Sodium in PDB 3cmj: Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome

All present enzymatic activity of Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome:
3.2.1.21;

The structure of Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome, PDB code: 3cmj was solved by K.Y.Hwang, K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.331, 71.002, 86.978, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 19.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome (pdb code 3cmj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 22 binding sites of Sodium where determined in the Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome, PDB code: 3cmj:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 22 in the Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:18.7 occ:1.00 O A:HOH579 2.7 12.1 1.0 O A:HOH570 2.8 13.2 1.0 O A:HOH489 2.8 9.3 1.0 O A:GLY60 2.8 10.4 1.0 C A:GLY60 3.6 11.2 1.0 N A:GLY60 3.7 10.4 1.0 NH2 A:ARG121 3.8 13.5 1.0 CA A:GLY60 3.9 10.7 1.0 O A:GLY88 4.0 10.9 1.0 CB A:GLU59 4.1 9.7 1.0 CA A:TRP62 4.1 12.5 1.0 CD1 A:TYR56 4.2 8.6 1.0 CB A:TRP62 4.3 13.4 1.0 CE A:LYS67 4.3 10.3 1.0 C A:GLU59 4.4 10.2 1.0 O A:SER55 4.4 9.3 1.0 N A:TRP62 4.4 11.9 1.0 O A:HOH547 4.5 13.6 1.0 O A:HOH519 4.6 11.5 1.0 CA A:TYR56 4.6 9.3 1.0 OE1 A:GLU59 4.6 10.5 1.0 CE1 A:TYR56 4.6 9.4 1.0 CA A:GLU59 4.7 9.8 1.0 C A:ALA61 4.7 11.1 1.0 O A:TYR56 4.8 9.5 1.0 N A:ALA61 4.8 10.9 1.0 CD A:LYS67 4.8 10.4 1.0 CZ A:ARG121 4.9 13.7 1.0 O A:ALA61 4.9 11.5 1.0 N A:GLU59 4.9 10.0 1.0 NZ A:LYS67 5.0 10.3 1.0

Sodium binding site 2 out of 22 in the Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2 b:31.9 occ:1.00 O A:HOH561 2.4 24.1 1.0 O A:HOH803 2.8 30.1 1.0 CA A:PRO79 3.6 15.3 1.0 O A:HOH565 3.7 13.2 1.0 CA A:GLY85 3.8 14.0 1.0 N A:GLY80 3.9 15.1 1.0 O A:HOH715 4.0 27.3 1.0 CB A:PRO79 4.1 15.9 1.0 O A:HOH823 4.3 39.6 1.0 C A:PRO79 4.3 15.3 1.0 O A:HOH613 4.5 13.7 1.0 N A:PRO79 4.6 15.8 1.0 N A:GLY85 4.7 13.8 1.0 O A:ILE78 4.8 16.0 1.0 C A:GLY85 4.8 14.4 1.0 O A:GLY85 4.9 14.8 1.0

Sodium binding site 3 out of 22 in the Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3 b:72.9 occ:1.00 O A:HOH819 2.9 40.2 1.0 O A:HOH583 3.5 18.4 1.0 O A:HOH804 4.1 39.0 1.0 O A:HOH818 4.1 36.5 1.0 O A:HOH561 4.3 24.1 1.0 CA A:GLY80 4.3 15.7 1.0 O A:GLY80 4.8 16.4 1.0 C A:GLY80 5.0 15.4 1.0 N A:GLY80 5.0 15.1 1.0

