Zinc in PDB 7vsp: Crystal Strcuture of the Tandem B-Box Domains of COL2

The structure of Crystal Strcuture of the Tandem B-Box Domains of COL2, PDB code: 7vsp was solved by X.Lv, R.Liu, J.Du, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.93 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.934, 44.478, 99.765, 90, 100.05, 90
R / Rfree (%)	17.9 / 20

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Crystal Strcuture of the Tandem B-Box Domains of COL2 (pdb code 7vsp). 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 Strcuture of the Tandem B-Box Domains of COL2, PDB code: 7vsp:
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 Strcuture of the Tandem B-Box Domains of COL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Strcuture of the Tandem B-Box Domains of COL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:33.4 occ:1.00 SG A:CYS36 2.3 30.7 1.0 SG A:CYS16 2.3 32.1 1.0 SG A:CYS39 2.3 35.0 1.0 SG A:CYS19 2.4 37.0 1.0 CB A:CYS19 3.1 38.8 1.0 CB A:CYS39 3.1 34.9 1.0 CB A:CYS16 3.1 33.8 1.0 CB A:CYS36 3.5 25.9 1.0 N A:CYS19 3.6 36.7 1.0 OG1 A:THR18 3.8 42.5 1.0 CA A:CYS19 3.9 41.6 1.0 N A:CYS36 4.0 24.8 1.0 N A:CYS39 4.3 31.4 1.0 CA A:CYS39 4.3 33.7 1.0 CA A:CYS36 4.3 34.6 1.0 CA A:CYS16 4.6 30.8 1.0 N A:ARG20 4.7 41.7 1.0 C A:CYS19 4.7 47.1 1.0 CB A:ALA22 4.8 42.4 1.0 C A:THR18 4.8 40.0 1.0 C A:CYS36 4.9 35.0 1.0 OG1 A:THR38 4.9 59.0 1.0 O A:CYS36 4.9 30.4 1.0

Zinc binding site 2 out of 12 in the Crystal Strcuture of the Tandem B-Box Domains of COL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Strcuture of the Tandem B-Box Domains of COL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:27.1 occ:1.00 OD2 A:ASP31 1.9 20.8 1.0 ND1 A:HIS53 2.2 23.7 1.0 NE2 A:HIS44 2.2 33.3 1.0 SG A:CYS28 2.2 20.9 1.0 CG A:ASP31 2.9 32.2 1.0 CD2 A:HIS44 3.1 29.3 1.0 CG A:HIS53 3.1 27.8 1.0 CE1 A:HIS53 3.2 33.8 1.0 CB A:CYS28 3.3 24.0 1.0 CE1 A:HIS44 3.3 29.9 1.0 CB A:HIS53 3.3 28.1 1.0 CB A:ASP31 3.6 24.8 1.0 OD1 A:ASP31 3.9 24.2 1.0 N A:ASP31 4.1 24.4 1.0 CD2 A:HIS53 4.3 29.8 1.0 CG A:HIS44 4.3 31.7 1.0 NE2 A:HIS53 4.3 28.1 1.0 ND1 A:HIS44 4.3 26.8 1.0 CA A:ASP31 4.4 25.2 1.0 CB A:ALA30 4.6 23.4 1.0 CA A:CYS28 4.6 24.1 1.0 CD A:ARG55 4.7 23.4 1.0 CG1 A:VAL43 4.7 25.1 1.0 O A:HOH322 4.8 32.7 1.0 CA A:HIS53 4.8 38.3 1.0 C A:ALA30 4.9 27.8 1.0 CG A:ARG55 5.0 28.1 1.0

