Calcium in PDB 2okx: Crystal Structure of GH78 Family Rhamnosidase of Bacillus Sp. GL1 at 1.9 A

All present enzymatic activity of Crystal Structure of GH78 Family Rhamnosidase of Bacillus Sp. GL1 at 1.9 A:
3.2.1.40;

The structure of Crystal Structure of GH78 Family Rhamnosidase of Bacillus Sp. GL1 at 1.9 A, PDB code: 2okx was solved by Z.Cui, B.Mikami, W.Hashimoto, K.Murata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.744, 119.985, 207.352, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.4

The binding sites of Calcium atom in the Crystal Structure of GH78 Family Rhamnosidase of Bacillus Sp. GL1 at 1.9 A (pdb code 2okx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of GH78 Family Rhamnosidase of Bacillus Sp. GL1 at 1.9 A, PDB code: 2okx:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of GH78 Family Rhamnosidase of Bacillus Sp. GL1 at 1.9 A


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 GH78 Family Rhamnosidase of Bacillus Sp. GL1 at 1.9 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4001 b:29.3 occ:1.00 O A:HOH4755 2.3 20.0 1.0 O A:HOH4757 2.3 25.6 1.0 O A:HOH4756 2.4 26.1 1.0 O A:VAL423 2.5 20.8 1.0 O1 A:GOL3040 2.5 50.5 1.0 O2 A:GOL3040 2.6 48.9 1.0 O A:HIS522 2.6 23.4 1.0 C1 A:GOL3040 3.0 51.2 1.0 C2 A:GOL3040 3.2 51.7 1.0 C A:HIS522 3.6 22.3 1.0 C A:VAL423 3.7 21.4 1.0 CA A:HIS522 4.0 21.6 1.0 CB A:HIS522 4.1 22.0 1.0 O A:LEU421 4.2 21.7 1.0 N A:VAL423 4.3 20.5 1.0 O A:PRO424 4.3 23.5 1.0 OE1 A:GLU523 4.4 32.1 1.0 C A:PRO424 4.4 22.7 1.0 O A:GLU425 4.4 23.2 1.0 CA A:PRO424 4.5 21.8 1.0 N A:PRO424 4.6 21.9 1.0 CB A:GLU523 4.6 22.5 1.0 C3 A:GOL3040 4.6 52.2 1.0 CA A:VAL423 4.6 19.4 1.0 N A:GLU523 4.7 20.0 1.0 O A:HOH4860 4.7 48.1 1.0 CD2 A:HIS522 4.7 26.1 1.0 CG A:HIS522 4.8 25.1 1.0 C A:GLU425 4.9 22.8 1.0 O A:HOH4506 4.9 18.9 1.0 O3 A:GOL3040 4.9 51.9 1.0 CG2 A:VAL423 4.9 19.1 1.0 O A:ASN418 4.9 19.7 1.0 CG A:GLU523 5.0 26.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of GH78 Family Rhamnosidase of Bacillus Sp. GL1 at 1.9 A


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 GH78 Family Rhamnosidase of Bacillus Sp. GL1 at 1.9 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4004 b:28.5 occ:1.00 O2 A:GOL3043 2.3 51.8 1.0 O A:LYS953 2.4 20.9 1.0 O3 A:GOL3043 2.4 47.7 1.0 O1 A:GOL3039 2.4 40.9 1.0 O2 A:GOL3039 2.4 38.3 1.0 C1 A:GOL3039 3.0 42.8 1.0 C3 A:GOL3043 3.1 52.0 1.0 C2 A:GOL3043 3.2 53.2 1.0 C2 A:GOL3039 3.2 43.2 1.0 C A:LYS953 3.5 23.0 1.0 C1 A:GOL3043 4.0 56.2 1.0 N A:LYS953 4.1 22.1 1.0 CA A:LYS953 4.3 21.9 1.0 C3 A:GOL3039 4.3 45.1 1.0 CB A:LYS953 4.4 24.9 1.0 N A:TYR954 4.5 20.5 1.0 O1 A:GOL3043 4.6 59.0 1.0 O A:HOH4734 4.7 56.6 1.0 CA A:TYR954 4.7 22.9 1.0 O A:HOH4580 4.8 29.4 1.0 CG1 A:VAL952 5.0 22.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of GH78 Family Rhamnosidase of Bacillus Sp. GL1 at 1.9 A


