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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 1yfj:

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

Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the T4DAM in Complex with Adohcy and 15-Mer Oligonucleotide Showing Semi- Specific and Specific Contact, PDB code: 1yfj:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 1yfj

Go back to Chlorine Binding Sites List in 1yfj
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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
1:Cl602

b:97.8
occ:1.00
 O4' 1:DT101 3.4 45.6 1.0
O2 1:DT101 3.6 38.9 1.0
C4' 1:DT101 4.1 48.2 1.0
C1' 1:DT101 4.3 47.4 1.0
C2 1:DT101 4.5 37.8 1.0
C5' 1:DT101 4.8 32.5 1.0
N1 1:DT101 4.9 43.1 1.0
CL 2:CL601 4.9 47.2 1.0

Chlorine binding site 2 out of 4 in 1yfj

Go back to Chlorine Binding Sites List in 1yfj
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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
2:Cl601

b:47.2
occ:1.00
 C2' 2:DG215 4.1 45.3 1.0
N3 2:DG215 4.1 27.0 1.0
O3' 2:DG215 4.4 57.2 1.0
C1' 2:DG215 4.4 40.8 1.0
C4 2:DG215 4.5 25.2 1.0
O2 1:DT101 4.6 38.9 1.0
C2 2:DG215 4.6 27.9 1.0
N9 2:DG215 4.7 27.8 1.0
N2 2:DG215 4.9 21.1 1.0
CL 1:CL602 4.9 97.8 1.0
C3' 2:DG215 4.9 48.5 1.0

Chlorine binding site 3 out of 4 in 1yfj

Go back to Chlorine Binding Sites List in 1yfj
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl603

b:54.3
occ:1.00
 N3 2:DT201 3.4 40.7 1.0
O4 2:DT201 3.4 33.9 1.0
C4 2:DT201 3.8 33.8 1.0
OE2 B:GLU85 4.0 40.4 1.0
CD B:GLU85 4.2 46.4 1.0
C2 2:DT201 4.4 43.5 1.0
OE1 B:GLU85 4.5 47.9 1.0
N3 1:DG115 4.5 41.9 1.0
O2 2:DT201 4.6 39.7 1.0
O 1:HOH117 4.8 33.9 1.0
CG B:GLU85 4.9 35.7 1.0
CE1 A:PHE111 4.9 15.5 1.0
C1' 1:DG115 4.9 26.2 1.0
C4 1:DG115 5.0 28.6 1.0

Chlorine binding site 4 out of 4 in 1yfj

Go back to Chlorine Binding Sites List in 1yfj
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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
8:Cl600

b:64.6
occ:1.00
 C5' 4:DT401 3.7 54.5 1.0
C2' 8:DG815 3.7 52.3 1.0
OG B:SER112 3.8 30.4 1.0
N3 8:DG815 3.8 36.2 1.0
O B:HOH465 4.0 44.6 1.0
C4' 4:DT401 4.0 54.1 1.0
C4 8:DG815 4.3 30.7 1.0
C1' 8:DG815 4.3 43.2 1.0
O4' 4:DT401 4.3 46.5 1.0
O2 7:DT701 4.4 32.3 1.0
C2 8:DG815 4.4 35.1 1.0
CB B:SER112 4.4 21.2 1.0
N9 8:DG815 4.5 39.0 1.0
O3' 8:DG815 4.6 56.4 1.0
N2 8:DG815 4.7 25.3 1.0
C3' 8:DG815 4.8 52.4 1.0
O5' 4:DT401 5.0 61.7 1.0

Reference:

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
Page generated: Sat Jul 20 04:11:37 2024

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