Zinc in PDB 9jiy: Macrophage Migration Inhibitory Factor S61H/Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(S61H/Y100H)-L)

All present enzymatic activity of Macrophage Migration Inhibitory Factor S61H/Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(S61H/Y100H)-L):
5.3.2.1; 5.3.3.12;

The structure of Macrophage Migration Inhibitory Factor S61H/Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(S61H/Y100H)-L), PDB code: 9jiy was solved by T.Himiyama, Y.Okamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.21 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.153, 68.211, 86.906, 90, 90, 90
R / Rfree (%)	15.5 / 17.4

The binding sites of Zinc atom in the Macrophage Migration Inhibitory Factor S61H/Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(S61H/Y100H)-L) (pdb code 9jiy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Macrophage Migration Inhibitory Factor S61H/Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(S61H/Y100H)-L), PDB code: 9jiy:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Macrophage Migration Inhibitory Factor S61H/Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(S61H/Y100H)-L)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Macrophage Migration Inhibitory Factor S61H/Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(S61H/Y100H)-L) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:22.2 occ:1.00 O1 A:CO3202 1.8 21.9 1.0 NE2 C:HIS63 2.0 19.9 1.0 NE2 A:HIS100 2.1 25.8 1.0 CE1 A:HIS100 2.6 22.4 1.0 C A:CO3202 2.7 14.2 1.0 O2 A:CO3202 3.0 22.3 1.0 CE1 C:HIS63 3.0 17.7 1.0 CD2 C:HIS63 3.0 17.0 1.0 ND1 A:HIS61 3.2 25.5 1.0 CE1 A:HIS61 3.2 22.4 1.0 CD2 A:HIS100 3.4 27.4 1.0 ND1 A:HIS100 3.8 28.0 1.0 O3 A:CO3202 3.9 21.9 1.0 ND1 C:HIS63 4.1 17.9 1.0 CG C:HIS63 4.1 15.8 1.0 CG A:HIS100 4.2 23.2 1.0 CG A:HIS61 4.3 19.8 1.0 CB A:ASN98 4.4 14.7 1.0 NE2 A:HIS61 4.5 24.9 1.0 CD2 C:HIS100 4.6 25.6 1.0 NE2 C:HIS100 4.7 23.1 1.0 CG C:HIS100 4.7 22.3 1.0 CG A:ASN98 4.7 17.9 1.0 ZN C:ZN201 4.7 23.0 1.0 ZN B:ZN201 4.7 22.6 1.0 ND1 C:HIS100 4.8 26.8 1.0 OD1 A:ASN98 4.9 27.9 1.0 CE1 C:HIS100 4.9 23.7 1.0 CD2 A:HIS61 5.0 22.9 1.0

Zinc binding site 2 out of 3 in the Macrophage Migration Inhibitory Factor S61H/Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(S61H/Y100H)-L)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Macrophage Migration Inhibitory Factor S61H/Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(S61H/Y100H)-L) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:22.6 occ:1.00 O2 A:CO3202 1.8 22.3 1.0 NE2 B:HIS100 2.0 23.6 1.0 NE2 A:HIS63 2.0 19.7 1.0 CE1 B:HIS100 2.6 22.7 1.0 C A:CO3202 2.7 14.2 1.0 O3 A:CO3202 2.9 21.9 1.0 CE1 A:HIS63 3.0 17.1 1.0 CD2 A:HIS63 3.1 17.3 1.0 CD2 B:HIS100 3.3 29.0 1.0 ND1 B:HIS61 3.3 23.7 1.0 CE1 B:HIS61 3.3 21.9 1.0 ND1 B:HIS100 3.8 26.8 1.0 O1 A:CO3202 3.9 21.9 1.0 CG B:HIS100 4.1 22.6 1.0 ND1 A:HIS63 4.1 17.4 1.0 CG A:HIS63 4.2 14.8 1.0 O B:HOH375 4.2 28.0 1.0 CG B:HIS61 4.3 19.9 1.0 CB B:ASN98 4.5 15.0 1.0 NE2 B:HIS61 4.5 23.0 1.0 CD2 A:HIS100 4.7 27.4 1.0 NE2 A:HIS100 4.7 25.8 1.0 ZN A:ZN201 4.7 22.2 1.0 CG A:HIS100 4.7 23.2 1.0 ZN C:ZN201 4.8 23.0 1.0 CG B:ASN98 4.9 18.5 1.0 ND1 A:HIS100 4.9 28.0 1.0 CE1 B:HIS63 4.9 19.2 1.0 CE1 A:HIS100 5.0 22.4 1.0 CD2 B:HIS61 5.0 22.7 1.0 NE2 B:HIS63 5.0 20.9 1.0

Zinc binding site 3 out of 3 in the Macrophage Migration Inhibitory Factor S61H/Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(S61H/Y100H)-L)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Macrophage Migration Inhibitory Factor S61H/Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(S61H/Y100H)-L) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:23.0 occ:1.00 O3 A:CO3202 1.9 21.9 1.0 NE2 B:HIS63 2.0 20.9 1.0 NE2 C:HIS100 2.1 23.1 1.0 CE1 C:HIS100 2.5 23.7 1.0 C A:CO3202 2.8 14.2 1.0 CE1 B:HIS63 2.9 19.2 1.0 O1 A:CO3202 3.0 21.9 1.0 CD2 B:HIS63 3.0 18.0 1.0 ND1 C:HIS61 3.2 26.5 1.0 CE1 C:HIS61 3.2 23.8 1.0 CD2 C:HIS100 3.4 25.6 1.0 ND1 C:HIS100 3.7 26.8 1.0 O2 A:CO3202 4.0 22.3 1.0 ND1 B:HIS63 4.1 18.6 1.0 CG B:HIS63 4.1 16.1 1.0 CG C:HIS100 4.1 22.3 1.0 CG C:HIS61 4.3 19.9 1.0 NE2 C:HIS61 4.4 26.1 1.0 CB C:ASN98 4.5 16.0 1.0 ZN A:ZN201 4.7 22.2 1.0 ZN B:ZN201 4.8 22.6 1.0 CD2 B:HIS100 4.8 29.0 1.0 CG C:ASN98 4.8 19.0 1.0 CG B:HIS100 4.8 22.6 1.0 NE2 B:HIS100 4.9 23.6 1.0 OD1 C:ASN98 4.9 28.6 1.0 CD2 C:HIS61 4.9 23.2 1.0 O B:HOH375 5.0 28.0 1.0

A.Ueno, F.Takida, T.Kita, T.Ishii, T.Himiyama, T.Mabuchi, Y.Okamoto. A Cytokine-Based Designer Enzyme with An Abiological Multinuclear Metal Center Exhibits Intrinsic and Extrinsic Catalysis Nat Commun 2025.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-025-61909-5