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Magnesium in PDB 1g8n: Molecular and Crystal Structure of D(CGCGAATF5UCGCG):5- Formyluridine/ Adenosine Base-Pairs in B-Dna

Protein crystallography data

The structure of Molecular and Crystal Structure of D(CGCGAATF5UCGCG):5- Formyluridine/ Adenosine Base-Pairs in B-Dna, PDB code: 1g8n was solved by M.Tsunoda, N.Karino, Y.Ueno, A.Matsuda, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 26.000, 39.500, 65.700, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 23.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Molecular and Crystal Structure of D(CGCGAATF5UCGCG):5- Formyluridine/ Adenosine Base-Pairs in B-Dna (pdb code 1g8n). 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 Molecular and Crystal Structure of D(CGCGAATF5UCGCG):5- Formyluridine/ Adenosine Base-Pairs in B-Dna, PDB code: 1g8n:

Magnesium binding site 1 out of 1 in 1g8n

Go back to Magnesium Binding Sites List in 1g8n
Magnesium binding site 1 out of 1 in the Molecular and Crystal Structure of D(CGCGAATF5UCGCG):5- Formyluridine/ Adenosine Base-Pairs in B-Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Molecular and Crystal Structure of D(CGCGAATF5UCGCG):5- Formyluridine/ Adenosine Base-Pairs in B-Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg25

b:13.2
occ:1.00
O A:HOH206 2.0 12.8 1.0
O A:HOH207 2.1 10.1 1.0
O A:HOH205 2.1 12.2 1.0
O A:HOH210 2.1 11.9 1.0
O A:HOH208 2.1 12.1 1.0
O A:HOH209 2.2 13.4 1.0
OP1 A:DA6 4.1 13.2 1.0
O A:HOH29 4.2 13.7 1.0
O A:HOH73 4.2 21.6 1.0
O A:HOH32 4.3 17.6 1.0
OP2 A:DT7 4.4 12.6 1.0
O A:HOH28 4.4 13.5 1.0
OP2 A:DA6 4.5 12.6 1.0
P A:DA6 4.6 12.2 1.0
O5' A:DA6 4.7 12.6 1.0
C3' A:DA6 4.9 12.4 1.0

Reference:

M.Tsunoda, N.Karino, Y.Ueno, A.Matsuda, A.Takenaka. Crystallization and Preliminary X-Ray Analysis of A Dna Dodecamer Containing 2'-Deoxy-5-Formyluridine; What Is the Role of Magnesium Cation in Crystallization of Dickerson-Type Dna Dodecamers? Acta Crystallogr.,Sect.D V. 57 345 2001.
ISSN: ISSN 0907-4449
PubMed: 11173500
DOI: 10.1107/S0907444900017583
Page generated: Mon Dec 14 05:57:29 2020

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