Iron in PDB 7lkj: Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda)

The structure of Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda), PDB code: 7lkj was solved by R.K.Harijan, M.Feng, J.B.Bonanno, S.C.Almo, V.L.Schramm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	155.73 / 2.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.295, 73.295, 157.495, 90, 98.59, 90
R / Rfree (%)	25.3 / 28.7

The binding sites of Iron atom in the Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) (pdb code 7lkj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda), PDB code: 7lkj:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:61.9 occ:1.00 NE2 A:HIS65 2.2 52.3 1.0 NE2 A:HIS207 2.3 44.4 1.0 NE2 A:HIS67 2.6 44.1 1.0 CD2 A:HIS207 2.8 44.5 1.0 CD2 A:HIS65 2.9 48.4 1.0 OD2 A:ASP314 3.0 51.2 1.0 CE1 A:HIS65 3.3 49.0 1.0 CE1 A:HIS67 3.4 44.0 1.0 CE1 A:HIS207 3.6 44.7 1.0 CD2 A:HIS67 3.6 43.9 1.0 CG A:ASP314 3.6 49.5 1.0 OD1 A:ASP314 3.7 50.6 1.0 NE2 A:HIS261 3.9 26.6 1.0 CG A:HIS207 4.1 43.7 1.0 CG A:HIS65 4.1 45.7 1.0 ND1 A:HIS65 4.3 48.6 1.0 ND1 A:HIS207 4.4 44.6 1.0 ND1 A:HIS67 4.5 44.3 1.0 CG A:HIS67 4.6 44.3 1.0 CE1 A:HIS261 4.7 28.5 1.0 CD2 A:HIS261 4.8 26.9 1.0 CG1 A:VAL260 4.8 26.4 1.0 CB A:ASP314 4.9 45.8 1.0 O A:HOH632 4.9 33.8 1.0

Iron binding site 2 out of 3 in the Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:64.8 occ:1.00 NE2 B:HIS207 2.1 59.2 1.0 CE1 B:HIS67 2.3 56.6 1.0 NE2 B:HIS67 2.4 57.1 1.0 NE2 B:HIS65 2.4 40.8 1.0 CE1 B:HIS207 2.6 55.6 1.0 CE1 B:HIS65 3.1 40.8 1.0 CD2 B:HIS207 3.4 55.4 1.0 ND1 B:HIS67 3.4 56.6 1.0 CD2 B:HIS65 3.5 40.6 1.0 CD2 B:HIS67 3.6 57.1 1.0 ND1 B:HIS207 3.9 55.1 1.0 CG B:HIS67 4.1 55.4 1.0 OD2 B:ASP314 4.2 69.2 1.0 ND1 B:HIS65 4.2 40.8 1.0 CG B:HIS207 4.3 52.5 1.0 OD1 B:ASP314 4.3 68.5 1.0 CG B:HIS65 4.5 41.0 1.0 CG B:ASP314 4.6 68.3 1.0 CE1 B:HIS261 4.8 29.8 1.0 OE1 B:GLU144 4.9 63.4 1.0

Iron binding site 3 out of 3 in the Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:81.0 occ:1.00 NE2 C:HIS67 2.3 49.4 1.0 NE2 C:HIS65 2.3 46.4 1.0 CE1 C:HIS207 2.5 42.2 1.0 CE1 C:HIS67 2.8 49.9 1.0 NE2 C:HIS207 2.9 41.4 1.0 CD2 C:HIS65 3.3 46.3 1.0 CE1 C:HIS65 3.3 46.5 1.0 CD2 C:HIS67 3.4 49.3 1.0 OD1 C:ASP314 3.5 59.9 1.0 ND1 C:HIS207 3.6 41.2 1.0 OD2 C:ASP314 3.9 59.9 1.0 ND1 C:HIS67 3.9 49.7 1.0 CG C:ASP314 4.0 58.0 1.0 CE1 C:HIS261 4.0 31.8 1.0 CD2 C:HIS207 4.1 40.9 1.0 CG C:HIS67 4.2 48.6 1.0 NE2 C:HIS261 4.4 31.5 1.0 ND1 C:HIS65 4.4 46.6 1.0 CG C:HIS65 4.4 44.9 1.0 CG C:HIS207 4.4 39.1 1.0 O C:HOH627 4.5 28.3 1.0

M.Feng, R.K.Harijan, L.D.Harris, P.C.Tyler, R.F.G.Frohlich, M.Brown, V.L.Schramm. Aminofutalosine Deaminase in the Menaquinone Pathway of Helicobacter Pylori Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 34077175
DOI: 10.1021/ACS.BIOCHEM.1C00215