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 GH78 Family Rhamnosidase of Bacillus Sp. GL1 at 1.9 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4002 b:31.6 occ:1.00 O B:HOH4875 2.2 30.5 1.0 O B:HOH4705 2.3 34.6 1.0 O3 B:GOL3041 2.4 59.6 1.0 O2 B:GOL3041 2.4 58.9 1.0 O B:LYS953 2.5 25.6 1.0 O B:HOH4874 2.6 41.8 1.0 C3 B:GOL3041 3.2 60.5 1.0 C2 B:GOL3041 3.3 61.4 1.0 C B:LYS953 3.6 25.1 1.0 N B:LYS953 4.2 22.3 1.0 C1 B:GOL3041 4.4 62.3 1.0 CA B:LYS953 4.4 23.9 1.0 N B:TYR954 4.6 23.2 1.0 O B:HOH4714 4.6 46.5 1.0 CB B:LYS953 4.7 26.4 1.0 CA B:TYR954 4.7 25.1 1.0 O1 B:GOL3041 4.8 64.3 1.0 O B:HOH4424 4.8 32.3 1.0 CG1 B:VAL952 4.9 23.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of GH78 Family Rhamnosidase of Bacillus Sp. GL1 at 1.9 A


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 GH78 Family Rhamnosidase of Bacillus Sp. GL1 at 1.9 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4003 b:30.1 occ:1.00 O B:HOH4700 2.2 20.0 1.0 O B:HOH4701 2.3 18.8 1.0 O B:VAL423 2.4 20.4 1.0 O B:HOH4702 2.5 24.8 1.0 O1 B:GOL3042 2.5 49.8 1.0 O2 B:GOL3042 2.5 47.8 1.0 O B:HIS522 2.5 19.6 1.0 C1 B:GOL3042 2.8 49.1 1.0 C2 B:GOL3042 3.2 49.9 1.0 C B:HIS522 3.6 22.1 1.0 C B:VAL423 3.6 20.5 1.0 O B:LEU421 4.1 22.1 1.0 CA B:HIS522 4.1 20.1 1.0 N B:VAL423 4.2 18.6 1.0 O B:GLU425 4.2 22.3 1.0 CB B:HIS522 4.2 21.7 1.0 O B:PRO424 4.3 22.1 1.0 C3 B:GOL3042 4.4 51.9 1.0 C B:PRO424 4.4 20.4 1.0 CA B:PRO424 4.5 20.5 1.0 OE2 B:GLU523 4.5 30.5 1.0 CB B:GLU523 4.5 19.6 1.0 N B:PRO424 4.5 21.3 1.0 CA B:VAL423 4.5 19.1 1.0 N B:GLU523 4.7 19.5 1.0 C B:GLU425 4.7 22.0 1.0 CD2 B:HIS522 4.7 27.3 1.0 CG2 B:VAL423 4.8 18.0 1.0 O B:ASN418 4.8 19.0 1.0 CG B:HIS522 4.9 25.8 1.0 N B:GLU425 5.0 20.7 1.0 CA B:PRO426 5.0 20.6 1.0

Z.Cui, Y.Maruyama, B.Mikami, W.Hashimoto, K.Murata. Crystal Structure of Glycoside Hydrolase Family 78 Alpha-L-Rhamnosidase From Bacillus Sp. GL1 J.Mol.Biol. V. 374 384 2007.
ISSN: ISSN 0022-2836
PubMed: 17936784
DOI: 10.1016/J.JMB.2007.09.003