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Chlorine in PDB 4hug: Structure of 5-Chlorouracil Modified A:U Base Pairs

Enzymatic activity of Structure of 5-Chlorouracil Modified A:U Base Pairs

All present enzymatic activity of Structure of 5-Chlorouracil Modified A:U Base Pairs:
3.1.26.4;

Protein crystallography data

The structure of Structure of 5-Chlorouracil Modified A:U Base Pairs, PDB code: 4hug was solved by A.Patra, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.23 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.829, 64.638, 116.286, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 22.2

Other elements in 4hug:

The structure of Structure of 5-Chlorouracil Modified A:U Base Pairs also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of 5-Chlorouracil Modified A:U Base Pairs (pdb code 4hug). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Structure of 5-Chlorouracil Modified A:U Base Pairs, PDB code: 4hug:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4hug

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Chlorine binding site 1 out of 8 in the Structure of 5-Chlorouracil Modified A:U Base Pairs


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of 5-Chlorouracil Modified A:U Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl7

b:49.8
occ:1.00
 CL C:UCL7 0.0 49.8 1.0
C5 C:UCL7 1.7 39.1 1.0
C6 C:UCL7 2.7 40.1 1.0
C4 C:UCL7 2.8 40.1 1.0
O4 C:UCL7 3.0 40.7 1.0
C8 C:DA6 3.5 32.1 1.0
N7 C:DA6 3.7 32.8 1.0
N9 C:DA6 3.9 36.4 1.0
N1 C:UCL7 3.9 41.1 1.0
N3 C:UCL7 4.0 40.3 1.0
C2' C:DA6 4.0 46.7 1.0
C5 C:DA6 4.1 31.6 1.0
C4 C:DA6 4.2 34.3 1.0
C2 C:UCL7 4.5 40.1 1.0
C1' C:DA6 4.5 40.3 1.0
O4 C:UCL8 4.7 49.9 1.0
CL C:UCL8 4.8 55.0 1.0
C6 C:DA6 4.9 32.8 1.0

Chlorine binding site 2 out of 8 in 4hug

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Chlorine binding site 2 out of 8 in the Structure of 5-Chlorouracil Modified A:U Base Pairs


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of 5-Chlorouracil Modified A:U Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl8

b:55.0
occ:1.00
 CL C:UCL8 0.0 55.0 1.0
C5 C:UCL8 1.7 45.8 1.0
C6 C:UCL8 2.7 43.2 1.0
C4 C:UCL8 2.8 44.0 1.0
O4 C:UCL8 3.0 49.9 1.0
C2' C:UCL7 3.4 55.1 1.0
C6 C:UCL7 3.7 40.1 1.0
N1 C:UCL7 3.8 41.1 1.0
N1 C:UCL8 3.9 45.8 1.0
N3 C:UCL8 4.0 46.0 1.0
C5 C:UCL7 4.1 39.1 1.0
C1' C:UCL7 4.2 44.5 1.0
C2 C:UCL7 4.3 40.1 1.0
C2 C:UCL8 4.5 44.2 1.0
C4 C:UCL7 4.5 40.1 1.0
N3 C:UCL7 4.6 40.3 1.0
C3' C:UCL7 4.7 55.3 1.0
CL C:UCL7 4.8 49.8 1.0
O2 C:UCL7 4.9 43.8 1.0
O1P C:UCL8 5.0 57.1 1.0

Chlorine binding site 3 out of 8 in 4hug

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Chlorine binding site 3 out of 8 in the Structure of 5-Chlorouracil Modified A:U Base Pairs


