Zinc in PDB 7wsj: Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans

The structure of Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans, PDB code: 7wsj was solved by P.Dahal, D.Pathak, E.Kwon, D.Y.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.93 / 2.40
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	159.09, 159.09, 55.01, 90, 90, 120
R / Rfree (%)	20.4 / 23.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans (pdb code 7wsj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans, PDB code: 7wsj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:62.4 occ:1.00 SG A:CYS43 2.3 36.5 1.0 SG A:CYS20 2.3 37.3 1.0 SG A:CYS23 2.3 42.1 1.0 SG A:CYS40 2.3 32.6 1.0 CB A:CYS43 3.1 26.7 1.0 CB A:CYS20 3.2 41.7 1.0 CB A:CYS23 3.3 38.0 1.0 CB A:CYS40 3.7 32.5 1.0 N A:CYS23 3.7 38.2 1.0 OG1 A:THR22 3.8 44.6 1.0 N A:CYS40 4.0 34.6 1.0 CA A:CYS23 4.0 43.0 1.0 N A:CYS43 4.2 30.9 1.0 CA A:CYS43 4.2 28.7 1.0 CA A:CYS40 4.4 37.2 1.0 C A:THR22 4.4 42.0 1.0 CB A:ASN26 4.5 53.6 1.0 CA A:CYS20 4.6 30.3 1.0 C A:CYS23 4.7 47.5 1.0 O A:HOH301 4.7 46.2 1.0 ND2 A:ASN26 4.7 46.6 1.0 O A:CYS23 4.7 53.5 1.0 N A:THR22 4.8 39.3 1.0 CB A:THR22 4.9 33.8 1.0 C A:CYS40 4.9 34.7 1.0 O A:CYS40 4.9 34.0 1.0 CA A:THR22 5.0 40.0 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:47.7 occ:1.00 OD2 A:ASP35 2.0 30.0 1.0 NE2 A:HIS48 2.3 26.4 1.0 SG A:CYS32 2.3 25.9 1.0 ND1 A:HIS57 2.3 32.5 1.0 CG A:ASP35 2.8 36.2 1.0 CD2 A:HIS48 3.1 26.5 1.0 CG A:HIS57 3.2 31.6 1.0 CE1 A:HIS57 3.3 29.8 1.0 CB A:HIS57 3.4 27.0 1.0 CE1 A:HIS48 3.4 25.0 1.0 CB A:CYS32 3.5 30.4 1.0 CB A:ASP35 3.5 30.3 1.0 OD1 A:ASP35 3.7 41.6 1.0 N A:ASP35 4.0 33.0 1.0 CG A:HIS48 4.3 32.3 1.0 CD2 A:HIS57 4.4 33.9 1.0 NE2 A:HIS57 4.4 49.9 1.0 CA A:ASP35 4.4 28.3 1.0 ND1 A:HIS48 4.4 32.9 1.0 O A:HOH337 4.6 52.5 1.0 CB A:ALA34 4.6 25.6 1.0 CG1 A:VAL47 4.6 24.6 1.0 C A:ALA34 4.9 33.5 1.0 CA A:CYS32 4.9 27.6 1.0 CA A:HIS57 4.9 35.8 1.0 O A:ALA54 5.0 31.1 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:63.6 occ:1.00 SG A:CYS86 2.3 44.0 1.0 SG A:CYS63 2.3 36.9 1.0 SG A:CYS83 2.3 38.0 1.0 SG A:CYS66 2.3 48.6 1.0 CB A:CYS86 3.1 34.4 1.0 CB A:CYS63 3.2 31.1 1.0 CB A:CYS66 3.3 33.7 1.0 CB A:CYS83 3.6 32.0 1.0 N A:CYS66 3.6 39.7 1.0 N A:CYS83 3.9 34.3 1.0 CA A:CYS66 4.1 40.2 1.0 CA A:CYS86 4.3 37.0 1.0 N A:CYS86 4.3 44.3 1.0 CA A:CYS83 4.3 36.0 1.0 CB A:ALA69 4.5 30.3 1.0 CB A:SER65 4.5 54.9 1.0 CA A:CYS63 4.6 37.4 1.0 C A:SER65 4.8 49.1 1.0 N A:GLU67 4.9 42.5 1.0 C A:CYS66 4.9 39.3 1.0 C A:CYS83 4.9 33.1 1.0 N A:SER65 4.9 51.2 1.0 O A:CYS83 4.9 47.2 1.0 CA A:SER65 5.0 47.1 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:71.4 occ:1.00 OD2 A:ASP78 2.0 58.5 1.0 NE2 A:HIS91 2.3 47.7 1.0 SG A:CYS75 2.3 40.9 1.0 ND1 A:HIS100 2.3 53.0 1.0 CG A:ASP78 2.7 50.0 1.0 CD2 A:HIS91 3.0 50.6 1.0 CG A:HIS100 3.1 55.2 1.0 CE1 A:HIS100 3.3 53.3 1.0 CB A:HIS100 3.4 40.7 1.0 CE1 A:HIS91 3.4 52.9 1.0 OD1 A:ASP78 3.4 58.0 1.0 CB A:ASP78 3.5 44.9 1.0 CB A:CYS75 3.5 38.0 1.0 N A:ASP78 4.0 44.4 1.0 CG A:HIS91 4.2 50.3 1.0 CD2 A:HIS100 4.3 55.0 1.0 NE2 A:HIS100 4.3 69.9 1.0 CA A:ASP78 4.3 38.0 1.0 ND1 A:HIS91 4.4 52.1 1.0 CB A:ALA77 4.7 43.4 1.0 CG1 A:VAL90 4.7 38.6 1.0 CD A:ARG102 4.9 57.1 1.0 CA A:HIS100 4.9 56.0 1.0 CA A:CYS75 4.9 37.4 1.0 C A:ALA77 4.9 51.9 1.0 CG A:ARG102 5.0 52.2 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:84.9 occ:1.00 SG B:CYS43 2.3 63.2 1.0 SG B:CYS23 2.3 68.3 1.0 SG B:CYS40 2.3 56.3 1.0 SG B:CYS20 2.3 58.5 1.0 CB B:CYS43 3.1 54.2 1.0 CB B:CYS20 3.2 54.5 1.0 CB B:CYS23 3.3 61.3 1.0 CB B:CYS40 3.6 49.9 1.0 N B:CYS40 3.9 44.7 1.0 N B:CYS23 3.9 66.0 1.0 OG1 B:THR22 4.0 57.4 1.0 CA B:CYS23 4.2 69.3 1.0 N B:CYS43 4.2 52.1 1.0 CA B:CYS40 4.3 53.4 1.0 CA B:CYS43 4.3 50.1 1.0 ND2 B:ASN26 4.5 75.2 1.0 C B:THR22 4.5 64.8 1.0 CB B:ASN26 4.6 73.7 1.0 CA B:CYS20 4.7 58.8 1.0 O B:CYS40 4.7 54.1 1.0 C B:CYS40 4.8 43.1 1.0 C B:CYS23 4.8 78.6 1.0 N B:THR22 4.9 56.8 1.0 C B:LEU39 5.0 50.0 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:72.1 occ:1.00 OD2 B:ASP35 2.0 61.2 1.0 SG B:CYS32 2.3 52.3 1.0 ND1 B:HIS57 2.3 63.3 1.0 NE2 B:HIS48 2.3 59.9 1.0 CG B:ASP35 3.0 61.6 1.0 CD2 B:HIS48 3.2 56.5 1.0 CG B:HIS57 3.2 59.1 1.0 CE1 B:HIS57 3.3 59.8 1.0 CE1 B:HIS48 3.3 57.2 1.0 CB B:HIS57 3.4 49.0 1.0 CB B:CYS32 3.4 48.6 1.0 CB B:ASP35 3.7 48.6 1.0 OD1 B:ASP35 3.8 68.9 1.0 N B:ASP35 4.0 49.2 1.0 CG B:HIS48 4.3 56.1 1.0 CB B:ALA34 4.4 51.9 1.0 ND1 B:HIS48 4.4 55.5 1.0 CD2 B:HIS57 4.4 61.8 1.0 NE2 B:HIS57 4.4 70.2 1.0 CA B:ASP35 4.5 48.6 1.0 CG1 B:VAL47 4.7 47.4 1.0 CA B:CYS32 4.8 58.6 1.0 C B:ALA34 4.8 64.5 1.0 CA B:HIS57 4.9 46.1 1.0 CG B:ARG59 4.9 56.2 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:72.0 occ:1.00 SG B:CYS86 2.3 52.1 1.0 SG B:CYS83 2.3 46.9 1.0 SG B:CYS63 2.3 47.0 1.0 SG B:CYS66 2.3 55.2 1.0 CB B:CYS86 3.1 37.4 1.0 CB B:CYS63 3.1 39.2 1.0 CB B:CYS66 3.4 42.5 1.0 CB B:CYS83 3.6 51.1 1.0 N B:CYS66 3.7 44.3 1.0 N B:CYS83 3.9 39.4 1.0 CA B:CYS66 4.1 46.1 1.0 CA B:CYS86 4.3 33.5 1.0 CA B:CYS83 4.3 47.1 1.0 N B:CYS86 4.3 49.6 1.0 CB B:SER65 4.6 53.5 1.0 CA B:CYS63 4.6 41.8 1.0 CB B:ALA69 4.7 44.5 1.0 N B:GLU67 4.8 55.2 1.0 C B:SER65 4.8 