Calcium in PDB 4mlg: Structure of RS223-Beta-Xylosidase

All present enzymatic activity of Structure of RS223-Beta-Xylosidase:
3.2.1.37;

The structure of Structure of RS223-Beta-Xylosidase, PDB code: 4mlg was solved by D.Jordan, J.Braker, K.Wagschal, C.Lee, I.Dubrovska, S.Anderson, Z.Wawrzak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.20 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	124.525, 148.702, 125.648, 90.00, 112.87, 90.00
R / Rfree (%)	21 / 25.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Structure of RS223-Beta-Xylosidase (pdb code 4mlg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Structure of RS223-Beta-Xylosidase, PDB code: 4mlg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Structure of RS223-Beta-Xylosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of RS223-Beta-Xylosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:62.5 occ:1.00 OD2 A:ASP85 2.4 49.4 1.0 NE2 A:HIS274 2.8 55.4 1.0 CG A:ASP85 3.2 49.8 1.0 OD1 A:ASP85 3.3 48.9 1.0 CD2 A:HIS274 3.5 55.3 1.0 CE1 A:HIS274 3.9 55.0 1.0 O A:HIS275 4.0 59.6 1.0 O A:SER225 4.0 51.3 1.0 CE3 A:TRP226 4.4 47.2 1.0 O A:PRO137 4.5 55.3 1.0 CB A:ASP85 4.6 51.8 1.0 O A:SER86 4.6 53.9 1.0 CZ3 A:TRP226 4.8 47.9 1.0 CG A:HIS274 4.8 54.8 1.0 O A:PRO16 4.8 56.1 1.0 ND1 A:HIS274 4.9 55.1 1.0 CA A:ALA224 5.0 50.9 1.0

Calcium binding site 2 out of 12 in the Structure of RS223-Beta-Xylosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of RS223-Beta-Xylosidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:73.2 occ:1.00 OD2 B:ASP85 2.4 73.1 1.0 OD1 B:ASP85 3.1 72.5 1.0 CG B:ASP85 3.1 70.9 1.0 NE2 B:HIS274 3.2 53.6 1.0 CD2 B:HIS274 3.9 54.1 1.0 O B:PRO137 4.0 68.0 1.0 O B:SER225 4.0 62.5 1.0 CE1 B:HIS274 4.2 54.1 1.0 O B:SER86 4.3 61.9 1.0 CE3 B:TRP226 4.3 63.1 1.0 O B:HIS275 4.4 72.5 1.0 CB B:ASP85 4.6 66.2 1.0 CZ3 B:TRP226 4.6 63.0 1.0 O B:HOH501 4.6 35.8 1.0 C B:PRO137 5.0 66.6 1.0

Calcium binding site 3 out of 12 in the Structure of RS223-Beta-Xylosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of RS223-Beta-Xylosidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:77.0 occ:1.00 OD2 C:ASP85 2.4 84.7 1.0 NE2 C:HIS274 2.6 67.0 1.0 CG C:ASP85 3.2 83.3 1.0 OD1 C:ASP85 3.4 85.7 1.0 CD2 C:HIS274 3.5 68.4 1.0 CE1 C:HIS274 3.5 65.6 1.0 O C:SER225 3.9 71.7 1.0 O C:HIS275 4.1 76.2 1.0 CE3 C:TRP226 4.3 78.6 1.0 O C:PRO137 4.6 68.2 1.0 CB C:ASP85 4.6 78.0 1.0 O C:SER86 4.6 78.0 1.0 O C:PRO16 4.6 70.2 1.0 ND1 C:HIS274 4.7 65.9 1.0 CG C:HIS274 4.7 67.7 1.0 CZ3 C:TRP226 4.7 84.0 1.0 CA C:ALA224 4.8 68.1 1.0 C C:ALA224 4.9 68.8 1.0 C C:SER225 4.9 68.5 1.0

