Atomistry » Chlorine » PDB 1y6q-1ylf » 1yfj
Atomistry »
  Chlorine »
    PDB 1y6q-1ylf »
      1yfj »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy