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Magnesium in PDB 9npv: [4,8,7-2] Shifted Tensegrity Triangle with An (Arm,Center,Arm) Distribution of (4,8,7) Base Pairs and 2 Nt Sticky Ends

Protein crystallography data

The structure of [4,8,7-2] Shifted Tensegrity Triangle with An (Arm,Center,Arm) Distribution of (4,8,7) Base Pairs and 2 Nt Sticky Ends, PDB code: 9npv was solved by A.Horvath, S.Vecchioni, K.Woloszyn, Y.P.Ohayon, R.Sha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.89 / 3.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 110.467, 110.467, 66.856, 90, 90, 120
R / Rfree (%) 18.7 / 22

Magnesium Binding Sites:

The binding sites of Magnesium atom in the [4,8,7-2] Shifted Tensegrity Triangle with An (Arm,Center,Arm) Distribution of (4,8,7) Base Pairs and 2 Nt Sticky Ends (pdb code 9npv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the [4,8,7-2] Shifted Tensegrity Triangle with An (Arm,Center,Arm) Distribution of (4,8,7) Base Pairs and 2 Nt Sticky Ends, PDB code: 9npv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 9npv

Go back to Magnesium Binding Sites List in 9npv
Magnesium binding site 1 out of 2 in the [4,8,7-2] Shifted Tensegrity Triangle with An (Arm,Center,Arm) Distribution of (4,8,7) Base Pairs and 2 Nt Sticky Ends


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of [4,8,7-2] Shifted Tensegrity Triangle with An (Arm,Center,Arm) Distribution of (4,8,7) Base Pairs and 2 Nt Sticky Ends within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:123.8
occ:1.00
O5' B:DG1 4.2 170.2 1.0
N7 B:DG3 4.4 148.1 1.0
O6 B:DG3 4.5 165.0 1.0
N7 B:DA2 4.6 139.9 1.0
O4 C:DT12 4.7 175.2 1.0
OP2 B:DA2 4.7 158.5 1.0
N6 B:DA4 4.8 183.5 1.0
C8 B:DA2 4.9 146.0 1.0

Magnesium binding site 2 out of 2 in 9npv

Go back to Magnesium Binding Sites List in 9npv
Magnesium binding site 2 out of 2 in the [4,8,7-2] Shifted Tensegrity Triangle with An (Arm,Center,Arm) Distribution of (4,8,7) Base Pairs and 2 Nt Sticky Ends


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of [4,8,7-2] Shifted Tensegrity Triangle with An (Arm,Center,Arm) Distribution of (4,8,7) Base Pairs and 2 Nt Sticky Ends within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:125.2
occ:1.00
OP1 B:DA2 4.2 170.1 1.0
O4' D:DT19 4.3 135.6 1.0
O4' C:DG8 4.4 193.6 1.0
C4' D:DT19 4.5 139.1 1.0
OP2 B:DG3 4.6 169.5 1.0
C4' C:DG8 4.6 168.5 1.0
N2 D:DG17 4.6 146.6 1.0
C1' D:DA18 4.8 170.9 1.0
C2' D:DA18 4.8 162.2 1.0
O5' B:DA2 4.8 163.8 1.0
C5' D:DT19 4.9 135.5 1.0
C5' C:DG8 5.0 133.0 1.0
O2 C:DC7 5.0 127.7 1.0

Reference:

A.Horvath, S.Vecchioni, K.Woloszyn, Y.P.Ohayon, R.Sha. Shifted Tensegrity Triangles To Be Published.
Page generated: Sat Aug 16 06:56:21 2025

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