Iron in PDB 3kef: Crystal Structure of Isph:Dmapp-Complex

All present enzymatic activity of Crystal Structure of Isph:Dmapp-Complex:
1.17.1.2;

The structure of Crystal Structure of Isph:Dmapp-Complex, PDB code: 3kef was solved by M.Groll, T.Graewert, I.Span, W.Eisenreich, A.Bacher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.120, 80.380, 110.840, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 23.7

The binding sites of Iron atom in the Crystal Structure of Isph:Dmapp-Complex (pdb code 3kef). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of Isph:Dmapp-Complex, PDB code: 3kef:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Crystal Structure of Isph:Dmapp-Complex


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 Isph:Dmapp-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe997 b:11.4 occ:1.00 FE1 A:F3S997 0.0 11.4 1.0 S3 A:F3S997 2.1 14.1 1.0 S1 A:F3S997 2.2 14.9 1.0 S2 A:F3S997 2.2 15.3 1.0 SG A:CYS197 2.3 11.3 1.0 FE3 A:F3S997 2.7 10.3 1.0 FE4 A:F3S997 2.7 12.1 1.0 CB A:CYS197 3.2 11.4 1.0 S4 A:F3S997 3.9 14.2 1.0 C4 A:DMA998 4.0 24.2 1.0 CB A:ALA199 4.3 10.8 1.0 OG1 A:THR200 4.5 11.4 1.0 OG1 A:THR167 4.5 13.0 1.0 CD1 A:LEU98 4.6 13.2 1.0 C3 A:DMA998 4.6 25.7 1.0 CA A:CYS197 4.7 10.2 1.0 C2 A:DMA998 4.7 23.9 1.0 CB A:THR167 4.7 13.5 1.0 SG A:CYS12 4.7 11.1 1.0 O A:HOH341 4.8 13.1 1.0 SG A:CYS96 4.9 11.0 1.0

Iron binding site 2 out of 6 in the Crystal Structure of Isph:Dmapp-Complex


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 Isph:Dmapp-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe997 b:10.3 occ:1.00 FE3 A:F3S997 0.0 10.3 1.0 S4 A:F3S997 2.2 14.2 1.0 S3 A:F3S997 2.2 14.1 1.0 S1 A:F3S997 2.2 14.9 1.0 SG A:CYS12 2.3 11.1 1.0 FE1 A:F3S997 2.7 11.4 1.0 FE4 A:F3S997 2.8 12.1 1.0 CB A:CYS12 3.3 11.2 1.0 C2 A:DMA998 3.7 23.9 1.0 S2 A:F3S997 4.0 15.3 1.0 C3 A:DMA998 4.1 25.7 1.0 C1 A:DMA998 4.1 21.5 1.0 N A:GLY14 4.2 11.0 1.0 CB A:ALA268 4.3 12.1 1.0 N A:VAL15 4.3 11.2 1.0 CA A:GLY14 4.4 11.3 1.0 C4 A:DMA998 4.4 24.2 1.0 CG2 A:VAL15 4.5 10.2 1.0 CB A:ALA199 4.6 10.8 1.0 CA A:CYS12 4.7 11.0 1.0 SG A:CYS197 4.7 11.3 1.0 C A:GLY14 4.8 10.9 1.0 SG A:CYS96 4.8 11.0 1.0 C5 A:DMA998 4.9 25.0 1.0 C A:CYS12 4.9 11.7 1.0 N A:ALA13 5.0 10.8 1.0

Iron binding site 3 out of 6 in the Crystal Structure of Isph:Dmapp-Complex


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 Isph:Dmapp-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe997 b:12.1 occ:1.00 FE4 A:F3S997 0.0 12.1 1.0 S3 A:F3S997 2.1 14.1 1.0 S4 A:F3S997 2.2 14.2 1.0 S2 A:F3S997 2.2 15.3 1.0 SG A:CYS96 2.3 11.0 1.0 FE1 A:F3S997 2.7 11.4 1.0 FE3 A:F3S997 2.8 10.3 1.0 CB A:CYS96 3.1 10.5 1.0 S1 A:F3S997 4.1 14.9 1.0 CA A:GLY14 4.1 11.3 1.0 C4 A:DMA998 4.1 24.2 1.0 CB A:LEU98 4.3 11.2 1.0 C3 A:DMA998 4.3 25.7 1.0 CD1 A:LEU98 4.4 13.2 1.0 N A:GLY14 4.4 11.0 1.0 CA A:CYS96 4.6 10.3 1.0 CG A:LEU98 4.6 13.2 1.0 C5 A:DMA998 4.7 25.0 1.0 SG A:CYS12 4.7 11.1 1.0 C2 A:DMA998 4.8 23.9 1.0 SG A:CYS197 4.9 11.3 1.0 N A:LEU98 5.0 12.4 1.0

