Zinc in PDB 7xt2: Crystal Structure of TRIM72

The structure of Crystal Structure of TRIM72, PDB code: 7xt2 was solved by C.Zhou, Y.M.Ma, L.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.14 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.571, 125.231, 174.537, 90, 91.45, 90
R / Rfree (%)	21.9 / 25.5

The binding sites of Zinc atom in the Crystal Structure of TRIM72 (pdb code 7xt2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of TRIM72, PDB code: 7xt2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of TRIM72


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 TRIM72 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:164.5 occ:1.00 ND1 B:HIS117 2.3 182.0 1.0 SG B:CYS97 2.3 187.0 1.0 ND1 B:HIS114 2.3 186.5 1.0 OD1 B:ASP100 2.6 191.6 1.0 CE1 B:HIS117 3.1 184.4 1.0 CG B:ASP100 3.1 191.3 1.0 CG B:HIS114 3.2 187.1 1.0 CB B:CYS97 3.3 188.5 1.0 CB B:HIS114 3.3 187.5 1.0 CE1 B:HIS114 3.3 189.7 1.0 CG B:HIS117 3.4 186.2 1.0 CB B:ASP100 3.5 192.0 1.0 CB B:HIS117 3.8 189.7 1.0 OD2 B:ASP100 3.9 190.9 1.0 CA B:HIS114 3.9 187.9 1.0 N B:ASP100 4.1 193.3 1.0 NE2 B:HIS117 4.3 186.0 1.0 CD2 B:HIS114 4.3 187.8 1.0 NE2 B:HIS114 4.4 190.0 1.0 CA B:ASP100 4.4 195.2 1.0 CD2 B:HIS117 4.4 186.2 1.0 O B:HIS114 4.6 186.6 1.0 C B:HIS114 4.7 187.1 1.0 CA B:CYS97 4.7 193.4 1.0 O B:SER113 4.7 188.5 1.0 CB B:GLN99 4.9 187.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of TRIM72


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 TRIM72 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:179.3 occ:1.00 NE2 B:HIS89 2.2 178.4 1.0 SG B:CYS108 2.3 163.5 1.0 SG B:CYS86 2.3 184.1 1.0 SG B:CYS105 2.3 190.8 1.0 CD2 B:HIS89 3.0 189.0 1.0 CE1 B:HIS89 3.1 177.4 1.0 CB B:CYS108 3.2 176.5 1.0 CB B:CYS86 3.4 190.5 1.0 CB B:CYS105 3.4 189.8 1.0 N B:CYS108 3.8 173.9 1.0 CA B:CYS108 4.0 178.0 1.0 CG B:HIS89 4.0 186.7 1.0 ND1 B:HIS89 4.0 183.0 1.0 N B:CYS105 4.1 188.2 1.0 CA B:CYS105 4.2 186.1 1.0 O B:CYS105 4.5 180.1 1.0 O B:HIS89 4.6 196.9 1.0 C B:CYS105 4.6 181.4 1.0 C B:VAL107 4.7 173.9 1.0 CB B:VAL107 4.8 173.1 1.0 CA B:CYS86 4.9 196.3 1.0 N B:HIS89 4.9 197.2 1.0 CB B:GLU88 5.0 182.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of TRIM72


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 TRIM72 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:143.8 occ:1.00 ND1 A:HIS89 2.1 147.9 1.0 SG A:CYS86 2.3 129.5 1.0 SG A:CYS108 2.3 121.5 1.0 SG A:CYS105 2.3 150.4 1.0 CE1 A:HIS89 3.1 146.1 1.0 CG A:HIS89 3.1 146.3 1.0 CB A:CYS108 3.3 135.1 1.0 CB A:CYS105 3.4 147.9 1.0 CB A:CYS86 3.4 146.3 1.0 CB A:HIS89 3.5 146.5 1.0 N A:CYS108 3.7 146.4 1.0 CA A:CYS108 3.9 139.3 1.0 N A:CYS105 4.1 137.3 1.0 CA A:CYS105 4.2 142.6 1.0 NE2 A:HIS89 4.2 148.1 1.0 CD2 A:HIS89 4.3 148.0 1.0 N A:HIS89 4.3 155.0 1.0 CA A:HIS89 4.5 149.4 1.0 C A:CYS105 4.5 143.7 1.0 O A:CYS105 4.6 141.8 1.0 C A:VAL107 4.6 150.4 1.0 CB A:VAL107 4.7 147.3 1.0 CA A:CYS86 4.8 150.8 1.0 N A:VAL107 5.0 149.4 1.0 CB A:GLU88 5.0 157.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of TRIM72


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 TRIM72 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:119.0 occ:1.00 ND1 A:HIS114 2.2 114.4 1.0 ND1 A:HIS117 2.3 141.6 1.0 SG A:CYS97 2.3 126.3 1.0 OD2 A:ASP100 2.7 135.8 1.0 CE1 A:HIS117 2.9 143.2 1.0 CG A:ASP100 3.0 132.3 1.0 CG A:HIS114 3.2 127.2 1.0 CE1 A:HIS114 3.2 118.4 1.0 CB A:CYS97 3.3 123.2 1.0 CB A:ASP100 3.4 129.1 1.0 CG A:HIS117 3.4 144.3 1.0 CB A:HIS114 3.4 137.0 1.0 OD1 A:ASP100 3.6 134.9 1.0 CA A:HIS114 3.8 142.3 1.0 CB A:HIS117 3.9 144.4 1.0 NE2 A:HIS117 4.1 143.9 1.0 N A:ASP100 4.1 120.9 1.0 NE2 A:HIS114 4.3 129.5 1.0 CD2 A:HIS114 4.3 127.8 1.0 CD2 A:HIS117 4.3 145.5 1.0 CA A:ASP100 4.4 122.5 1.0 CA A:CYS97 4.7 122.3 1.0 N A:HIS114 4.8 143.1 1.0 C A:HIS114 4.8 149.6 1.0 O A:HIS114 4.9 156.1 1.0 CB A:GLN99 5.0 135.6 1.0

Y.Ma, L.Ding, Z.Li, C.Zhou. Structural Basis For TRIM72 Oligomerization During Membrane Damage Repair Nat Commun V. 14 1555 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-37198-1