Atomistry » Manganese » PDB 5wly-5yvs » 5yty
Atomistry »
  Manganese »
    PDB 5wly-5yvs »
      5yty »

Manganese in PDB 5yty: Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex

Protein crystallography data

The structure of Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex, PDB code: 5yty was solved by M.H.Hou, P.C.Wu, Y.F.Kao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.60 / 1.58
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 46.362, 46.362, 48.005, 90.00, 90.00, 120.00
R / Rfree (%) 22.2 / 26.3

Other elements in 5yty:

The structure of Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex (pdb code 5yty). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex, PDB code: 5yty:

Manganese binding site 1 out of 1 in 5yty

Go back to Manganese Binding Sites List in 5yty
Manganese binding site 1 out of 1 in the Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Echinomycin-D(Acgacgt/Acgtcgt) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn101

b:11.5
occ:1.00
O B:HOH211 2.1 11.3 1.0
N7 B:DG3 2.2 11.0 1.0
C8 B:DG3 3.1 12.8 1.0
C5 B:DG3 3.3 13.0 1.0
O6 B:DG3 3.7 10.8 1.0
C6 B:DG3 3.9 10.0 1.0
O F:HOH202 4.2 20.9 1.0
N9 B:DG3 4.4 14.1 1.0
C4 B:DG3 4.5 15.3 1.0
OP2 B:DG3 4.5 14.9 1.0
N4 F:QUI101 4.9 15.4 1.0
C3 F:QUI101 5.0 14.1 1.0

Reference:

P.C.Wu, S.L.Tzeng, C.K.Chang, Y.F.Kao, M.J.Waring, M.H.Hou. Cooperative Recognition of T:T Mismatch By Echinomycin Causes Structural Distortions in Dna Duplex Nucleic Acids Res. V. 46 7396 2018.
ISSN: ESSN 1362-4962
PubMed: 29741655
DOI: 10.1093/NAR/GKY345
Page generated: Tue Dec 15 04:49:26 2020

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