Atomistry » Magnesium » PDB 1xyl-1ydf » 1y95
Atomistry »
  Magnesium »
    PDB 1xyl-1ydf »
      1y95 »

Magnesium in PDB 1y95: Hiv-1 Dis(Mal) Duplex Pb-Soaked

Protein crystallography data

The structure of Hiv-1 Dis(Mal) Duplex Pb-Soaked, PDB code: 1y95 was solved by E.Ennifar, P.Walter, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.97 / 2.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 59.200, 59.200, 65.800, 90.00, 90.00, 120.00
R / Rfree (%) 22.6 / 25.3

Other elements in 1y95:

The structure of Hiv-1 Dis(Mal) Duplex Pb-Soaked also contains other interesting chemical elements:

Lead (Pb) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Hiv-1 Dis(Mal) Duplex Pb-Soaked (pdb code 1y95). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Hiv-1 Dis(Mal) Duplex Pb-Soaked, PDB code: 1y95:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 1y95

Go back to Magnesium Binding Sites List in 1y95
Magnesium binding site 1 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hiv-1 Dis(Mal) Duplex Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg30

b:56.9
occ:1.00
 O6 A:G7 3.8 53.4 1.0
N7 A:G7 3.9 54.2 1.0
O4 A:U6 4.0 51.5 1.0
O B:HOH126 4.0 77.0 0.8
C5 A:U6 4.5 49.4 1.0
C4 A:U6 4.5 49.8 1.0
C6 A:G7 4.5 53.9 1.0
C5 A:G7 4.6 54.1 1.0

Magnesium binding site 2 out of 10 in 1y95

Go back to Magnesium Binding Sites List in 1y95
Magnesium binding site 2 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hiv-1 Dis(Mal) Duplex Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg32

b:46.0
occ:1.00
 MG B:MG41 2.1 63.4 0.8
O6 A:G4 2.9 53.8 1.0
O4 A:U3 3.1 54.7 1.0
MG A:MG40 3.6 67.1 1.0
C4 A:U3 3.9 54.6 1.0
C6 A:G4 4.0 54.7 1.0
C5 A:U3 4.3 55.4 1.0
N7 A:G4 4.5 56.5 1.0
C5 A:G4 4.6 55.7 1.0
N6 B:A21 4.7 49.9 1.0
N4 A:C5 4.7 54.0 1.0
N4 B:C20 4.8 55.6 1.0
O6 B:G19 4.9 44.4 1.0
N3 A:U3 5.0 54.1 1.0

Magnesium binding site 3 out of 10 in 1y95

Go back to Magnesium Binding Sites List in 1y95
Magnesium binding site 3 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hiv-1 Dis(Mal) Duplex Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg37

b:50.0
occ:0.98
 O B:HOH143 3.4 68.0 0.8
O6 A:G12 3.7 51.9 1.0
O4 A:U11 3.9 52.6 1.0
C4 A:U11 4.5 52.9 1.0
C6 A:G12 4.7 52.1 1.0
O6 B:G12 4.7 55.5 1.0
N7 A:G12 4.7 53.0 1.0
C5 A:U11 4.8 52.7 1.0
N4 A:C13 4.9 58.8 1.0
N4 B:C13 5.0 56.6 1.0

Magnesium binding site 4 out of 10 in 1y95

Go back to Magnesium Binding Sites List in 1y95
Magnesium binding site 4 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hiv-1 Dis(Mal) Duplex Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg38

b:57.4
occ:0.98
 N7 A:G23 3.7 40.6 1.0
O6 A:G23 3.8 41.5 1.0
N7 A:A22 4.4 41.2 1.0
C5 A:G23 4.5 39.9 1.0
C6 A:G23 4.5 39.9 1.0
C8 A:G23 4.8 39.8 1.0

Magnesium binding site 5 out of 10 in 1y95

Go back to Magnesium Binding Sites List in 1y95
Magnesium binding site 5 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Hiv-1 Dis(Mal) Duplex Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg40

b:67.1
occ:1.00
 N7 A:G4 3.4 56.5 1.0
MG A:MG32 3.6 46.0 1.0
OP2 A:G4 3.8 62.5 1.0
C5 A:U3 3.8 55.4 1.0
C8 A:G4 4.2 57.5 1.0
C6 A:U3 4.3 55.7 1.0
C4 A:U3 4.4 54.6 1.0
C5 A:G4 4.6 55.7 1.0
OP2 A:U3 4.6 58.9 1.0
O4 A:U3 4.6 54.7 1.0
O6 A:G4 4.7 53.8 1.0

Magnesium binding site 6 out of 10 in 1y95

Go back to Magnesium Binding Sites List in 1y95
Magnesium binding site 6 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Hiv-1 Dis(Mal) Duplex Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg43

b:39.5
occ:1.00
 N7 A:G19 3.7 37.4 1.0
N7 A:A18 4.1 48.8 1.0
N4 A:C20 4.2 42.2 1.0
MG B:MG33 4.2 34.9 1.0
O6 A:G19 4.3 38.5 1.0
C8 A:A18 4.6 47.6 1.0
C8 A:G19 4.6 37.9 1.0
C5 A:G19 4.6 37.2 1.0
C5 A:A18 4.7 47.0 1.0
C6 A:G19 4.9 38.2 1.0
OP2 A:A18 4.9 50.7 1.0
N6 A:A18 5.0 43.7 1.0

Magnesium binding site 7 out of 10 in 1y95

Go back to Magnesium Binding Sites List in 1y95
Magnesium binding site 7 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Hiv-1 Dis(Mal) Duplex Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg33

b:34.9
occ:1.00
 O B:HOH127 3.3 47.9 1.0
O6 B:G4 3.4 42.9 1.0
O4 B:U3 3.4 50.5 1.0
C4 B:U3 4.2 48.3 1.0
MG A:MG43 4.2 39.5 1.0
C6 B:G4 4.4 41.6 1.0
C5 B:U3 4.5 47.3 1.0
N7 B:G4 4.5 41.8 1.0
N4 A:C20 4.9 42.2 1.0
C5 B:G4 4.9 41.0 1.0

Magnesium binding site 8 out of 10 in 1y95

Go back to Magnesium Binding Sites List in 1y95
Magnesium binding site 8 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Hiv-1 Dis(Mal) Duplex Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg34

b:67.1
occ:1.00
 O B:HOH116 2.5 41.2 1.0
O6 B:G7 3.2 50.8 0.5
O6 B:G7 3.5 47.7 0.5
O4 B:U6 3.6 39.8 1.0
N4 A:C17 4.3 44.4 1.0
C6 B:G7 4.3 49.2 0.5
C4 B:U6 4.4 36.4 1.0
N7 B:G7 4.4 46.7 0.5
C6 B:G7 4.5 47.0 0.5
N6 A:A16 4.6 48.4 1.0
N7 B:G7 4.7 47.9 0.5
C5 B:G7 4.8 46.9 0.5
C5 B:G7 4.9 48.5 0.5
C5 B:U6 4.9 36.4 1.0
O B:HOH123 4.9 44.7 0.8
N6 A:A18 4.9 43.7 1.0

Magnesium binding site 9 out of 10 in 1y95

Go back to Magnesium Binding Sites List in 1y95
Magnesium binding site 9 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Hiv-1 Dis(Mal) Duplex Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg41

b:63.4
occ:0.79
 MG A:MG32 2.1 46.0 1.0
O6 A:G4 3.7 53.8 1.0
O6 B:G19 3.9 44.4 1.0
N4 B:C20 4.1 55.6 1.0
N6 B:A18 4.5 51.0 1.0
N7 B:A18 4.6 53.3 1.0
N7 B:G19 4.7 47.6 1.0
N4 A:C5 4.8 54.0 1.0
O4 A:U3 4.8 54.7 1.0
C6 B:G19 4.9 44.9 1.0
C6 A:G4 4.9 54.7 1.0

Magnesium binding site 10 out of 10 in 1y95

Go back to Magnesium Binding Sites List in 1y95
Magnesium binding site 10 out of 10 in the Hiv-1 Dis(Mal) Duplex Pb-Soaked


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Hiv-1 Dis(Mal) Duplex Pb-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg42

b:56.5
occ:0.88
 O B:HOH119 4.0 35.0 0.9
O5' B:C1 4.8 52.0 1.0

Reference:

E.Ennifar, P.Walter, P.Dumas. A Crystallographic Study of the Binding of 13 Metal Ions to Two Related Rna Duplexes Nucleic Acids Res. V. 31 2671 2003.
ISSN: ISSN 0305-1048
PubMed: 12736317
DOI: 10.1093/NAR/GKG350
Page generated: Mon Dec 14 07:06:35 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