Sodium binding site 4 out of 22 in the Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na4 b:33.8 occ:1.00 OD2 A:ASP86 2.7 17.5 1.0 O A:GLU444 3.1 11.5 1.0 N A:SER447 3.3 13.6 1.0 O A:LYS83 3.4 14.7 1.0 CB A:SER447 3.4 14.0 1.0 N A:TYR446 3.5 12.3 1.0 CB A:ASN84 3.5 14.5 1.0 CB A:LYS83 3.6 15.5 1.0 C A:LYS83 3.7 14.6 1.0 CG A:ASP86 3.8 16.8 1.0 CA A:SER447 3.8 13.4 1.0 OG A:SER447 4.0 14.3 1.0 C A:TYR446 4.0 13.6 1.0 C A:GLY445 4.1 12.4 1.0 C A:GLU444 4.1 11.9 1.0 CA A:GLY445 4.1 12.0 1.0 N A:ASN84 4.2 14.2 1.0 CA A:TYR446 4.2 12.8 1.0 CA A:LYS83 4.3 14.8 1.0 CA A:ASN84 4.5 14.5 1.0 N A:GLY445 4.5 11.7 1.0 OD1 A:ASP86 4.5 17.3 1.0 CG A:ASN84 4.6 17.4 1.0 ND2 A:ASN84 4.7 18.7 1.0 CB A:ASP86 4.8 14.9 1.0 CG A:LYS83 4.8 18.1 1.0 CD A:LYS83 4.8 20.9 1.0 CB A:TYR446 4.9 12.8 1.0 O A:TYR446 4.9 15.4 1.0

Sodium binding site 5 out of 22 in the Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na5 b:34.7 occ:1.00 O A:HOH512 2.6 17.6 1.0 OG A:SER87 2.8 13.2 1.0 O A:HOH792 2.9 34.8 1.0 O A:HOH734 2.9 33.6 1.0 CB A:SER87 3.6 12.6 1.0 N A:SER87 3.6 12.4 1.0 CA A:SER87 4.1 12.2 1.0 OD2 A:ASP89 4.3 15.9 1.0 O A:HOH505 4.3 12.6 1.0 C A:ASP86 4.3 13.5 1.0 O A:GLY85 4.4 14.8 1.0 O A:SER87 4.5 11.6 1.0 O A:HOH791 4.5 32.4 1.0 CG A:ASP89 4.5 15.3 1.0 CB A:ASP89 4.6 12.6 1.0 CA A:ASP86 4.6 14.3 1.0 C A:SER87 4.6 11.9 1.0 O A:HOH647 4.6 25.8 1.0 O A:HOH808 4.7 30.8 1.0

Sodium binding site 6 out of 22 in the Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na6 b:30.1 occ:1.00 O A:HOH674 2.7 30.6 1.0 O A:ARG106 3.0 10.6 1.0 O A:HOH726 3.0 41.5 1.0 CA A:GLY109 3.5 10.8 1.0 CG A:ARG106 3.8 11.6 1.0 C A:ARG106 3.9 10.9 1.0 CA A:ARG106 4.0 11.0 1.0 O A:HOH723 4.1 26.5 1.0 N A:GLY109 4.1 11.0 1.0 C A:GLY109 4.4 10.4 1.0 CB A:ARG106 4.5 10.7 1.0 O A:HOH603 4.6 18.6 1.0 O A:HOH801 4.7 38.3 1.0 O A:ARG148 4.8 14.7 1.0 O A:HOH812 4.9 33.2 1.0 O A:GLY109 4.9 10.8 1.0 N A:LEU110 5.0 10.4 1.0

Sodium binding site 7 out of 22 in the Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na7 b:31.4 occ:1.00 O A:HOH507 2.6 30.8 1.0 O A:HOH559 2.9 20.4 1.0 OD2 A:ASP167 3.0 20.8 1.0 CB A:TRP164 3.8 12.1 1.0 CB A:ASP167 3.9 15.2 1.0 CG A:ASP167 3.9 16.9 1.0 CB A:SER126 3.9 15.7 1.0 CA A:TRP164 3.9 11.9 1.0 OG A:SER126 4.1 16.4 1.0 O A:TRP164 4.5 12.6 1.0 O A:HOH747 4.6 30.1 1.0 C A:TRP164 4.7 12.1 1.0 N A:SER126 4.9 14.4 1.0 N A:TRP164 4.9 11.4 1.0 CA A:SER126 5.0 15.2 1.0

