Atomistry » Magnesium » PDB 1xyl-1ydf » 1y84
Atomistry »
  Magnesium »
    PDB 1xyl-1ydf »
      1y84 »

Magnesium in PDB 1y84: Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Imidazolyl)Ethyl] Thymidine (T*)

Protein crystallography data

The structure of Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Imidazolyl)Ethyl] Thymidine (T*), PDB code: 1y84 was solved by M.Egli, G.Minasov, V.Tereshko, P.S.Pallan, M.Teplova, G.B.Inamati, E.A.Lesnik, S.R.Owens, B.S.Ross, T.P.Prakash, M.Manoharan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 24.097, 43.071, 46.260, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Imidazolyl)Ethyl] Thymidine (T*) (pdb code 1y84). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Imidazolyl)Ethyl] Thymidine (T*), PDB code: 1y84:

Magnesium binding site 1 out of 1 in 1y84

Go back to Magnesium Binding Sites List in 1y84
Magnesium binding site 1 out of 1 in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Imidazolyl)Ethyl] Thymidine (T*)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Imidazolyl)Ethyl] Thymidine (T*) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:20.6
occ:1.00
O B:HOH107 2.0 23.7 1.0
O A:HOH104 2.0 23.1 1.0
O A:HOH103 2.0 24.5 1.0
O A:HOH106 2.1 19.0 1.0
O A:HOH102 2.1 14.7 1.0
O B:HOH105 2.3 26.5 1.0
O6 A:DG3 4.0 10.3 1.0
O B:HOH123 4.0 19.6 1.0
O A:HOH130 4.1 30.8 1.0
O A:HOH167 4.1 20.1 1.0
O A:HOH176 4.2 20.8 1.0
O B:HOH187 4.2 34.3 1.0
O A:HOH139 4.2 22.2 0.7
N7 A:DG3 4.3 9.6 1.0
O4 A:DT4 4.4 11.2 1.0
O4 B:EIT16 4.4 10.0 1.0
N6 A:DA5 4.4 8.8 1.0
O B:HOH153 4.5 21.6 1.0
C6 A:DG3 4.7 9.9 1.0
C5 A:DG3 4.8 10.0 1.0
O A:HOH175 4.8 23.1 1.0
N4 A:DC2 4.9 13.9 1.0
N6 B:DA17 4.9 10.5 1.0

Reference:

M.Egli, G.Minasov, V.Tereshko, P.S.Pallan, M.Teplova, G.B.Inamati, E.A.Lesnik, S.R.Owens, B.S.Ross, T.P.Prakash, M.Manoharan. Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the Rna Affinity, Nuclease Resistance, and Crystal Structure of Ten 2'-O-Ribonucleic Acid Modifications. Biochemistry V. 44 9045 2005.
ISSN: ISSN 0006-2960
PubMed: 15966728
DOI: 10.1021/BI050574M
Page generated: Sun Aug 10 07:42:32 2025

Last articles

Mg in 4AWN
Mg in 4AQY
Mg in 4APZ
Mg in 4AV6
Mg in 4AVA
Mg in 4AV3
Mg in 4AUX
Mg in 4ATB
Mg in 4AUI
Mg in 4AT9
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy