Chlorine in PDB 5vpf: Transcription Factor Fosb/Jund Bzip Domain in Complex with Cognate Dna, Type-II Crystal

The structure of Transcription Factor Fosb/Jund Bzip Domain in Complex with Cognate Dna, Type-II Crystal, PDB code: 5vpf was solved by Z.Yin, G.Rudenko, M.Machius, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.59 / 2.69
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	119.637, 119.637, 249.970, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 24.8

The structure of Transcription Factor Fosb/Jund Bzip Domain in Complex with Cognate Dna, Type-II Crystal also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Transcription Factor Fosb/Jund Bzip Domain in Complex with Cognate Dna, Type-II Crystal (pdb code 5vpf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Transcription Factor Fosb/Jund Bzip Domain in Complex with Cognate Dna, Type-II Crystal, PDB code: 5vpf:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Transcription Factor Fosb/Jund Bzip Domain in Complex with Cognate Dna, Type-II Crystal


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Transcription Factor Fosb/Jund Bzip Domain in Complex with Cognate Dna, Type-II Crystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl304 b:57.9 occ:1.00 HH21 A:ARG164 1.9 56.6 1.0 HH11 A:ARG161 2.3 68.2 1.0 NH2 A:ARG164 2.7 47.1 1.0 NH1 A:ARG161 2.8 56.8 1.0 HE A:ARG164 2.9 48.5 1.0 HD3 A:ARG161 3.0 55.9 1.0 HH12 A:ARG161 3.1 68.2 1.0 H3' E:DC4 3.2 54.8 1.0 HH22 A:ARG164 3.3 56.6 1.0 H6 E:DC4 3.4 60.8 1.0 HD2 A:ARG161 3.4 55.9 1.0 OP2 E:DC4 3.5 55.0 1.0 NE A:ARG164 3.5 40.4 1.0 OP2 E:DG5 3.5 43.5 1.0 CZ A:ARG164 3.6 42.0 1.0 CD A:ARG161 3.6 46.5 1.0 CZ A:ARG161 3.7 51.7 1.0 O5' E:DC4 3.8 85.4 1.0 N7 E:DG5 3.8 42.0 1.0 H2' E:DC4 3.9 52.7 1.0 H8 E:DG5 3.9 48.3 1.0 NE A:ARG161 3.9 44.3 1.0 C6 E:DC4 4.0 50.6 1.0 C3' E:DC4 4.1 45.9 1.0 H5 E:DC4 4.2 64.0 1.0 C8 E:DG5 4.3 40.5 1.0 P E:DC4 4.3 74.7 1.0 C5 E:DC4 4.4 53.3 1.0 C2' E:DC4 4.5 44.2 1.0 H2'' E:DT3 4.5 88.6 1.0 HB2 A:ARG164 4.6 33.9 1.0 NH2 A:ARG161 4.7 26.8 1.0 HA A:ARG161 4.7 31.2 1.0 HE A:ARG161 4.7 53.2 1.0 H2' E:DT3 4.7 88.6 1.0 P E:DG5 4.8 49.8 1.0 HH22 A:ARG161 4.8 32.2 1.0 NH1 A:ARG164 4.8 48.6 1.0 N1 E:DC4 4.9 46.5 1.0 O A:HOH405 4.9 27.2 1.0 CD A:ARG164 4.9 28.9 1.0 O3' E:DC4 5.0 45.3 1.0 CG A:ARG161 5.0 25.1 1.0 C5' E:DC4 5.0 88.9 1.0 HD2 A:ARG164 5.0 34.7 1.0

Chlorine binding site 2 out of 2 in the Transcription Factor Fosb/Jund Bzip Domain in Complex with Cognate Dna, Type-II Crystal


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Transcription Factor Fosb/Jund Bzip Domain in Complex with Cognate Dna, Type-II Crystal within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl402 b:39.9 occ:1.00 HD22 B:ASN278 2.3 24.5 1.0 N7 F:DG6 2.8 17.1 1.0 O F:HOH208 2.9 13.6 1.0 HA B:ASN278 2.9 23.2 1.0 HB3 B:ALA281 3.0 38.7 1.0 ND2 B:ASN278 3.2 20.7 1.0 HB2 B:ALA281 3.3 38.7 1.0 H8 F:DG5 3.4 24.9 1.0 CB B:ALA281 3.4 32.2 1.0 H2' F:DG5 3.5 31.6 1.0 C8 F:DG5 3.5 20.7 1.0 HB1 B:ALA281 3.5 38.7 1.0 HD21 B:ASN278 3.6 24.5 1.0 HB2 B:ASN278 3.7 25.1 1.0 C8 F:DG6 3.7 17.1 1.0 O6 F:DG6 3.8 22.7 1.0 N7 F:DG5 3.8 26.5 1.0 CA B:ASN278 3.8 19.5 1.0 C5 F:DG6 3.8 17.4 1.0 H8 F:DG6 3.8 20.4 1.0 H2'' F:DG5 3.9 31.6 1.0 H73 F:DT7 4.0 28.5 1.0 N9 F:DG5 4.0 21.9 1.0 CB B:ASN278 4.1 20.9 1.0 C2' F:DG5 4.1 26.3 1.0 CG B:ASN278 4.1 25.8 1.0 O4 F:DT7 4.1 24.4 1.0 C6 F:DG6 4.2 17.8 1.0 C5 F:DG5 4.4 22.6 1.0 O B:ARG277 4.4 20.0 1.0 N B:ASN278 4.5 20.1 1.0 H71 F:DT7 4.6 28.5 1.0 C4 F:DG5 4.6 22.1 1.0 C1' F:DG5 4.6 19.7 1.0 C7 F:DT7 4.7 23.7 1.0 C B:ARG277 4.7 22.9 1.0 H61 E:DA13 4.8 27.6 1.0 O B:ASN278 4.8 18.2 1.0 C B:ASN278 4.8 19.9 1.0 H B:ALA281 4.8 22.2 1.0 CA B:ALA281 4.9 18.4 1.0 C4 F:DT7 4.9 27.6 1.0 H B:ASN278 5.0 24.2 1.0 N9 F:DG6 5.0 17.3 1.0

Z.Yin, M.Machius, E.J.Nestler, G.Rudenko. Activator Protein-1: Redox Switch Controlling Structure and Dna-Binding. Nucleic Acids Res. V. 45 11425 2017.
ISSN: ESSN 1362-4962
PubMed: 28981703
DOI: 10.1093/NAR/GKX795