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Magnesium in PDB 3hxm: Structure of An Argonaute Complexed with Guide Dna and Target Rna Duplex Containing Two Mismatches.

Protein crystallography data

The structure of Structure of An Argonaute Complexed with Guide Dna and Target Rna Duplex Containing Two Mismatches., PDB code: 3hxm was solved by Y.Wang, H.Li, G.Sheng, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 121.839, 118.867, 59.186, 90.00, 114.79, 90.00
R / Rfree (%) 22.1 / 27.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of An Argonaute Complexed with Guide Dna and Target Rna Duplex Containing Two Mismatches. (pdb code 3hxm). 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 Structure of An Argonaute Complexed with Guide Dna and Target Rna Duplex Containing Two Mismatches., PDB code: 3hxm:

Magnesium binding site 1 out of 1 in 3hxm

Go back to Magnesium Binding Sites List in 3hxm
Magnesium binding site 1 out of 1 in the Structure of An Argonaute Complexed with Guide Dna and Target Rna Duplex Containing Two Mismatches.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of An Argonaute Complexed with Guide Dna and Target Rna Duplex Containing Two Mismatches. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg30

b:15.3
occ:1.00
OP1 C:DA3 2.2 51.1 1.0
O A:VAL685 2.5 54.0 1.0
OXT A:VAL685 2.5 54.5 1.0
OP3 C:DT1 2.8 55.6 1.0
C A:VAL685 2.8 52.8 1.0
P C:DT1 3.2 58.8 1.0
OP1 C:DT1 3.2 57.7 1.0
O5' C:DT1 3.3 55.1 1.0
P C:DA3 3.4 52.4 1.0
OE1 A:GLN433 3.4 39.8 1.0
NZ A:LYS457 3.6 41.9 1.0
O3' C:DG2 3.7 53.2 1.0
NE2 A:GLN433 4.1 42.7 1.0
C5' C:DT1 4.2 59.1 1.0
CD A:GLN433 4.2 41.2 1.0
OP2 C:DA3 4.2 52.8 1.0
CA A:VAL685 4.3 51.5 1.0
CE A:LYS457 4.6 41.3 1.0
O5' C:DA3 4.7 50.8 1.0
OP2 C:DT1 4.7 62.5 1.0
CG2 A:VAL685 4.8 52.2 1.0
C5' C:DA3 4.9 49.8 1.0
CB A:VAL685 4.9 52.2 1.0

Reference:

Y.Wang, S.Juranek, H.Li, G.Sheng, G.S.Wardle, T.Tuschl, D.J.Patel. Nucleation, Propagation and Cleavage of Target Rnas in Ago Silencing Complexes. Nature V. 461 754 2009.
ISSN: ISSN 0028-0836
PubMed: 19812667
DOI: 10.1038/NATURE08434
Page generated: Mon Dec 14 08:15:01 2020

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