Zinc in PDB 4rul: Crystal Structure of Full-Length E.Coli Topoisomerase I in Complex with Ssdna

All present enzymatic activity of Crystal Structure of Full-Length E.Coli Topoisomerase I in Complex with Ssdna:
5.99.1.2;

The structure of Crystal Structure of Full-Length E.Coli Topoisomerase I in Complex with Ssdna, PDB code: 4rul was solved by K.Tan, B.Chen, Y.C.Tse-Dinh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.73 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	85.613, 80.295, 97.475, 90.00, 91.26, 90.00
R / Rfree (%)	20.9 / 25.9

The binding sites of Zinc atom in the Crystal Structure of Full-Length E.Coli Topoisomerase I in Complex with Ssdna (pdb code 4rul). 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 Full-Length E.Coli Topoisomerase I in Complex with Ssdna, PDB code: 4rul:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Full-Length E.Coli Topoisomerase I in Complex with Ssdna


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 Full-Length E.Coli Topoisomerase I in Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:1.0 occ:1.00 SG A:CYS630 2.3 92.3 1.0 SG A:CYS602 2.4 0.9 1.0 SG A:CYS619 2.4 0.9 1.0 SG A:CYS599 2.4 85.0 1.0 CB A:CYS619 2.7 0.3 1.0 CB A:CYS599 3.0 93.4 1.0 CB A:CYS630 3.1 0.6 1.0 OG1 A:THR632 3.6 83.3 1.0 CB A:CYS602 3.7 0.5 1.0 N A:CYS602 4.1 0.8 1.0 CA A:CYS619 4.2 0.5 1.0 CA A:CYS602 4.4 0.1 1.0 CA A:CYS599 4.5 97.4 1.0 CA A:CYS630 4.6 0.4 1.0 C A:CYS602 4.8 0.8 1.0 CB A:ARG604 4.8 0.5 1.0 NE A:ARG604 4.9 0.4 1.0 CB A:THR632 5.0 84.7 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Full-Length E.Coli Topoisomerase I in Complex with Ssdna


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 Full-Length E.Coli Topoisomerase I in Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:83.5 occ:1.00 SG A:CYS689 2.3 91.0 1.0 SG A:CYS665 2.3 76.9 1.0 SG A:CYS662 2.3 82.3 1.0 SG A:CYS683 2.4 86.6 1.0 CB A:CYS662 3.0 71.2 1.0 CB A:CYS683 3.1 68.6 1.0 CB A:CYS689 3.1 73.8 1.0 CB A:CYS665 3.5 81.6 1.0 N A:CYS665 3.9 79.5 1.0 CA A:CYS665 4.3 78.7 1.0 CA A:CYS683 4.4 67.6 1.0 CA A:CYS662 4.5 72.1 1.0 CA A:CYS689 4.5 82.7 1.0 CB A:LYS664 4.6 76.3 1.0 CA A:GLY691 4.7 82.7 1.0 CB A:THR667 4.7 67.6 1.0 N A:GLY691 4.8 86.0 1.0 OG1 A:THR667 4.8 72.6 1.0 C A:LYS664 4.8 88.1 1.0 C A:CYS689 4.9 90.1 1.0 N A:GLY666 4.9 82.0 1.0 C A:CYS665 5.0 80.6 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Full-Length E.Coli Topoisomerase I in Complex with Ssdna


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 Full-Length E.Coli Topoisomerase I in Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:98.2 occ:1.00 SG A:CYS736 2.2 0.6 1.0 SG A:CYS711 2.3 0.8 1.0 SG A:CYS714 2.3 0.2 1.0 SG A:CYS731 2.5 91.6 1.0 CB A:CYS711 2.9 92.6 1.0 CB A:CYS731 3.3 77.8 1.0 CB A:CYS714 3.7 0.7 1.0 CB A:CYS736 3.9 0.5 1.0 OG A:SER716 3.9 0.1 1.0 N A:CYS714 3.9 0.2 1.0 CA A:CYS714 4.4 0.4 1.0 CA A:CYS711 4.4 94.0 1.0 CB A:LYS713 4.6 0.1 1.0 CA A:CYS731 4.7 99.3 1.0 CB A:ASN733 4.7 0.1 1.0 N A:GLY715 4.7 0.3 1.0 C A:LYS713 5.0 0.8 1.0 CB A:ASN738 5.0 0.3 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Full-Length E.Coli Topoisomerase I in Complex with Ssdna


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 Full-Length E.Coli Topoisomerase I in Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:0.4 occ:0.64 ZN A:ZN1004 0.0 0.4 0.6 ZN A:ZN1004 1.3 0.3 0.4 NE2 A:HIS566 2.2 78.0 0.5 CE1 A:HIS566 2.3 78.3 0.5 NE2 A:HIS566 2.7 75.7 0.5 CE1 A:HIS566 3.0 74.4 0.5 CD2 A:HIS566 3.4 75.5 0.5 ND1 A:HIS566 3.5 75.7 0.5 CD2 A:HIS566 4.1 70.5 0.5 OD2 A:ASP570 4.2 92.2 1.0 ND1 A:HIS566 4.2 70.3 0.5 CG A:HIS566 4.4 68.8 0.5 CG A:HIS566 4.4 68.6 0.5 OD1 A:ASP570 4.6 0.4 1.0 CG A:ASP570 4.8 95.1 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Full-Length E.Coli Topoisomerase I in Complex with Ssdna


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 Full-Length E.Coli Topoisomerase I in Complex with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:0.3 occ:0.36 ZN A:ZN1004 0.0 0.3 0.4 ZN A:ZN1004 1.3 0.4 0.6 NE2 A:HIS566 2.2 78.0 0.5 NE2 A:HIS566 2.2 75.7 0.5 CE1 A:HIS566 2.3 78.3 0.5 CE1 A:HIS566 2.4 74.4 0.5 OD2 A:ASP570 3.5 92.2 1.0 CD2 A:HIS566 3.5 75.5 0.5 CD2 A:HIS566 3.6 70.5 0.5 ND1 A:HIS566 3.6 75.7 0.5 ND1 A:HIS566 3.7 70.3 0.5 CG A:HIS566 4.2 68.8 0.5 CG A:HIS566 4.2 68.6 0.5 CG A:ASP570 4.4 95.1 1.0 OD1 A:ASP570 4.5 0.4 1.0

K.Tan, Q.Zhou, B.Cheng, Z.Zhang, A.Joachimiak, Y.C.Tse-Dinh. Structural Basis For Suppression of Hypernegative Dna Supercoiling By E. Coli Topoisomerase I. Nucleic Acids Res. V. 43 11031 2015.
ISSN: ISSN 0305-1048
PubMed: 26490962
DOI: 10.1093/NAR/GKV1073