Zinc in PDB 5od9: Structure of the Engineered Metalloesterase MID1SC9

The structure of Structure of the Engineered Metalloesterase MID1SC9, PDB code: 5od9 was solved by S.Studer, P.R.E.Mittl, D.Hilvert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.00 / 1.13
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	43.820, 104.959, 33.604, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Structure of the Engineered Metalloesterase MID1SC9 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Zinc atom in the Structure of the Engineered Metalloesterase MID1SC9 (pdb code 5od9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the Engineered Metalloesterase MID1SC9, PDB code: 5od9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the Engineered Metalloesterase MID1SC9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Engineered Metalloesterase MID1SC9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3001 b:11.3 occ:1.00 ND1 A:HIS1061 2.0 13.1 1.0 NE2 A:HIS1039 2.0 12.7 1.0 NE2 B:HIS2065 2.1 13.2 1.0 OE2 A:GLU1058 2.1 15.1 1.0 OE1 A:GLU1058 2.2 14.2 1.0 CD A:GLU1058 2.5 13.5 1.0 CE1 A:HIS1061 2.9 14.6 1.0 CE1 A:HIS1039 3.0 14.0 1.0 CD2 B:HIS2065 3.0 13.9 1.0 CD2 A:HIS1039 3.1 13.3 1.0 CG A:HIS1061 3.1 14.1 1.0 CE1 B:HIS2065 3.1 13.3 1.0 CB A:HIS1061 3.5 15.2 1.0 CG A:GLU1058 4.0 14.2 1.0 NE2 A:HIS1061 4.0 13.0 1.0 CD2 A:HIS1061 4.1 14.4 1.0 ND1 A:HIS1039 4.1 13.4 1.0 CG B:HIS2065 4.2 13.2 1.0 ND1 B:HIS2065 4.2 13.2 1.0 CG A:HIS1039 4.2 13.3 1.0 O A:GLU1058 4.2 12.3 1.0 NE1 A:TRP1038 4.3 15.8 1.0 CD1 A:TRP1038 4.3 16.8 1.0 N A:VAL1062 4.5 12.8 1.0 CG2 A:VAL1062 4.6 15.6 1.0 C A:HIS1061 4.7 13.5 1.0 CA A:HIS1061 4.8 13.1 1.0 CA A:GLU1058 4.9 13.1 1.0 CB A:GLU1058 4.9 13.8 1.0 C A:GLU1058 5.0 12.8 1.0

Zinc binding site 2 out of 4 in the Structure of the Engineered Metalloesterase MID1SC9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Engineered Metalloesterase MID1SC9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3002 b:11.1 occ:1.00 ND1 A:HIS1035 2.0 12.9 1.0 NE2 A:HIS1061 2.0 13.0 1.0 NE2 A:HIS1065 2.0 13.7 1.0 CL A:CL3003 2.2 13.6 1.0 CE1 A:HIS1061 2.9 14.6 1.0 CE1 A:HIS1035 2.9 13.8 1.0 CE1 A:HIS1065 3.0 13.5 1.0 CD2 A:HIS1065 3.1 14.0 1.0 CG A:HIS1035 3.1 14.0 1.0 CD2 A:HIS1061 3.1 14.4 1.0 CB A:HIS1035 3.5 14.6 1.0 O A:HOH3185 4.0 26.8 1.0 ND1 A:HIS1061 4.1 13.1 1.0 NE2 A:HIS1035 4.1 12.9 1.0 CG A:HIS1061 4.2 14.1 1.0 ND1 A:HIS1065 4.2 13.2 1.0 CD2 A:HIS1035 4.2 14.8 1.0 CG A:HIS1065 4.2 13.6 1.0 O A:HOH3119 4.3 25.2 1.0 CA A:HIS1035 4.4 14.3 1.0 CE1 B:HIS2065 4.6 13.3 1.0 O A:GLN1031 4.8 15.2 1.0

