Chlorine in PDB 4mgw: Comparison of the Structural and Dynamic Effects of 5-Methylcytosine and 5-Chlorocytosine in A Cpg Dinucleotide Sequence

The structure of Comparison of the Structural and Dynamic Effects of 5-Methylcytosine and 5-Chlorocytosine in A Cpg Dinucleotide Sequence, PDB code: 4mgw was solved by J.A.Theruvathu, Y.Whitney, B.Montgomery Pettitt, L.C.Sowers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.99 / 1.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.629, 39.918, 65.364, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 26.3

The structure of Comparison of the Structural and Dynamic Effects of 5-Methylcytosine and 5-Chlorocytosine in A Cpg Dinucleotide Sequence also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Chlorine atom in the Comparison of the Structural and Dynamic Effects of 5-Methylcytosine and 5-Chlorocytosine in A Cpg Dinucleotide Sequence (pdb code 4mgw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Comparison of the Structural and Dynamic Effects of 5-Methylcytosine and 5-Chlorocytosine in A Cpg Dinucleotide Sequence, PDB code: 4mgw:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Comparison of the Structural and Dynamic Effects of 5-Methylcytosine and 5-Chlorocytosine in A Cpg Dinucleotide Sequence


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Comparison of the Structural and Dynamic Effects of 5-Methylcytosine and 5-Chlorocytosine in A Cpg Dinucleotide Sequence within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl3 b:50.4 occ:1.00 CL A:2GF3 0.0 50.4 1.0 C5 A:2GF3 1.7 35.3 1.0 H41 A:2GF3 2.6 37.4 1.0 C6 A:2GF3 2.7 30.8 1.0 C4 A:2GF3 2.7 31.1 1.0 H6 A:2GF3 2.8 37.0 1.0 N4 A:2GF3 3.0 31.2 1.0 O A:HOH218 3.0 52.5 1.0 H2'' A:DG2 3.1 45.3 1.0 H2' A:DG2 3.6 45.3 1.0 O B:HOH116 3.7 37.0 1.0 C2' A:DG2 3.8 37.7 1.0 H42 A:2GF3 3.9 37.4 1.0 H8 A:DG2 3.9 40.3 1.0 N1 A:2GF3 4.0 28.7 1.0 N3 A:2GF3 4.0 32.0 1.0 C8 A:DG2 4.0 33.6 1.0 N9 A:DG2 4.2 34.8 1.0 C1' A:DG2 4.4 35.0 1.0 C2 A:2GF3 4.5 29.3 1.0 O6 A:DG4 4.5 35.3 1.0 H1' A:DG2 4.6 42.0 1.0 N7 A:DG2 4.6 32.6 1.0 H2' A:2GF3 4.8 45.3 1.0 OP2 A:2GF3 4.8 44.0 1.0 C4 A:DG2 5.0 31.8 1.0

Chlorine binding site 2 out of 2 in the Comparison of the Structural and Dynamic Effects of 5-Methylcytosine and 5-Chlorocytosine in A Cpg Dinucleotide Sequence


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Comparison of the Structural and Dynamic Effects of 5-Methylcytosine and 5-Chlorocytosine in A Cpg Dinucleotide Sequence within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl15 b:54.6 occ:1.00 CL B:2GF15 0.0 54.6 1.0 C5 B:2GF15 1.7 37.7 1.0 H42 B:2GF15 2.6 40.6 1.0 C6 B:2GF15 2.7 31.9 1.0 C4 B:2GF15 2.7 32.6 1.0 H6 B:2GF15 2.8 38.2 1.0 H2' B:DG14 2.9 50.5 1.0 N4 B:2GF15 3.0 33.8 1.0 C2' B:DG14 3.8 42.1 1.0 H2'' B:DG14 3.8 50.5 1.0 H41 B:2GF15 3.9 40.6 1.0 N3 B:2GF15 4.0 30.4 1.0 N1 B:2GF15 4.0 31.7 1.0 H8 B:DG14 4.1 42.6 1.0 C8 B:DG14 4.2 35.5 1.0 H3' B:DG14 4.3 44.2 1.0 OP2 B:2GF15 4.4 37.9 1.0 C2 B:2GF15 4.5 27.9 1.0 N9 B:DG14 4.5 37.3 1.0 N7 B:DG14 4.6 38.5 1.0 C3' B:DG14 4.6 36.8 1.0 C1' B:DG14 4.8 37.6 1.0 O5' B:2GF15 4.9 36.0 1.0 H2' B:2GF15 4.9 41.6 1.0

J.A.Theruvathu, Y.W.Yin, B.M.Pettitt, L.C.Sowers. Comparison of the Structural and Dynamic Effects of 5-Methylcytosine and 5-Chlorocytosine in A Cpg Dinucleotide Sequence. Biochemistry V. 52 8590 2013.
ISSN: ISSN 0006-2960
PubMed: 24147911
DOI: 10.1021/BI400980C