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

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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

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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

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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

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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

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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: Tue Jul 30 12:38:35 2024

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