Calcium in PDB 7jjt: Ruminococcus Bromii Amylase AMY5 (RBR_07800)

All present enzymatic activity of Ruminococcus Bromii Amylase AMY5 (RBR_07800):
3.2.1.1;

The structure of Ruminococcus Bromii Amylase AMY5 (RBR_07800), PDB code: 7jjt was solved by F.Cerqueira, N.Koropatkin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.00 / 1.66
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.46, 98.46, 196.22, 90, 90, 90
R / Rfree (%)	16 / 18.1

The binding sites of Calcium atom in the Ruminococcus Bromii Amylase AMY5 (RBR_07800) (pdb code 7jjt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Ruminococcus Bromii Amylase AMY5 (RBR_07800), PDB code: 7jjt:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Ruminococcus Bromii Amylase AMY5 (RBR_07800)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ruminococcus Bromii Amylase AMY5 (RBR_07800) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca624 b:23.6 occ:1.00 O A:HOH732 2.3 26.4 1.0 O A:THR48 2.3 23.9 1.0 OD2 A:ASP50 2.3 23.1 1.0 OD1 A:ASN44 2.4 24.1 1.0 OD1 A:ASP42 2.4 23.2 1.0 OD1 A:ASP46 2.4 23.9 1.0 CG A:ASP42 3.3 24.0 1.0 CG A:ASP46 3.3 25.9 1.0 H A:ASN44 3.4 29.4 1.0 HB3 A:ASP50 3.4 27.7 1.0 H A:THR48 3.4 26.6 1.0 CG A:ASP50 3.4 21.2 1.0 HA A:ASP42 3.5 28.0 1.0 C A:THR48 3.5 24.4 1.0 CG A:ASN44 3.5 25.8 1.0 H A:SER43 3.6 28.8 1.0 HG22 A:THR48 3.6 37.4 1.0 H A:ASP46 3.7 30.0 1.0 OD2 A:ASP46 3.8 24.8 1.0 HD21 A:ASN44 3.9 31.1 1.0 HB A:THR48 3.9 32.4 1.0 CB A:ASP50 4.0 23.1 1.0 OD2 A:ASP42 4.1 25.6 1.0 N A:THR48 4.1 22.2 1.0 N A:ASN44 4.1 24.5 1.0 H21 A:EDO604 4.1 45.5 1.0 ND2 A:ASN44 4.1 25.9 1.0 CB A:ASP42 4.1 25.0 1.0 CA A:ASP42 4.2 23.3 1.0 N A:SER43 4.2 24.0 1.0 CA A:THR48 4.2 22.7 1.0 HB2 A:ASP42 4.2 30.0 1.0 HG A:SER43 4.3 31.1 1.0 CG2 A:THR48 4.4 31.1 1.0 CB A:THR48 4.4 27.0 1.0 HA2 A:GLY49 4.4 25.6 1.0 H A:GLY45 4.4 29.4 1.0 N A:ASP46 4.5 25.0 1.0 OD1 A:ASP50 4.5 22.4 1.0 N A:GLY49 4.5 23.4 1.0 H22 A:EDO604 4.5 45.5 1.0 C A:GLY49 4.5 22.3 1.0 CB A:ASP46 4.6 24.7 1.0 O A:ASP102 4.6 28.2 1.0 H12 A:EDO604 4.6 46.8 1.0 HB2 A:ASP50 4.6 27.7 1.0 C A:ASP42 4.6 23.1 1.0 CB A:ASN44 4.6 26.2 1.0 HB3 A:ASP46 4.7 29.7 1.0 CA A:ASN44 4.7 25.8 1.0 N A:ASP50 4.7 23.6 1.0 H A:GLU47 4.7 29.7 1.0 CA A:GLY49 4.7 21.3 1.0 N A:GLY45 4.7 24.4 1.0 O A:GLY49 4.8 22.3 1.0 HG23 A:THR48 4.8 37.4 1.0 C A:ASN44 4.8 24.6 1.0 C2 A:EDO604 4.8 37.9 1.0 HB3 A:ASN44 4.9 31.5 1.0 CA A:ASP46 4.9 24.1 1.0 HD22 A:ASN44 5.0 31.1 1.0 H A:ASP50 5.0 28.3 1.0 N A:GLU47 5.0 24.7 1.0

