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Zinc in PDB 4ddu: Thermotoga Maritima Reverse Gyrase, C2 Form 1

Enzymatic activity of Thermotoga Maritima Reverse Gyrase, C2 Form 1

All present enzymatic activity of Thermotoga Maritima Reverse Gyrase, C2 Form 1:
3.6.4.12; 5.99.1.3;

Protein crystallography data

The structure of Thermotoga Maritima Reverse Gyrase, C2 Form 1, PDB code: 4ddu 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) 44.22 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 169.961, 73.912, 111.371, 90.00, 116.59, 90.00
R / Rfree (%) 21.5 / 27.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Thermotoga Maritima Reverse Gyrase, C2 Form 1 (pdb code 4ddu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Thermotoga Maritima Reverse Gyrase, C2 Form 1, PDB code: 4ddu:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4ddu

Go back to Zinc Binding Sites List in 4ddu
Zinc binding site 1 out of 3 in the Thermotoga Maritima Reverse Gyrase, C2 Form 1


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, C2 Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1201

b:80.7
occ:1.00
SG A:CYS624 2.2 79.9 1.0
SG A:CYS638 2.2 0.1 1.0
SG A:CYS621 2.3 96.4 1.0
SG A:CYS635 2.3 80.7 1.0
CB A:CYS621 3.0 50.7 1.0
CB A:CYS635 3.1 94.2 1.0
CB A:CYS624 3.5 76.9 1.0
CB A:CYS638 3.5 0.6 1.0
N A:CYS624 3.9 79.0 1.0
N A:CYS638 3.9 0.1 1.0
CA A:CYS638 4.2 0.3 1.0
CA A:CYS624 4.2 73.1 1.0
CA A:CYS621 4.5 72.3 1.0
CA A:CYS635 4.6 95.6 1.0
N A:GLY625 4.7 57.7 1.0
CB A:ASP623 4.7 91.0 1.0
CB A:SER640 4.8 0.1 1.0
C A:CYS638 4.8 1.0 1.0
CB A:TYR626 4.9 75.5 1.0
C A:CYS624 4.9 63.1 1.0
N A:TYR626 4.9 58.8 1.0
CB A:VAL637 4.9 88.3 1.0
N A:SER639 5.0 0.9 1.0
N A:SER640 5.0 0.0 1.0

Zinc binding site 2 out of 3 in 4ddu

Go back to Zinc Binding Sites List in 4ddu
Zinc binding site 2 out of 3 in the Thermotoga Maritima Reverse Gyrase, C2 Form 1


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, C2 Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1202

b:71.1
occ:1.00
SG A:CYS32 2.2 52.3 1.0
SG A:CYS14 2.3 56.6 1.0
SG A:CYS29 2.3 46.5 1.0
SG A:CYS11 2.4 68.9 1.0
CB A:CYS14 2.9 43.9 1.0
CB A:CYS32 3.3 38.2 1.0
CB A:CYS11 3.5 46.4 1.0
CB A:CYS29 3.5 33.4 1.0
N A:CYS14 3.7 50.6 1.0
N A:CYS29 3.8 39.5 1.0
CA A:CYS14 3.9 47.4 1.0
N A:CYS32 4.1 46.5 1.0
CA A:CYS29 4.2 36.1 1.0
CA A:CYS32 4.3 49.2 1.0
ND2 A:ASN13 4.7 39.6 1.0
C A:CYS14 4.7 53.5 1.0
CB A:PRO28 4.7 41.4 1.0
C A:CYS29 4.8 42.2 1.0
O A:CYS29 4.8 54.5 1.0
C A:ASN13 4.8 45.9 1.0
C A:PRO28 4.8 43.9 1.0
CA A:CYS11 4.9 54.0 1.0
N A:GLY15 4.9 57.8 1.0

Zinc binding site 3 out of 3 in 4ddu

Go back to Zinc Binding Sites List in 4ddu
Zinc binding site 3 out of 3 in the Thermotoga Maritima Reverse Gyrase, C2 Form 1


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, C2 Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1203

b:81.0
occ:1.00
N A:ALA2 2.0 45.5 1.0
OE1 A:GLU24 2.0 80.4 1.0
OE2 A:GLU24 2.3 86.9 1.0
CD A:GLU24 2.5 76.4 1.0
CA A:ALA2 3.0 46.0 1.0
CB A:ALA2 3.1 53.4 1.0
CG A:GLU24 3.9 65.2 1.0
CE2 A:PHE716 4.1 36.1 1.0
C A:ALA2 4.2 47.5 1.0
O A:ALA2 4.4 49.4 1.0
CZ A:PHE716 4.5 30.0 1.0
CB A:GLU24 4.7 58.1 1.0
CD2 A:PHE716 4.7 35.6 1.0

Reference:

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
Page generated: Wed Dec 16 05:10:58 2020

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