Calcium in PDB 3om6: Crystal Structure of B. Megaterium Levansucrase Mutant Y247A

All present enzymatic activity of Crystal Structure of B. Megaterium Levansucrase Mutant Y247A:
2.4.1.10;

The structure of Crystal Structure of B. Megaterium Levansucrase Mutant Y247A, PDB code: 3om6 was solved by C.P.Strube, A.Homann, M.Gamer, D.Jahn, J.Seibel, D.W.Heinz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 1.96
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	93.786, 100.018, 95.544, 90.00, 90.59, 90.00
R / Rfree (%)	22.2 / 23

The binding sites of Calcium atom in the Crystal Structure of B. Megaterium Levansucrase Mutant Y247A (pdb code 3om6). 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 B. Megaterium Levansucrase Mutant Y247A, PDB code: 3om6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of B. Megaterium Levansucrase Mutant Y247A


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 B. Megaterium Levansucrase Mutant Y247A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:13.6 occ:1.00 O A:LEU318 2.4 9.4 1.0 O A:HOH598 2.4 13.8 1.0 OE1 A:GLN282 2.4 8.6 1.0 OD1 A:ASN320 2.4 8.2 1.0 OD1 A:ASP251 2.5 16.9 1.0 OD1 A:ASP349 2.6 10.7 1.0 OD2 A:ASP349 2.6 10.8 1.0 CG A:ASP349 2.9 10.8 1.0 CD A:GLN282 3.4 8.3 1.0 CG A:ASN320 3.4 8.4 1.0 CG A:ASP251 3.5 16.9 1.0 C A:LEU318 3.6 9.5 1.0 OD2 A:ASP251 3.7 16.9 1.0 ND2 A:ASN274 4.0 7.6 1.0 N A:ASN320 4.0 8.7 1.0 O A:ASN252 4.1 16.0 1.0 NE2 A:GLN282 4.1 8.7 1.0 ND2 A:ASN320 4.1 8.2 1.0 CA A:LEU318 4.4 9.8 1.0 CB A:ASP349 4.4 10.7 1.0 CB A:GLN282 4.4 7.8 1.0 N A:ASN252 4.5 16.5 1.0 CB A:ASN320 4.5 8.6 1.0 CG A:GLN282 4.5 8.2 1.0 CB A:LEU318 4.5 9.8 1.0 NE2 A:GLN236 4.6 12.4 1.0 N A:ALA319 4.6 9.2 1.0 CG A:ASN274 4.6 8.2 1.0 CA A:ASN320 4.7 8.6 1.0 CA A:ALA319 4.7 8.9 1.0 C A:ALA319 4.7 8.8 1.0 C A:ASN252 4.8 16.0 1.0 CB A:ASP251 4.8 16.9 1.0 OE1 A:GLN236 4.9 12.0 1.0 CB A:ASN274 4.9 8.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of B. Megaterium Levansucrase Mutant Y247A


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 B. Megaterium Levansucrase Mutant Y247A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1 b:12.8 occ:1.00 O B:LEU318 2.3 3.8 1.0 OD1 B:ASN320 2.3 4.0 1.0 OE1 B:GLN282 2.4 4.3 1.0 OD1 B:ASP251 2.5 18.3 1.0 OD1 B:ASP349 2.5 8.6 1.0 O B:HOH1120 2.5 20.8 1.0 OD2 B:ASP349 3.0 9.4 1.0 CG B:ASP349 3.1 8.6 1.0 CG B:ASN320 3.4 3.4 1.0 C B:LEU318 3.5 4.1 1.0 CD B:GLN282 3.5 5.1 1.0 CG B:ASP251 3.6 18.2 1.0 OD2 B:ASP251 3.9 18.3 1.0 N B:ASN320 4.0 3.4 1.0 ND2 B:ASN274 4.0 8.1 1.0 ND2 B:ASN320 4.2 3.7 1.0 NE2 B:GLN282 4.2 5.3 1.0 CB B:GLN282 4.3 6.1 1.0 CA B:LEU318 4.3 4.6 1.0 CB B:ASN320 4.4 3.3 1.0 O B:ASN252 4.4 16.9 1.0 N B:ALA319 4.4 3.5 1.0 CB B:ASP349 4.5 8.4 1.0 CG B:GLN282 4.5 6.4 1.0 CB B:LEU318 4.5 4.7 1.0 CA B:ALA319 4.6 3.4 1.0 C B:ALA319 4.6 3.3 1.0 OE1 B:GLN236 4.6 10.2 1.0 CA B:ASN320 4.6 3.4 1.0 CG B:ASN274 4.7 8.0 1.0 N B:ASN252 4.7 17.6 1.0 O B:HOH671 4.7 15.6 1.0 CB B:ASP251 4.9 18.3 1.0 NE2 B:GLN236 5.0 10.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of B. Megaterium Levansucrase Mutant Y247A


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 B. Megaterium Levansucrase Mutant Y247A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1 b:10.8 occ:1.00 OD1 C:ASP251 2.3 12.1 1.0 O C:HOH822 2.3 16.9 1.0 O C:LEU318 2.3 8.0 1.0 OD1 C:ASN320 2.3 6.4 1.0 OD1 C:ASP349 2.4 9.7 1.0 OE1 C:GLN282 2.6 6.5 1.0 OD2 C:ASP349 2.6 9.5 1.0 CG C:ASP349 2.9 9.8 1.0 CG C:ASP251 3.4 12.0 1.0 CG C:ASN320 3.5 6.8 1.0 C C:LEU318 3.5 8.1 1.0 CD C:GLN282 3.7 6.9 1.0 OD2 C:ASP251 3.7 12.1 1.0 ND2 C:ASN274 4.0 7.5 1.0 N C:ASN320 4.0 7.4 1.0 O C:ASN252 4.1 10.7 1.0 ND2 C:ASN320 4.3 6.5 1.0 CB C:ASP349 4.4 10.1 1.0 N C:ASN252 4.4 11.4 1.0 CA C:LEU318 4.4 8.2 1.0 NE2 C:GLN282 4.4 6.8 1.0 N C:ALA319 4.5 7.8 1.0 CB C:GLN282 4.5 7.3 1.0 CA C:ALA319 4.6 7.6 1.0 CB C:ASN320 4.6 7.2 1.0 CB C:LEU318 4.6 8.4 1.0 CG C:ASN274 4.6 7.2 1.0 C C:ALA319 4.6 7.6 1.0 NE2 C:GLN236 4.6 8.2 1.0 CB C:ASP251 4.7 12.1 1.0 CG C:GLN282 4.7 7.2 1.0 CA C:ASN320 4.7 7.3 1.0 C C:ASN252 4.8 10.8 1.0 OE1 C:GLN236 4.8 7.8 1.0 CB C:ASN274 4.8 7.1 1.0 O C:HOH769 4.9 15.5 1.0 CA C:ASP251 4.9 12.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of B. Megaterium Levansucrase Mutant Y247A


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 B. Megaterium Levansucrase Mutant Y247A within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1 b:14.7 occ:1.00 O D:HOH562 2.3 7.8 1.0 OE1 D:GLN282 2.3 11.0 1.0 OD1 D:ASP251 2.4 16.3 1.0 OD1 D:ASN320 2.4 7.5 1.0 O D:LEU318 2.4 9.8 1.0 OD1 D:ASP349 2.7 10.5 1.0 OD2 D:ASP349 2.8 10.1 1.0 CG D:ASP349 3.1 10.4 1.0 CG D:ASP251 3.4 16.4 1.0 CG D:ASN320 3.5 8.0 1.0 CD D:GLN282 3.5 10.9 1.0 C D:LEU318 3.6 9.9 1.0 OD2 D:ASP251 3.8 16.2 1.0 ND2 D:ASN320 4.1 7.7 1.0 N D:ASN320 4.1 8.5 1.0 O D:ASN252 4.2 15.0 1.0 NE2 D:GLN282 4.2 10.7 1.0 ND2 D:ASN274 4.2 6.7 1.0 CB D:GLN282 4.4 11.6 1.0 CA D:LEU318 4.4 10.2 1.0 NE2 D:GLN236 4.5 6.2 1.0 CG D:GLN282 4.5 11.5 1.0 CB D:ASN320 4.5 8.3 1.0 N D:ASN252 4.6 15.7 1.0 CB D:ASP349 4.6 10.6 1.0 CB D:LEU318 4.6 10.3 1.0 N D:ALA319 4.6 9.5 1.0 CG D:ASN274 4.7 7.2 1.0 OE1 D:GLN236 4.8 6.3 1.0 CA D:ALA319 4.8 9.1 1.0 CB D:ASP251 4.8 16.4 1.0 CA D:ASN320 4.8 8.3 1.0 C D:ALA319 4.8 8.8 1.0 O D:HOH1018 4.9 22.2 1.0 C D:ASN252 4.9 14.9 1.0 CB D:ASN274 5.0 7.7 1.0

C.P.Strube, A.Homann, M.Gamer, D.Jahn, J.Seibel, D.W.Heinz. Polysaccharide Synthesis of the Levansucrase Sacb From Bacillus Megaterium Is Controlled By Distinct Surface Motifs. J.Biol.Chem. V. 286 17593 2011.
ISSN: ISSN 0021-9258
PubMed: 21454585
DOI: 10.1074/JBC.M110.203166