59.1 1.0 C B:CYS83 4.9 45.6 1.0 C B:CYS66 4.9 43.6 1.0 N B:SER65 5.0 48.7 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:57.1 occ:1.00 OD2 B:ASP78 2.0 36.6 1.0 NE2 B:HIS91 2.3 36.3 1.0 SG B:CYS75 2.3 40.2 1.0 ND1 B:HIS100 2.3 40.1 1.0 CG B:ASP78 2.9 34.3 1.0 CD2 B:HIS91 3.0 32.3 1.0 CG B:HIS100 3.1 38.9 1.0 CB B:HIS100 3.3 33.4 1.0 CE1 B:HIS100 3.3 33.4 1.0 CB B:CYS75 3.4 46.1 1.0 CE1 B:HIS91 3.4 38.3 1.0 CB B:ASP78 3.6 32.5 1.0 OD1 B:ASP78 3.7 40.6 1.0 N B:ASP78 4.2 35.6 1.0 CG B:HIS91 4.2 41.6 1.0 CD2 B:HIS100 4.3 44.8 1.0 NE2 B:HIS100 4.4 46.5 1.0 O B:HOH308 4.4 41.9 1.0 ND1 B:HIS91 4.4 44.6 1.0 CA B:ASP78 4.5 32.7 1.0 CG1 B:VAL90 4.6 27.6 1.0 CD B:ARG102 4.8 43.2 1.0 CA B:HIS100 4.8 47.1 1.0 CB B:ALA77 4.8 42.0 1.0 CA B:CYS75 4.8 37.3 1.0 O B:ALA97 4.8 42.8 1.0 CG B:ARG102 4.9 49.5 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:125.6 occ:1.00 SG C:CYS40 2.3 89.8 1.0 SG C:CYS43 2.3 91.2 1.0 SG C:CYS23 2.3 114.3 1.0 SG C:CYS20 2.3 95.0 1.0 CB C:CYS43 3.1 68.2 1.0 CB C:CYS40 3.3 84.9 1.0 CB C:CYS20 3.4 95.0 1.0 CB C:CYS23 3.4 93.2 1.0 N C:CYS23 3.6 90.4 1.0 N C:CYS40 3.8 73.6 1.0 CA C:CYS23 4.0 96.9 1.0 CA C:CYS40 4.1 79.4 1.0 O C:CYS23 4.3 105.9 1.0 CA C:CYS43 4.3 77.1 1.0 N C:CYS43 4.3 80.5 1.0 CB C:THR22 4.3 79.0 1.0 C C:THR22 4.5 95.3 1.0 CB C:ASN26 4.5 96.6 1.0 C C:CYS23 4.6 103.5 1.0 C C:CYS40 4.6 85.6 1.0 O C:CYS40 4.7 90.6 1.0 OG C:SER42 4.8 90.1 1.0 CA C:THR22 4.8 90.0 1.0 CA C:CYS20 4.8 90.4 1.0 N C:THR22 4.8 88.2 1.0 ND2 C:ASN26 4.9 109.5 1.0 C C:LEU39 5.0 85.3 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Tandem B-Box Domain of Arabidopsis Thaliana Constans within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:82.4 occ:1.00 OD2 C:ASP35 2.0 66.0 1.0 NE2 C:HIS48 2.3 72.9 1.0 SG C:CYS32 2.3 69.5 1.0 ND1 C:HIS57 2.3 60.3 1.0 CG C:ASP35 2.7 63.1 1.0 CD2 C:HIS48 3.1 67.4 1.0 CG C:HIS57 3.1 55.3 1.0 CB C:HIS57 3.2 45.8 1.0 CE1 C:HIS57 3.3 50.1 1.0 CE1 C:HIS48 3.3 62.8 1.0 OD1 C:ASP35 3.4 63.6 1.0 CB C:CYS32 3.4 58.5 1.0 CB C:ASP35 3.5 62.4 1.0 N C:ASP35 3.9 48.2 1.0 CG C:HIS48 4.2 66.8 1.0 CD2 C:HIS57 4.3 47.0 1.0 CA C:ASP35 4.3 60.0 1.0 ND1 C:HIS48 4.3 69.1 1.0 NE2 C:HIS57 4.3 57.7 1.0 CB C:ALA34 4.4 43.9 1.0 CA C:HIS57 4.7 59.5 1.0 C C:ALA34 4.8 57.6 1.0 CD C:ARG59 4.8 72.0 1.0 CA C:CYS32 4.8 71.8 1.0 CG C:ARG59 4.8 66.1 1.0 O C:ALA54 4.9 73.5 1.0

P.Dahal, E.Kwon, D.Pathak, D.Y.Kim. Crystal Structure of A Tandem B-Box Domain From Arabidopsis Constans. Biochem.Biophys.Res.Commun. V. 599 38 2022.
ISSN: ESSN 1090-2104
PubMed: 35168062
DOI: 10.1016/J.BBRC.2022.02.025