Zinc in PDB 5zmu: Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids

The structure of Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids, PDB code: 5zmu was solved by S.Dong, X.Liu, X.Wang, Y.Feng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.35 / 1.50
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.490, 94.250, 94.360, 90.00, 95.90, 90.00
R / Rfree (%)	14.9 / 17

The binding sites of Zinc atom in the Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids (pdb code 5zmu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids, PDB code: 5zmu:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids


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 A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:14.7 occ:0.50 OE2 A:GLU34 2.0 23.1 1.0 O A:HOH535 2.1 18.7 1.0 NE2 A:HIS69 2.2 14.8 1.0 NE2 A:HIS67 2.2 14.2 1.0 O A:HOH581 2.2 17.8 1.0 O A:HOH712 2.2 17.5 1.0 CD A:GLU34 2.9 16.5 1.0 CE1 A:HIS69 3.1 21.4 1.0 OE1 A:GLU34 3.1 18.8 1.0 CE1 A:HIS67 3.1 16.5 1.0 CD2 A:HIS67 3.2 12.0 1.0 HE1 A:HIS69 3.2 25.6 1.0 CD2 A:HIS69 3.2 13.9 1.0 HE1 A:HIS67 3.3 19.8 1.0 HD2 A:HIS67 3.3 14.4 1.0 HD2 A:HIS69 3.4 16.7 1.0 HH12 A:ARG31 3.6 19.4 1.0 HB A:THR102 3.9 18.2 1.0 HH22 A:ARG31 4.0 18.8 1.0 HG1 A:THR102 4.0 20.8 1.0 O A:HOH748 4.1 22.5 1.0 HA A:GLU34 4.1 15.3 1.0 ND1 A:HIS69 4.2 19.8 1.0 NH1 A:ARG31 4.2 16.1 1.0 ND1 A:HIS67 4.3 14.2 1.0 CG A:GLU34 4.3 14.8 1.0 OG1 A:THR102 4.3 17.4 1.0 O A:HOH603 4.3 21.5 1.0 CG A:HIS67 4.3 13.4 1.0 CG A:HIS69 4.3 14.9 1.0 HG2 A:GLU34 4.4 17.7 1.0 NH2 A:ARG31 4.5 15.7 1.0 CB A:THR102 4.6 15.2 1.0 O A:HOH811 4.6 34.0 1.0 O A:HOH659 4.6 14.6 1.0 HZ2 A:LYS247 4.7 40.5 1.0 O A:HOH612 4.7 19.5 1.0 O A:HOH528 4.7 26.4 1.0 CZ A:ARG31 4.7 15.7 1.0 HH11 A:ARG31 4.7 19.4 1.0 HG3 A:PRO133 4.8 17.9 1.0 HB3 A:GLU34 4.9 14.7 1.0 HG3 A:GLU34 4.9 17.7 1.0 HA A:THR102 4.9 16.1 1.0 CA A:GLU34 5.0 12.8 1.0 HD1 A:HIS69 5.0 23.8 1.0 CB A:GLU34 5.0 12.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids


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 A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:15.9 occ:0.53 OE2 B:GLU34 2.0 20.3 1.0 NE2 B:HIS69 2.1 16.4 1.0 NE2 B:HIS67 2.1 13.1 1.0 O B:HOH522 2.2 18.0 1.0 O B:HOH604 2.2 17.4 1.0 O B:HOH701 2.2 19.3 1.0 CD B:GLU34 2.9 17.8 1.0 CE1 B:HIS69 3.0 22.5 1.0 CE1 B:HIS67 3.1 15.2 1.0 OE1 B:GLU34 3.1 21.6 1.0 CD2 B:HIS67 3.1 12.1 1.0 HE1 B:HIS69 3.2 27.0 1.0 CD2 B:HIS69 3.2 15.2 1.0 HE1 B:HIS67 3.3 18.2 1.0 HD2 B:HIS67 3.3 14.5 1.0 HD2 B:HIS69 3.4 18.2 1.0 HH12 B:ARG31 3.6 18.9 1.0 HB B:THR102 3.9 20.9 1.0 HH22 B:ARG31 4.0 18.4 1.0 O B:HOH746 4.2 21.0 1.0 HA B:GLU34 4.2 15.2 1.0 ND1 B:HIS69 4.2 19.0 1.0 HG1 B:THR102 4.2 23.0 1.0 ND1 B:HIS67 4.2 14.4 1.0 NH1 B:ARG31 4.2 15.7 1.0 CG B:GLU34 4.3 16.0 1.0 CG B:HIS67 4.3 11.6 1.0 CG B:HIS69 4.3 15.3 1.0 OG1 B:THR102 4.4 19.2 1.0 O B:HOH543 4.4 20.6 1.0 HG2 B:GLU34 4.4 19.1 1.0 CB B:THR102 4.6 17.4 1.0 NH2 B:ARG31 4.6 15.3 1.0 O B:HOH654 4.6 15.3 1.0 O B:HOH798 4.7 37.0 1.0 HZ2 B:LYS247 4.7 39.2 1.0 O B:HOH598 4.7 21.9 1.0 O B:HOH519 4.7 29.0 1.0 CZ B:ARG31 4.7 13.4 1.0 HH11 B:ARG31 4.7 18.9 1.0 HG3 B:PRO133 4.8 17.3 1.0 HB3 B:GLU34 4.9 16.8 1.0 HG3 B:GLU34 4.9 19.1 1.0 HD1 B:HIS69 5.0 22.8 1.0 CB B:GLU34 5.0 14.0 1.0 HA B:THR102 5.0 17.1 1.0 HD1 B:HIS67 5.0 17.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids


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 A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn400 b:16.7 occ:0.61 OE2 C:GLU34 2.0 20.9 1.0 NE2 C:HIS67 2.1 12.5 1.0 NE2 C:HIS69 2.2 13.6 1.0 O C:HOH519 2.2 20.7 1.0 O C:HOH735 2.2 19.8 1.0 O C:HOH559 2.3 17.5 1.0 CD C:GLU34 2.8 15.8 1.0 OE1 C:GLU34 3.0 18.5 1.0 CD2 C:HIS67 3.1 11.5 1.0 CE1 C:HIS69 3.1 16.0 1.0 CE1 C:HIS67 3.1 16.0 1.0 CD2 C:HIS69 3.2 13.0 1.0 HD2 C:HIS67 3.2 13.8 1.0 HE1 C:HIS69 3.2 19.1 1.0 HE1 C:HIS67 3.3 19.1 1.0 HD2 C:HIS69 3.4 15.6 1.0 HH12 C:ARG31 3.5 16.6 1.0 HG1 C:THR102 3.8 21.6 1.0 HB C:THR102 3.8 20.0 1.0 HH22 C:ARG31 3.9 15.4 1.0 HA C:GLU34 4.1 15.1 1.0 O C:HOH761 4.1 25.9 1.0 NH1 C:ARG31 4.1 13.8 1.0 CG C:GLU34 4.2 14.2 1.0 ND1 C:HIS67 4.2 13.4 1.0 CG C:HIS67 4.2 10.8 1.0 ND1 C:HIS69 4.2 14.6 1.0 OG1 C:THR102 4.3 18.0 1.0 CG C:HIS69 4.3 12.4 1.0 HG2 C:GLU34 4.4 17.0 1.0 NH2 C:ARG31 4.4 12.9 1.0 O C:HOH582 4.5 21.0 1.0 HZ2 C:LYS247 4.5 44.2 1.0 CB C:THR102 4.5 16.7 1.0 O C:HOH657 4.6 15.0 1.0 CZ C:ARG31 4.6 13.3 1.0 HH11 C:ARG31 4.6 16.6 1.0 O C:HOH823 4.6 45.4 1.0 O C:HOH545 4.8 29.6 1.0 O C:HOH637 4.8 22.2 1.0 HB3 C:GLU34 4.8 14.4 1.0 HG3 C:GLU34 4.8 17.0 1.0 CB C:GLU34 4.9 12.0 1.0 CA C:GLU34 4.9 12.6 1.0 HA C:THR102 4.9 16.3 1.0 HG3 C:PRO133 5.0 15.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids


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 A Cis-Epoxysuccinate Hydrolase Producing D(-)- Tartaric Acids within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn400 b:15.5 occ:0.53 OE2 D:GLU34 2.1 20.9 1.0 NE2 D:HIS67 2.1 13.0 1.0 O D:HOH523 2.2 19.0 1.0 O D:HOH587 2.2 15.8 1.0 NE2 D:HIS69 2.2 17.0 1.0 O D:HOH697 2.2 17.2 1.0 CD D:GLU34 2.9 17.0 1.0 CE1 D:HIS67 3.1 13.1 1.0 CE1 D:HIS69 3.1 19.4 1.0 CD2 D:HIS67 3.1 12.0 1.0 OE1 D:GLU34 3.1 19.5 1.0 HE1 D:HIS69 3.2 23.2 1.0 CD2 D:HIS69 3.2 15.2 1.0 HE1 D:HIS67 3.2 15.6 1.0 HD2 D:HIS67 3.3 14.4 1.0 HD2 D:HIS69 3.4 18.2 1.0 HH12 D:ARG31 3.6 17.7 1.0 HG1 D:THR102 3.7 19.9 1.0 HB D:THR102 3.9 20.2 1.0 HH22 D:ARG31 4.0 18.9 1.0 O D:HOH750 4.1 21.9 1.0 HA D:GLU34 4.2 15.7 1.0 NH1 D:ARG31 4.2 14.8 1.0 ND1 D:HIS67 4.2 13.1 1.0 ND1 D:HIS69 4.3 17.9 1.0 CG D:HIS67 4.3 11.7 1.0 CG D:GLU34 4.3 14.0 1.0 OG1 D:THR102 4.3 16.6 1.0 O D:HOH586 4.3 20.1 1.0 CG D:HIS69 4.3 14.6 1.0 HG2 D:GLU34 4.4 16.8 1.0 NH2 D:ARG31 4.5 15.8 1.0 CB D:THR102 4.5 16.8 1.0 O D:HOH656 4.6 14.1 1.0 O D:HOH803 4.6 30.1 1.0 O D:HOH525 4.7 25.2 1.0 O D:HOH576 4.7 20.5 1.0 HH11 D:ARG31 4.7 17.7 1.0 HZ2 D:LYS247 4.7 36.9 1.0 CZ D:ARG31 4.7 13.6 1.0 HG3 D:PRO133 4.8 18.1 1.0 HB3 D:GLU34 4.9 14.9 1.0 HG3 D:GLU34 4.9 16.8 1.0 HA D:THR102 5.0 16.6 1.0 HD1 D:HIS67 5.0 15.7 1.0

S.Dong, X.Liu, G.Z.Cui, Q.Cui, X.Wang, Y.Feng. Structural Insight Into the Catalytic Mechanism of A Cis-Epoxysuccinate Hydrolase Producing Enantiomerically Pure D(-)-Tartaric Acid. Chem. Commun. (Camb.) V. 54 8482 2018.
ISSN: ESSN 1364-548X
PubMed: 30003205
DOI: 10.1039/C8CC04398A