Atomistry » Chlorine » PDB 8sbx-8sxr » 8sv3
Atomistry »
  Chlorine »
    PDB 8sbx-8sxr »
      8sv3 »

Chlorine in PDB 8sv3: 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex

Enzymatic activity of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex

All present enzymatic activity of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex:
3.1.26.4;

Protein crystallography data

The structure of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex, PDB code: 8sv3 was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.54 / 1.51
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.983, 89, 72.566, 90, 100.44, 90
R / Rfree (%) 17.7 / 21

Other elements in 8sv3:

The structure of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex also contains other interesting chemical elements:

Fluorine (F) 10 atoms
Magnesium (Mg) 1 atom
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex (pdb code 8sv3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex, PDB code: 8sv3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8sv3

Go back to Chlorine Binding Sites List in 8sv3
Chlorine binding site 1 out of 5 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl7

b:16.7
occ:1.00
 CL D:UCL7 0.0 16.7 1.0
C5 D:UCL7 1.8 14.2 1.0
C6 D:UCL7 2.7 13.6 1.0
C4 D:UCL7 2.7 13.5 1.0
O4 D:UCL7 3.0 15.9 1.0
C8 D:7DA6 3.5 14.0 1.0
O D:HOH305 3.5 26.2 1.0
O D:HOH352 3.5 35.9 1.0
O D:HOH315 3.6 27.3 1.0
C7 D:7DA6 3.7 12.6 1.0
O D:HOH340 3.7 26.1 1.0
CL D:UCL8 3.7 16.5 0.5
O4 D:UCL8 3.8 16.0 0.5
O D:HOH344 3.9 24.1 1.0
N1 D:UCL7 4.0 16.7 1.0
N3 D:UCL7 4.0 14.1 1.0
N9 D:7DA6 4.1 14.0 1.0
CL D:UCL8 4.1 16.4 0.5
C2' D:7DA6 4.2 15.3 1.0
O4 D:UCL8 4.3 13.1 0.5
C5 D:7DA6 4.3 12.8 1.0
C2 D:UCL7 4.5 17.0 1.0
C4 D:7DA6 4.5 13.9 1.0
C4 D:UCL8 4.5 16.0 0.5
C5 D:UCL8 4.6 15.8 0.5
C1' D:7DA6 4.8 15.2 1.0

Chlorine binding site 2 out of 5 in 8sv3

Go back to Chlorine Binding Sites List in 8sv3
Chlorine binding site 2 out of 5 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl8

b:16.4
occ:0.50
 CL D:UCL8 0.0 16.4 0.5
CL D:UCL8 0.9 16.5 0.5
C5 D:UCL8 1.5 15.8 0.5
C5 D:UCL8 1.8 13.8 0.5
C6 D:UCL8 2.1 16.9 0.5
C6 D:UCL8 2.7 16.1 0.5
C4 D:UCL8 2.7 16.0 0.5
C4 D:UCL8 2.8 14.4 0.5
O4 D:UCL8 3.0 13.1 0.5
O4 D:UCL8 3.3 16.0 0.5
C6 D:UCL7 3.3 13.6 1.0
O D:HOH359 3.3 37.5 1.0
N1 D:UCL8 3.4 18.8 0.5
C2' D:UCL7 3.5 21.6 1.0
O D:HOH344 3.6 24.1 1.0
C5 D:UCL7 3.6 14.2 1.0
O D:HOH326 3.7 23.2 1.0
N1 D:UCL7 3.7 16.7 1.0
N3 D:UCL8 3.8 15.7 0.5
N1 D:UCL8 4.0 15.5 0.5
O D:HOH305 4.0 26.2 1.0
N3 D:UCL8 4.0 14.2 0.5
C2 D:UCL8 4.1 18.4 0.5
CL D:UCL7 4.1 16.7 1.0
C1' D:UCL7 4.2 20.4 1.0
C4 D:UCL7 4.3 13.5 1.0
F D:C379 4.3 22.2 0.5
C2 D:UCL7 4.3 17.0 1.0
C2 D:UCL8 4.5 15.4 0.5
C3' D:UCL7 4.5 22.1 1.0
C1' D:UCL8 4.6 19.3 0.5
N3 D:UCL7 4.6 14.1 1.0
N4 D:C379 4.7 17.9 0.5
F D:C379 4.7 16.1 0.5
O4' D:UCL8 4.7 17.0 0.5
O2P D:UCL8 4.9 28.1 1.0
O5' D:UCL8 4.9 19.6 0.5
N4 D:C379 4.9 14.0 0.5
O5' D:UCL8 5.0 19.6 0.5

