Magnesium in PDB 8e5d: Crystal Structure of Double-Stranded Dna Deaminase Toxin Ddda in Complex with Dna with the Target Cytosine Parked in the Major Groove

The structure of Crystal Structure of Double-Stranded Dna Deaminase Toxin Ddda in Complex with Dna with the Target Cytosine Parked in the Major Groove, PDB code: 8e5d was solved by L.L.Yin, K.Shi, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.77 / 2.39
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	31.699, 94.611, 138.465, 90, 90, 90
R / Rfree (%)	19.8 / 23.3

The structure of Crystal Structure of Double-Stranded Dna Deaminase Toxin Ddda in Complex with Dna with the Target Cytosine Parked in the Major Groove also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Double-Stranded Dna Deaminase Toxin Ddda in Complex with Dna with the Target Cytosine Parked in the Major Groove (pdb code 8e5d). 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 Crystal Structure of Double-Stranded Dna Deaminase Toxin Ddda in Complex with Dna with the Target Cytosine Parked in the Major Groove, PDB code: 8e5d:

Magnesium binding site 1 out of 1 in the Crystal Structure of Double-Stranded Dna Deaminase Toxin Ddda in Complex with Dna with the Target Cytosine Parked in the Major Groove


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 Double-Stranded Dna Deaminase Toxin Ddda in Complex with Dna with the Target Cytosine Parked in the Major Groove within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1502 b:49.1 occ:1.00 O A:ASN1417 2.3 48.5 1.0 OD1 A:ASN1415 2.4 50.0 1.0 O A:ASN1415 2.4 56.5 1.0 O A:LEU1384 2.4 38.1 1.0 O A:THR1382 2.4 38.1 1.0 O A:GLU1381 2.5 36.7 1.0 C A:THR1382 3.2 44.9 1.0 C A:ASN1415 3.3 46.9 1.0 C A:ASN1417 3.4 41.4 1.0 CA A:THR1382 3.4 34.7 1.0 CG A:ASN1415 3.4 52.9 1.0 N A:ASN1415 3.5 38.9 1.0 C A:GLU1381 3.6 37.9 1.0 C A:LEU1384 3.6 41.1 1.0 NH2 A:ARG1355 3.8 39.9 1.0 N A:ASN1417 3.8 45.7 1.0 CA A:ASN1415 3.9 41.9 1.0 N A:THR1382 4.0 39.2 1.0 N A:LEU1384 4.1 39.5 1.0 CA A:ASN1417 4.1 37.8 1.0 CB A:ASN1415 4.3 37.8 1.0 N A:LEU1383 4.3 43.0 1.0 ND2 A:ASN1415 4.3 42.6 1.0 N A:SER1416 4.4 53.1 1.0 C A:SER1416 4.4 37.2 1.0 CA A:LEU1384 4.4 31.1 1.0 N A:SER1418 4.4 38.8 1.0 C A:LEU1383 4.4 36.5 1.0 C A:GLY1414 4.5 41.7 1.0 CB A:ASN1417 4.6 44.0 1.0 N A:PRO1385 4.6 32.7 1.0 CA A:PRO1385 4.7 29.9 1.0 CA A:SER1418 4.7 43.1 1.0 CB A:THR1382 4.7 33.8 1.0 CA A:GLY1414 4.8 40.1 1.0 CA A:SER1416 4.8 49.8 1.0 C A:PRO1385 4.8 39.9 1.0 O A:LEU1383 4.8 47.7 1.0 CB A:LEU1384 4.9 28.5 1.0 CA A:LEU1383 4.9 33.8 1.0 CG2 A:THR1382 4.9 36.3 1.0 CA A:GLU1381 4.9 35.9 1.0 N A:GLU1386 5.0 44.7 1.0

L.L.Yin, K.Shi, H.Aihara. Structural Basis of Sequence-Specific Cytosine Deamination By Double-Stranded Dna Deaminase Toxin Ddda To Be Published.