Calcium binding site 4 out of 12 in the Structure of RS223-Beta-Xylosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of RS223-Beta-Xylosidase within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:65.6 occ:1.00 OD2 D:ASP85 2.3 74.6 1.0 NE2 D:HIS274 3.0 66.0 1.0 CG D:ASP85 3.3 73.0 1.0 OD1 D:ASP85 3.6 74.6 1.0 O D:SER225 3.7 57.7 1.0 CD2 D:HIS274 3.8 65.9 1.0 CE1 D:HIS274 4.0 66.9 1.0 CE3 D:TRP226 4.1 52.0 1.0 O D:PRO137 4.2 59.8 1.0 O D:HIS275 4.2 59.3 1.0 CZ3 D:TRP226 4.6 54.1 1.0 O D:SER86 4.6 61.7 1.0 CB D:ASP85 4.6 69.0 1.0 CA D:ALA224 4.7 58.6 1.0 C D:ALA224 4.7 58.6 1.0 C D:SER225 4.8 57.0 1.0 N D:SER225 4.8 58.5 1.0

Calcium binding site 5 out of 12 in the Structure of RS223-Beta-Xylosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of RS223-Beta-Xylosidase within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca401 b:70.4 occ:1.00 OD2 E:ASP85 2.3 68.7 1.0 NE2 E:HIS274 2.5 51.8 1.0 CG E:ASP85 3.1 68.2 1.0 OD1 E:ASP85 3.1 70.4 1.0 CD2 E:HIS274 3.4 53.4 1.0 CE1 E:HIS274 3.6 52.8 1.0 O E:SER225 4.0 53.3 1.0 O E:HIS275 4.2 57.5 1.0 O E:PRO137 4.5 57.5 1.0 CB E:ASP85 4.5 65.5 1.0 CE3 E:TRP226 4.5 47.8 1.0 O E:HOH501 4.6 33.5 1.0 CG E:HIS274 4.6 54.6 1.0 ND1 E:HIS274 4.7 53.9 1.0 O E:SER86 4.7 58.5 1.0 CA E:ALA224 4.8 56.9 1.0 CZ3 E:TRP226 4.8 48.1 1.0 C E:ALA224 4.9 55.2 1.0

Calcium binding site 6 out of 12 in the Structure of RS223-Beta-Xylosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of RS223-Beta-Xylosidase within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca401 b:84.3 occ:1.00 OD2 F:ASP85 2.4 84.7 1.0 NE2 F:HIS274 2.5 78.3 1.0 CG F:ASP85 3.0 83.5 1.0 OD1 F:ASP85 3.1 85.3 1.0 CE1 F:HIS274 3.3 77.6 1.0 CD2 F:HIS274 3.6 78.0 1.0 O F:SER225 3.9 68.4 1.0 O F:HIS275 4.1 71.5 1.0 CB F:ASP85 4.4 78.7 1.0 CE3 F:TRP226 4.4 64.6 1.0 O F:PRO137 4.5 68.6 1.0 ND1 F:HIS274 4.5 76.9 1.0 O F:SER86 4.6 64.7 1.0 CG F:HIS274 4.7 76.6 1.0 O F:HOH521 4.8 51.7 1.0 CZ3 F:TRP226 4.8 65.2 1.0 CA F:ALA224 4.9 64.8 1.0 CB F:ALA17 5.0 77.6 1.0 C F:ALA224 5.0 67.0 1.0

Calcium binding site 7 out of 12 in the Structure of RS223-Beta-Xylosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of RS223-Beta-Xylosidase within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca401 b:77.9 occ:1.00 OD2 G:ASP85 2.4 76.2 1.0 CE1 G:HIS274 2.9 71.7 1.0 OD1 G:ASP85 3.1 82.4 1.0 CG G:ASP85 3.1 78.8 1.0 NE2 G:HIS274 3.4 70.8 1.0 O G:SER86 4.0 72.0 1.0 O G:SER225 4.0 62.8 1.0 ND1 G:HIS274 4.1 73.6 1.0 O G:PRO137 4.2 67.4 1.0 CE3 G:TRP226 4.3 68.2 1.0 CZ3 G:TRP226 4.5 70.0 1.0 CB G:ASP85 4.6 77.5 1.0 O G:HIS275 4.6 72.6 1.0 CB G:ALA17 4.7 71.0 1.0 CD2 G:HIS274 4.7 72.3 1.0 C G:SER86 5.0 71.5 1.0

