Zinc in PDB 8ofb: Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch, Hexagonal Form

All present enzymatic activity of Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch, Hexagonal Form:
3.6.4.12; 5.6.2.2;

The structure of Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch, Hexagonal Form, PDB code: 8ofb was solved by D.Klostermeier, R.Rasche, V.Mhaindarkar, D.Kummel, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.85 / 2.39
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.833, 90.833, 571.878, 90, 90, 120
R / Rfree (%)	24.3 / 27.2

The structure of Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch, Hexagonal Form also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch, Hexagonal Form (pdb code 8ofb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch, Hexagonal Form, PDB code: 8ofb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch, Hexagonal Form


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 T. Maritima Reverse Gyrase with A Minimal Latch, Hexagonal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:70.6 occ:1.00 SG A:CYS29 2.3 72.5 1.0 SG A:CYS14 2.3 71.4 1.0 SG A:CYS11 2.3 71.5 1.0 SG A:CYS32 2.3 95.8 1.0 CB A:CYS14 3.4 72.9 1.0 CB A:CYS11 3.4 61.3 1.0 CB A:CYS29 3.5 72.3 1.0 CB A:CYS32 3.7 78.6 1.0 N A:CYS14 3.7 77.5 1.0 N A:CYS29 3.9 75.0 1.0 CA A:CYS14 4.1 69.3 1.0 CA A:CYS29 4.2 75.0 1.0 N A:CYS32 4.3 91.5 1.0 O A:CYS29 4.5 91.2 1.0 CB A:ASN13 4.5 72.0 1.0 CA A:CYS32 4.6 83.8 1.0 CB A:PRO28 4.7 69.3 1.0 C A:ASN13 4.7 74.8 1.0 C A:CYS29 4.7 81.2 1.0 C A:CYS14 4.8 68.2 1.0 CA A:CYS11 4.8 57.4 1.0 N A:GLY15 4.9 78.8 1.0 N A:GLY16 4.9 68.7 1.0 N A:ASN13 4.9 61.9 1.0 CA A:ASN13 5.0 68.1 1.0 C A:PRO28 5.0 76.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of T. Maritima Reverse Gyrase with A Minimal Latch, Hexagonal Form


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 T. Maritima Reverse Gyrase with A Minimal Latch, Hexagonal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1103 b:52.3 occ:1.00 SG A:CYS563 2.3 58.2 1.0 SG A:CYS577 2.3 59.5 1.0 SG A:CYS560 2.3 62.4 1.0 SG A:CYS574 2.3 59.9 1.0 CB A:CYS560 3.0 46.6 1.0 CB A:CYS574 3.0 52.7 1.0 CB A:CYS563 3.5 63.3 1.0 CB A:CYS577 3.8 52.2 1.0 N A:CYS563 3.9 70.7 1.0 N A:CYS577 4.0 45.0 1.0 CA A:CYS563 4.2 67.7 1.0 CA A:CYS577 4.4 57.6 1.0 CA A:CYS560 4.5 49.9 1.0 CA A:CYS574 4.5 46.8 1.0 CB A:SER579 4.5 63.3 1.0 CB A:TYR565 4.6 44.5 1.0 CB A:VAL576 4.7 47.2 1.0 N A:GLY564 4.8 61.0 1.0 C A:CYS563 4.8 60.7 1.0 N A:TYR565 4.8 51.8 1.0 CB A:ASP562 4.9 67.1 1.0 N A:SER579 4.9 63.6 1.0 C A:CYS577 4.9 60.2 1.0

V.Mhaindarkar, R.Rasche, D.Kummel, M.G.Rudolph, D.Klostermeier. Structure of Reverse Gyrase with A Minimal Latch That Supports Atp-Dependent Positive Supercoiling Without Specific Interactions with the Topoisomerase Domain Acta Crystallogr.,Sect.D 2023.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798323002565