Calcium in PDB 7nsn: Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex

The structure of Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex, PDB code: 7nsn was solved by B.M.Kolaczkowski, O.V.Moroz, E.Blagova, G.J.Davies, K.S.Wilson, M.S.Moeler, A.S.Meyer, P.Westh, K.Jensen, K.B.R.M.Krogh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.92 / 2.29
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	94.605, 151.937, 114.007, 90, 94.63, 90
R / Rfree (%)	20.5 / 24.6

The binding sites of Calcium atom in the Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex (pdb code 7nsn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex, PDB code: 7nsn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1501 b:25.0 occ:1.00 O A:HOH1840 2.3 21.6 1.0 OD2 A:ASP1058 2.3 23.0 1.0 O A:HOH1670 2.3 26.4 1.0 O2 A:MVL1505 2.3 28.4 1.0 OD1 A:ASN1013 2.3 26.6 1.0 O A:HOH1689 2.4 18.3 1.0 O3 A:MVL1505 2.4 26.1 1.0 OE1 A:GLN1014 2.4 22.4 1.0 C2 A:MVL1505 3.4 26.5 1.0 CG A:ASP1058 3.4 24.8 1.0 CD A:GLN1014 3.4 23.5 1.0 C3 A:MVL1505 3.5 26.2 1.0 CG A:ASN1013 3.5 27.4 1.0 NE2 A:GLN1014 3.8 23.6 1.0 OD1 A:ASP1058 3.8 23.4 1.0 CB A:ASP1056 4.0 22.6 1.0 C1 A:MVL1505 4.1 28.0 1.0 ND2 A:ASN1013 4.3 24.1 1.0 OD1 A:ASP748 4.3 23.5 1.0 O A:HOH1690 4.4 17.5 1.0 C4 A:MVL1505 4.5 25.5 1.0 N1 A:MVL1505 4.5 28.7 1.0 OE1 A:GLU944 4.5 31.1 1.0 O A:ASP1056 4.6 19.7 1.0 CA A:ASN1013 4.6 23.2 1.0 CB A:ASP1058 4.6 22.2 1.0 CB A:ASN1013 4.6 24.0 1.0 N A:GLN1014 4.7 20.9 1.0 OE2 A:GLU997 4.7 27.8 1.0 CZ3 A:TRP747 4.7 17.9 1.0 CG A:GLN1014 4.8 23.3 1.0 OD2 A:ASP1056 4.8 27.6 1.0 CG A:ASP1056 4.9 23.2 1.0 O A:SER1012 4.9 20.4 1.0

Calcium binding site 2 out of 9 in the Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1502 b:29.1 occ:1.00 O A:GLY257 2.3 23.6 1.0 O A:SER48 2.3 30.9 1.0 OG A:SER48 2.3 31.0 1.0 O A:THR254 2.3 28.3 1.0 OD2 A:ASP389 2.4 33.4 1.0 OD1 A:ASP389 2.4 30.3 1.0 OE2 A:GLU50 2.4 39.3 1.0 CG A:ASP389 2.7 32.8 1.0 C A:SER48 3.3 31.7 1.0 C A:GLY257 3.4 23.7 1.0 CB A:SER48 3.5 31.4 1.0 CD A:GLU50 3.6 36.8 1.0 C A:THR254 3.6 28.2 1.0 CA A:SER48 3.7 31.5 1.0 OD1 A:ASP390 3.9 42.5 1.0 N A:GLY257 4.1 28.7 1.0 CG A:GLU50 4.2 37.8 1.0 OG1 A:THR254 4.2 31.4 1.0 CB A:ASP389 4.2 26.7 1.0 CA A:GLY257 4.3 24.7 1.0 N A:THR254 4.4 29.0 1.0 N A:ALA258 4.4 22.8 1.0 CA A:GLY252 4.4 25.4 1.0 CA A:GLY255 4.5 26.1 1.0 N A:GLY255 4.5 24.7 1.0 N A:PHE49 4.5 29.9 1.0 CA A:THR254 4.5 28.9 1.0 C A:GLY255 4.5 29.3 1.0 CA A:ALA258 4.6 25.6 1.0 OE1 A:GLU50 4.6 37.9 1.0 O A:GLY255 4.8 30.8 1.0 N A:TRP253 4.9 25.8 1.0 N A:LEU256 4.9 27.7 1.0 C A:PHE49 4.9 34.2 1.0 CG A:ASP390 4.9 38.9 1.0 CB A:ALA258 4.9 25.4 1.0 N A:GLU50 5.0 32.7 1.0

Calcium binding site 3 out of 9 in the Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1503 b:39.5 occ:1.00 OD1 A:ASN1209 2.3 29.7 1.0 OD2 A:ASP1182 2.3 31.1 1.0 OD1 A:ASP1185 2.3 37.3 1.0 O A:HOH1613 2.3 27.7 1.0 O A:HOH1640 2.3 30.5 1.0 O A:HOH1780 2.4 31.9 1.0 CG A:ASN1209 3.2 30.1 1.0 CG A:ASP1182 3.2 27.1 1.0 CG A:ASP1185 3.6 41.2 1.0 CB A:ASP1182 3.6 24.2 1.0 ND2 A:ASN1209 3.6 28.7 1.0 OG1 A:THR1184 4.0 25.9 1.0 OE2 A:GLU1313 4.2 27.5 1.0 OD2 A:ASP1185 4.3 35.9 1.0 CG A:GLU1315 4.4 31.8 1.0 OD1 A:ASP1182 4.4 30.1 1.0 O A:PHE846 4.4 19.3 1.0 CB A:PHE846 4.5 18.5 1.0 O A:LEU1314 4.5 23.8 1.0 CB A:ASN1209 4.5 25.8 1.0 CA A:ASP1185 4.6 30.0 1.0 O A:PHE1207 4.6 26.0 1.0 CB A:ASP1185 4.6 35.4 1.0 OE2 A:GLU1315 4.6 34.2 1.0 CA A:ASN1209 4.6 27.4 1.0 N A:ASP1185 4.7 29.6 1.0 N A:ASN1209 4.8 27.6 1.0 O A:ASP1182 5.0 21.8 1.0 C A:PHE1207 5.0 27.4 1.0 CB A:GLU1315 5.0 24.6 1.0 CD A:GLU1315 5.0 33.8 1.0

Calcium binding site 4 out of 9 in the Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1504 b:21.4 occ:1.00 O A:ALA1312 2.3 21.4 1.0 O A:LEU1205 2.3 30.1 1.0 OE1 A:GLU1313 2.3 24.8 1.0 OG1 A:THR1213 2.3 22.1 1.0 O A:THR1210 2.4 25.0 1.0 O A:THR1213 2.4 26.2 1.0 OD1 A:ASP1208 2.4 25.3 1.0 C A:THR1213 3.4 24.3 1.0 C A:LEU1205 3.5 30.3 1.0 C A:ALA1312 3.5 24.2 1.0 CG A:ASP1208 3.5 28.1 1.0 C A:THR1210 3.6 27.2 1.0 CB A:THR1213 3.6 23.5 1.0 CD A:GLU1313 3.6 28.9 1.0 OD2 A:ASP1208 3.9 30.6 1.0 CA A:THR1213 4.0 23.4 1.0 N A:THR1213 4.1 28.0 1.0 N A:THR1210 4.3 24.6 1.0 CA A:LEU1205 4.3 28.6 1.0 N A:LEU1206 4.4 27.0 1.0 CA A:ALA1312 4.4 23.8 1.0 CB A:GLU1313 4.4 29.0 1.0 N A:GLN1214 4.4 23.9 1.0 CA A:LEU1206 4.4 26.8 1.0 N A:GLU1313 4.5 22.2 1.0 OE2 A:GLU1313 4.5 27.5 1.0 CA A:THR1210 4.5 26.6 1.0 CA A:GLU1313 4.5 26.4 1.0 N A:SER1211 4.5 24.6 1.0 CG A:GLU1313 4.6 28.3 1.0 CG2 A:THR1210 4.6 25.9 1.0 CA A:SER1211 4.7 26.8 1.0 N A:ASP1208 4.7 24.1 1.0 C A:LEU1206 4.7 29.4 1.0 CG2 A:THR1213 4.8 21.2 1.0 N A:PHE1207 4.8 26.8 1.0 CB A:LEU1205 4.8 26.3 1.0 CA A:GLN1214 4.8 25.3 1.0 CB A:ASP1208 4.8 26.8 1.0 CB A:ALA1312 4.9 22.9 1.0

Calcium binding site 5 out of 9 in the Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1507 b:25.9 occ:1.00 O A:LYS109 2.3 24.3 1.0 O A:ASP114 2.3 26.7 1.0 OE1 A:GLU216 2.4 31.2 1.0 O A:THR117 2.4 22.9 1.0 OG1 A:THR117 2.4 23.0 1.0 OD1 A:ASP112 2.4 26.3 1.0 O A:ALA215 2.4 25.9 1.0 C A:THR117 3.4 22.4 1.0 C A:ASP114 3.4 30.8 1.0 CG A:ASP112 3.4 26.8 1.0 C A:LYS109 3.5 23.7 1.0 C A:ALA215 3.6 22.6 1.0 CB A:THR117 3.6 22.4 1.0 CD A:GLU216 3.6 38.8 1.0 OD2 A:ASP112 3.7 28.1 1.0 CA A:THR117 3.9 22.7 1.0 N A:ASP114 4.0 30.0 1.0 N A:THR117 4.1 22.9 1.0 CA A:ASP114 4.1 30.4 1.0 CA A:LYS109 4.3 24.0 1.0 N A:PRO115 4.3 28.3 1.0 CB A:LYS109 4.4 23.1 1.0 CB A:ASP114 4.4 31.5 1.0 N A:LYS118 4.4 23.6 1.0 N A:LEU110 4.5 24.4 1.0 OE2 A:GLU216 4.5 43.7 1.0 CA A:ALA215 4.5 22.3 1.0 N A:GLU216 4.6 23.8 1.0 CB A:GLU216 4.6 31.0 1.0 CA A:PRO115 4.6 26.4 1.0 CG A:GLU216 4.6 33.7 1.0 CA A:LEU110 4.6 22.9 1.0 CA A:GLU216 4.6 27.6 1.0 N A:GLY113 4.7 31.4 1.0 N A:ASP112 4.7 31.7 1.0 C A:LEU110 4.7 24.7 1.0 CB A:ASP112 4.7 27.6 1.0 C A:PRO115 4.8 27.8 1.0 CG2 A:THR117 4.8 21.8 1.0 CA A:LYS118 4.9 25.5 1.0 CB A:ALA215 4.9 20.0 1.0 N A:THR116 4.9 29.0 1.0

