Calcium in PDB 2pyh: Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide

The structure of Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide, PDB code: 2pyh was solved by H.J.Rozeboom, T.M.Bjerkan, K.H.Kalk, H.Ertesvag, S.Holtan, F.L.Aachman, S.Valla, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.40 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	169.551, 121.790, 45.068, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 27.9

The binding sites of Calcium atom in the Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide (pdb code 2pyh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide, PDB code: 2pyh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:12.8 occ:0.25 O A:GLU95 2.0 64.0 1.0 OD2 A:ASP133 2.3 58.3 1.0 OG1 A:THR97 2.4 59.6 1.0 OG A:SER91 2.7 55.6 1.0 N A:THR97 2.7 61.8 1.0 CG A:ASP133 2.9 58.2 1.0 CB A:THR97 2.9 59.5 1.0 OD1 A:ASP133 2.9 57.1 1.0 C A:GLU95 3.2 64.1 1.0 O A:ALA92 3.3 63.4 1.0 CA A:THR97 3.4 60.8 1.0 CB A:SER91 3.7 57.1 1.0 C A:GLU96 3.7 62.0 1.0 O A:GLY124 3.7 53.3 1.0 CA A:GLU96 3.9 61.7 1.0 N A:GLU96 4.0 63.2 1.0 OE1 A:GLU95 4.2 72.8 1.0 CB A:ASP133 4.2 57.3 1.0 CA A:GLU95 4.3 65.3 1.0 N A:ALA92 4.3 60.8 1.0 CB A:GLU95 4.3 67.7 1.0 C A:GLY124 4.3 55.5 1.0 CG2 A:THR97 4.3 59.3 1.0 C A:THR97 4.4 61.1 1.0 C A:ALA92 4.4 63.2 1.0 O A:THR97 4.4 60.6 1.0 C A:SER91 4.5 59.2 1.0 CA A:ASP133 4.6 58.4 1.0 N A:GLU95 4.7 65.3 1.0 CG A:GLU95 4.7 70.3 1.0 CA A:SER91 4.7 57.5 1.0 O A:GLU96 4.8 62.6 1.0 N A:GLY124 4.8 53.0 1.0 CA A:ALA92 4.8 61.8 1.0 N A:TYR125 4.9 56.8 1.0 CD A:GLU95 4.9 72.1 1.0 CA A:TYR125 5.0 58.6 1.0

Calcium binding site 2 out of 7 in the Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:80.9 occ:1.00 OD1 A:ASP112 4.2 69.7 1.0 OD2 A:ASP112 4.4 67.9 1.0 OD1 A:ASP169 4.5 49.6 1.0 OE1 A:GLU145 4.5 50.4 1.0 NH2 A:ARG111 4.6 62.1 1.0 CG A:ASP112 4.7 68.5 1.0 OE2 A:GLU145 4.7 49.4 1.0 NE A:ARG111 4.9 62.7 1.0

Calcium binding site 3 out of 7 in the Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:84.7 occ:1.00 OE2 A:GLU229 3.3 80.5 1.0 OE1 A:GLU229 3.6 80.7 1.0 CD A:GLU229 3.8 80.4 1.0

Calcium binding site 4 out of 7 in the Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:53.2 occ:0.75 O B:GLU95 2.2 63.2 1.0 OD2 B:ASP133 2.3 52.3 1.0 OG B:SER91 2.6 55.6 1.0 O B:ALA92 2.6 60.6 1.0 OG1 B:THR97 3.0 56.3 1.0 O B:GLY124 3.1 52.5 1.0 CG B:ASP133 3.1 52.4 1.0 OD1 B:ASP133 3.1 51.4 1.0 C B:GLU95 3.4 61.2 1.0 C B:GLY124 3.5 53.0 1.0 N B:THR97 3.7 56.9 1.0 C B:ALA92 3.8 60.3 1.0 CB B:SER91 3.8 55.1 1.0 CB B:THR97 4.0 56.4 1.0 N B:TYR125 4.0 54.5 1.0 N B:ALA92 4.1 57.3 1.0 CA B:TYR125 4.1 56.5 1.0 N B:GLU95 4.1 62.9 1.0 N B:GLY124 4.2 50.4 1.0 CA B:GLU95 4.2 63.1 1.0 N B:GLU96 4.3 58.7 1.0 CA B:GLY124 4.3 52.2 1.0 CA B:GLU96 4.4 56.5 1.0 CB B:GLU95 4.4 66.0 1.0 C B:SER91 4.4 55.7 1.0 CA B:ALA92 4.5 58.9 1.0 CA B:THR97 4.5 56.9 1.0 C B:GLU96 4.5 56.8 1.0 CB B:ASP133 4.5 52.7 1.0 OE1 B:GLU95 4.7 71.1 1.0 CA B:SER91 4.7 54.5 1.0 N B:TYR93 4.8 61.1 1.0 O B:SER91 4.9 54.7 1.0

Calcium binding site 5 out of 7 in the Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:82.4 occ:1.00 O B:THR114 2.4 60.5 1.0 O B:ARG111 2.6 64.6 1.0 C B:THR114 3.6 59.4 1.0 C B:ARG111 3.8 63.5 1.0 N B:THR114 4.2 60.4 1.0 CA B:THR114 4.5 59.6 1.0 N B:SER115 4.5 57.8 1.0 O B:ASP112 4.5 64.7 1.0 C B:ASP112 4.5 63.8 1.0 CA B:SER115 4.5 57.6 1.0 CA B:ARG111 4.7 62.2 1.0 CA B:ASP112 4.7 64.0 1.0 N B:ASP112 4.8 63.9 1.0 OG B:SER115 4.8 58.8 1.0 OG1 B:THR114 4.8 58.8 1.0 N B:ASN113 5.0 62.7 1.0

Calcium binding site 6 out of 7 in the Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:90.4 occ:1.00 OD2 B:ASP112 3.6 66.5 1.0 OD1 B:ASP112 3.8 66.1 1.0 CG B:ASP112 4.2 65.8 1.0 OD1 B:ASP169 4.2 48.7 1.0 OE1 B:GLU145 4.2 52.4 1.0 OE2 B:GLU145 4.4 49.5 1.0 NH2 B:ARG111 4.5 59.3 1.0 CD B:GLU145 4.8 50.8 1.0 NE B:ARG111 4.8 59.9 1.0

Calcium binding site 7 out of 7 in the Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Azotobacter Vinelandii Mannuronan C-5 Epimerase ALGE4 A-Module Complexed with Mannuronan Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:0.8 occ:0.50 OG1 B:THR310 3.0 60.0 1.0 CB B:THR310 3.8 59.7 1.0 O B:THR310 4.4 59.2 1.0 C B:THR310 4.5 58.8 1.0 CB B:ALA311 4.8 57.5 1.0 CA B:THR310 4.8 59.2 1.0 N B:ALA311 4.8 58.4 1.0 CG2 B:THR310 4.8 59.0 1.0

H.J.Rozeboom, T.M.Bjerkan, K.H.Kalk, H.Ertesvag, S.Holtan, F.L.Aachmann, S.Valla, B.W.Dijkstra. Structural and Mutational Characterization of the Catalytic A-Module of the Mannuronan C-5-Epimerase ALGE4 From Azotobacter Vinelandii. J.Biol.Chem. V. 283 23819 2008.
ISSN: ISSN 0021-9258
PubMed: 18574239
DOI: 10.1074/JBC.M804119200