Zinc binding site 3 out of 12 in the Crystal Strcuture of the Tandem B-Box Domains of COL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Strcuture of the Tandem B-Box Domains of COL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:27.4 occ:1.00 SG A:CYS79 2.3 25.0 1.0 SG A:CYS82 2.3 30.9 1.0 SG A:CYS59 2.4 24.6 1.0 SG A:CYS62 2.4 26.7 1.0 CB A:CYS82 3.0 22.8 1.0 CB A:CYS59 3.2 23.4 1.0 CB A:CYS62 3.3 29.6 1.0 CB A:CYS79 3.4 27.1 1.0 N A:CYS62 3.6 27.3 1.0 N A:CYS79 3.9 27.6 1.0 CA A:CYS62 4.0 18.9 1.0 N A:CYS82 4.1 25.4 1.0 CA A:CYS82 4.1 27.9 1.0 CA A:CYS79 4.2 27.5 1.0 CB A:SER61 4.5 33.8 1.0 O C:HOH301 4.5 35.7 1.0 CA A:CYS59 4.7 23.3 1.0 CB A:ALA65 4.7 23.9 1.0 C A:SER61 4.7 32.4 1.0 OG A:SER61 4.8 26.9 1.0 N A:GLU63 4.8 29.6 1.0 C A:CYS62 4.9 24.3 1.0 C A:CYS79 4.9 29.4 1.0 CA A:SER61 5.0 33.2 1.0

Zinc binding site 4 out of 12 in the Crystal Strcuture of the Tandem B-Box Domains of COL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Strcuture of the Tandem B-Box Domains of COL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:25.5 occ:1.00 OD2 A:ASP74 2.0 31.8 1.0 NE2 A:HIS87 2.1 25.5 1.0 ND1 A:HIS96 2.2 25.0 1.0 SG A:CYS71 2.3 25.5 1.0 CD2 A:HIS87 2.9 22.4 1.0 CG A:ASP74 3.0 33.6 1.0 CG A:HIS96 3.1 24.0 1.0 CE1 A:HIS96 3.2 26.2 1.0 CE1 A:HIS87 3.2 24.5 1.0 CB A:HIS96 3.3 23.6 1.0 CB A:CYS71 3.3 23.0 1.0 CB A:ASP74 3.7 23.2 1.0 OD1 A:ASP74 3.8 27.4 1.0 CG A:HIS87 4.1 28.2 1.0 N A:ASP74 4.2 29.5 1.0 ND1 A:HIS87 4.2 23.0 1.0 CD2 A:HIS96 4.2 28.6 1.0 NE2 A:HIS96 4.3 27.5 1.0 CD A:ARG98 4.6 28.9 1.0 CA A:ASP74 4.6 32.5 1.0 O A:HOH333 4.6 34.6 1.0 CG2 A:ILE86 4.7 28.6 1.0 CB A:ALA73 4.7 30.4 1.0 CA A:CYS71 4.7 23.7 1.0 CG A:ARG98 4.8 24.2 1.0 CA A:HIS96 4.8 28.1 1.0

Zinc binding site 5 out of 12 in the Crystal Strcuture of the Tandem B-Box Domains of COL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Strcuture of the Tandem B-Box Domains of COL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:50.5 occ:1.00 CB B:CYS19 1.8 57.5 1.0 SG B:CYS36 2.3 45.9 1.0 SG B:CYS39 2.3 47.5 1.0 SG B:CYS16 2.4 42.3 1.0 SG B:CYS19 2.9 83.0 1.0 CA B:CYS19 3.1 69.2 1.0 CB B:CYS39 3.1 36.6 1.0 N B:CYS19 3.4 65.6 1.0 CB B:CYS16 3.4 58.4 1.0 CB B:CYS36 3.5 47.1 1.0 OG1 B:THR18 4.0 55.2 1.0 N B:CYS36 4.1 38.5 1.0 N B:CYS39 4.1 40.6 1.0 C B:CYS19 4.2 68.3 1.0 CA B:CYS39 4.3 37.2 1.0 CA B:CYS36 4.3 41.3 1.0 CB B:ALA22 4.4 57.9 1.0 N B:ARG20 4.5 70.1 1.0 C B:THR18 4.6 62.0 1.0 CA B:CYS16 4.8 50.8 1.0 C B:CYS36 4.9 45.8 1.0

