Manganese in PDB 3ivd: Putative 5'-Nucleotidase (C4898) From Escherichia Coli in Complex with Uridine

The structure of Putative 5'-Nucleotidase (C4898) From Escherichia Coli in Complex with Uridine, PDB code: 3ivd was solved by U.A.Ramagopal, R.Toro, S.K.Burley, S.C.Almo, New York Sgx Research Centerfor Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.597, 67.281, 86.417, 74.04, 77.55, 83.76
R / Rfree (%)	16.7 / 21

The structure of Putative 5'-Nucleotidase (C4898) From Escherichia Coli in Complex with Uridine also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Manganese atom in the Putative 5'-Nucleotidase (C4898) From Escherichia Coli in Complex with Uridine (pdb code 3ivd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Putative 5'-Nucleotidase (C4898) From Escherichia Coli in Complex with Uridine, PDB code: 3ivd:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Putative 5'-Nucleotidase (C4898) From Escherichia Coli in Complex with Uridine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Putative 5'-Nucleotidase (C4898) From Escherichia Coli in Complex with Uridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:23.4 occ:1.00 OD1 A:ASP32 2.1 17.7 1.0 O A:HOH758 2.2 27.2 1.0 NE2 A:HIS34 2.2 16.8 1.0 OD2 A:ASP79 2.3 14.5 1.0 NE2 A:HIS253 2.3 18.0 1.0 CG A:ASP32 3.1 18.5 1.0 CE1 A:HIS34 3.1 17.6 1.0 CG A:ASP79 3.2 13.5 1.0 CD2 A:HIS34 3.2 16.4 1.0 CE1 A:HIS253 3.3 18.8 1.0 CD2 A:HIS253 3.3 18.8 1.0 FE A:FE601 3.4 19.1 1.0 CB A:ASP79 3.4 12.6 1.0 CB A:ASP32 3.7 16.3 1.0 OD2 A:ASP32 4.2 18.7 1.0 CD2 A:HIS112 4.2 15.4 1.0 O A:HIS251 4.2 18.1 1.0 ND1 A:HIS34 4.3 17.1 1.0 CA A:ASP32 4.3 16.6 1.0 CG A:HIS34 4.3 16.3 1.0 CA A:HIS251 4.4 16.8 1.0 OD1 A:ASP79 4.4 13.6 1.0 ND1 A:HIS253 4.4 19.4 1.0 CG A:HIS253 4.5 18.6 1.0 NE2 A:HIS212 4.6 13.2 1.0 CE1 A:HIS212 4.6 14.2 1.0 C A:HIS251 4.7 17.1 1.0 NH2 A:ARG375 4.7 19.9 1.0 O5' A:URI603 4.7 19.8 1.0 NE2 A:HIS112 4.7 17.6 1.0 N A:HIS251 4.8 17.3 1.0 CA A:ASP79 4.9 14.0 1.0

Manganese binding site 2 out of 2 in the Putative 5'-Nucleotidase (C4898) From Escherichia Coli in Complex with Uridine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Putative 5'-Nucleotidase (C4898) From Escherichia Coli in Complex with Uridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn602 b:19.9 occ:1.00 O B:HOH706 2.1 25.3 1.0 OD1 B:ASP32 2.2 13.6 1.0 NE2 B:HIS34 2.3 12.5 1.0 NE2 B:HIS253 2.4 11.7 1.0 OD2 B:ASP79 2.4 13.9 1.0 O B:HOH698 3.0 36.3 1.0 CG B:ASP32 3.1 15.1 1.0 CE1 B:HIS34 3.2 12.9 1.0 CD2 B:HIS34 3.2 13.4 1.0 CG B:ASP79 3.3 12.3 1.0 CE1 B:HIS253 3.3 11.7 1.0 CD2 B:HIS253 3.4 13.0 1.0 FE B:FE601 3.4 15.5 1.0 CB B:ASP79 3.4 12.0 1.0 CB B:ASP32 3.6 13.2 1.0 OD2 B:ASP32 4.1 16.8 1.0 O B:HIS251 4.2 14.0 1.0 CD2 B:HIS112 4.3 14.7 1.0 CA B:ASP32 4.3 12.4 1.0 ND1 B:HIS34 4.3 12.2 1.0 CA B:HIS251 4.3 13.9 1.0 CG B:HIS34 4.4 12.1 1.0 CE1 B:HIS212 4.4 12.2 1.0 NE2 B:HIS212 4.4 10.4 1.0 OD1 B:ASP79 4.4 12.6 1.0 ND1 B:HIS253 4.5 13.4 1.0 CG B:HIS253 4.5 13.6 1.0 C B:HIS251 4.6 14.8 1.0 NH2 B:ARG375 4.6 16.7 1.0 N B:HIS251 4.7 13.2 1.0 NE2 B:HIS112 4.8 15.3 1.0 O5' B:URI603 4.9 18.2 1.0 CA B:ASP79 5.0 11.8 1.0 ND1 B:HIS251 5.0 17.6 1.0

U.A.Ramagopal, R.Toro, S.K.Burley, S.C.Almo. Putative 5'-Nucleotidase (C4898) From Escherichia Coli in Complex with Uridine To Be Published.