Calcium binding site 2 out of 3 in the Ruminococcus Bromii Amylase AMY5 (RBR_07800)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ruminococcus Bromii Amylase AMY5 (RBR_07800) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca625 b:21.0 occ:1.00 OD1 A:ASN130 2.4 19.8 1.0 O A:HOH932 2.4 21.7 1.0 O A:HOH894 2.4 22.1 1.0 OE1 A:GLU191 2.4 22.8 1.0 O A:TYR225 2.4 21.3 1.0 O A:HOH800 2.5 20.7 1.0 O A:HOH955 2.6 22.4 1.0 HB3 A:GLU191 3.4 25.2 1.0 HB3 A:TYR225 3.5 25.1 1.0 CG A:ASN130 3.5 20.6 1.0 C A:TYR225 3.6 19.0 1.0 CD A:GLU191 3.6 23.2 1.0 HD22 A:ASN228 3.7 31.6 1.0 HD21 A:ASN130 3.8 25.3 1.0 HA A:PHE226 3.9 24.4 1.0 ND2 A:ASN130 4.1 21.1 1.0 CB A:GLU191 4.3 20.9 1.0 ND2 A:ASN228 4.3 26.3 1.0 HD11 A:LEU194 4.3 30.9 1.0 CB A:TYR225 4.3 20.9 1.0 O A:ASN130 4.4 20.8 1.0 OE1 A:GLU182 4.4 27.4 1.0 HA A:ASN130 4.4 23.5 1.0 N A:PHE226 4.4 19.6 1.0 HG A:LEU194 4.4 30.6 1.0 HD21 A:ASN228 4.4 31.6 1.0 OE2 A:GLU191 4.5 23.7 1.0 CA A:PHE226 4.5 20.3 1.0 CG A:GLU191 4.5 26.5 1.0 CA A:TYR225 4.5 20.1 1.0 HD22 A:ASN184 4.5 30.3 1.0 HB2 A:GLU191 4.5 25.2 1.0 O A:PHE226 4.6 23.7 1.0 HB2 A:TYR225 4.6 25.1 1.0 HB3 A:ASN228 4.6 28.7 1.0 O A:TRP192 4.6 21.6 1.0 HD12 A:LEU194 4.7 30.9 1.0 HA A:TYR225 4.7 24.1 1.0 CB A:ASN130 4.7 19.7 1.0 CD A:GLU182 4.7 24.1 1.0 C A:PHE226 4.7 23.3 1.0 OE2 A:GLU182 4.7 26.2 1.0 O A:HOH877 4.7 21.8 1.0 HD1 A:PHE226 4.7 24.7 1.0 O A:HOH778 4.8 25.3 1.0 CD1 A:LEU194 4.9 25.7 1.0 HG2 A:GLU191 4.9 31.8 1.0 HB2 A:ASN130 4.9 23.7 1.0 HD22 A:ASN130 4.9 25.3 1.0 HD21 A:ASN184 4.9 30.3 1.0 CA A:ASN130 5.0 19.6 1.0

Calcium binding site 3 out of 3 in the Ruminococcus Bromii Amylase AMY5 (RBR_07800)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ruminococcus Bromii Amylase AMY5 (RBR_07800) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca626 b:27.7 occ:1.00 O A:ASP65 2.3 23.1 1.0 O A:SER68 2.3 31.3 1.0 O A:HOH747 2.3 28.0 1.0 OD1 A:ASP71 2.4 25.7 1.0 OD1 A:ASP63 2.4 24.3 1.0 O A:HOH1163 2.6 32.0 1.0 OD2 A:ASP63 2.7 29.5 1.0 CG A:ASP63 2.9 27.5 1.0 CG A:ASP71 3.2 23.4 1.0 OD2 A:ASP71 3.4 24.8 1.0 C A:ASP65 3.4 21.4 1.0 HA3 A:GLY69 3.4 41.6 1.0 C A:SER68 3.5 31.7 1.0 H A:SER68 3.6 33.3 1.0 H A:ASP65 3.6 33.0 1.0 HA A:PRO66 3.7 34.5 1.0 HB3 A:ASP65 3.8 37.5 1.0 H A:ASP71 4.0 28.7 1.0 H A:ASP63 4.1 29.1 1.0 CA A:GLY69 4.1 34.6 1.0 CA A:ASP65 4.2 29.7 1.0 N A:ASP65 4.2 27.4 1.0 N A:GLY69 4.2 30.1 1.0 N A:SER68 4.3 27.7 1.0 N A:PRO66 4.3 27.3 1.0 CA A:PRO66 4.3 28.7 1.0 O A:HOH956 4.3 25.7 1.0 CB A:ASP63 4.4 24.2 1.0 CB A:ASP65 4.5 31.2 1.0 C A:GLY69 4.5 29.8 1.0 CA A:SER68 4.5 29.0 1.0 O A:HOH1314 4.6 22.4 1.0 O A:HOH1130 4.6 37.2 1.0 CB A:ASP71 4.6 22.0 1.0 C A:PRO66 4.6 27.3 1.0 O A:HOH1182 4.6 32.2 1.0 HB3 A:ASP71 4.7 26.4 1.0 HB3 A:ASP63 4.7 29.0 1.0 HG A:SER68 4.8 57.2 1.0 O A:HOH1272 4.8 42.2 1.0 H A:ASN67 4.8 30.0 1.0 N A:ASP71 4.8 23.9 1.0 N A:ASN67 4.8 25.0 1.0 N A:ASP63 4.9 24.2 1.0 O A:GLY69 4.9 33.9 1.0 HB2 A:ASP63 4.9 29.0 1.0 N A:ASP70 5.0 27.5 1.0 HA2 A:GLY69 5.0 41.6 1.0

D.W.Cockburn, F.M.Cerqueira, C.M.E.Bahr, N.M.Koropatkin. The Structures of the GH13_36 Amylases From Eubacterium Rectale and Ruminococcus Bromii Reveal Subsite Architectures That Favor Maltose Production Amylase V. 4 24 2020.
ISSN: ESSN 2450-9728
DOI: 10.1515/AMYLASE-2020-0003