Iron in PDB 3kem: Crystal Structure of Isph:Ipp Complex

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

The structure of Crystal Structure of Isph:Ipp Complex, PDB code: 3kem 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)	9.99 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.475, 80.645, 70.157, 90.00, 94.68, 90.00
R / Rfree (%)	22.6 / 27.5

The binding sites of Iron atom in the Crystal Structure of Isph:Ipp Complex (pdb code 3kem). 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:Ipp Complex, PDB code: 3kem:
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:Ipp 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:Ipp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe997 b:10.5 occ:1.00 FE1 A:F3S997 0.0 10.5 1.0 S3 A:F3S997 2.1 15.5 1.0 S1 A:F3S997 2.2 18.6 1.0 S2 A:F3S997 2.2 11.8 1.0 SG A:CYS96 2.4 13.3 1.0 FE3 A:F3S997 2.8 14.6 1.0 FE4 A:F3S997 2.9 12.2 1.0 CB A:CYS96 3.2 12.2 1.0 C5 A:IPE998 3.6 24.9 1.0 S4 A:F3S997 4.0 15.3 1.0 CA A:GLY14 4.1 7.2 1.0 CB A:LEU98 4.2 9.9 1.0 C3 A:IPE998 4.2 22.7 1.0 N A:GLY14 4.5 5.8 1.0 C4 A:IPE998 4.5 22.3 1.0 CD2 A:LEU98 4.6 7.3 1.0 CA A:CYS96 4.6 10.6 1.0 SG A:CYS12 4.7 12.5 1.0 N A:LEU98 5.0 9.0 1.0

Iron binding site 2 out of 6 in the Crystal Structure of Isph:Ipp 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:Ipp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe997 b:14.6 occ:1.00 FE3 A:F3S997 0.0 14.6 1.0 S3 A:F3S997 2.2 15.5 1.0 S4 A:F3S997 2.2 15.3 1.0 S1 A:F3S997 2.2 18.6 1.0 SG A:CYS197 2.3 13.6 1.0 FE1 A:F3S997 2.8 10.5 1.0 FE4 A:F3S997 3.0 12.2 1.0 CB A:CYS197 3.1 11.9 1.0 S2 A:F3S997 4.1 11.8 1.0 CB A:ALA199 4.1 11.4 1.0 C5 A:IPE998 4.1 24.9 1.0 OG1 A:THR200 4.4 8.2 1.0 CA A:CYS197 4.6 11.0 1.0 CD2 A:LEU98 4.6 7.3 1.0 OG1 A:THR167 4.7 7.3 1.0 CB A:THR167 4.7 8.7 1.0 O A:THR167 4.9 5.9 1.0 CB A:LEU98 4.9 9.9 1.0 O A:HOH350 4.9 14.0 1.0 N A:THR200 4.9 8.2 1.0 N A:ALA199 4.9 9.9 1.0 SG A:CYS96 5.0 13.3 1.0 SG A:CYS12 5.0 12.5 1.0

Iron binding site 3 out of 6 in the Crystal Structure of Isph:Ipp 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:Ipp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe997 b:12.2 occ:1.00 FE4 A:F3S997 0.0 12.2 1.0 S3 A:F3S997 2.1 15.5 1.0 S4 A:F3S997 2.2 15.3 1.0 S2 A:F3S997 2.2 11.8 1.0 SG A:CYS12 2.2 12.5 1.0 FE1 A:F3S997 2.9 10.5 1.0 FE3 A:F3S997 3.0 14.6 1.0 CB A:CYS12 3.2 8.6 1.0 C1 A:IPE998 3.9 16.1 1.0 S1 A:F3S997 4.2 18.6 1.0 CG2 A:VAL15 4.2 6.9 1.0 CB A:ALA268 4.2 8.0 1.0 C5 A:IPE998 4.2 24.9 1.0 N A:VAL15 4.3 9.7 1.0 N A:GLY14 4.3 5.8 1.0 C3 A:IPE998 4.4 22.7 1.0 CA A:GLY14 4.4 7.2 1.0 CA A:CYS12 4.6 7.7 1.0 C2 A:IPE998 4.6 20.6 1.0 CB A:ALA199 4.6 11.4 1.0 C A:GLY14 4.8 8.5 1.0 C A:CYS12 4.9 8.4 1.0 SG A:CYS96 4.9 13.3 1.0 O1 A:IPE998 4.9 13.0 1.0 CB A:VAL15 4.9 10.0 1.0 SG A:CYS197 5.0 13.6 1.0

