Zinc in PDB 7dq0: Crystal Structure of Actinomycin D-Echinomycin-D(Acgtgct/Agctcgt) Complex

Protein crystallography data

The structure of Crystal Structure of Actinomycin D-Echinomycin-D(Acgtgct/Agctcgt) Complex, PDB code: 7dq0 was solved by 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) 25.22 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 30.188, 30.188, 137.608, 90, 90, 90
R / Rfree (%) 23.2 / 24.9

Other elements in 7dq0:

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

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Actinomycin D-Echinomycin-D(Acgtgct/Agctcgt) Complex (pdb code 7dq0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Actinomycin D-Echinomycin-D(Acgtgct/Agctcgt) Complex, PDB code: 7dq0:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7dq0

Go back to Zinc Binding Sites List in 7dq0
Zinc binding site 1 out of 3 in the Crystal Structure of Actinomycin D-Echinomycin-D(Acgtgct/Agctcgt) 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(Acgtgct/Agctcgt) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:60.3
occ:1.00
O A:HOH205 1.7 35.3 1.0
N7 A:DA1 2.3 22.8 1.0
C5 A:DA1 3.3 21.2 1.0
C8 A:DA1 3.3 22.8 1.0
N6 A:DA1 3.4 19.3 1.0
C6 A:DA1 3.8 22.1 1.0
O A:HOH201 3.8 27.8 1.0
O A:HOH207 4.5 23.4 1.0
C4 A:DA1 4.5 22.2 1.0
N9 A:DA1 4.5 21.4 1.0
O6 A:DG2 4.9 18.8 1.0

Zinc binding site 2 out of 3 in 7dq0

Go back to Zinc Binding Sites List in 7dq0
Zinc binding site 2 out of 3 in the Crystal Structure of Actinomycin D-Echinomycin-D(Acgtgct/Agctcgt) 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(Acgtgct/Agctcgt) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:21.1
occ:1.00
N7 A:DG6 2.0 16.3 1.0
O A:HOH203 2.2 14.3 1.0
CL A:CL103 2.3 16.1 1.0
C8 A:DG6 2.9 16.5 1.0
C5 A:DG6 3.1 18.4 1.0
O6 A:DG6 3.5 15.0 1.0
C6 A:DG6 3.7 16.4 1.0
O D:HOH201 4.1 19.2 1.0
N9 A:DG6 4.1 21.1 1.0
C4 A:DG6 4.2 20.1 1.0
C5 A:DC5 4.3 17.9 1.0
N4 A:DC5 4.6 15.1 1.0
O A:HOH210 4.6 28.3 1.0
C4 A:DC5 4.8 17.0 1.0
O A:HOH215 4.9 34.3 1.0

Zinc binding site 3 out of 3 in 7dq0

Go back to Zinc Binding Sites List in 7dq0
Zinc binding site 3 out of 3 in the Crystal Structure of Actinomycin D-Echinomycin-D(Acgtgct/Agctcgt) 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(Acgtgct/Agctcgt) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:14.6
occ:0.49
O B:HOH202 2.1 12.2 1.0
N7 B:DG3 2.2 15.5 1.0
O B:HOH204 2.2 15.3 1.0
C8 B:DG3 3.1 16.2 1.0
C5 B:DG3 3.3 20.2 1.0
O6 B:DG3 3.7 12.3 1.0
C6 B:DG3 3.9 17.0 1.0
O B:HOH205 3.9 16.1 1.0
N9 B:DG3 4.3 20.2 1.0
N4 D:QUI102 4.3 22.5 1.0
C4 B:DG3 4.4 22.1 1.0
C3 D:QUI102 4.9 19.9 1.0
C5 B:DC2 4.9 15.9 1.0

Reference:

R.B.Satange, M.H.Hou. Crystal Structure of Actinomycin D-Echinomycin-D(Acgtgct/Agctcgt) Complex To Be Published.
Page generated: Thu Mar 31 05:21:53 2022

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