Calcium binding site 6 out of 9 in the Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1501 b:22.8 occ:1.00 O B:HOH1773 2.3 18.7 1.0 OE1 B:GLN1014 2.3 18.5 1.0 O2 B:MVL1505 2.3 23.6 1.0 OD2 B:ASP1058 2.3 29.1 1.0 O B:HOH1677 2.3 17.5 1.0 O B:HOH1678 2.3 23.7 1.0 O3 B:MVL1505 2.3 20.0 1.0 OD1 B:ASN1013 2.4 31.0 1.0 C2 B:MVL1505 3.4 22.4 1.0 CD B:GLN1014 3.4 20.9 1.0 CG B:ASP1058 3.4 31.3 1.0 C3 B:MVL1505 3.4 22.4 1.0 CG B:ASN1013 3.6 29.0 1.0 NE2 B:GLN1014 3.8 19.0 1.0 OD1 B:ASP1058 3.9 31.6 1.0 CB B:ASP1056 4.1 23.5 1.0 C1 B:MVL1505 4.1 24.6 1.0 OD1 B:ASP748 4.3 32.4 1.0 ND2 B:ASN1013 4.3 29.6 1.0 C4 B:MVL1505 4.4 21.4 1.0 O B:HOH1633 4.5 21.4 1.0 CA B:ASN1013 4.5 22.9 1.0 N1 B:MVL1505 4.5 27.1 1.0 O B:ASP1056 4.6 21.0 1.0 N B:GLN1014 4.6 23.5 1.0 CB B:ASN1013 4.6 24.2 1.0 CB B:ASP1058 4.6 27.6 1.0 OE1 B:GLU944 4.6 25.9 1.0 CZ3 B:TRP747 4.6 23.2 1.0 OD2 B:ASP1056 4.7 29.9 1.0 CG B:GLN1014 4.7 19.6 1.0 CG B:ASP1056 4.8 27.9 1.0 OE2 B:GLU997 4.8 23.4 1.0 O B:SER1012 4.9 23.8 1.0

Calcium binding site 7 out of 9 in the Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1502 b:24.0 occ:1.00 O B:SER48 2.3 26.8 1.0 O B:GLY257 2.3 23.2 1.0 OG B:SER48 2.3 26.4 1.0 O B:THR254 2.4 20.9 1.0 OE2 B:GLU50 2.4 31.5 1.0 OD1 B:ASP389 2.4 23.9 1.0 OD2 B:ASP389 2.4 22.5 1.0 CG B:ASP389 2.8 21.9 1.0 C B:SER48 3.3 24.8 1.0 CB B:SER48 3.4 24.7 1.0 C B:GLY257 3.5 24.2 1.0 CD B:GLU50 3.6 29.8 1.0 C B:THR254 3.6 22.0 1.0 CA B:SER48 3.6 24.0 1.0 OD1 B:ASP390 3.9 21.0 1.0 O B:HOH1767 4.1 27.4 1.0 OG1 B:THR254 4.1 22.4 1.0 N B:GLY257 4.2 26.4 1.0 CG B:GLU50 4.2 25.3 1.0 CB B:ASP389 4.3 20.8 1.0 CA B:GLY257 4.3 23.6 1.0 N B:THR254 4.4 21.1 1.0 N B:ALA258 4.4 20.3 1.0 N B:GLY255 4.5 22.6 1.0 N B:PHE49 4.5 22.2 1.0 CA B:GLY255 4.5 20.9 1.0 CA B:GLY252 4.5 22.1 1.0 CA B:THR254 4.5 21.3 1.0 OE1 B:GLU50 4.6 32.0 1.0 CA B:ALA258 4.6 21.4 1.0 C B:GLY255 4.6 23.7 1.0 O B:GLY255 4.9 22.6 1.0 CG B:ASP390 4.9 21.8 1.0 N B:LEU256 4.9 24.9 1.0 CB B:ALA258 5.0 19.2 1.0 C B:PHE49 5.0 24.2 1.0 N B:TRP253 5.0 20.9 1.0

Calcium binding site 8 out of 9 in the Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1503 b:54.4 occ:1.00 OD1 B:ASN1209 2.3 54.0 1.0 OD2 B:ASP1182 2.3 44.2 1.0 O B:HOH1614 2.3 38.8 1.0 O B:HOH1601 2.3 51.1 1.0 OD1 B:ASP1185 2.3 65.1 1.0 O B:HOH1668 2.4 39.0 1.0 CG B:ASN1209 3.2 46.2 1.0 CG B:ASP1182 3.2 47.7 1.0 ND2 B:ASN1209 3.5 41.7 1.0 CB B:ASP1182 3.6 49.6 1.0 CG B:ASP1185 3.6 63.8 1.0 OG1 B:THR1184 4.1 59.1 1.0 O B:PHE846 4.2 40.1 1.0 CG B:GLU1315 4.2 53.1 1.0 OD2 B:ASP1185 4.3 49.3 1.0 OE2 B:GLU1313 4.3 44.8 1.0 OD1 B:ASP1182 4.4 54.6 1.0 OE2 B:GLU1315 4.4 71.1 1.0 CB B:PHE846 4.4 42.7 1.0 O B:LEU1314 4.5 40.6 1.0 CB B:ASN1209 4.5 44.2 1.0 CA B:ASN1209 4.7 45.8 1.0 CB B:ASP1185 4.7 62.5 1.0 CA B:ASP1185 4.7 56.2 1.0 O B:PHE1207 4.7 40.1 1.0 N B:ASN1209 4.9 38.7 1.0 CD B:GLU1315 4.9 60.0 1.0 N B:ASP1185 4.9 49.5 1.0 CB B:GLU1315 4.9 46.9 1.0 C B:PHE846 4.9 41.6 1.0 CA B:PHE846 5.0 42.6 1.0

Calcium binding site 9 out of 9 in the Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis: Mannoimidazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1504 b:36.2 occ:1.00 OG1 B:THR1213 2.3 32.6 1.0 O B:ALA1312 2.3 32.5 1.0 O B:THR1213 2.3 44.7 1.0 O B:THR1210 2.3 59.2 1.0 O B:LEU1205 2.4 49.7 1.0 OE1 B:GLU1313 2.4 42.1 1.0 OD1 B:ASP1208 2.4 36.7 1.0 C B:THR1213 3.3 52.2 1.0 CG B:ASP1208 3.5 33.7 1.0 C B:ALA1312 3.5 43.5 1.0 C B:LEU1205 3.5 48.7 1.0 C B:THR1210 3.6 53.6 1.0 CB B:THR1213 3.6 40.8 1.0 CD B:GLU1313 3.7 47.5 1.0 CA B:THR1213 3.9 47.2 1.0 OD2 B:ASP1208 4.0 34.9 1.0 N B:THR1213 4.1 57.0 1.0 N B:THR1210 4.3 50.3 1.0 CA B:ALA1312 4.4 46.2 1.0 CA B:LEU1205 4.4 51.2 1.0 N B:GLN1214 4.4 60.7 1.0 CA B:THR1210 4.4 49.2 1.0 CB B:GLU1313 4.4 52.2 1.0 N B:LEU1206 4.4 42.9 1.0 OE2 B:GLU1313 4.5 44.8 1.0 CA B:LEU1206 4.5 42.7 1.0 N B:GLU1313 4.5 42.5 1.0 N B:SER1211 4.5 45.2 1.0 CG2 B:THR1210 4.5 55.6 1.0 CA B:GLU1313 4.5 49.0 1.0 CA B:SER1211 4.6 43.6 1.0 CG B:GLU1313 4.6 45.8 1.0 N B:ASP1208 4.7 36.6 1.0 C B:LEU1206 4.7 42.6 1.0 CG2 B:THR1213 4.7 36.6 1.0 CA B:GLN1214 4.8 61.7 1.0 CB B:ASP1208 4.8 36.3 1.0 CB B:LEU1205 4.8 49.2 1.0 N B:PHE1207 4.9 41.0 1.0 CB B:ALA1312 4.9 45.8 1.0

B.M.Kolaczkowski, O.V.Moroz, E.Blagova, G.J.Davies, K.S.Wilson, M.S.Moeler, A.S.Meyer, P.Westh, K.Jensen, K.B.R.M.Krogh. Structural and Functional Characterization of Multi-Domain GH92 Alpha-1,2-Mannosidase From Neobacillus Novalis To Be Published.