Calcium binding site 8 out of 12 in the Structure of RS223-Beta-Xylosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of RS223-Beta-Xylosidase within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca401 b:72.0 occ:1.00 OD2 H:ASP85 2.3 69.8 1.0 NE2 H:HIS274 3.0 60.8 1.0 CG H:ASP85 3.2 68.6 1.0 OD1 H:ASP85 3.4 69.3 1.0 O H:SER225 3.6 71.1 1.0 CD2 H:HIS274 3.7 61.1 1.0 CE1 H:HIS274 4.0 60.6 1.0 CE3 H:TRP226 4.3 70.3 1.0 O H:HIS275 4.3 65.8 1.0 O H:PRO137 4.4 65.8 1.0 O H:SER86 4.5 56.7 1.0 CB H:ASP85 4.6 65.6 1.0 CB H:CYS138 4.7 68.1 1.0 CZ3 H:TRP226 4.7 71.5 1.0 C H:SER225 4.8 71.7 1.0 O H:HOH501 4.8 28.6 1.0 CA H:ALA224 4.9 65.8 1.0 C H:ALA224 4.9 68.2 1.0 N H:SER225 4.9 70.0 1.0 CG H:HIS274 5.0 61.8 1.0 C H:PRO137 5.0 65.2 1.0

Calcium binding site 9 out of 12 in the Structure of RS223-Beta-Xylosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of RS223-Beta-Xylosidase within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca401 b:78.6 occ:1.00 OD2 I:ASP85 2.4 69.8 1.0 CE1 I:HIS274 2.7 73.0 1.0 CG I:ASP85 3.1 68.0 1.0 OD1 I:ASP85 3.1 66.3 1.0 NE2 I:HIS274 3.3 72.4 1.0 ND1 I:HIS274 3.8 74.1 1.0 O I:SER225 3.9 61.6 1.0 O I:HIS275 4.1 86.0 1.0 CE3 I:TRP226 4.2 60.0 1.0 CB I:ASP85 4.5 68.4 1.0 CZ3 I:TRP226 4.6 61.1 1.0 CD2 I:HIS274 4.6 73.3 1.0 O I:SER86 4.7 80.5 1.0 O I:PRO137 4.7 65.9 1.0 CG I:HIS274 4.9 74.8 1.0 CA I:ALA224 4.9 66.7 1.0 O I:HOH501 4.9 45.1 1.0 O I:PRO16 4.9 69.9 1.0 C I:ALA224 5.0 66.5 1.0 CB I:CYS138 5.0 66.0 1.0

Calcium binding site 10 out of 12 in the Structure of RS223-Beta-Xylosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of RS223-Beta-Xylosidase within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca401 b:70.2 occ:1.00 OD1 J:ASP85 2.4 65.3 1.0 NE2 J:HIS274 2.6 64.0 1.0 CG J:ASP85 3.2 65.6 1.0 OD2 J:ASP85 3.3 67.3 1.0 CD2 J:HIS274 3.5 64.6 1.0 CE1 J:HIS274 3.5 63.7 1.0 O J:SER225 3.7 68.3 1.0 O J:HIS275 4.2 65.0 1.0 O J:PRO137 4.3 56.7 1.0 CE3 J:TRP226 4.3 62.1 1.0 CA J:ALA224 4.5 66.8 1.0 CB J:ASP85 4.6 64.3 1.0 C J:ALA224 4.6 68.4 1.0 ND1 J:HIS274 4.7 63.7 1.0 CG J:HIS274 4.7 64.3 1.0 CZ3 J:TRP226 4.7 62.5 1.0 C J:SER225 4.8 68.0 1.0 N J:SER225 4.8 68.0 1.0 O J:SER86 4.8 60.3 1.0 O J:HOH501 4.9 42.3 1.0 CB J:ALA224 5.0 67.0 1.0

D.Jordan, J.Braker, K.Wagschal, C.Lee, I.Dubrovska, S.Anderson, Z.Wawrzak. Structure of RS223-Beta-Xylosidase To Be Published.