1 1.0 CA B:ASP171 4.3 42.7 1.0 CB B:ASP179 4.4 36.9 1.0 CB B:LYS177 4.4 44.1 1.0 N B:GLU180 4.4 37.8 1.0 CB B:ASP171 4.4 46.1 1.0 N B:ASN175 4.4 49.3 1.0 N B:ALA178 4.5 32.3 1.0 OD2 B:ASP171 4.5 48.0 1.0 CB B:ASN173 4.5 44.6 1.0 CA B:ASP179 4.5 39.5 1.0 CA B:ALA178 4.7 39.0 1.0 CB B:ASN175 4.7 51.8 1.0 C B:ALA178 4.8 42.5 1.0 N B:ASN173 4.8 44.3 1.0 C B:ASP171 4.8 44.9 1.0 N B:GLY174 4.8 47.2 1.0 C B:ASP179 4.9 38.6 1.0 CA B:ASN175 4.9 46.1 1.0 N B:GLY176 4.9 51.0 1.0 C B:ASN173 4.9 48.0 1.0 CA B:ASN173 5.0 44.3 1.0

Calcium binding site 5 out of 6 in the Structure of Alginate-Binding Protein ALGQ2 in Complex with An Alginate Pentasaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Alginate-Binding Protein ALGQ2 in Complex with An Alginate Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca507 b:59.6 occ:1.00 O2 B:BEM504 2.3 32.0 1.0 O B:HOH733 2.7 29.7 1.0 O4 B:BEM505 3.0 40.8 1.0 O B:HOH783 3.3 40.8 1.0 C2 B:BEM504 3.4 34.6 1.0 O5 B:BEM504 3.4 30.2 1.0 C1 B:BEM504 3.5 34.6 1.0 O6B B:BEM504 3.7 34.9 1.0 C4 B:BEM504 4.0 26.6 1.0 NZ B:LYS251 4.1 45.0 1.0 C6 B:BEM504 4.1 30.9 1.0 O B:HOH621 4.1 31.2 1.0 C5 B:BEM504 4.1 28.8 1.0 C3 B:BEM505 4.1 46.0 1.0 C4 B:BEM505 4.1 41.4 1.0 O3 B:BEM505 4.2 38.6 1.0 C3 B:BEM504 4.3 32.4 1.0 OD1 B:ASP189 4.4 32.0 1.0 O6A B:BEM504 4.4 36.7 1.0 OD2 B:ASP21 4.7 31.3 1.0 O3 B:BEM504 4.7 36.2 1.0 CE B:LYS251 4.9 38.5 1.0 CD B:PRO188 4.9 20.9 1.0

Calcium binding site 6 out of 6 in the Structure of Alginate-Binding Protein ALGQ2 in Complex with An Alginate Pentasaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Alginate-Binding Protein ALGQ2 in Complex with An Alginate Pentasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca508 b:38.6 occ:1.00 O B:HOH700 2.4 25.4 1.0 O B:GLY133 2.6 27.6 1.0 O B:HOH812 2.7 35.5 1.0 O B:HOH837 2.7 36.3 1.0 C B:GLY133 3.7 23.0 1.0 O B:HOH851 4.0 37.6 1.0 N B:GLY133 4.3 21.3 1.0 O B:GLN310 4.6 18.1 1.0 CA B:VAL134 4.6 19.9 1.0 N B:VAL134 4.6 28.0 1.0 O B:HOH695 4.7 34.3 1.0 CA B:GLY133 4.7 24.2 1.0 CB B:ARG309 4.7 26.4 1.0 O B:ARG309 4.8 25.6 1.0

A.Kaneko, K.Uenishi, Y.Maruyama, N.Mizuno, S.Baba, T.Kumasaka, B.Mikami, K.Murata, W.Hashimoto. A Solute-Binding Protein in the Closed Conformation Induces Atp Hydrolysis in A Bacterial Atp-Binding Cassette Transporter Involved in the Import of Alginate J. Biol. Chem. V. 292 15681 2017.
ISSN: ESSN 1083-351X
PubMed: 28768763
DOI: 10.1074/JBC.M117.793992