Iodine in PDB 7l4h: Crystal Structure of the DRM2-Ctg Dna Complex

All present enzymatic activity of Crystal Structure of the DRM2-Ctg Dna Complex:
2.1.1.37;

The structure of Crystal Structure of the DRM2-Ctg Dna Complex, PDB code: 7l4h was solved by J.Fang, J.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	115.19 / 2.56
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	116.888, 230.379, 54.244, 90, 90, 90
R / Rfree (%)	20.9 / 24.8

The structure of Crystal Structure of the DRM2-Ctg Dna Complex also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Iodine atom in the Crystal Structure of the DRM2-Ctg Dna Complex (pdb code 7l4h). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Crystal Structure of the DRM2-Ctg Dna Complex, PDB code: 7l4h:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in the Crystal Structure of the DRM2-Ctg Dna Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of the DRM2-Ctg Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I1006 b:85.9 occ:1.00 NH1 A:ARG471 3.7 58.9 1.0 CG A:PRO450 3.8 58.9 1.0 CG A:ARG471 3.9 53.6 1.0 CB A:ARG471 4.0 52.7 1.0 NH1 A:ARG474 4.1 69.1 1.0 NH2 A:ARG465 4.1 65.8 1.0 CD A:ARG471 4.2 59.2 1.0 CD A:PRO450 4.3 63.0 1.0 CB A:PRO450 4.3 61.1 1.0 CD A:ARG474 4.3 64.9 1.0 CA A:ARG471 4.5 55.4 1.0 CZ A:ARG474 4.6 61.0 1.0 NE A:ARG474 4.7 64.4 1.0 CZ A:ARG465 4.7 69.7 1.0 CZ A:ARG471 4.8 60.5 1.0 NE A:ARG471 4.9 61.3 1.0

Iodine binding site 2 out of 5 in the Crystal Structure of the DRM2-Ctg Dna Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of the DRM2-Ctg Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I1007 b:73.4 occ:1.00 CB A:PRO586 3.9 50.6 1.0 C8 A:SAH1001 3.9 49.7 1.0 O A:HOH1134 4.0 58.4 1.0 CG A:GLN605 4.2 48.0 1.0 CG A:PRO586 4.2 49.5 1.0 C2' A:SAH1001 4.2 50.5 1.0 CB A:GLN605 4.5 55.8 1.0 C3' A:SAH1001 4.6 52.0 1.0 CA A:PRO586 4.8 56.4 1.0 CG A:ASN588 4.8 79.8 1.0 N7 A:SAH1001 4.8 45.9 1.0 N9 A:SAH1001 4.9 49.7 1.0 OD1 A:ASN588 4.9 94.3 1.0

Iodine binding site 3 out of 5 in the Crystal Structure of the DRM2-Ctg Dna Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of the DRM2-Ctg Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I1008 b:100.3 occ:1.00 N A:ILE357 3.8 54.1 1.0 N A:ARG297 4.0 76.1 1.0 CA A:PRO356 4.1 54.2 1.0 CG1 A:ILE357 4.1 59.8 1.0 O A:ARG297 4.2 75.7 1.0 CA A:HIS296 4.2 83.7 1.0 O A:THR295 4.2 73.3 1.0 CB A:PRO356 4.3 54.5 1.0 OD1 A:ASN358 4.3 71.8 1.0 CD2 A:HIS296 4.4 105.4 1.0 C A:PRO356 4.5 56.0 1.0 N A:ASN358 4.6 60.2 1.0 C A:HIS296 4.7 82.8 1.0 CG A:HIS296 4.7 109.5 1.0 CG A:ARG297 4.7 66.1 1.0 CA A:ILE357 4.8 57.2 1.0 CB A:HIS296 4.9 92.0 1.0 CB A:ILE357 5.0 56.3 1.0 CB A:ASN358 5.0 67.3 1.0 CD1 A:ILE357 5.0 60.4 1.0

Iodine binding site 4 out of 5 in the Crystal Structure of the DRM2-Ctg Dna Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of the DRM2-Ctg Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I1009 b:101.6 occ:1.00 CD2 A:HIS519 3.6 53.1 1.0 CG A:PRO460 3.7 54.0 1.0 CD A:ARG520 3.8 50.8 1.0 CD A:PRO460 3.9 56.3 1.0 CB A:PRO460 4.3 55.5 1.0 CG A:ARG520 4.3 49.5 1.0 CG1 A:VAL516 4.3 46.8 1.0 NE2 A:HIS519 4.3 55.4 1.0 CE1 A:PHE544 4.3 51.6 1.0 CG A:HIS519 4.7 55.5 1.0 NE A:ARG520 4.8 50.3 1.0

Iodine binding site 5 out of 5 in the Crystal Structure of the DRM2-Ctg Dna Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of the DRM2-Ctg Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I1010 b:139.4 occ:1.00 OE2 A:GLU412 2.8 120.0 1.0 ND2 A:ASN443 3.6 78.7 1.0 CD A:GLU412 3.7 114.4 1.0 CG A:GLU412 4.1 99.1 1.0 CG A:ARG408 4.1 73.4 1.0 O A:LYS442 4.1 70.5 1.0 ND2 A:ASN415 4.2 88.1 1.0 CB A:ASN443 4.3 77.0 1.0 CG A:ASN443 4.4 79.7 1.0 CG A:LYS442 4.5 66.4 1.0 O A:ARG408 4.7 77.8 1.0 CD A:ARG408 4.7 75.9 1.0 OD1 A:ASN415 4.7 83.5 1.0 CB A:GLU412 4.8 91.3 1.0 OE1 A:GLU412 4.8 113.5 1.0 CD A:LYS442 4.8 67.5 1.0 CG A:ASN415 4.9 87.4 1.0 C A:LYS442 4.9 71.8 1.0 CA A:GLU412 4.9 89.3 1.0

J.Fang, S.M.Leichter, J.Jiang, M.Biswal, J.Lu, Z.M.Zhang, W.Ren, J.Zhai, Q.Cui, X.Zhong, J.Song. Substrate Deformation Regulates DRM2-Mediated Dna Methylation in Plants. Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
PubMed: 34078593
DOI: 10.1126/SCIADV.ABD9224