Chlorine binding site 3 out of 5 in 8sv3

Go back to Chlorine Binding Sites List in 8sv3
Chlorine binding site 3 out of 5 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl8

b:16.5
occ:0.50
 CL D:UCL8 0.0 16.5 0.5
CL D:UCL8 0.9 16.4 0.5
C5 D:UCL8 1.8 15.8 0.5
C5 D:UCL8 2.4 13.8 0.5
C4 D:UCL8 2.7 16.0 0.5
C6 D:UCL8 2.8 16.9 0.5
O4 D:UCL8 2.9 13.1 0.5
O4 D:UCL8 2.9 16.0 0.5
C4 D:UCL8 3.0 14.4 0.5
O D:HOH305 3.2 26.2 1.0
O D:HOH326 3.3 23.2 1.0
O D:HOH359 3.4 37.5 1.0
C6 D:UCL8 3.5 16.1 0.5
C6 D:UCL7 3.5 13.6 1.0
C5 D:UCL7 3.5 14.2 1.0
O D:HOH344 3.6 24.1 1.0
CL D:UCL7 3.7 16.7 1.0
N3 D:UCL8 4.0 15.7 0.5
N1 D:UCL8 4.1 18.8 0.5
N1 D:UCL7 4.2 16.7 1.0
C4 D:UCL7 4.2 13.5 1.0
O E:HOH135 4.2 35.6 1.0
C2' D:UCL7 4.3 21.6 1.0
N3 D:UCL8 4.3 14.2 0.5
N4 D:C379 4.4 17.9 0.5
F D:C379 4.5 22.2 0.5
C2 D:UCL8 4.5 18.4 0.5
N1 D:UCL8 4.7 15.5 0.5
C2 D:UCL7 4.8 17.0 1.0
N3 D:UCL7 4.8 14.1 1.0
N4 D:C379 4.8 14.0 0.5
C1' D:UCL7 4.8 20.4 1.0
O4 D:UCL7 4.9 15.9 1.0
F D:C379 5.0 16.1 0.5

Chlorine binding site 4 out of 5 in 8sv3

Go back to Chlorine Binding Sites List in 8sv3
Chlorine binding site 4 out of 5 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl7

b:17.6
occ:1.00
 CL E:UCL7 0.0 17.6 1.0
C5 E:UCL7 1.8 14.8 1.0
C6 E:UCL7 2.7 13.7 1.0
C4 E:UCL7 2.8 14.7 1.0
O4 E:UCL7 3.0 14.6 1.0
C2' E:7DA6 3.4 21.9 1.0
C8 E:7DA6 3.5 18.0 1.0
N9 E:7DA6 3.5 19.1 1.0
O E:HOH120 3.6 21.7 1.0
C7 E:7DA6 3.7 16.2 1.0
O E:HOH147 3.7 38.3 1.0
C4 E:7DA6 3.7 18.3 1.0
C5 E:7DA6 3.8 14.2 1.0
O E:HOH115 4.0 22.9 1.0
O E:HOH111 4.0 27.1 1.0
N1 E:UCL7 4.0 14.4 1.0
C1' E:7DA6 4.0 22.9 1.0
N3 E:UCL7 4.0 13.4 1.0
CL E:UCL8 4.1 15.8 1.0
O E:HOH101 4.1 32.5 1.0
O1P E:UCL7 4.4 24.2 1.0
N3 E:7DA6 4.4 21.4 1.0
C2 E:UCL7 4.5 14.9 1.0
O E:HOH128 4.6 28.2 1.0
C6 E:7DA6 4.6 15.1 1.0
O4 E:UCL8 4.7 14.0 1.0
C3' E:7DA6 4.8 22.2 1.0
O5' E:UCL7 4.9 15.6 1.0
C5 E:UCL8 4.9 12.9 1.0

Chlorine binding site 5 out of 5 in 8sv3

Go back to Chlorine Binding Sites List in 8sv3
Chlorine binding site 5 out of 5 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl8

b:15.8
occ:1.00
 CL E:UCL8 0.0 15.8 1.0
C5 E:UCL8 1.8 12.9 1.0
C6 E:UCL8 2.7 12.2 1.0
C4 E:UCL8 2.8 13.3 1.0
O4 E:UCL8 3.0 14.0 1.0
O E:HOH148 3.5 20.8 1.0
C6 E:UCL7 3.6 13.7 1.0
O E:HOH115 3.6 22.9 1.0
O E:HOH144 3.6 23.0 1.0
O E:HOH128 3.6 28.2 1.0
C5 E:UCL7 3.6 14.8 1.0
N1 E:UCL7 3.9 14.4 1.0
N1 E:UCL8 4.0 11.1 1.0
N3 E:UCL8 4.0 12.7 1.0
C4 E:UCL7 4.0 14.7 1.0
CL E:UCL7 4.1 17.6 1.0
O E:HOH134 4.1 24.4 1.0
C2' E:UCL7 4.2 15.4 1.0
C2 E:UCL7 4.3 14.9 1.0
N3 E:UCL7 4.3 13.4 1.0
C2 E:UCL8 4.5 12.0 1.0
O4 E:UCL7 4.6 14.6 1.0
C1' E:UCL7 4.7 16.1 1.0
F E:C379 4.7 14.2 1.0
N4 E:C379 4.9 12.3 1.0

Reference:

P.S.Pallan, T.P.Lybrand, E.Rozners, M.Abramov, G.Schepers, E.Eremeeva, P.Herdewijn, M.Egli. Conformational Morphing By A Dna Analogue Featuring 7-Deazapurines and 5-Halogenpyrimidines and the Origins of Adenine-Tract Geometry. Biochemistry 2023.
ISSN: ISSN 0006-2960
PubMed: 37694722
DOI: 10.1021/ACS.BIOCHEM.3C00327
Page generated: Thu Dec 28 03:29:49 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy