Magnesium in PDB 5w1z: Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)

Protein crystallography data

The structure of Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4), PDB code: 5w1z was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.24 / 1.55
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 24.884, 32.798, 34.034, 90.25, 107.32, 111.04
R / Rfree (%) 20.7 / 23.4

Other elements in 5w1z:

The structure of Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4) also contains other interesting chemical elements:

Bromine (Br) 4 atoms
Sodium (Na) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4) (pdb code 5w1z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4), PDB code: 5w1z:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5w1z

Go back to Magnesium Binding Sites List in 5w1z
Magnesium binding site 1 out of 3 in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:27.9
occ:0.70
O A:HOH203 1.9 16.2 0.5
O A:HOH233 2.0 31.6 1.0
O A:HOH231 2.2 11.0 0.3
O2 A:DC1 4.1 20.4 1.0
C5' A:DC2 4.3 23.5 1.0
O4' A:DC2 4.4 20.0 1.0
C4' A:DC2 4.5 23.6 1.0

Magnesium binding site 2 out of 3 in 5w1z

Go back to Magnesium Binding Sites List in 5w1z
Magnesium binding site 2 out of 3 in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:23.0
occ:1.00
O C:HOH223 1.9 24.4 1.0
O D:HOH213 2.2 21.9 1.0
O C:HOH224 2.2 27.5 1.0
O D:HOH233 2.2 24.4 1.0
O C:HOH209 2.3 23.5 1.0
O4' D:DA13 4.1 25.2 1.0
O D:HOH211 4.1 27.0 1.0
O D:HOH212 4.3 16.5 0.5
N3 C:DI10 4.3 19.1 1.0
O2 D:DC12 4.3 19.0 1.0
C4' D:DA13 4.6 27.1 1.0
O4' C:DI10 4.6 20.7 1.0
O3' C:DI10 4.7 24.3 1.0
C1' C:DI10 4.8 20.2 1.0
C4' C:DI10 4.9 22.4 1.0
C2 C:DI10 4.9 20.1 1.0
O4' D:DC12 5.0 24.1 0.5

Magnesium binding site 3 out of 3 in 5w1z

Go back to Magnesium Binding Sites List in 5w1z
Magnesium binding site 3 out of 3 in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:33.7
occ:1.00
O D:HOH228 2.1 33.8 1.0
O D:HOH212 4.2 16.5 0.5
OP1 D:DC12 4.3 28.6 0.5
OP1 D:DC12 4.5 29.5 0.5
C5' D:DC12 4.5 26.7 0.5
O3' D:DC11 4.6 29.2 1.0
C5' D:DC12 4.8 27.0 0.5

Reference:

J.P.Peters, E.A.Kowal, P.S.Pallan, M.Egli, L.J.Maher 3Rd.. Comparative Analysis of Inosine-Substituted Duplex Dna By Circular Dichroism and X-Ray Crystallography. J. Biomol. Struct. Dyn. V. 36 2753 2018.
ISSN: ESSN 1538-0254
PubMed: 28818035
DOI: 10.1080/07391102.2017.1369164
Page generated: Mon Dec 14 21:20:03 2020

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