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Magnesium in PDB 3jxq: X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2

Protein crystallography data

The structure of X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2, PDB code: 3jxq was solved by D.A.Adamiak, J.Milecki, R.W.Adamiak, W.Rypniewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.45
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 21.224, 26.486, 29.310, 97.56, 105.47, 109.38
R / Rfree (%) 17.1 / 20.5

Other elements in 3jxq:

The structure of X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2 also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2 (pdb code 3jxq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2, PDB code: 3jxq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3jxq

Go back to Magnesium Binding Sites List in 3jxq
Magnesium binding site 1 out of 4 in the X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg7

b:25.0
occ:0.83
O A:HOH119 1.9 29.4 1.0
O A:HOH118 2.0 28.0 1.0
O A:HOH18 2.3 22.1 1.0
O A:HOH109 2.3 34.4 1.0
O B:HOH93 3.7 34.8 1.0
O A:HOH21 3.8 24.5 1.0
O B:HOH40 3.9 24.2 1.0
O A:HOH32 4.0 21.5 1.0
O A:HOH97 4.1 39.7 1.0
O6 A:G4 4.2 13.7 1.0
N4 A:C3 4.3 13.6 1.0
O A:HOH24 4.3 24.1 1.0
O A:HOH129 4.4 41.0 1.0
N7 A:G4 4.6 14.6 1.0
O A:HOH51 4.6 28.8 1.0
C5 A:C3 4.7 14.0 1.0
O A:HOH81 4.8 44.6 1.0
O B:HOH110 4.9 36.6 1.0
C4 A:C3 4.9 14.6 1.0

Magnesium binding site 2 out of 4 in 3jxq

Go back to Magnesium Binding Sites List in 3jxq
Magnesium binding site 2 out of 4 in the X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg7

b:44.1
occ:0.83
O B:HOH121 1.7 19.7 1.0
O B:HOH132 1.9 8.0 1.0
O B:HOH120 2.2 29.2 1.0
O B:HOH108 2.2 35.0 1.0
O B:HOH71 2.3 22.0 1.0
O B:HOH10 2.4 19.1 1.0
O A:HOH10 3.8 18.7 1.0
O A:HOH8 3.9 15.0 1.0
O4' B:G4 4.8 14.4 1.0
O2' B:G4 4.9 14.4 1.0

Magnesium binding site 3 out of 4 in 3jxq

Go back to Magnesium Binding Sites List in 3jxq
Magnesium binding site 3 out of 4 in the X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg7

b:40.0
occ:0.83
O K:HOH115 2.1 21.4 1.0
O K:HOH41 2.2 24.1 1.0
O B:HOH96 2.3 26.9 1.0
O B:HOH53 2.4 34.9 1.0
O B:HOH94 2.5 30.7 1.0
O K:HOH64 4.0 31.4 1.0
O6 K:G6 4.1 15.8 1.0
O B:HOH12 4.1 22.2 1.0
O K:HOH8 4.3 17.6 1.0
O B:HOH34 4.4 29.3 1.0
N7 K:G6 4.5 14.5 1.0
O B:HOH101 4.5 28.6 1.0
O B:HOH43 4.5 28.8 1.0
O K:HOH73 4.6 27.1 1.0
N4 B:5CF5 4.7 14.4 1.0
O6 B:G6 4.7 24.8 1.0
O K:HOH46 4.7 31.6 1.0
F5 K:5CF5 4.8 15.9 1.0
C6 K:G6 4.9 13.5 1.0
F5 B:5CF5 4.9 15.1 1.0
O B:HOH84 4.9 28.7 1.0

Magnesium binding site 4 out of 4 in 3jxq

Go back to Magnesium Binding Sites List in 3jxq
Magnesium binding site 4 out of 4 in the X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg7

b:36.2
occ:0.83
O L:HOH123 2.2 30.4 1.0
OP2 L:G6 2.2 23.3 1.0
O L:HOH122 2.2 30.5 1.0
O L:HOH116 2.2 31.6 1.0
O L:HOH112 2.3 38.6 1.0
P L:G6 3.6 25.7 1.0
O L:HOH86 4.0 33.0 1.0
OP2 L:5CF5 4.2 22.3 1.0
OP1 L:G6 4.4 32.0 1.0
O5' L:5CF5 4.4 18.9 1.0
O3' L:5CF5 4.4 27.8 1.0
C3' L:5CF5 4.5 22.4 1.0
O5' L:G6 4.5 23.0 1.0
OP1 L:5CF5 4.6 28.9 1.0
P L:5CF5 4.6 22.2 1.0

Reference:

D.A.Adamiak, J.Milecki, R.W.Adamiak, W.Rypniewski. The Hydration and Unusual Hydrogen Bonding in the Crystal Structure of An Rna Duplex Containing Alternating Cg Base Pairs New J.Chem. V. 34 903 2010.
ISSN: ISSN 1144-0546
DOI: 10.1039/B9NJ00601J
Page generated: Mon Dec 14 08:20:53 2020

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