Iron 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:

Manganese	(Mn)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron where determined in the Putative 5'-Nucleotidase (C4898) From Escherichia Coli in Complex with Uridine, PDB code: 3ivd:
Jump to Iron binding site number: 1; 2;

Iron 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 Iron with other atoms in the Fe 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:Fe601 b:19.1 occ:1.00 OD1 A:ASN111 2.0 18.4 1.0 OD2 A:ASP79 2.1 14.5 1.0 O A:HOH758 2.2 27.2 1.0 NE2 A:HIS212 2.3 13.2 1.0 ND1 A:HIS251 2.3 15.4 1.0 CG A:ASP79 3.1 13.5 1.0 CG A:ASN111 3.1 15.8 1.0 CE1 A:HIS251 3.2 16.5 1.0 CD2 A:HIS212 3.2 13.4 1.0 CE1 A:HIS212 3.3 14.2 1.0 CG A:HIS251 3.3 15.2 1.0 MN A:MN602 3.4 23.4 1.0 OD1 A:ASP79 3.5 13.6 1.0 ND2 A:ASN111 3.6 16.4 1.0 CA A:HIS251 3.6 16.8 1.0 CB A:HIS251 3.7 15.7 1.0 OD1 A:ASP32 4.0 17.7 1.0 CD2 A:HIS112 4.1 15.4 1.0 O A:HIS251 4.3 18.1 1.0 NE2 A:HIS251 4.3 16.2 1.0 N A:ASN111 4.3 13.5 1.0 CB A:ASP79 4.3 12.6 1.0 ND1 A:HIS212 4.4 14.5 1.0 CG A:HIS212 4.4 15.1 1.0 CB A:ASN111 4.4 13.8 1.0 CD2 A:HIS251 4.4 15.3 1.0 C A:HIS251 4.5 17.1 1.0 N A:HIS251 4.5 17.3 1.0 NE2 A:HIS112 4.7 17.6 1.0 O5' A:URI603 4.8 19.8 1.0 CA A:ASN111 4.9 12.8 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe601 b:15.5 occ:1.00 O B:HOH706 1.9 25.3 1.0 OD1 B:ASN111 2.0 14.1 1.0 OD2 B:ASP79 2.1 13.9 1.0 NE2 B:HIS212 2.1 10.4 1.0 ND1 B:HIS251 2.3 17.6 1.0 CD2 B:HIS212 3.1 9.7 1.0 CG B:ASP79 3.1 12.3 1.0 CG B:ASN111 3.1 13.9 1.0 CE1 B:HIS212 3.1 12.2 1.0 CE1 B:HIS251 3.1 17.9 1.0 CG B:HIS251 3.3 16.5 1.0 MN B:MN602 3.4 19.9 1.0 OD1 B:ASP79 3.4 12.6 1.0 ND2 B:ASN111 3.5 14.1 1.0 CA B:HIS251 3.6 13.9 1.0 CB B:HIS251 3.7 14.4 1.0 OD1 B:ASP32 3.9 13.6 1.0 CD2 B:HIS112 4.1 14.7 1.0 ND1 B:HIS212 4.2 11.8 1.0 CG B:HIS212 4.2 10.4 1.0 NE2 B:HIS251 4.3 17.8 1.0 O B:HIS251 4.3 14.0 1.0 CB B:ASP79 4.3 12.0 1.0 N B:ASN111 4.4 12.6 1.0 CB B:ASN111 4.4 12.1 1.0 CD2 B:HIS251 4.4 15.7 1.0 C B:HIS251 4.5 14.8 1.0 N B:HIS251 4.5 13.2 1.0 O B:HOH698 4.6 36.3 1.0 NE2 B:HIS112 4.7 15.3 1.0 O5' B:URI603 4.9 18.2 1.0 CA B:ASN111 5.0 12.9 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.