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of 5-Chlorouracil Modified A:U Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl19

b:50.0
occ:1.00
 CL D:UCL19 0.0 50.0 1.0
C5 D:UCL19 1.7 35.2 1.0
C6 D:UCL19 2.7 44.0 1.0
C4 D:UCL19 2.8 38.3 1.0
O4 D:UCL19 3.0 39.5 1.0
C8 D:DA18 3.6 48.7 1.0
C2' D:DA18 3.8 59.6 1.0
N7 D:DA18 3.9 43.4 1.0
N9 D:DA18 3.9 46.8 1.0
N1 D:UCL19 4.0 39.6 1.0
N3 D:UCL19 4.0 40.2 1.0
C5 D:DA18 4.3 42.2 1.0
C4 D:DA18 4.3 41.6 1.0
C1' D:DA18 4.4 56.1 1.0
C2 D:UCL19 4.5 39.7 1.0
CL D:UCL20 4.6 50.0 1.0
O4 D:UCL20 4.6 35.1 1.0
O D:HOH204 4.8 39.8 1.0

Chlorine binding site 4 out of 8 in 4hug

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Chlorine binding site 4 out of 8 in the Structure of 5-Chlorouracil Modified A:U Base Pairs


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of 5-Chlorouracil Modified A:U Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl20

b:50.0
occ:1.00
 CL D:UCL20 0.0 50.0 1.0
C5 D:UCL20 1.7 33.4 1.0
C6 D:UCL20 2.7 38.4 1.0
C4 D:UCL20 2.8 32.8 1.0
O4 D:UCL20 3.0 35.1 1.0
C6 D:UCL19 3.7 44.0 1.0
O D:HOH210 3.7 34.5 1.0
C2' D:UCL19 3.8 51.8 1.0
N1 D:UCL19 3.9 39.6 1.0
C5 D:UCL19 3.9 35.2 1.0
N1 D:UCL20 4.0 36.2 1.0
N3 D:UCL20 4.0 30.3 1.0
O D:HOH204 4.1 39.8 1.0
C2 D:UCL19 4.4 39.7 1.0
N4 D:DC21 4.4 26.5 1.0
C4 D:UCL19 4.4 38.3 1.0
O C:HOH115 4.4 39.3 1.0
C1' D:UCL19 4.4 49.5 1.0
C2 D:UCL20 4.5 34.5 1.0
CL D:UCL19 4.6 50.0 1.0
N3 D:UCL19 4.6 40.2 1.0
C3' D:UCL19 5.0 58.9 1.0

Chlorine binding site 5 out of 8 in 4hug

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Chlorine binding site 5 out of 8 in the Structure of 5-Chlorouracil Modified A:U Base Pairs


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of 5-Chlorouracil Modified A:U Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl7

b:55.6
occ:1.00
 CL E:UCL7 0.0 55.6 1.0
C5 E:UCL7 1.7 52.5 1.0
C6 E:UCL7 2.7 57.3 1.0
C4 E:UCL7 2.8 57.1 1.0
O4 E:UCL7 3.1 59.8 1.0
C8 E:DA6 3.7 44.5 1.0
N7 E:DA6 3.9 42.3 1.0
N1 E:UCL7 3.9 60.7 1.0
N3 E:UCL7 4.0 56.1 1.0
N9 E:DA6 4.1 46.8 1.0
C2' E:DA6 4.2 58.5 1.0
C5 E:DA6 4.3 41.8 1.0
C4 E:DA6 4.4 47.5 1.0
C2 E:UCL7 4.5 58.2 1.0
CL E:UCL8 4.6 69.0 1.0
C1' E:DA6 4.7 54.8 1.0
O4 E:UCL8 5.0 64.1 1.0

Chlorine binding site 6 out of 8 in 4hug

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Chlorine binding site 6 out of 8 in the Structure of 5-Chlorouracil Modified A:U Base Pairs


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of 5-Chlorouracil Modified A:U Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl8

b:69.0
occ:1.00
 CL E:UCL8 0.0 69.0 1.0
C5 E:UCL8 1.7 66.0 1.0
C6 E:UCL8 2.7 70.1 1.0
C4 E:UCL8 2.8 65.9 1.0
O4 E:UCL8 3.1 64.1 1.0
C2' E:UCL7 3.5 72.2 1.0
C6 E:UCL7 3.5 57.3 1.0
N1 E:UCL7 3.7 60.7 1.0
C5 E:UCL7 3.8 52.5 1.0
N1 E:UCL8 4.0 69.5 1.0
N3 E:UCL8 4.0 65.5 1.0
C2 E:UCL7 4.1 58.2 1.0
C1' E:UCL7 4.2 63.1 1.0
C4 E:UCL7 4.2 57.1 1.0
N3 E:UCL7 4.3 56.1 1.0
C2 E:UCL8 4.5 65.6 1.0
CL E:UCL7 4.6 55.6 1.0
O2 E:UCL7 4.7 58.9 1.0
C3' E:UCL7 4.7 74.4 1.0
O4 E:UCL7 5.0 59.8 1.0
O6 F:DG16 5.0 70.1 1.0

Chlorine binding site 7 out of 8 in 4hug

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Chlorine binding site 7 out of 8 in the Structure of 5-Chlorouracil Modified A:U Base Pairs


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of 5-Chlorouracil Modified A:U Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl19

b:67.8
occ:1.00
 CL F:UCL19 0.0 67.8 1.0
C5 F:UCL19 1.7 59.0 1.0
C6 F:UCL19 2.7 63.6 1.0
C4 F:UCL19 2.8 58.7 1.0
O4 F:UCL19 3.1 57.0 1.0
C8 F:DA18 3.7 69.3 1.0
C2' F:DA18 3.9 75.5 1.0
N9 F:DA18 3.9 66.3 1.0
N1 F:UCL19 3.9 63.6 1.0
N7 F:DA18 4.0 68.4 1.0
N3 F:UCL19 4.0 52.3 1.0
C4 F:DA18 4.3 64.0 1.0
C5 F:DA18 4.4 65.5 1.0
C1' F:DA18 4.4 74.5 1.0
C2 F:UCL19 4.5 57.6 1.0
CL F:UCL20 4.6 55.9 1.0
O4 F:UCL20 4.9 48.2 1.0
O1P F:UCL19 4.9 82.5 1.0

Chlorine binding site 8 out of 8 in 4hug

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Chlorine binding site 8 out of 8 in the Structure of 5-Chlorouracil Modified A:U Base Pairs


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of 5-Chlorouracil Modified A:U Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl20

b:55.9
occ:1.00
 CL F:UCL20 0.0 55.9 1.0
C5 F:UCL20 1.7 50.3 1.0
C6 F:UCL20 2.7 55.2 1.0
C4 F:UCL20 2.8 48.7 1.0
O4 F:UCL20 3.0 48.2 1.0
C6 F:UCL19 3.6 63.6 1.0
N1 F:UCL19 3.7 63.6 1.0
C2' F:UCL19 3.8 67.7 1.0
C5 F:UCL19 3.8 59.0 1.0
N1 F:UCL20 4.0 57.6 1.0
O F:HOH206 4.0 40.5 1.0
N3 F:UCL20 4.0 38.6 1.0
C2 F:UCL19 4.2 57.6 1.0
C1' F:UCL19 4.2 67.1 1.0
C4 F:UCL19 4.3 58.7 1.0
N3 F:UCL19 4.4 52.3 1.0
C2 F:UCL20 4.5 52.6 1.0
CL F:UCL19 4.6 67.8 1.0
O2 F:UCL19 4.8 56.0 1.0

Reference:

A.Patra, J.Harp, P.S.Pallan, L.Zhao, M.Abramov, P.Herdewijn, M.Egli. Structure, Stability and Function of 5-Chlorouracil Modified A:U and G:U Base Pairs. Nucleic Acids Res. V. 41 2689 2013.
ISSN: ISSN 0305-1048
PubMed: 23275540
DOI: 10.1093/NAR/GKS1316
Page generated: Sun Jul 21 16:07:01 2024

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