Sodium in PDB 3wfa: Catalytic Role of the Calcium Ion in GH97 Inverting Glycoside Hydrolase

The structure of Catalytic Role of the Calcium Ion in GH97 Inverting Glycoside Hydrolase, PDB code: 3wfa was solved by M.Okuyama, T.Yoshida, H.Hondoh, H.Mori, M.Yao, A.Kimura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.81 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.520, 111.960, 102.360, 90.00, 100.49, 90.00
R / Rfree (%)	17.1 / 20

The binding sites of Sodium atom in the Catalytic Role of the Calcium Ion in GH97 Inverting Glycoside Hydrolase (pdb code 3wfa). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Catalytic Role of the Calcium Ion in GH97 Inverting Glycoside Hydrolase, PDB code: 3wfa:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Catalytic Role of the Calcium Ion in GH97 Inverting Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Catalytic Role of the Calcium Ion in GH97 Inverting Glycoside Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na801 b:29.2 occ:1.00 OE1 A:GLU532 2.1 18.4 1.0 OE2 A:GLU526 2.2 11.5 1.0 O A:HOH1320 2.4 21.6 1.0 OE2 A:GLU194 2.4 19.5 1.0 O A:HOH1405 2.5 19.5 1.0 OE1 A:GLU508 2.8 9.8 1.0 CD A:GLU526 3.2 11.4 1.0 CD A:GLU532 3.2 17.9 1.0 OE1 A:GLU526 3.4 10.7 1.0 CD A:GLU194 3.4 15.9 1.0 O A:HOH1030 3.5 16.1 1.0 OE1 A:GLU194 3.8 14.1 1.0 OE2 A:GLU532 3.8 18.9 1.0 O A:HOH1031 3.9 7.4 1.0 CD A:GLU508 4.0 10.0 1.0 O A:HOH1029 4.2 10.6 1.0 O A:HOH1522 4.2 33.9 1.0 ND1 A:HIS507 4.3 6.3 1.0 CG A:GLU532 4.4 17.3 1.0 CG A:GLU526 4.5 9.5 1.0 CG A:GLU194 4.7 13.2 1.0 CG A:GLU508 4.8 9.9 1.0 CE2 A:TYR533 4.9 15.5 1.0 OE2 A:GLU508 4.9 10.0 1.0 CB A:HIS507 5.0 7.8 1.0

Sodium binding site 2 out of 2 in the Catalytic Role of the Calcium Ion in GH97 Inverting Glycoside Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Catalytic Role of the Calcium Ion in GH97 Inverting Glycoside Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na801 b:22.4 occ:1.00 OE1 B:GLU532 2.1 16.5 1.0 OE2 B:GLU526 2.3 9.0 1.0 OE2 B:GLU194 2.3 19.7 1.0 O B:HOH1412 2.4 23.5 1.0 O B:HOH1292 2.4 19.5 1.0 OE1 B:GLU508 2.9 8.5 1.0 CD B:GLU526 3.2 9.5 1.0 CD B:GLU532 3.2 18.0 1.0 CD B:GLU194 3.4 16.2 1.0 OE1 B:GLU526 3.4 7.7 1.0 O B:HOH1065 3.5 16.8 1.0 O B:HOH1450 3.8 28.8 1.0 OE1 B:GLU194 3.8 16.5 1.0 OE2 B:GLU532 3.9 19.8 1.0 O B:HOH1058 4.0 5.9 1.0 CD B:GLU508 4.1 8.2 1.0 O B:HOH1063 4.3 10.8 1.0 CG B:GLU532 4.3 16.3 1.0 ND1 B:HIS507 4.5 5.7 1.0 CG B:GLU526 4.6 7.5 1.0 CG B:GLU194 4.6 14.1 1.0 CE2 B:TYR533 4.8 13.0 1.0 CG B:GLU508 4.9 9.5 1.0

M.Okuyama, T.Yoshida, H.Hondoh, H.Mori, M.Yao, A.Kimura. Catalytic Role of the Calcium Ion in GH97 Inverting Glycoside Hydrolase To Be Published.