Zinc in PDB 4ddw: Thermotoga Maritima Reverse Gyrase, C-Centered Orthorhombic Form

All present enzymatic activity of Thermotoga Maritima Reverse Gyrase, C-Centered Orthorhombic Form:
3.6.4.12; 5.99.1.3;

The structure of Thermotoga Maritima Reverse Gyrase, C-Centered Orthorhombic Form, PDB code: 4ddw was solved by M.G.Rudolph, D.Klostermeier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.75 / 3.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	174.325, 175.646, 104.135, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 28.9

The structure of Thermotoga Maritima Reverse Gyrase, C-Centered Orthorhombic Form also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Thermotoga Maritima Reverse Gyrase, C-Centered Orthorhombic Form (pdb code 4ddw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Thermotoga Maritima Reverse Gyrase, C-Centered Orthorhombic Form, PDB code: 4ddw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Thermotoga Maritima Reverse Gyrase, C-Centered Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermotoga Maritima Reverse Gyrase, C-Centered Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1201 b:0.5 occ:1.00 SG A:CYS638 2.2 0.8 1.0 SG A:CYS624 2.3 0.1 1.0 SG A:CYS621 2.3 0.8 1.0 SG A:CYS635 2.3 0.0 1.0 CB A:CYS621 2.9 0.8 1.0 CB A:CYS635 3.1 0.5 1.0 CB A:CYS638 3.6 0.9 1.0 CB A:CYS624 3.7 0.2 1.0 N A:CYS638 4.0 0.5 1.0 N A:CYS624 4.0 0.9 1.0 CA A:CYS638 4.4 0.6 1.0 CA A:CYS621 4.4 0.3 1.0 CA A:CYS624 4.4 0.1 1.0 CA A:CYS635 4.6 0.1 1.0 CB A:VAL637 4.6 0.3 1.0 CB A:ASP623 4.7 0.1 1.0 N A:GLY625 4.7 0.5 1.0 N A:TYR626 4.9 0.3 1.0 C A:CYS638 5.0 0.2 1.0

Zinc binding site 2 out of 2 in the Thermotoga Maritima Reverse Gyrase, C-Centered Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thermotoga Maritima Reverse Gyrase, C-Centered Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1202 b:0.6 occ:1.00 SG A:CYS29 2.3 0.3 1.0 SG A:CYS14 2.3 0.9 1.0 SG A:CYS11 2.4 0.7 1.0 SG A:CYS32 2.4 0.5 1.0 CB A:CYS14 2.9 0.2 1.0 CB A:CYS11 3.4 0.9 1.0 CB A:CYS29 3.7 0.9 1.0 CB A:CYS32 3.7 0.1 1.0 N A:CYS14 3.7 0.5 1.0 N A:CYS29 3.8 0.2 1.0 CA A:CYS14 3.9 0.7 1.0 CA A:CYS29 4.3 0.8 1.0 N A:CYS32 4.4 0.9 1.0 CB A:PRO28 4.6 0.9 1.0 C A:CYS14 4.6 0.3 1.0 CA A:CYS32 4.6 0.9 1.0 C A:ASN13 4.8 0.8 1.0 N A:GLY15 4.8 0.7 1.0 CA A:CYS11 4.9 0.6 1.0 C A:PRO28 4.9 0.9 1.0 C A:CYS29 5.0 0.2 1.0

M.G.Rudolph, Y.Del Toro Duany, S.P.Jungblut, A.Ganguly, D.Klostermeier. Crystal Structures of Thermotoga Maritima Reverse Gyrase: Inferences For the Mechanism of Positive Dna Supercoiling. Nucleic Acids Res. V. 41 1058 2013.
ISSN: ISSN 0305-1048
PubMed: 23209025
DOI: 10.1093/NAR/GKS1073