Iron in PDB 7lkk: Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin

The structure of Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin, PDB code: 7lkk 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)	28.59 / 1.89
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.905, 73.072, 157.44, 90, 98.3, 90
R / Rfree (%)	23.1 / 26.9

The binding sites of Iron atom in the Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin (pdb code 7lkk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin, PDB code: 7lkk:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin


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) in Complex with Methylthio-Coformycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:27.3 occ:1.00 O8 A:MCF506 2.0 30.8 1.0 NE2 A:HIS67 2.0 23.0 1.0 NE2 A:HIS65 2.1 18.4 1.0 NE2 A:HIS207 2.4 23.8 1.0 OD1 A:ASP314 2.7 23.1 1.0 CE1 A:HIS67 2.9 25.0 1.0 C8 A:MCF506 2.9 28.4 1.0 CD2 A:HIS67 3.0 26.4 1.0 CE1 A:HIS65 3.0 20.3 1.0 CD2 A:HIS65 3.1 19.5 1.0 CD2 A:HIS207 3.3 23.6 1.0 C9 A:MCF506 3.3 24.5 1.0 CE1 A:HIS207 3.4 18.5 1.0 CG A:ASP314 3.6 23.7 1.0 C10 A:MCF506 3.8 25.4 1.0 OD2 A:ASP314 3.9 19.9 1.0 N1 A:MCF506 3.9 26.4 1.0 ND1 A:HIS67 4.0 23.8 1.0 N4 A:MCF506 4.1 24.7 1.0 CG A:HIS67 4.1 22.9 1.0 ND1 A:HIS65 4.1 14.7 1.0 CG A:HIS65 4.2 18.7 1.0 NE2 A:HIS261 4.2 20.3 1.0 C7 A:MCF506 4.3 25.6 1.0 CG A:HIS207 4.4 19.3 1.0 C5 A:MCF506 4.4 26.5 1.0 ND1 A:HIS207 4.5 19.4 1.0 N6 A:MCF506 4.6 25.3 1.0 N3 A:MCF506 4.6 23.5 1.0 C2 A:MCF506 4.7 26.4 1.0 O A:HOH603 4.9 28.7 1.0 CE1 A:HIS261 4.9 20.2 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin


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) in Complex with Methylthio-Coformycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:26.9 occ:1.00 O8 B:MCF504 1.9 33.0 1.0 NE2 B:HIS67 2.0 24.7 1.0 NE2 B:HIS65 2.1 20.2 1.0 NE2 B:HIS207 2.3 24.1 1.0 OD1 B:ASP314 2.7 22.7 1.0 C8 B:MCF504 2.9 25.1 1.0 CE1 B:HIS67 3.0 22.5 1.0 CD2 B:HIS67 3.0 21.7 1.0 CE1 B:HIS65 3.0 17.1 1.0 CD2 B:HIS65 3.1 22.4 1.0 CD2 B:HIS207 3.1 26.1 1.0 CE1 B:HIS207 3.3 22.1 1.0 C9 B:MCF504 3.3 23.4 1.0 CG B:ASP314 3.6 23.3 1.0 OD2 B:ASP314 3.9 29.2 1.0 C10 B:MCF504 3.9 23.6 1.0 N1 B:MCF504 4.0 24.2 1.0 ND1 B:HIS67 4.1 20.4 1.0 CG B:HIS67 4.1 25.0 1.0 N4 B:MCF504 4.1 23.7 1.0 ND1 B:HIS65 4.1 14.8 1.0 NE2 B:HIS261 4.2 18.9 1.0 CG B:HIS65 4.2 14.2 1.0 C7 B:MCF504 4.3 26.4 1.0 CG B:HIS207 4.3 23.2 1.0 ND1 B:HIS207 4.4 23.5 1.0 C5 B:MCF504 4.4 23.9 1.0 N6 B:MCF504 4.5 26.1 1.0 N3 B:MCF504 4.7 23.5 1.0 C2 B:MCF504 4.7 26.0 1.0 CE1 B:HIS261 4.9 20.8 1.0 O B:HOH624 4.9 22.2 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin


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) in Complex with Methylthio-Coformycin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:28.9 occ:1.00 O8 C:MCF504 2.0 37.5 1.0 NE2 C:HIS67 2.1 23.7 1.0 NE2 C:HIS65 2.1 23.9 1.0 NE2 C:HIS207 2.4 24.9 1.0 OD1 C:ASP314 2.6 25.3 1.0 C8 C:MCF504 2.9 29.5 1.0 CE1 C:HIS67 3.0 25.4 1.0 CD2 C:HIS65 3.0 22.9 1.0 CD2 C:HIS67 3.1 26.5 1.0 CE1 C:HIS65 3.1 21.7 1.0 CD2 C:HIS207 3.2 25.5 1.0 C9 C:MCF504 3.3 27.2 1.0 CE1 C:HIS207 3.5 22.5 1.0 CG C:ASP314 3.6 26.4 1.0 OD2 C:ASP314 3.8 24.7 1.0 C10 C:MCF504 3.9 26.8 1.0 N1 C:MCF504 3.9 27.6 1.0 NE2 C:HIS261 4.1 25.1 1.0 ND1 C:HIS67 4.1 25.2 1.0 CG C:HIS67 4.2 27.1 1.0 N4 C:MCF504 4.2 25.1 1.0 ND1 C:HIS65 4.2 23.1 1.0 CG C:HIS65 4.2 22.5 1.0 C7 C:MCF504 4.3 28.2 1.0 CG C:HIS207 4.4 22.6 1.0 ND1 C:HIS207 4.5 23.3 1.0 C5 C:MCF504 4.5 26.3 1.0 N6 C:MCF504 4.6 28.5 1.0 N3 C:MCF504 4.7 26.3 1.0 C2 C:MCF504 4.7 24.2 1.0 CE1 C:HIS261 4.8 24.6 1.0 CG1 C:VAL260 4.9 20.2 1.0 O C:HOH616 4.9 27.0 1.0 CB C:ASP314 4.9 19.1 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:32.6 occ:1.00 NE2 D:HIS67 2.0 27.5 1.0 O8 D:MCF507 2.0 37.2 1.0 NE2 D:HIS65 2.0 24.3 1.0 NE2 D:HIS207 2.4 27.7 1.0 OD1 D:ASP314 2.7 30.2 1.0 CE1 D:HIS65 3.0 23.6 1.0 CD2 D:HIS67 3.0 29.1 1.0 C8 D:MCF507 3.0 31.3 1.0 CE1 D:HIS67 3.0 27.0 1.0 CD2 D:HIS65 3.1 22.9 1.0 CD2 D:HIS207 3.3 29.1 1.0 C9 D:MCF507 3.3 28.1 1.0 CE1 D:HIS207 3.5 25.1 1.0 CG D:ASP314 3.6 28.0 1.0 N1 D:MCF507 3.9 29.4 1.0 C10 D:MCF507 3.9 30.7 1.0 OD2 D:ASP314 3.9 27.1 1.0 ND1 D:HIS65 4.1 19.6 1.0 ND1 D:HIS67 4.1 25.0 1.0 CG D:HIS67 4.1 28.9 1.0 CG D:HIS65 4.2 23.5 1.0 N4 D:MCF507 4.2 27.2 1.0 NE2 D:HIS261 4.2 24.1 1.0 C7 D:MCF507 4.4 27.1 1.0 CG D:HIS207 4.5 22.2 1.0 ND1 D:HIS207 4.5 24.4 1.0 C5 D:MCF507 4.6 26.4 1.0 N3 D:MCF507 4.6 31.6 1.0 C2 D:MCF507 4.6 30.3 1.0 N6 D:MCF507 4.7 26.9 1.0 CE1 D:HIS261 4.9 25.3 1.0 CG1 D:VAL260 4.9 21.5 1.0 CB D:ASP314 5.0 25.8 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