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Magnesium in PDB 4rnk: Sequence and Structure of A Self-Assembled 3-D Dna Crystal: D(Ggaaaatttggag)

Protein crystallography data

The structure of Sequence and Structure of A Self-Assembled 3-D Dna Crystal: D(Ggaaaatttggag), PDB code: 4rnk was solved by M.M.Saoji, P.J.Paukstelis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.41 / 2.08
Space group P 64
Cell size a, b, c (Å), α, β, γ (°) 39.729, 39.729, 55.989, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Sequence and Structure of A Self-Assembled 3-D Dna Crystal: D(Ggaaaatttggag) (pdb code 4rnk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Sequence and Structure of A Self-Assembled 3-D Dna Crystal: D(Ggaaaatttggag), PDB code: 4rnk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4rnk

Go back to Magnesium Binding Sites List in 4rnk
Magnesium binding site 1 out of 2 in the Sequence and Structure of A Self-Assembled 3-D Dna Crystal: D(Ggaaaatttggag)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sequence and Structure of A Self-Assembled 3-D Dna Crystal: D(Ggaaaatttggag) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:74.0
occ:1.00
O A:HOH207 1.9 58.8 1.0
O A:HOH206 2.1 77.0 1.0
OP1 A:DA3 4.0 55.2 1.0
OP2 A:DA3 4.1 54.1 1.0
P A:DA3 4.6 52.6 1.0
C3' A:DG2 5.0 50.3 1.0

Magnesium binding site 2 out of 2 in 4rnk

Go back to Magnesium Binding Sites List in 4rnk
Magnesium binding site 2 out of 2 in the Sequence and Structure of A Self-Assembled 3-D Dna Crystal: D(Ggaaaatttggag)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sequence and Structure of A Self-Assembled 3-D Dna Crystal: D(Ggaaaatttggag) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:62.9
occ:1.00
O A:HOH209 2.5 50.5 1.0
C5' A:DA3 3.7 51.4 1.0
O4' A:DA3 3.9 47.6 1.0
C4' A:DG2 4.0 51.3 1.0
O4' A:DG2 4.1 48.6 1.0
C4' A:DA3 4.1 49.9 1.0
O3' A:DG2 4.3 51.8 1.0
O5' A:DA3 4.7 52.0 1.0
C1' A:DG2 4.7 47.2 1.0
C5' A:DG2 4.8 55.3 1.0
C3' A:DG2 4.9 50.3 1.0

Reference:

M.Saoji, D.Zhang, P.J.Paukstelis. Probing the Role of Sequence in the Assembly of Three-Dimensional Dna Crystals. Biopolymers V. 103 618 2015.
ISSN: ISSN 0006-3525
PubMed: 26015367
DOI: 10.1002/BIP.22688
Page generated: Tue Aug 20 03:13:41 2024

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