Iron binding site 4 out of 6 in the Crystal Structure of Isph:Dmapp-Complex


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 Isph:Dmapp-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe997 b:11.4 occ:1.00 FE1 B:F3S997 0.0 11.4 1.0 S3 B:F3S997 2.1 13.7 1.0 S1 B:F3S997 2.2 16.0 1.0 S2 B:F3S997 2.2 14.1 1.0 SG B:CYS197 2.3 11.3 1.0 FE3 B:F3S997 2.7 10.7 1.0 FE4 B:F3S997 2.8 11.1 1.0 CB B:CYS197 3.2 12.3 1.0 S4 B:F3S997 3.9 14.5 1.0 CB B:ALA199 4.2 11.4 1.0 C4 B:DMA998 4.3 22.7 1.0 OG1 B:THR200 4.5 11.8 1.0 OG1 B:THR167 4.5 12.6 1.0 CA B:CYS197 4.7 10.8 1.0 CB B:THR167 4.7 12.5 1.0 CD1 B:LEU98 4.7 12.2 1.0 C3 B:DMA998 4.7 23.4 1.0 C2 B:DMA998 4.7 22.3 1.0 SG B:CYS12 4.8 11.0 1.0 O B:HOH333 4.8 14.2 1.0 SG B:CYS96 4.9 10.2 1.0

Iron binding site 5 out of 6 in the Crystal Structure of Isph:Dmapp-Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Isph:Dmapp-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe997 b:10.7 occ:1.00 FE3 B:F3S997 0.0 10.7 1.0 S4 B:F3S997 2.2 14.5 1.0 S3 B:F3S997 2.2 13.7 1.0 S1 B:F3S997 2.2 16.0 1.0 SG B:CYS12 2.3 11.0 1.0 FE1 B:F3S997 2.7 11.4 1.0 FE4 B:F3S997 2.8 11.1 1.0 CB B:CYS12 3.3 11.5 1.0 C2 B:DMA998 3.8 22.3 1.0 S2 B:F3S997 4.0 14.1 1.0 C1 B:DMA998 4.2 20.8 1.0 N B:GLY14 4.2 11.2 1.0 C3 B:DMA998 4.2 23.4 1.0 CB B:ALA268 4.3 9.2 1.0 CA B:GLY14 4.3 10.8 1.0 N B:VAL15 4.3 10.5 1.0 CG2 B:VAL15 4.5 9.8 1.0 CB B:ALA199 4.6 11.4 1.0 CA B:CYS12 4.6 11.5 1.0 C4 B:DMA998 4.7 22.7 1.0 SG B:CYS197 4.7 11.3 1.0 SG B:CYS96 4.8 10.2 1.0 C B:GLY14 4.8 9.9 1.0 C B:CYS12 4.9 12.0 1.0 C5 B:DMA998 4.9 23.2 1.0

Iron binding site 6 out of 6 in the Crystal Structure of Isph:Dmapp-Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Isph:Dmapp-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe997 b:11.1 occ:1.00 FE4 B:F3S997 0.0 11.1 1.0 S3 B:F3S997 2.1 13.7 1.0 S4 B:F3S997 2.2 14.5 1.0 S2 B:F3S997 2.2 14.1 1.0 SG B:CYS96 2.3 10.2 1.0 FE1 B:F3S997 2.8 11.4 1.0 FE3 B:F3S997 2.8 10.7 1.0 CB B:CYS96 3.1 9.1 1.0 CA B:GLY14 4.1 10.8 1.0 S1 B:F3S997 4.1 16.0 1.0 CB B:LEU98 4.3 11.9 1.0 C4 B:DMA998 4.4 22.7 1.0 N B:GLY14 4.4 11.2 1.0 C3 B:DMA998 4.5 23.4 1.0 CD1 B:LEU98 4.5 12.2 1.0 CA B:CYS96 4.6 10.0 1.0 CG B:LEU98 4.6 12.5 1.0 SG B:CYS12 4.7 11.0 1.0 C5 B:DMA998 4.7 23.2 1.0 SG B:CYS197 4.9 11.3 1.0 C2 B:DMA998 4.9 22.3 1.0 N B:LEU98 5.0 10.5 1.0

T.Grawert, I.Span, W.Eisenreich, F.Rohdich, J.Eppinger, A.Bacher, M.Groll. Probing the Reaction Mechanism of Isph Protein By X-Ray Structure Analysis. Proc.Natl.Acad.Sci.Usa V. 107 1077 2010.
ISSN: ISSN 0027-8424
PubMed: 20080550
DOI: 10.1073/PNAS.0913045107