Zinc in PDB 7x97: Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex

Protein crystallography data

The structure of Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex, PDB code: 7x97 was solved by S.H.Kao, R.B.Satange, M.H.Hou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.57 / 1.95
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 43.452, 43.452, 139.365, 90, 90, 120
R / Rfree (%) 22.9 / 28.2

Other elements in 7x97:

The structure of Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex (pdb code 7x97). 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 Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex, PDB code: 7x97:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 7x97

Go back to Zinc Binding Sites List in 7x97
Zinc binding site 1 out of 5 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex


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 Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:54.9
occ:0.33
O A:HOH214 2.6 19.6 1.0
O A:HOH210 4.3 21.9 1.0
C5 A:DC4 4.5 14.1 1.0
C6 A:DC4 4.9 14.2 1.0

Zinc binding site 2 out of 5 in 7x97

Go back to Zinc Binding Sites List in 7x97
Zinc binding site 2 out of 5 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex


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 Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:55.6
occ:1.00
N7 A:DA1 2.4 38.2 1.0
N6 A:DA1 3.3 37.7 1.0
C5 A:DA1 3.3 37.3 1.0
C8 A:DA1 3.5 38.4 1.0
C6 A:DA1 3.7 36.9 1.0
O6 A:DG2 4.1 23.0 1.0
C4 A:DA1 4.6 36.8 1.0
N9 A:DA1 4.6 37.8 1.0
N4 B:DC6 4.9 29.8 1.0

Zinc binding site 3 out of 5 in 7x97

Go back to Zinc Binding Sites List in 7x97
Zinc binding site 3 out of 5 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex


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 Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn103

b:116.6
occ:1.00
N7 A:DG6 2.5 17.5 1.0
C5 A:DG6 3.5 16.1 1.0
C8 A:DG6 3.5 18.2 1.0
O6 A:DG6 3.5 15.3 1.0
C6 A:DG6 3.9 15.4 1.0
N4 G:QUI102 4.7 11.4 1.0
N9 A:DG6 4.7 18.1 1.0
C4 A:DG6 4.7 16.5 1.0
C3 G:QUI102 5.0 11.1 1.0

Zinc binding site 4 out of 5 in 7x97

Go back to Zinc Binding Sites List in 7x97
Zinc binding site 4 out of 5 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex


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 Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:16.1
occ:1.00
O B:HOH205 2.1 13.5 1.0
O B:HOH206 2.1 7.2 1.0
N7 B:DG4 2.2 20.6 1.0
C8 B:DG4 3.1 23.6 1.0
C5 B:DG4 3.3 19.6 1.0
O6 B:DG4 3.7 20.1 1.0
C6 B:DG4 3.9 19.7 1.0
O B:HOH204 4.0 16.4 1.0
O6 B:DG5 4.2 20.5 1.0
OP2 B:DG4 4.4 27.6 1.0
N9 B:DG4 4.4 22.9 1.0
C4 B:DG4 4.5 19.6 1.0

Zinc binding site 5 out of 5 in 7x97

Go back to Zinc Binding Sites List in 7x97
Zinc binding site 5 out of 5 in the Crystal Structure of Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex


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 Actinomycin D-Echinomycin-D(Agcccgt/Acgggct) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn102

b:16.6
occ:1.00
N7 B:DG3 2.0 20.5 1.0
CL B:CL103 2.2 28.2 1.0
C8 B:DG3 2.9 21.3 1.0
C5 B:DG3 3.1 19.7 1.0
O6 B:DG3 3.5 18.3 1.0
C6 B:DG3 3.7 20.6 1.0
O G:HOH201 4.1 13.8 1.0
N9 B:DG3 4.1 21.0 1.0
C4 B:DG3 4.2 20.0 1.0
C5 B:DC2 4.8 21.1 1.0
C6 B:DC2 4.8 22.2 1.0

Reference:

R.Satange, S.H.Kao, C.M.Chien, S.H.Chou, C.C.Lin, S.Neidle, M.H.Hou. Staggered Intercalation of Dna Duplexes with Base-Pair Modulation By Two Distinct Drug Molecules Induces Asymmetric Backbone Twisting and Structure Polymorphism. Nucleic Acids Res. V. 50 8867 2022.
ISSN: ESSN 1362-4962
PubMed: 35871296
DOI: 10.1093/NAR/GKAC629
Page generated: Sat Apr 8 05:36:46 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy