Zinc in PDB 6own: Crystal Structure of Msm DNAB1 Intein Splicing Domain Bound with Zinc

All present enzymatic activity of Crystal Structure of Msm DNAB1 Intein Splicing Domain Bound with Zinc:
3.6.4.12;

The structure of Crystal Structure of Msm DNAB1 Intein Splicing Domain Bound with Zinc, PDB code: 6own was solved by V.R.Bacot-Davis, M.Belfort, C.Lennon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.48 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.050, 56.914, 64.727, 90.00, 106.60, 90.00
R / Rfree (%)	20.9 / 24.4

The binding sites of Zinc atom in the Crystal Structure of Msm DNAB1 Intein Splicing Domain Bound with Zinc (pdb code 6own). 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 Msm DNAB1 Intein Splicing Domain Bound with Zinc, PDB code: 6own:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Msm DNAB1 Intein Splicing Domain Bound with Zinc


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 Msm DNAB1 Intein Splicing Domain Bound with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:40.2 occ:1.00 NE1 A:TRP14 3.1 20.2 1.0 CE2 A:TRP14 3.9 19.1 1.0 CZ2 A:TRP14 4.0 20.7 1.0 CD1 A:TRP14 4.2 15.8 1.0 CE A:MET134 4.3 19.4 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Msm DNAB1 Intein Splicing Domain Bound with Zinc


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 Msm DNAB1 Intein Splicing Domain Bound with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:69.6 occ:1.00 SG A:CYS118 2.3 52.2 1.0 OH A:TYR128 2.7 21.5 1.0 N A:VAL119 2.9 20.7 1.0 O A:VAL119 2.9 27.5 1.0 CB A:CYS118 3.4 28.9 1.0 CA A:CYS118 3.4 22.8 1.0 CZ A:TYR128 3.6 20.6 1.0 CE1 A:TYR128 3.6 22.7 1.0 C A:CYS118 3.7 26.6 1.0 OXT A:ASN139 3.7 50.3 1.0 C A:VAL119 3.8 26.8 1.0 CE1 A:HIS65 3.9 24.9 1.0 CA A:VAL119 3.9 22.7 1.0 CA A:ASN139 3.9 27.7 1.0 CG2 A:VAL119 4.1 27.2 1.0 C A:ASN139 4.2 45.0 1.0 O A:HIS138 4.3 28.0 1.0 ND1 A:HIS65 4.4 20.5 1.0 CE A:MET17 4.4 15.9 1.0 CB A:ASN139 4.5 35.6 1.0 O A:HOH348 4.6 26.5 1.0 CB A:ALA1 4.7 16.9 1.0 CB A:VAL119 4.7 19.3 1.0 N A:CYS118 4.8 19.2 1.0 CE2 A:TYR128 4.8 19.8 1.0 O A:ARG117 4.9 14.4 1.0 O A:CYS118 4.9 24.7 1.0 CD1 A:TYR128 4.9 21.3 1.0 N A:ASN139 5.0 25.3 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Msm DNAB1 Intein Splicing Domain Bound with Zinc


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 Msm DNAB1 Intein Splicing Domain Bound with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:36.5 occ:1.00 O B:HOH390 3.0 28.4 1.0 NE1 B:TRP14 3.1 20.9 1.0 OH A:TYR49 3.1 19.0 1.0 NH1 A:ARG110 3.3 19.8 1.0 NH2 A:ARG110 3.3 18.3 1.0 CB A:ALA63 3.5 20.3 1.0 CZ A:ARG110 3.7 17.9 1.0 CE2 B:TRP14 3.9 19.2 1.0 CB A:PRO47 3.9 22.8 1.0 CG A:PRO47 4.0 25.6 1.0 CZ2 B:TRP14 4.0 20.3 1.0 CE1 A:TYR49 4.0 18.3 1.0 CZ A:TYR49 4.0 15.4 1.0 CD1 B:TRP14 4.2 21.3 1.0 CE B:MET134 4.2 19.0 1.0 CB A:ALA77 4.6 24.4 1.0 CA A:ALA63 4.8 18.6 1.0 O B:HOH334 4.9 41.6 1.0 NE A:ARG110 5.0 13.6 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Msm DNAB1 Intein Splicing Domain Bound with Zinc


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 Msm DNAB1 Intein Splicing Domain Bound with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:80.2 occ:1.00 SG B:CYS118 2.3 62.0 1.0 OH B:TYR128 2.8 23.9 1.0 N B:VAL119 3.0 24.5 1.0 O B:VAL119 3.3 31.9 1.0 CB B:CYS118 3.3 35.5 1.0 CA B:CYS118 3.4 26.9 1.0 C B:CYS118 3.7 33.0 1.0 CZ B:TYR128 3.7 21.1 1.0 CE1 B:TYR128 3.8 21.8 1.0 OXT B:ASN139 3.8 52.7 1.0 CE1 B:HIS65 3.8 27.3 1.0 CA B:VAL119 4.1 23.5 1.0 C B:VAL119 4.1 29.0 1.0 CG2 B:VAL119 4.1 22.5 1.0 O B:HIS138 4.2 35.3 1.0 ND1 B:HIS65 4.2 21.7 1.0 O B:HOH344 4.2 30.9 1.0 CB B:ALA1 4.2 28.6 1.0 CE B:MET17 4.4 18.8 1.0 C B:ASN139 4.5 44.1 1.0 CA B:ASN139 4.7 41.5 1.0 N B:CYS118 4.7 20.6 1.0 O B:ARG117 4.7 23.4 1.0 CB B:VAL119 4.7 23.6 1.0 O B:CYS118 4.9 26.4 1.0 NE2 B:HIS65 5.0 25.4 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Msm DNAB1 Intein Splicing Domain Bound with Zinc


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 Msm DNAB1 Intein Splicing Domain Bound with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:86.4 occ:1.00 SG C:CYS118 2.4 54.8 1.0 OH C:TYR128 2.6 32.9 1.0 N C:VAL119 2.9 25.1 1.0 O C:VAL119 3.0 34.9 1.0 CA C:CYS118 3.4 27.9 1.0 CZ C:TYR128 3.4 37.9 1.0 CB C:CYS118 3.4 32.5 1.0 CE1 C:TYR128 3.4 36.4 1.0 C C:CYS118 3.6 25.4 1.0 C C:VAL119 3.8 30.9 1.0 CA C:VAL119 3.8 29.0 1.0 CG2 C:VAL119 4.0 31.4 1.0 CE C:MET17 4.0 29.4 1.0 O C:ASN139 4.0 60.2 1.0 CA C:ASN139 4.2 56.3 1.0 CE1 C:HIS65 4.3 30.8 1.0 C C:ASN139 4.4 67.8 1.0 O C:HIS138 4.4 49.9 1.0 CB C:VAL119 4.5 25.9 1.0 ND2 C:ASN139 4.6 51.1 1.0 CE2 C:TYR128 4.7 41.0 1.0 N C:CYS118 4.7 28.4 1.0 CD1 C:TYR128 4.8 36.4 1.0 O C:ARG117 4.8 26.1 1.0 O C:CYS118 4.8 26.1 1.0 ND1 C:HIS65 4.8 25.7 1.0

V.R.Bacot-Davis, M.Belfort. Characterization of Novel Antimycobacterial Small Molecule and Nanoparticle Intein Splicing Inhibitors To Be Published.