Zinc binding site 6 out of 12 in the Crystal Strcuture of the Tandem B-Box Domains of COL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Strcuture of the Tandem B-Box Domains of COL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:27.7 occ:1.00 CE1 B:HIS44 1.8 41.1 1.0 OD2 B:ASP31 1.8 26.5 1.0 ND1 B:HIS53 2.2 23.0 1.0 SG B:CYS28 2.4 27.2 1.0 NE2 B:HIS44 2.4 34.2 1.0 CG B:ASP31 2.8 32.1 1.0 ND1 B:HIS44 3.0 38.6 1.0 CG B:HIS53 3.2 24.8 1.0 CE1 B:HIS53 3.2 23.8 1.0 CB B:CYS28 3.4 26.7 1.0 CB B:HIS53 3.4 34.4 1.0 CB B:ASP31 3.5 23.2 1.0 CD2 B:HIS44 3.7 25.3 1.0 OD1 B:ASP31 3.8 30.6 1.0 CG B:HIS44 4.0 35.7 1.0 N B:ASP31 4.1 31.5 1.0 NE2 B:HIS53 4.3 25.7 1.0 CD2 B:HIS53 4.3 24.8 1.0 CG1 B:VAL43 4.4 26.6 1.0 CA B:ASP31 4.4 29.2 1.0 CB B:ALA30 4.7 27.0 1.0 CD B:ARG55 4.7 43.4 1.0 CG B:ARG55 4.8 34.4 1.0 CA B:CYS28 4.8 29.3 1.0 C B:ALA30 4.9 34.7 1.0 CA B:HIS53 4.9 38.7 1.0 O B:ALA50 5.0 28.2 1.0

Zinc binding site 7 out of 12 in the Crystal Strcuture of the Tandem B-Box Domains of COL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Strcuture of the Tandem B-Box Domains of COL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:33.1 occ:1.00 SG B:CYS62 2.3 38.9 1.0 SG B:CYS59 2.3 30.8 1.0 SG B:CYS79 2.3 26.1 1.0 SG B:CYS82 2.4 39.5 1.0 CB B:CYS62 3.2 37.1 1.0 CB B:CYS82 3.2 26.0 1.0 CB B:CYS59 3.2 24.7 1.0 N B:CYS62 3.5 36.6 1.0 CB B:CYS79 3.6 29.5 1.0 CA B:CYS62 3.9 41.4 1.0 N B:CYS79 4.1 30.3 1.0 N B:CYS82 4.3 27.2 1.0 CA B:CYS82 4.3 28.3 1.0 CB B:SER61 4.4 37.9 1.0 CA B:CYS79 4.4 26.3 1.0 CB B:ALA65 4.6 39.8 1.0 C B:SER61 4.6 46.9 1.0 CA B:CYS59 4.6 27.0 1.0 OG B:SER61 4.7 38.4 1.0 N B:GLU63 4.8 42.5 1.0 C B:CYS62 4.8 52.1 1.0 CA B:SER61 4.9 39.4 1.0 N B:SER61 4.9 37.0 1.0

Zinc binding site 8 out of 12 in the Crystal Strcuture of the Tandem B-Box Domains of COL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Strcuture of the Tandem B-Box Domains of COL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:26.2 occ:1.00 OD2 B:ASP74 1.8 24.3 1.0 ND1 B:HIS96 2.2 22.9 1.0 NE2 B:HIS87 2.2 28.9 1.0 SG B:CYS71 2.3 27.1 1.0 CG B:ASP74 2.8 34.2 1.0 CD2 B:HIS87 3.1 22.4 1.0 CG B:HIS96 3.2 23.2 1.0 CE1 B:HIS96 3.2 24.4 1.0 CE1 B:HIS87 3.3 22.4 1.0 CB B:CYS71 3.3 26.6 1.0 CB B:HIS96 3.4 21.4 1.0 CB B:ASP74 3.5 23.5 1.0 OD1 B:ASP74 3.7 30.0 1.0 N B:ASP74 4.1 26.2 1.0 NE2 B:HIS96 4.3 21.9 1.0 CG B:HIS87 4.3 28.1 1.0 CD2 B:HIS96 4.3 24.3 1.0 O B:HOH321 4.3 35.3 1.0 ND1 B:HIS87 4.4 20.2 1.0 CA B:ASP74 4.4 23.1 1.0 CG2 B:ILE86 4.6 25.7 1.0 CA B:CYS71 4.7 27.6 1.0 CD B:ARG98 4.8 31.8 1.0 CB B:ALA73 4.9 24.1 1.0 CG B:ARG98 4.9 28.7 1.0 CA B:HIS96 4.9 28.4 1.0 C B:ALA73 5.0 30.9 1.0

