Zinc in PDB 4ddx: Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic Form

All present enzymatic activity of Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic Form:
3.6.4.12; 5.99.1.3;

The structure of Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic Form, PDB code: 4ddx 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)	48.43 / 4.17
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	125.815, 104.896, 126.181, 90.00, 91.72, 90.00
R / Rfree (%)	24.5 / 30.5

The binding sites of Zinc atom in the Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic Form (pdb code 4ddx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic Form, PDB code: 4ddx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic 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, Primitive Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1201 b:0.7 occ:1.00 SG A:CYS624 2.3 0.1 1.0 SG A:CYS638 2.3 0.8 1.0 SG A:CYS621 2.5 0.1 1.0 SG A:CYS635 2.5 0.2 1.0 CB A:CYS624 3.0 0.8 1.0 CB A:CYS635 3.1 0.6 1.0 CB A:CYS621 3.2 0.7 1.0 N A:CYS624 3.5 0.2 1.0 CB A:CYS638 3.7 0.9 1.0 CA A:CYS624 3.9 0.0 1.0 N A:CYS638 4.2 0.8 1.0 N A:GLY625 4.3 1.0 1.0 CB A:SER640 4.4 0.3 1.0 CA A:CYS638 4.5 0.9 1.0 CB A:ASP623 4.6 0.5 1.0 C A:CYS624 4.6 1.0 1.0 CA A:CYS635 4.6 0.3 1.0 C A:ASP623 4.7 0.4 1.0 CA A:CYS621 4.7 0.5 1.0 N A:SER640 4.7 0.1 1.0 CB A:VAL637 4.8 0.5 1.0 N A:TYR626 4.8 0.9 1.0 C A:CYS638 4.9 0.5 1.0 O A:CYS635 5.0 0.6 1.0 N A:SER639 5.0 0.8 1.0 CB A:TYR626 5.0 0.8 1.0

Zinc binding site 2 out of 4 in the Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic 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, Primitive Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1202 b:0.3 occ:1.00 SG A:CYS29 2.2 0.5 1.0 SG A:CYS14 2.3 0.3 1.0 SG A:CYS32 2.3 1.0 1.0 SG A:CYS11 2.4 0.2 1.0 CB A:CYS14 3.3 0.7 1.0 N A:CYS14 3.5 0.7 1.0 CB A:CYS29 3.5 0.1 1.0 CB A:CYS11 3.6 0.6 1.0 CB A:CYS32 3.7 0.3 1.0 N A:CYS29 3.8 0.2 1.0 CA A:CYS14 3.9 0.6 1.0 CB A:ASN13 4.2 0.8 1.0 CA A:CYS29 4.2 0.8 1.0 N A:CYS32 4.4 0.3 1.0 C A:ASN13 4.6 0.1 1.0 CA A:CYS32 4.6 0.3 1.0 ND2 A:ASN13 4.7 0.7 1.0 C A:CYS14 4.7 1.0 1.0 N A:GLY15 4.8 0.6 1.0 CA A:ASN13 4.8 0.1 1.0 CB A:PRO28 4.8 0.2 1.0 C A:PRO28 4.9 0.5 1.0 CG A:ASN13 5.0 0.2 1.0 N A:ASN13 5.0 0.1 1.0 C A:CYS29 5.0 0.5 1.0 CA A:CYS11 5.0 0.4 1.0

Zinc binding site 3 out of 4 in the Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:0.4 occ:1.00 SG B:CYS624 2.3 0.4 1.0 SG B:CYS638 2.3 0.7 1.0 SG B:CYS635 2.4 0.3 1.0 SG B:CYS621 2.5 0.6 1.0 CB B:CYS624 3.1 0.2 1.0 CB B:CYS635 3.1 0.7 1.0 CB B:CYS621 3.2 0.1 1.0 N B:CYS624 3.6 0.5 1.0 CB B:CYS638 3.7 0.9 1.0 CA B:CYS624 3.9 0.3 1.0 N B:CYS638 4.1 0.8 1.0 N B:GLY625 4.3 0.7 1.0 CB B:SER640 4.4 0.1 1.0 CA B:CYS638 4.5 0.8 1.0 CA B:CYS635 4.6 0.4 1.0 CB B:ASP623 4.6 0.5 1.0 C B:CYS624 4.6 0.3 1.0 CA B:CYS621 4.7 0.9 1.0 N B:SER640 4.7 1.0 1.0 C B:ASP623 4.8 0.5 1.0 CB B:VAL637 4.8 0.8 1.0 N B:TYR626 4.8 0.5 1.0 C B:CYS638 4.9 0.5 1.0 O B:CYS635 5.0 0.7 1.0 CB B:TYR626 5.0 0.4 1.0 N B:SER639 5.0 0.7 1.0

Zinc binding site 4 out of 4 in the Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1202 b:0.7 occ:1.00 SG B:CYS29 2.2 0.5 1.0 SG B:CYS14 2.3 0.1 1.0 SG B:CYS32 2.3 0.3 1.0 SG B:CYS11 2.4 0.9 1.0 CB B:CYS14 3.3 0.5 1.0 N B:CYS14 3.5 0.5 1.0 CB B:CYS29 3.5 0.1 1.0 CB B:CYS11 3.5 0.2 1.0 CB B:CYS32 3.7 0.6 1.0 N B:CYS29 3.8 0.2 1.0 CA B:CYS14 4.0 0.5 1.0 CB B:ASN13 4.2 0.7 1.0 CA B:CYS29 4.2 0.8 1.0 N B:CYS32 4.4 0.6 1.0 C B:ASN13 4.6 0.9 1.0 CA B:CYS32 4.6 0.6 1.0 C B:CYS14 4.7 0.8 1.0 ND2 B:ASN13 4.7 0.5 1.0 N B:GLY15 4.8 0.6 1.0 CA B:ASN13 4.8 0.9 1.0 CB B:PRO28 4.8 0.0 1.0 C B:PRO28 4.9 0.3 1.0 N B:ASN13 5.0 0.0 1.0 CG B:ASN13 5.0 0.1 1.0 CA B:CYS11 5.0 0.1 1.0 C B:CYS29 5.0 0.5 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