Atomistry » Iron » PDB 3i9t-3j7b » 3ivd
Atomistry »
  Iron »
    PDB 3i9t-3j7b »
      3ivd »

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

Protein crystallography data

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

Other elements in 3ivd:

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

Iron Binding Sites:

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 3ivd

Go back to Iron Binding Sites List in 3ivd
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 3ivd

Go back to Iron Binding Sites List in 3ivd
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

Reference:

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.
Page generated: Sun Dec 13 15:09:11 2020

Last articles

Zn in 7O75
Zn in 7O73
Zn in 7O4I
Zn in 7O72
Zn in 7O4J
Zn in 7NVR
Zn in 7NVY
Zn in 7NVZ
Zn in 7NW0
Zn in 7O4K
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy