Zinc in PDB 6j4b: Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate

The structure of Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate, PDB code: 6j4b was solved by Y.Hou, B.Liu, K.Hu, R.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.78 / 1.58
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	43.627, 43.627, 99.973, 90.00, 90.00, 120.00
R / Rfree (%)	14.6 / 17.7

The binding sites of Zinc atom in the Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate (pdb code 6j4b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate, PDB code: 6j4b:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:10.4 occ:1.00 O A:HOH316 1.9 9.3 1.0 OXT A:ACY209 2.0 11.8 1.0 O A:HOH332 2.0 9.5 1.0 NE2 A:HIS62 2.0 9.8 1.0 C A:ACY209 2.9 10.9 1.0 CE1 A:HIS62 2.9 10.6 1.0 CD2 A:HIS62 3.1 11.2 1.0 ZN A:ZN204 3.2 10.7 1.0 ZN A:ZN205 3.3 10.4 1.0 O A:ACY209 3.3 11.2 1.0 O3 A:GOL207 3.5 13.8 1.0 O2 A:GOL207 3.7 16.9 1.0 CE1 A:HIS25 3.7 9.4 1.0 OH A:TYR70 3.9 13.2 1.0 O A:HOH371 3.9 13.8 1.0 NE2 A:HIS25 4.0 8.2 1.0 ND1 A:HIS62 4.1 10.2 1.0 NE2 A:HIS107 4.1 9.4 1.0 NE2 A:HIS64 4.2 10.4 1.0 CG A:HIS62 4.2 11.1 1.0 CE1 A:HIS64 4.2 10.9 1.0 CH3 A:ACY209 4.2 11.6 1.0 C3 A:GOL207 4.2 14.9 1.0 CD2 A:HIS107 4.6 9.0 1.0 C2 A:GOL207 4.6 17.7 1.0 OXT A:ACY208 4.7 13.3 1.0 OE2 A:GLU68 4.9 12.6 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:14.7 occ:1.00 NE2 A:HIS26 2.1 9.6 1.0 CD2 A:HIS26 3.0 10.2 1.0 CE1 A:HIS26 3.0 8.9 1.0 O A:HOH365 4.0 20.5 1.0 ND1 A:HIS26 4.1 9.9 1.0 CG A:HIS26 4.2 8.8 1.0 O A:HOH350 4.2 28.6 1.0 OE1 A:GLN27 4.6 23.1 1.0 O A:HOH307 4.8 10.8 1.0 CG A:GLN27 5.0 17.2 1.0 O A:PRO57 5.0 13.2 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:17.6 occ:1.00 O A:HOH347 2.1 34.0 1.0 NE2 A:HIS91 2.1 19.1 1.0 CD2 A:HIS91 3.1 18.3 1.0 CE1 A:HIS91 3.1 17.3 1.0 ND1 A:HIS91 4.2 17.3 1.0 CG A:HIS91 4.2 16.3 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:10.7 occ:1.00 O A:HOH332 1.9 9.5 1.0 OXT A:ACY208 2.0 13.3 1.0 NE2 A:HIS25 2.0 8.2 1.0 O A:ACY209 2.0 11.2 1.0 C A:ACY208 2.7 15.2 1.0 O A:ACY208 2.8 14.8 1.0 C A:ACY209 2.9 10.9 1.0 CE1 A:HIS25 3.0 9.4 1.0 CD2 A:HIS25 3.1 9.4 1.0 OXT A:ACY209 3.2 11.8 1.0 ZN A:ZN201 3.2 10.4 1.0 O2 A:GOL207 3.8 16.9 1.0 CG2 A:VAL58 3.9 10.4 1.0 C3 A:GOL207 4.0 14.9 1.0 ND1 A:HIS25 4.1 8.5 1.0 CG A:HIS25 4.2 8.8 1.0 CH3 A:ACY208 4.2 14.0 1.0 CB A:ALA29 4.2 9.4 1.0 O3 A:GOL207 4.3 13.8 1.0 CH3 A:ACY209 4.3 11.6 1.0 O A:HOH371 4.4 13.8 1.0 NE2 A:HIS62 4.4 9.8 1.0 O1 A:GOL207 4.5 20.4 1.0 O A:HOH316 4.6 9.3 1.0 C2 A:GOL207 4.6 17.7 1.0 CE1 A:HIS62 4.8 10.6 1.0 CB A:VAL58 4.9 9.5 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Marh, An Epimerase For Biosynthesis of Maremycins in Streptomyces, Under 400 Mm Zinc Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:10.4 occ:1.00 OE1 A:GLU68 1.9 9.9 1.0 O A:HOH316 2.0 9.3 1.0 NE2 A:HIS64 2.0 10.4 1.0 NE2 A:HIS107 2.1 9.4 1.0 CD A:GLU68 2.7 10.9 1.0 OE2 A:GLU68 2.8 12.6 1.0 CD2 A:HIS64 2.9 11.4 1.0 CE1 A:HIS107 3.0 8.8 1.0 CE1 A:HIS64 3.1 10.9 1.0 CD2 A:HIS107 3.1 9.0 1.0 ZN A:ZN201 3.3 10.4 1.0 OH A:TYR70 3.8 13.2 1.0 CE1 A:TYR70 3.9 14.9 1.0 OXT A:ACY209 3.9 11.8 1.0 O3 A:GOL207 3.9 13.8 1.0 NE2 A:HIS62 4.0 9.8 1.0 CG A:GLU68 4.1 9.4 1.0 ND1 A:HIS107 4.1 8.7 1.0 CG A:HIS64 4.1 10.5 1.0 ND1 A:HIS64 4.2 10.7 1.0 CG A:HIS107 4.2 8.8 1.0 CZ A:TYR70 4.3 14.3 1.0 CD2 A:HIS62 4.4 11.2 1.0 CB A:GLU68 4.6 9.3 1.0 C A:ACY209 4.8 10.9 1.0 CG2 A:ILE101 4.8 12.0 1.0 O A:HOH317 4.8 15.1 1.0

B.Liu, Y.Hou, X.Wang, X.Ma, S.Fang, T.Huang, Y.Chen, Z.Bai, S.Lin, R.Zhang, K.Hu. Structural Basis of the Mechanism of Beta-Methyl Epimerization By Enzyme Marh. Org.Biomol.Chem. V. 17 9605 2019.
ISSN: ESSN 1477-0539
PubMed: 31681917
DOI: 10.1039/C9OB01996K