Sodium binding site 8 out of 22 in the Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8 b:25.2 occ:1.00 O A:HOH491 2.6 14.0 1.0 OE2 A:GLU182 2.7 15.0 1.0 NE2 A:GLN123 3.0 14.6 1.0 CB A:GLU182 3.3 11.6 1.0 CB A:ARG128 3.6 18.6 1.0 CD A:GLU182 3.6 13.1 1.0 CD A:ARG128 3.8 26.3 1.0 CD A:GLN123 3.9 13.6 1.0 NE A:ARG128 3.9 30.4 1.0 OE1 A:GLN123 3.9 12.7 1.0 CG A:GLU182 4.0 11.7 1.0 CG A:ARG128 4.3 22.5 1.0 O A:ARG128 4.5 17.7 1.0 NE A:ARG179 4.6 10.2 1.0 O A:ARG179 4.6 10.0 1.0 CA A:GLU182 4.6 11.2 1.0 CA A:ARG128 4.6 18.0 1.0 OE1 A:GLU182 4.7 15.9 1.0 CD A:ARG179 4.7 9.5 1.0 C A:GLU182 4.7 10.7 1.0 CH2 A:TRP164 4.8 12.5 1.0 N A:TYR183 4.8 10.5 1.0

Sodium binding site 9 out of 22 in the Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na9 b:39.7 occ:1.00 O A:HOH808 2.3 30.8 1.0 O A:HOH587 2.4 19.1 1.0 O A:HOH655 3.1 24.3 1.0 CB A:PHE457 3.5 17.4 1.0 CE2 A:TYR446 3.6 12.1 1.0 CD2 A:TYR446 3.8 12.0 1.0 CZ A:TYR446 3.9 12.0 1.0 CG A:PHE457 3.9 16.1 1.0 CD2 A:PHE457 4.0 16.3 1.0 O A:HOH780 4.2 24.7 1.0 CG A:TYR446 4.2 11.9 1.0 O A:HOH505 4.2 12.6 1.0 CE1 A:TYR446 4.2 11.6 1.0 OH A:TYR446 4.4 12.7 1.0 CD1 A:TYR446 4.4 12.3 1.0 O A:HOH512 4.5 17.6 1.0 O A:PHE457 4.5 20.3 1.0 O A:HOH827 4.5 34.0 1.0 CA A:PHE457 4.7 17.7 1.0 O A:ALA91 4.7 11.4 1.0 CD1 A:PHE457 4.9 15.9 1.0 C A:PHE457 4.9 19.0 1.0 CE2 A:PHE457 5.0 15.6 1.0

Sodium binding site 10 out of 22 in the Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Engineered Beta-Glucosidase From Soil Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na10 b:32.3 occ:1.00 NA A:NA11 2.5 37.1 1.0 O A:HOH809 2.7 29.6 1.0 O A:GLU143 2.8 13.3 1.0 N A:LYS147 3.6 15.9 1.0 C A:GLU143 3.6 13.2 1.0 CB A:HIS146 3.8 15.9 1.0 CA A:GLU143 3.9 13.8 1.0 CA A:LYS147 4.1 16.6 1.0 CE A:LYS147 4.1 22.8 1.0 CB A:LYS147 4.1 17.1 1.0 C A:HIS146 4.1 15.9 1.0 CB A:GLU143 4.2 14.5 1.0 CA A:HIS146 4.5 15.7 1.0 CG A:GLU143 4.6 19.1 1.0 CD A:LYS147 4.7 20.4 1.0 O A:HOH623 4.7 35.8 1.0 NZ A:LYS147 4.8 23.2 1.0 O A:HIS146 4.9 15.7 1.0 N A:GLY144 4.9 12.7 1.0 CG A:LYS147 4.9 19.8 1.0 N A:HIS146 4.9 14.4 1.0

K.H.Nam, S.J.Kim, M.Y.Kim, J.H.Kim, Y.S.Yeo, C.M.Lee, H.K.Jun, K.Y.Hwang. Crystal Structure of Engineered Beta-Glucosidase From A Soil Metagenome. Proteins V. 73 788 2008.
ISSN: ISSN 0887-3585
PubMed: 18712828
DOI: 10.1002/PROT.22199