Zinc binding site 9 out of 12 in the Crystal Strcuture of the Tandem B-Box Domains of COL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Strcuture of the Tandem B-Box Domains of COL2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:34.6 occ:1.00 SG C:CYS36 2.2 32.0 1.0 SG C:CYS39 2.3 36.0 1.0 SG C:CYS16 2.4 30.8 1.0 SG C:CYS19 2.4 36.8 1.0 CB C:CYS39 3.0 34.9 1.0 CB C:CYS16 3.2 30.1 1.0 CB C:CYS19 3.4 30.9 1.0 CB C:CYS36 3.4 33.0 1.0 N C:CYS19 3.8 38.5 1.0 N C:CYS36 3.9 29.5 1.0 N C:CYS39 4.1 37.5 1.0 CA C:CYS39 4.2 36.9 1.0 CA C:CYS19 4.2 39.1 1.0 CA C:CYS36 4.2 35.0 1.0 CB C:ALA22 4.6 34.4 1.0 CB C:THR18 4.6 35.6 1.0 CA C:CYS16 4.7 33.5 1.0 C C:CYS36 4.8 34.6 1.0 N C:ARG20 4.9 39.6 1.0 C C:THR18 4.9 39.7 1.0 O C:CYS36 4.9 28.5 1.0 C C:CYS19 4.9 45.3 1.0

Zinc binding site 10 out of 12 in the Crystal Strcuture of the Tandem B-Box Domains of COL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Strcuture of the Tandem B-Box Domains of COL2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:26.4 occ:1.00 OD2 C:ASP31 2.0 27.6 1.0 NE2 C:HIS44 2.1 24.2 1.0 ND1 C:HIS53 2.2 26.6 1.0 SG C:CYS28 2.3 25.8 1.0 CD2 C:HIS44 2.9 31.0 1.0 CG C:ASP31 3.0 31.6 1.0 CG C:HIS53 3.1 26.9 1.0 CE1 C:HIS53 3.2 26.3 1.0 CB C:HIS53 3.2 26.9 1.0 CE1 C:HIS44 3.3 29.8 1.0 CB C:CYS28 3.4 22.7 1.0 CB C:ASP31 3.7 23.1 1.0 OD1 C:ASP31 3.9 25.7 1.0 CG C:HIS44 4.1 38.4 1.0 N C:ASP31 4.2 25.9 1.0 CD2 C:HIS53 4.2 25.9 1.0 ND1 C:HIS44 4.3 28.5 1.0 NE2 C:HIS53 4.3 27.6 1.0 CB C:ALA30 4.6 24.6 1.0 CA C:ASP31 4.6 28.2 1.0 CG1 C:VAL43 4.6 26.7 1.0 CD C:ARG55 4.7 30.4 1.0 O C:HOH319 4.7 26.8 1.0 CA C:CYS28 4.8 23.0 1.0 CA C:HIS53 4.8 33.0 1.0 O C:ALA50 4.9 29.9 1.0 CG C:ARG55 4.9 25.9 1.0

X.Zeng, X.Lv, R.Liu, H.He, S.Liang, L.Chen, F.Zhang, L.Chen, Y.He, J.Du. Molecular Basis of Constans Oligomerization in Flowering Locus T Activation. J Integr Plant Biol V. 64 731 2022.
ISSN: ISSN 1744-7909
PubMed: 35023269
DOI: 10.1111/JIPB.13223