Calcium in PDB 1yfj: T4DAM in Complex with Adohcy and 15-Mer Oligonucleotide Showing Semi- Specific and Specific Contact

All present enzymatic activity of T4DAM in Complex with Adohcy and 15-Mer Oligonucleotide Showing Semi- Specific and Specific Contact:
2.1.1.72;

The structure of T4DAM in Complex with Adohcy and 15-Mer Oligonucleotide Showing Semi- Specific and Specific Contact, PDB code: 1yfj was solved by J.R.Horton, K.Liebert, S.Hattman, A.Jeltsch, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.78 / 2.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	111.200, 133.000, 189.200, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 25

The structure of T4DAM in Complex with Adohcy and 15-Mer Oligonucleotide Showing Semi- Specific and Specific Contact also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Calcium atom in the T4DAM in Complex with Adohcy and 15-Mer Oligonucleotide Showing Semi- Specific and Specific Contact (pdb code 1yfj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the T4DAM in Complex with Adohcy and 15-Mer Oligonucleotide Showing Semi- Specific and Specific Contact, PDB code: 1yfj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the T4DAM in Complex with Adohcy and 15-Mer Oligonucleotide Showing Semi- Specific and Specific Contact


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of T4DAM in Complex with Adohcy and 15-Mer Oligonucleotide Showing Semi- Specific and Specific Contact within 5.0Å range: probe atom residue distance (Å) B Occ 2:Ca502 b:28.8 occ:1.00 O 2:HOH606 2.4 31.3 1.0 O 1:HOH605 2.5 30.3 1.0 O 1:HOH607 2.5 31.1 1.0 O 1:HOH604 2.5 21.9 1.0 O B:HOH503 2.6 32.0 1.0 O 2:HOH609 2.6 25.6 1.0 O B:HOH502 2.6 24.1 1.0 O B:HOH504 2.8 25.4 1.0 O 2:HOH241 4.3 46.6 1.0 N3 2:DA203 4.4 33.3 1.0 O 1:HOH117 4.5 33.9 1.0 C2 2:DA203 4.5 43.3 1.0 OE1 B:GLU92 4.6 42.4 1.0 OE2 B:GLU92 4.6 36.9 1.0 O4' 2:DC204 4.6 41.7 1.0 C4' 2:DC204 4.7 42.9 1.0 N2 1:DG115 4.7 28.1 1.0 N3 1:DG115 4.8 41.9 1.0 C5' 2:DC204 4.9 41.9 1.0 O4' 1:DG115 4.9 30.5 1.0 CD B:GLU92 5.0 43.9 1.0

Calcium binding site 2 out of 2 in the T4DAM in Complex with Adohcy and 15-Mer Oligonucleotide Showing Semi- Specific and Specific Contact


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of T4DAM in Complex with Adohcy and 15-Mer Oligonucleotide Showing Semi- Specific and Specific Contact within 5.0Å range: probe atom residue distance (Å) B Occ 4:Ca508 b:31.9 occ:1.00 O 4:HOH614 2.4 29.0 1.0 O 3:HOH615 2.4 29.0 1.0 O A:HOH497 2.5 28.4 1.0 O 3:HOH613 2.5 29.1 1.0 O 3:HOH612 2.6 25.7 1.0 O A:HOH498 2.6 17.4 1.0 O A:HOH499 2.6 22.3 1.0 O 4:HOH619 2.8 27.1 1.0 OE2 A:GLU92 4.1 49.7 1.0 OE1 A:GLU92 4.4 51.0 1.0 O4' 4:DC404 4.5 36.9 1.0 O 3:HOH257 4.5 24.4 1.0 C4' 4:DC404 4.6 34.8 1.0 N3 4:DA403 4.6 46.0 1.0 CD A:GLU92 4.7 45.0 1.0 C2 4:DA403 4.8 49.1 1.0 C5' 4:DC404 4.8 37.2 1.0 O4' 3:DG315 5.0 27.5 1.0 N3 3:DG315 5.0 30.6 1.0

J.R.Horton, K.Liebert, S.Hattman, A.Jeltsch, X.Cheng. Transition From Nonspecific to Specific Dna Interactions Along the Substrate-Recognition Pathway of Dam Methyltransferase. Cell(Cambridge,Mass.) V. 121 349 2005.
ISSN: ISSN 0092-8674
PubMed: 15882618
DOI: 10.1016/J.CELL.2005.02.021