Atomistry » Mercury » PDB 3kbc-3wa8 » 3px7
Atomistry »
  Mercury »
    PDB 3kbc-3wa8 »
      3px7 »

Mercury in PDB 3px7: Crystal Structure of Covalent Complex of Topoisomerase 1A with Substrate

Enzymatic activity of Crystal Structure of Covalent Complex of Topoisomerase 1A with Substrate

All present enzymatic activity of Crystal Structure of Covalent Complex of Topoisomerase 1A with Substrate:
5.99.1.2;

Protein crystallography data

The structure of Crystal Structure of Covalent Complex of Topoisomerase 1A with Substrate, PDB code: 3px7 was solved by Z.Zhang, Y.C.Tse-Dinh, B.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 500.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.602, 91.759, 141.976, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 26.9

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Covalent Complex of Topoisomerase 1A with Substrate (pdb code 3px7). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 3 binding sites of Mercury where determined in the Crystal Structure of Covalent Complex of Topoisomerase 1A with Substrate, PDB code: 3px7:
Jump to Mercury binding site number: 1; 2; 3;

Mercury binding site 1 out of 3 in 3px7

Go back to Mercury Binding Sites List in 3px7
Mercury binding site 1 out of 3 in the Crystal Structure of Covalent Complex of Topoisomerase 1A with Substrate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of Covalent Complex of Topoisomerase 1A with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg596

b:34.0
occ:0.70
SG A:CYS401 2.7 35.2 1.0
O A:CYS401 2.9 28.4 1.0
O A:GLY281 3.1 31.1 1.0
CB A:CYS401 3.3 21.2 1.0
CA A:CYS401 3.5 26.9 1.0
C A:CYS401 3.5 28.7 1.0
CD2 A:TYR355 3.5 48.7 1.0
CE2 A:TYR355 3.7 49.5 1.0
C A:GLY281 3.9 31.7 1.0
CA A:ALA282 4.1 29.5 1.0
CG A:TYR355 4.3 50.8 1.0
N A:ALA282 4.4 30.8 1.0
NE2 A:GLN402 4.5 36.3 1.0
CZ A:TYR355 4.6 47.8 1.0
CD A:PRO283 4.6 30.6 1.0
CB A:ASN353 4.6 47.8 1.0
N A:GLN402 4.7 28.4 1.0
CG A:PRO280 4.7 38.4 1.0
O A:PRO280 4.8 36.1 1.0
N A:CYS401 4.9 25.4 1.0
C A:ALA282 5.0 31.2 1.0
CB A:TYR355 5.0 52.2 1.0

Mercury binding site 2 out of 3 in 3px7

Go back to Mercury Binding Sites List in 3px7
Mercury binding site 2 out of 3 in the Crystal Structure of Covalent Complex of Topoisomerase 1A with Substrate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of Covalent Complex of Topoisomerase 1A with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg6

b:52.4
occ:0.30
O4 B:DT1 1.8 78.4 1.0
C4 B:DT1 2.5 79.7 1.0
N3 B:DT1 2.7 79.8 1.0
O4 B:DT2 2.7 80.4 1.0
O4 C:DT8 3.2 46.5 1.0
C4 B:DT2 3.4 80.7 1.0
HG C:HG9 3.5 52.0 0.3
C4 C:DT8 3.7 43.7 1.0
N3 C:DT8 3.7 45.4 1.0
N3 B:DT2 3.8 81.0 1.0
C5 B:DT1 3.8 80.2 1.0
C2 B:DT1 4.0 79.3 1.0
C5 B:DT2 4.4 80.3 1.0
C7 B:DT1 4.5 77.7 1.0
O2 B:DT1 4.6 79.0 1.0
C6 B:DT1 4.7 80.8 1.0
C7 B:DT2 4.8 77.7 1.0
C2 C:DT8 4.8 44.6 1.0
C5 C:DT8 4.8 44.1 1.0
N1 B:DT1 4.8 80.0 1.0
C2 B:DT2 4.9 80.8 1.0

Mercury binding site 3 out of 3 in 3px7

Go back to Mercury Binding Sites List in 3px7
Mercury binding site 3 out of 3 in the Crystal Structure of Covalent Complex of Topoisomerase 1A with Substrate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of Covalent Complex of Topoisomerase 1A with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg9

b:52.0
occ:0.30
N3 C:DT8 2.5 45.4 1.0
O4 C:DT8 3.2 46.5 1.0
C4 C:DT8 3.2 43.7 1.0
C2 C:DT8 3.4 44.6 1.0
O2 C:DT8 3.4 42.1 1.0
HG B:HG6 3.5 52.4 0.3
O C:HOH63 3.6 56.2 1.0
N3 B:DT1 4.1 79.8 1.0
CD1 A:LEU86 4.2 69.6 1.0
O4 B:DT1 4.6 78.4 1.0
C5 C:DT8 4.6 44.1 1.0
N1 C:DT8 4.6 44.8 1.0
N3 C:DC7 4.7 41.2 1.0
C4 B:DT1 4.8 79.7 1.0
O2 B:DT1 4.8 79.0 1.0
C2 B:DT1 5.0 79.3 1.0

Reference:

Y.C.Tse-Dinh, Z.Zhang, B.Cheng. Structure of E. Coli Topoisomerase I Trapped As Covalent Complex Intermediate with Cleaved Dna To Be Published.
Page generated: Sun Dec 13 19:10:20 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy