Manganese in PDB 3lhl: Crystal Structure of A Putative Agmatinase From Clostridium Difficile

The structure of Crystal Structure of A Putative Agmatinase From Clostridium Difficile, PDB code: 3lhl was solved by K.Palani, S.K.Burley, S.Swaminathan, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.68 / 2.30
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	77.350, 77.350, 166.118, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 23.8

The binding sites of Manganese atom in the Crystal Structure of A Putative Agmatinase From Clostridium Difficile (pdb code 3lhl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of A Putative Agmatinase From Clostridium Difficile, PDB code: 3lhl:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of A Putative Agmatinase From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of A Putative Agmatinase From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:18.2 occ:1.00 OD2 A:ASP134 2.2 13.8 1.0 OD2 A:ASP215 2.2 15.6 1.0 ND1 A:HIS111 2.2 12.3 1.0 OD2 A:ASP138 2.3 15.6 1.0 MN A:MN303 2.9 41.2 1.0 CG A:ASP134 3.1 16.0 1.0 CE1 A:HIS111 3.1 9.8 1.0 MN A:MN302 3.2 17.8 1.0 CG A:ASP215 3.2 16.8 1.0 CG A:HIS111 3.3 12.9 1.0 CG A:ASP138 3.3 16.2 1.0 OD1 A:ASP134 3.3 9.9 1.0 CB A:ASP215 3.6 15.1 1.0 OD1 A:ASP138 3.6 18.0 1.0 CB A:HIS111 3.6 13.1 1.0 NE2 A:HIS111 4.3 12.0 1.0 O A:HIS150 4.3 16.3 1.0 CD2 A:HIS111 4.4 11.9 1.0 OD1 A:ASP215 4.4 19.1 1.0 CB A:ASP134 4.5 14.1 1.0 CE1 A:HIS132 4.5 19.4 1.0 CG A:GLU261 4.7 14.2 1.0 CB A:ASP138 4.7 16.3 1.0 OE2 A:GLU261 4.8 19.5 1.0 CA A:ASP215 4.9 14.3 1.0 OD2 A:ASP217 5.0 20.7 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of A Putative Agmatinase From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of A Putative Agmatinase From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:17.8 occ:1.00 OD2 A:ASP217 2.0 20.7 1.0 OD1 A:ASP134 2.3 9.9 1.0 OD2 A:ASP215 2.4 15.6 1.0 ND1 A:HIS136 2.4 16.4 1.0 CG A:ASP217 2.7 20.2 1.0 OD1 A:ASP217 2.7 21.2 1.0 CG A:ASP215 3.0 16.8 1.0 MN A:MN303 3.2 41.2 1.0 MN A:MN301 3.2 18.2 1.0 CE1 A:HIS136 3.2 18.1 1.0 CG A:ASP134 3.3 16.0 1.0 OD1 A:ASP215 3.3 19.1 1.0 CG A:HIS136 3.5 18.7 1.0 OD2 A:ASP134 3.6 13.8 1.0 CB A:HIS136 3.9 15.8 1.0 N A:HIS136 4.0 16.1 1.0 CB A:ASP215 4.1 15.1 1.0 CB A:ASP217 4.2 18.2 1.0 N A:ALA135 4.2 15.1 1.0 NE2 A:HIS136 4.4 16.8 1.0 O A:HOH382 4.5 14.5 1.0 CD2 A:HIS136 4.6 16.8 1.0 CA A:HIS136 4.6 17.7 1.0 CB A:ASP134 4.6 14.1 1.0 O A:HOH345 4.7 28.3 1.0 CB A:ALA135 4.7 14.3 1.0 CG A:GLU261 4.8 14.2 1.0 OD1 A:ASP138 4.9 18.0 1.0 OD2 A:ASP138 4.9 15.6 1.0 C A:ALA135 4.9 17.7 1.0 CA A:ALA135 4.9 15.4 1.0 CA A:ASP134 5.0 15.5 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of A Putative Agmatinase From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of A Putative Agmatinase From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:41.2 occ:1.00 MN A:MN301 2.9 18.2 1.0 MN A:MN302 3.2 17.8 1.0 OD2 A:ASP215 3.4 15.6 1.0 OE2 A:GLU261 3.4 19.5 1.0 CD2 A:HIS150 3.6 16.2 1.0 OD1 A:ASP138 3.7 18.0 1.0 O A:HOH345 3.7 28.3 1.0 O A:HIS150 3.9 16.3 1.0 OD2 A:ASP138 4.0 15.6 1.0 CD A:GLU261 4.2 19.1 1.0 CG A:ASP138 4.3 16.2 1.0 CG A:HIS150 4.3 16.6 1.0 CB A:HIS150 4.3 17.0 1.0 CG A:GLU261 4.3 14.2 1.0 C A:HIS150 4.3 17.2 1.0 ND1 A:HIS136 4.4 16.4 1.0 OD2 A:ASP217 4.4 20.7 1.0 CB A:HIS111 4.4 13.1 1.0 CG A:ASP215 4.6 16.8 1.0 ND1 A:HIS111 4.6 12.3 1.0 OD1 A:ASP134 4.7 9.9 1.0 OD2 A:ASP134 4.7 13.8 1.0 NE2 A:HIS150 4.7 17.1 1.0 N A:ALA151 4.9 16.9 1.0 CG A:HIS136 4.9 18.7 1.0 CA A:HIS150 5.0 18.3 1.0 CB A:HIS136 5.0 15.8 1.0 CA A:ALA151 5.0 16.9 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of A Putative Agmatinase From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of A Putative Agmatinase From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn304 b:29.7 occ:0.33 ND2 A:ASN236 3.6 23.8 1.0 CB A:ASN236 4.6 19.6 1.0 CG A:ASN236 4.6 22.3 1.0 O A:HOH384 4.8 19.0 1.0 O A:HOH445 4.9 34.6 1.0

K.Palani, S.K.Burley, S.Swaminathan. Crystal Structure of A Putative Agmatinase From Clostridium Difficile To Be Published.