Iron binding site 4 out of 6 in the Crystal Structure of Isph:Ipp 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:Ipp 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 15.7 1.0 S1 B:F3S997 2.2 14.8 1.0 S2 B:F3S997 2.2 16.4 1.0 SG B:CYS197 2.4 9.8 1.0 FE3 B:F3S997 2.8 13.4 1.0 FE4 B:F3S997 2.8 11.6 1.0 CB B:CYS197 3.3 10.3 1.0 C5 B:IPE998 3.9 17.5 1.0 S4 B:F3S997 3.9 14.7 1.0 OG1 B:THR200 4.3 10.1 1.0 CB B:ALA199 4.4 9.5 1.0 OG1 B:THR167 4.5 8.0 1.0 CB B:THR167 4.6 4.9 1.0 CD2 B:LEU98 4.7 4.2 1.0 CA B:CYS197 4.7 9.6 1.0 O B:HOH320 4.9 9.6 1.0 O B:THR167 4.9 7.8 1.0 SG B:CYS12 4.9 8.6 1.0 C3 B:IPE998 4.9 16.9 1.0 SG B:CYS96 4.9 7.8 1.0 N B:THR200 5.0 9.1 1.0 CG2 B:THR168 5.0 7.7 1.0

Iron binding site 5 out of 6 in the Crystal Structure of Isph:Ipp 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:Ipp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe997 b:13.4 occ:1.00 FE3 B:F3S997 0.0 13.4 1.0 S4 B:F3S997 2.2 14.7 1.0 S1 B:F3S997 2.2 14.8 1.0 S3 B:F3S997 2.2 15.7 1.0 SG B:CYS12 2.4 8.6 1.0 FE1 B:F3S997 2.8 11.4 1.0 FE4 B:F3S997 3.0 11.6 1.0 CB B:CYS12 3.2 9.1 1.0 C5 B:IPE998 4.0 17.5 1.0 C1 B:IPE998 4.0 10.7 1.0 S2 B:F3S997 4.1 16.4 1.0 CB B:ALA268 4.2 4.4 1.0 C3 B:IPE998 4.2 16.9 1.0 C2 B:IPE998 4.5 16.6 1.0 N B:GLY14 4.5 8.1 1.0 CG2 B:VAL15 4.5 8.9 1.0 N B:VAL15 4.5 9.0 1.0 CA B:GLY14 4.6 8.2 1.0 CA B:CYS12 4.7 9.3 1.0 CB B:ALA199 4.7 9.5 1.0 SG B:CYS197 4.8 9.8 1.0 O1 B:IPE998 4.9 13.7 1.0 SG B:CYS96 5.0 7.8 1.0 O B:HOH320 5.0 9.6 1.0

Iron binding site 6 out of 6 in the Crystal Structure of Isph:Ipp 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:Ipp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe997 b:11.6 occ:1.00 FE4 B:F3S997 0.0 11.6 1.0 S3 B:F3S997 2.1 15.7 1.0 S4 B:F3S997 2.2 14.7 1.0 S2 B:F3S997 2.2 16.4 1.0 SG B:CYS96 2.3 7.8 1.0 FE1 B:F3S997 2.8 11.4 1.0 FE3 B:F3S997 3.0 13.4 1.0 CB B:CYS96 3.1 7.4 1.0 C5 B:IPE998 3.3 17.5 1.0 CB B:LEU98 4.0 8.3 1.0 C3 B:IPE998 4.1 16.9 1.0 S1 B:F3S997 4.2 14.8 1.0 CA B:GLY14 4.3 8.2 1.0 C4 B:IPE998 4.4 16.4 1.0 CD2 B:LEU98 4.5 4.2 1.0 CA B:CYS96 4.6 7.8 1.0 N B:GLY14 4.7 8.1 1.0 CG2 B:VAL99 4.7 4.4 1.0 SG B:CYS12 4.9 8.6 1.0 N B:LEU98 4.9 7.6 1.0 CG B:LEU98 4.9 9.0 1.0 CA B:LEU98 5.0 8.2 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