Calcium in PDB 6gsz: Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus

All present enzymatic activity of Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus:
3.2.1.40;

The structure of Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus, PDB code: 6gsz was solved by P.Pachl, P.Rezacova, J.Skerlova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.82 / 1.38
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.260, 106.248, 119.832, 90.00, 90.00, 90.00
R / Rfree (%)	13.4 / 16.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus (pdb code 6gsz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 21 binding sites of Calcium where determined in the Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus, PDB code: 6gsz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 21 in the Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca927 b:13.3 occ:1.00 O A:VAL64 2.3 12.0 1.0 O A:HOH1813 2.4 17.0 1.0 O A:HOH1913 2.4 17.4 1.0 OD2 A:ASP62 2.4 13.2 1.0 O A:HOH1570 2.4 13.1 1.0 O A:HOH1920 2.4 16.6 1.0 OD1 A:ASP62 2.5 12.9 1.0 CG A:ASP62 2.8 13.4 1.0 C A:VAL64 3.5 11.1 1.0 CB A:VAL64 4.2 12.7 1.0 CA A:VAL64 4.2 11.3 1.0 O A:HOH1203 4.3 41.8 1.0 CB A:ASP62 4.3 12.5 1.0 N A:VAL64 4.3 11.0 1.0 O A:LEU65 4.4 11.4 1.0 O A:HOH1309 4.5 14.8 1.0 C A:LEU65 4.5 9.6 1.0 N A:LEU65 4.5 11.0 1.0 O A:HOH1611 4.5 21.2 1.0 O A:HOH1808 4.6 19.0 1.0 CB A:LEU65 4.6 11.1 1.0 CG1 A:VAL64 4.6 16.4 1.0 CA A:LEU65 4.8 10.6 1.0 O A:HOH1586 4.8 14.1 1.0

Calcium binding site 2 out of 21 in the Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca928 b:22.4 occ:0.80 OE2 A:GLU385 2.3 29.5 1.0 O A:HOH1479 2.3 25.0 1.0 O A:HOH1889 2.4 32.6 1.0 O A:HOH1358 2.4 35.1 1.0 OE1 A:GLU385 2.4 28.4 1.0 O A:HOH1269 2.5 26.7 1.0 CD A:GLU385 2.7 25.1 1.0 CG A:GLU385 4.2 28.4 1.0 O A:HOH1189 4.4 32.1 1.0 O A:HOH1794 4.5 29.5 1.0 O A:HOH1485 4.5 34.9 1.0 O A:HOH1115 4.6 40.5 1.0 O A:SER272 4.6 17.2 1.0 O A:ARG273 4.6 18.6 1.0 O A:GLU275 4.8 20.3 1.0 CB A:SER383 5.0 20.4 1.0

Calcium binding site 3 out of 21 in the Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca929 b:20.7 occ:0.70 O A:HOH1421 2.3 20.3 1.0 OD2 A:ASP487 2.3 18.5 1.0 O2 A:PG0957 2.3 36.5 1.0 OTT A:PG0957 2.3 33.4 1.0 O1 A:PG0957 2.4 28.0 1.0 O A:HOH1811 2.4 28.4 1.0 O A:HOH1348 2.5 24.8 1.0 C3 A:PG0957 3.2 32.6 1.0 C4 A:PG0957 3.2 33.1 1.0 C1 A:PG0957 3.3 33.6 1.0 C2 A:PG0957 3.3 29.0 1.0 CG A:ASP487 3.4 13.9 1.0 O A:HOH1064 3.7 31.9 1.0 OD1 A:ASP487 4.0 13.6 1.0 NH1 A:ARG29 4.2 20.8 0.5 O A:HOH1089 4.3 33.0 1.0 O A:HOH1761 4.5 23.5 0.5 O A:HOH1560 4.6 21.1 1.0 CB A:ASP487 4.6 12.4 1.0 ND1 A:HIS12 4.7 11.3 1.0 CZ A:ARG29 4.8 26.9 0.5 NH2 A:ARG29 4.8 30.3 0.5 O A:HOH1438 4.8 29.9 1.0 NE2 A:GLN7 4.9 21.4 1.0

Calcium binding site 4 out of 21 in the Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca930 b:31.5 occ:0.80 OD2 A:ASP189 2.3 20.8 1.0 O A:HOH1792 2.4 31.1 0.5 O A:HOH1974 2.6 47.4 1.0 O A:HOH1172 2.7 47.6 1.0 O A:HOH1959 2.8 44.2 1.0 O A:HOH1954 3.3 42.4 1.0 CG A:ASP189 3.4 16.9 1.0 O A:HOH1792 3.9 33.4 0.5 CB A:ASP189 4.0 13.7 1.0 O A:HOH2185 4.2 34.8 1.0 OD1 A:ASP189 4.4 16.2 1.0 O A:HOH1641 4.4 22.6 1.0 O A:HOH1123 4.7 45.3 1.0 O A:HOH2188 4.8 50.7 1.0

Calcium binding site 5 out of 21 in the Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca931 b:40.8 occ:1.00 O A:HOH1129 2.3 36.5 0.5 O A:HOH1978 2.4 60.1 1.0 OE1 A:GLU792 2.4 32.9 1.0 OE2 A:GLU792 2.4 33.2 1.0 O A:HOH1323 2.6 72.3 1.0 O A:HOH1858 2.7 50.3 1.0 O A:HOH1879 2.7 58.1 1.0 CD A:GLU792 2.8 25.2 1.0 CG A:GLU792 4.3 18.6 1.0 O A:HOH2072 4.6 46.9 1.0 O A:HOH1581 4.7 46.6 1.0 ND2 A:ASN790 4.7 20.6 0.6

Calcium binding site 6 out of 21 in the Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca932 b:36.2 occ:0.60 O A:HOH1061 2.0 65.3 1.0 O A:HOH1857 2.2 42.2 1.0 O7 A:NAG906 2.4 44.2 1.0 O2 A:MAN909 2.4 35.2 0.7 O A:HOH1700 2.5 28.4 1.0 O A:HOH1656 2.5 39.0 1.0 O A:HOH1121 2.7 45.1 1.0 CA A:CA935 3.5 32.6 0.5 O A:HOH1009 3.6 26.6 0.6 C7 A:NAG906 3.6 39.3 1.0 C2 A:MAN909 3.6 37.0 0.7 CB A:ASP667 4.0 16.2 1.0 OD2 A:ASP667 4.2 37.1 1.0 O4 A:NAG905 4.2 29.6 1.0 C1 A:MAN909 4.5 36.6 0.7 CE1 A:HIS634 4.5 20.4 1.0 C8 A:NAG906 4.5 42.5 1.0 CG A:ASP667 4.6 20.4 1.0 N2 A:NAG906 4.6 33.9 1.0 O A:HOH1372 4.7 44.3 1.0 C2 A:NAG906 4.7 38.3 1.0 O A:ASP667 4.8 16.4 1.0 O A:PHE666 4.8 14.2 1.0 OD1 A:ASP612 4.9 22.7 1.0 C3 A:MAN909 4.9 41.0 0.7 O3 A:MAN909 4.9 41.0 0.7 O A:HOH2144 4.9 49.1 1.0 C3 A:NAG905 4.9 22.4 1.0 OD2 A:ASP612 5.0 21.3 1.0

Calcium binding site 7 out of 21 in the Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca933 b:37.6 occ:0.50 O A:HOH1856 2.3 60.0 1.0 OE2 A:GLU269 2.3 33.6 1.0 OE1 A:GLU269 2.4 24.9 1.0 O A:HOH2179 2.4 55.6 1.0 CD A:GLU269 2.7 24.7 1.0 CG A:GLU269 4.1 18.7 1.0 O A:HOH1162 4.4 28.4 1.0 O A:HOH1749 4.4 43.4 1.0 O A:HOH1076 4.6 34.2 1.0

Calcium binding site 8 out of 21 in the Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca934 b:35.2 occ:0.60 O A:HOH1355 2.2 34.9 1.0 O A:HOH1893 2.3 32.8 1.0 O A:HOH2211 2.4 68.4 1.0 O A:HOH2087 2.5 54.6 1.0 O A:HOH2015 2.6 65.0 1.0 O A:HOH1989 3.0 55.0 1.0 O A:HOH1441 3.4 31.3 1.0 O A:HOH1825 3.6 52.7 1.0 O A:HOH2169 4.1 54.7 1.0 OE1 A:GLU541 4.2 25.6 1.0 O A:HOH2022 4.2 42.7 1.0 OE2 A:GLU541 4.3 22.6 1.0 O A:HOH1182 4.5 44.8 1.0 CD A:GLU541 4.6 17.1 1.0 O A:HOH1651 4.7 30.1 1.0 CD A:PRO784 4.7 14.7 1.0 CG A:PRO784 5.0 17.4 1.0 O A:ALA782 5.0 18.8 1.0

Calcium binding site 9 out of 21 in the Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca935 b:32.6 occ:0.50 O A:HOH1372 2.1 44.3 1.0 O A:HOH1700 2.3 28.4 1.0 O A:ASP667 2.3 16.4 1.0 O3 A:MAN909 2.3 41.0 0.7 O2 A:MAN909 2.4 35.2 0.7 O A:HOH1121 2.5 45.1 1.0 O A:HOH1280 2.8 27.3 1.0 C3 A:MAN909 3.2 41.0 0.7 C2 A:MAN909 3.2 37.0 0.7 C A:ASP667 3.5 14.7 1.0 CA A:CA932 3.5 36.2 0.6 C4 A:MAN909 3.8 40.4 0.7 CB A:ASP667 3.9 16.2 1.0 CE1 A:HIS634 4.2 20.4 1.0 O A:HOH1574 4.3 33.5 1.0 CA A:ASP667 4.4 15.2 1.0 O A:HOH1985 4.4 44.8 1.0 N A:LEU668 4.5 13.2 1.0 O A:PHE666 4.6 14.2 1.0 C1 A:MAN909 4.6 36.6 0.7 OG1 A:THR638 4.6 19.3 1.0 CG2 A:THR638 4.6 20.3 1.0 O4 A:MAN909 4.6 47.8 0.7 O A:HOH1061 4.7 65.3 1.0 CA A:LEU668 4.7 13.3 1.0 O5 A:MAN909 4.9 37.4 0.7 O A:HOH1857 4.9 42.2 1.0 ND1 A:HIS634 4.9 20.0 1.0

Calcium binding site 10 out of 21 in the Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Native Alfa-L-Rhamnosidase From Aspergillus Terreus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca936 b:46.7 occ:0.50 OE2 A:GLU415 2.3 61.3 1.0 OE1 A:GLU415 2.3 44.9 1.0 CD A:GLU415 2.7 53.3 1.0 CG A:GLU415 4.2 44.5 1.0 CB A:ASP414 5.0 31.2 1.0

P.Pachl, J.Skerlova, D.Simcikova, M.Kotik, A.Krenkova, P.Mader, J.Brynda, J.Kapesova, V.Kren, Z.Otwinowski, P.Rezacova. Crystal Structure of Native Alpha-L-Rhamnosidase From Aspergillus Terreus. Acta Crystallogr D Struct V. 74 1078 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30387766
DOI: 10.1107/S2059798318013049