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Chlorine in PDB 9jj0: Macrophage Migration Inhibitory Factor Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(Y100H))

Enzymatic activity of Macrophage Migration Inhibitory Factor Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(Y100H))

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

Protein crystallography data

The structure of Macrophage Migration Inhibitory Factor Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(Y100H)), PDB code: 9jj0 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) 48.16 / 1.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.906, 68.32, 87.629, 90, 90, 90
R / Rfree (%) 11.8 / 14.6

Other elements in 9jj0:

The structure of Macrophage Migration Inhibitory Factor Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(Y100H)) also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Macrophage Migration Inhibitory Factor Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(Y100H)) (pdb code 9jj0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Macrophage Migration Inhibitory Factor Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(Y100H)), PDB code: 9jj0:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 9jj0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Macrophage Migration Inhibitory Factor Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(Y100H)) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:17.5
occ:1.00
 ZN A:ZN202 2.2 14.8 1.0
O A:HOH417 3.2 38.4 1.0
NE2 C:HIS63 3.4 14.9 1.0
NE2 A:HIS100 3.4 14.6 1.0
CB A:SER61 3.5 14.2 1.0
O1 A:CO3204 3.5 15.5 1.0
OD1 A:ASN98 3.5 19.6 1.0
O2 A:CO3204 3.6 14.8 1.0
CD2 A:HIS100 3.6 15.4 1.0
O A:HOH419 3.7 40.6 1.0
CB A:ASN98 3.7 13.8 1.0
CE1 C:HIS63 3.8 16.1 1.0
O A:HOH347 3.8 45.7 1.0
C A:CO3204 3.9 14.7 1.0
CG A:ASN98 4.0 17.0 1.0
OG A:SER61 4.1 15.1 1.0
O A:HOH357 4.2 41.2 1.0
CD2 C:HIS63 4.4 14.0 1.0
CE1 A:HIS63 4.5 15.2 1.0
O C:HOH309 4.6 41.6 1.0
O A:HOH452 4.7 38.5 1.0
CE1 A:HIS100 4.7 16.9 1.0
CA A:SER61 4.7 13.2 1.0
ND1 C:HIS63 4.8 15.4 1.0
O A:ASN98 4.9 14.4 1.0
CG A:HIS100 5.0 14.3 1.0

Chlorine binding site 2 out of 3 in 9jj0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Macrophage Migration Inhibitory Factor Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(Y100H)) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:18.4
occ:1.00
 ZN A:ZN201 2.2 15.1 1.0
O A:HOH418 3.2 38.6 1.0
NE2 A:HIS63 3.4 14.3 1.0
CB B:SER61 3.4 13.7 1.0
O2 A:CO3204 3.5 14.8 1.0
NE2 B:HIS100 3.5 14.8 1.0
O B:HOH332 3.6 48.8 1.0
O3 A:CO3204 3.6 15.0 1.0
O A:HOH417 3.6 38.4 1.0
OD1 B:ASN98 3.6 19.4 1.0
CD2 B:HIS100 3.7 15.1 1.0
CE1 A:HIS63 3.8 15.2 1.0
CB B:ASN98 3.8 13.6 1.0
C A:CO3204 3.9 14.7 1.0
OG B:SER61 4.0 15.0 1.0
CG B:ASN98 4.1 15.7 1.0
O B:HOH345 4.2 35.3 1.0
CD2 A:HIS63 4.4 13.7 1.0
CE1 B:HIS63 4.4 15.2 1.0
CA B:SER61 4.7 12.2 1.0
O B:HOH445 4.7 39.1 1.0
O A:HOH347 4.7 45.7 1.0
CE1 B:HIS100 4.8 16.5 1.0
ND1 A:HIS63 4.9 14.8 1.0
O B:ASN98 5.0 13.7 1.0

Chlorine binding site 3 out of 3 in 9jj0

Go back to Chlorine Binding Sites List in 9jj0
Chlorine binding site 3 out of 3 in the Macrophage Migration Inhibitory Factor Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(Y100H))


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Macrophage Migration Inhibitory Factor Y100H Mutant Complexed with Three Zinc Ions (ZN3-Mif(Y100H)) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:18.5
occ:1.00
 ZN B:ZN201 2.2 15.3 1.0
O A:HOH419 3.1 40.6 1.0
NE2 C:HIS100 3.4 16.0 1.0
NE2 B:HIS63 3.4 14.3 1.0
O C:HOH309 3.4 41.6 1.0
CB C:SER61 3.5 15.8 1.0
OD1 C:ASN98 3.5 20.5 1.0
O3 A:CO3204 3.5 15.0 1.0
O1 A:CO3204 3.6 15.5 1.0
CD2 C:HIS100 3.6 15.8 1.0
O A:HOH418 3.6 38.6 1.0
CB C:ASN98 3.7 14.7 1.0
CE1 B:HIS63 3.8 15.2 1.0
C A:CO3204 4.0 14.7 1.0
CG C:ASN98 4.0 16.3 1.0
O C:HOH329 4.1 43.3 1.0
OG C:SER61 4.1 15.9 1.0
CD2 B:HIS63 4.4 14.4 1.0
CE1 C:HIS63 4.5 16.1 1.0
O C:HOH436 4.5 45.6 1.0
CE1 C:HIS100 4.7 17.7 1.0
CA C:SER61 4.7 14.2 1.0
ND1 B:HIS63 4.8 15.1 1.0
O B:HOH332 4.9 48.8 1.0
O C:ASN98 4.9 15.7 1.0
CG C:HIS100 5.0 16.0 1.0

Reference:

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
Page generated: Sat Aug 23 00:45:23 2025

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