Zinc binding site 3 out of 4 in the Structure of the Engineered Metalloesterase MID1SC9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Engineered Metalloesterase MID1SC9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3011 b:11.4 occ:1.00 NE2 B:HIS2035 2.0 13.4 1.0 NE2 B:HIS2039 2.0 13.9 1.0 ND1 A:HIS1065 2.0 13.2 1.0 CL A:CL3004 2.2 13.4 0.9 CD2 B:HIS2039 2.9 15.2 1.0 CE1 A:HIS1065 2.9 13.5 1.0 CE1 B:HIS2035 3.0 15.5 1.0 CD2 B:HIS2035 3.0 14.0 1.0 CG A:HIS1065 3.1 13.6 1.0 CE1 B:HIS2039 3.1 17.0 1.0 CB A:HIS1065 3.6 13.8 1.0 NE2 A:HIS1065 4.1 13.7 1.0 ND1 B:HIS2065 4.1 13.2 1.0 CG B:HIS2039 4.1 15.7 1.0 CD2 A:HIS1065 4.1 14.0 1.0 ND1 B:HIS2039 4.1 16.5 1.0 ND1 B:HIS2035 4.2 13.4 1.0 CG B:HIS2035 4.2 13.8 1.0 O A:HOH3112 4.4 47.2 1.0 O B:HOH2210 4.5 47.6 1.0 O B:HIS2061 4.6 14.1 1.0 CB B:HIS2061 4.6 15.1 1.0 C B:HIS2061 4.7 13.8 1.0 CB B:HIS2065 4.8 13.5 1.0 O A:HOH3155 4.8 24.1 1.0 O A:HOH3213 4.8 24.4 1.0 CG B:HIS2065 4.9 13.2 1.0 CA A:HIS1065 4.9 13.7 1.0 N B:VAL2062 4.9 14.2 1.0 CE1 B:HIS2065 5.0 13.3 1.0

Zinc binding site 4 out of 4 in the Structure of the Engineered Metalloesterase MID1SC9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Engineered Metalloesterase MID1SC9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3012 b:10.7 occ:1.00 OE1 B:GLU2032 2.0 13.2 1.0 NE2 A:HIS1035 2.0 12.9 1.0 ND1 B:HIS2035 2.0 13.4 1.0 CL B:CL2101 2.3 11.8 0.9 CD B:GLU2032 2.7 14.8 1.0 CE1 B:HIS2035 2.9 15.5 1.0 OE2 B:GLU2032 2.9 13.4 1.0 CE1 A:HIS1035 2.9 13.8 1.0 CD2 A:HIS1035 3.1 14.8 1.0 CG B:HIS2035 3.1 13.8 1.0 CB B:HIS2035 3.5 15.0 1.0 ND1 A:HIS1039 3.8 13.4 1.0 O B:HOH2230 3.9 28.1 1.0 CE1 A:HIS1039 3.9 14.0 1.0 O B:HOH2241 4.0 19.3 1.0 NE2 B:HIS2035 4.1 13.4 1.0 ND1 A:HIS1035 4.1 12.9 1.0 CG B:GLU2032 4.1 15.3 1.0 CD2 B:HIS2035 4.1 14.0 1.0 NH2 B:ARG2068 4.2 17.8 1.0 CG A:HIS1035 4.2 14.0 1.0 O B:GLU2032 4.6 20.1 1.0 NE B:ARG2068 4.6 17.3 1.0 CB B:GLU2032 4.7 17.8 1.0 CA B:GLU2032 4.7 16.1 1.0 CZ B:ARG2068 4.9 19.1 1.0

S.Studer, D.A.Hansen, Z.L.Pianowski, P.R.E.Mittl, A.Debon, S.L.Guffy, B.S.Der, B.Kuhlman, D.Hilvert. Evolution of A Highly Active and Enantiospecific Metalloenzyme From Short Peptides. Science V. 362 1285 2018.
ISSN: ESSN 1095-9203
PubMed: 30545884
DOI: 10.1126/SCIENCE.AAU3744