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Chlorine in PDB 4gqd: Dna Holliday Junction Stabilized By Chlorine Halogen Bond.

Protein crystallography data

The structure of Dna Holliday Junction Stabilized By Chlorine Halogen Bond., PDB code: 4gqd was solved by M.Carter, P.S.Ho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.68 / 1.94
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 65.692, 23.565, 37.286, 90.00, 110.92, 90.00
R / Rfree (%) 26.4 / 30

Other elements in 4gqd:

The structure of Dna Holliday Junction Stabilized By Chlorine Halogen Bond. also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dna Holliday Junction Stabilized By Chlorine Halogen Bond. (pdb code 4gqd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Dna Holliday Junction Stabilized By Chlorine Halogen Bond., PDB code: 4gqd:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4gqd

Go back to Chlorine Binding Sites List in 4gqd
Chlorine binding site 1 out of 2 in the Dna Holliday Junction Stabilized By Chlorine Halogen Bond.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dna Holliday Junction Stabilized By Chlorine Halogen Bond. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl7

b:1.6
occ:0.63
CL A:UCL7 0.0 1.6 0.6
C5 A:UCL7 1.7 1.6 0.6
C5 C:DC27 1.8 1.6 0.4
C4 A:UCL7 2.7 2.2 0.6
C4 C:DC27 2.7 2.2 0.4
C6 A:UCL7 2.7 1.6 0.6
C6 C:DC27 2.8 2.1 0.4
N4 C:DC27 2.9 1.6 0.4
OP1 A:DA6 2.9 14.9 0.6
OP1 C:DA26 2.9 21.3 0.4
O4 A:UCL7 2.9 1.6 0.6
O5' C:DA26 3.0 20.5 0.4
O5' A:DA6 3.0 14.6 0.6
P A:DA6 3.2 16.6 0.6
P C:DA26 3.2 22.2 0.4
OP2 A:DA6 3.4 16.1 0.6
OP2 C:DA26 3.5 21.9 0.4
O C:HOH102 3.6 11.2 1.0
C5' C:DA26 3.8 17.0 0.4
C5' A:DA6 3.8 9.8 0.6
N3 A:UCL7 3.9 1.6 0.6
N3 C:DC27 4.0 2.3 0.4
N1 A:UCL7 4.0 3.0 0.6
N1 C:DC27 4.1 4.0 0.4
C3' C:DA26 4.2 15.2 0.4
C3' A:DA6 4.2 9.7 0.6
C2 A:UCL7 4.5 1.6 0.6
C2 C:DC27 4.5 2.8 0.4
C4' C:DA26 4.6 15.9 0.4
C2' A:DA6 4.6 6.8 0.6
C4' A:DA6 4.6 9.6 0.6
C2' C:DA26 4.6 14.1 0.4
O3' A:DT5 4.8 14.5 0.6
O3' C:DT25 4.8 22.0 0.4
O5' A:UCL7 4.9 15.7 0.6
N4 C:DC28 5.0 16.8 0.4
O5' C:DC27 5.0 15.7 0.4

Chlorine binding site 2 out of 2 in 4gqd

Go back to Chlorine Binding Sites List in 4gqd
Chlorine binding site 2 out of 2 in the Dna Holliday Junction Stabilized By Chlorine Halogen Bond.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dna Holliday Junction Stabilized By Chlorine Halogen Bond. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl37

b:13.8
occ:0.37
CL D:UCL37 0.0 13.8 0.4
C5 D:UCL37 1.7 15.0 0.4
C5 B:DC17 1.7 13.2 0.6
C4 B:DC17 2.5 13.3 0.6
N4 B:DC17 2.5 13.6 0.6
C4 D:UCL37 2.7 15.2 0.4
C6 D:UCL37 2.7 15.6 0.4
C6 B:DC17 2.9 13.2 0.6
O4 D:UCL37 2.9 14.9 0.4
C8 B:DA16 3.3 24.8 0.6
C8 D:DA36 3.6 26.4 0.4
N7 B:DA16 3.7 24.6 0.6
N9 B:DA16 3.7 24.2 0.6
N3 B:DC17 3.8 13.7 0.6
N3 D:UCL37 3.9 16.1 0.4
N9 D:DA36 3.9 25.4 0.4
C2' D:DA36 4.0 23.7 0.4
N1 D:UCL37 4.0 16.2 0.4
N7 D:DA36 4.0 26.3 0.4
C2' B:DA16 4.0 21.7 0.6
N4 D:DC38 4.0 18.1 0.4
N1 B:DC17 4.1 13.5 0.6
N4 B:DC18 4.1 7.3 0.6
O1P D:UCL37 4.2 22.6 0.4
C5 B:DA16 4.2 26.0 0.6
C1' B:DA16 4.2 22.7 0.6
C4 B:DA16 4.3 24.8 0.6
O6 A:DG3 4.3 20.9 0.6
C1' D:DA36 4.3 24.4 0.4
C2 B:DC17 4.4 15.0 0.6
OP2 B:DC17 4.4 20.4 0.6
O6 C:DG23 4.5 26.0 0.4
C4 D:DA36 4.5 26.1 0.4
C5 D:DA36 4.5 26.7 0.4
C2 D:UCL37 4.5 16.8 0.4
O B:HOH220 4.5 9.8 1.0
O B:HOH209 4.6 25.7 1.0
C4 D:DC38 4.8 17.0 0.4
C4 B:DC18 4.8 5.0 0.6
N3 B:DC18 5.0 5.6 0.6
N3 D:DC38 5.0 17.2 0.4

Reference:

M.Carter, A.R.Voth, M.R.Scholfield, B.Rummel, L.C.Sowers, P.S.Ho. Enthalpy-Entropy Compensation in Biomolecular Halogen Bonds Measured in Dna Junctions. Biochemistry V. 52 4891 2013.
ISSN: ISSN 0006-2960
PubMed: 23789744
DOI: 10.1021/BI400590H
Page generated: Sun Jul 21 14:55:50 2024

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