Zinc in PDB 7dh7: Crystal Structure of Apo Xczur

The structure of Crystal Structure of Apo Xczur, PDB code: 7dh7 was solved by F.M.Liu, Z.H.Su, P.Chen, X.L.Tian, L.J.Wu, D.J.Tang, P.F.Li, H.T.Deng, J.L.Tang, Z.H.Ming, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.94 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	153.391, 77.871, 73.063, 90, 103.07, 90
R / Rfree (%)	21.9 / 27.6

The binding sites of Zinc atom in the Crystal Structure of Apo Xczur (pdb code 7dh7). 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 Apo Xczur, PDB code: 7dh7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Apo Xczur


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 Apo Xczur within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:29.0 occ:1.00 SG A:CYS164 2.1 37.6 1.0 SG A:CYS127 2.4 28.9 1.0 SG A:CYS124 2.5 25.4 1.0 SG A:CYS167 2.7 43.9 1.0 CB A:CYS127 2.9 31.0 1.0 CB A:CYS164 3.1 30.8 1.0 CB A:CYS124 3.2 20.2 1.0 CB A:CYS167 3.5 39.4 1.0 N A:CYS127 3.8 26.6 1.0 CA A:CYS127 3.9 33.5 1.0 N A:CYS164 4.0 30.2 1.0 CA A:CYS164 4.1 26.8 1.0 N A:CYS167 4.2 69.2 1.0 CA A:CYS167 4.4 44.9 1.0 CA A:CYS124 4.7 19.7 1.0 CB A:ARG126 4.7 39.3 1.0 C A:CYS127 4.7 33.5 1.0 C A:ARG126 4.8 31.4 1.0 C A:CYS164 4.9 31.0 1.0 O A:CYS164 5.0 26.8 1.0 N A:HIS128 5.0 27.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Apo Xczur


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 Apo Xczur within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:39.7 occ:1.00 SG B:CYS164 2.2 58.6 1.0 SG B:CYS127 2.3 64.9 1.0 SG B:CYS167 2.4 33.8 1.0 SG B:CYS124 2.5 44.1 1.0 CB B:CYS164 2.9 43.5 1.0 CB B:CYS127 3.0 41.9 1.0 CB B:CYS124 3.1 32.4 1.0 CB B:CYS167 3.3 34.4 1.0 N B:CYS127 3.4 33.7 1.0 CA B:CYS127 3.8 40.6 1.0 CA B:CYS164 4.1 35.0 1.0 N B:CYS164 4.1 32.8 1.0 N B:CYS167 4.2 45.1 1.0 CA B:CYS167 4.4 35.2 1.0 CB B:ARG126 4.5 49.6 1.0 C B:ARG126 4.5 35.9 1.0 CA B:CYS124 4.6 26.7 1.0 C B:CYS127 4.8 38.7 1.0 C B:CYS164 4.9 40.8 1.0 CA B:ARG126 4.9 39.6 1.0 N B:ARG126 4.9 38.7 1.0 N B:HIS128 5.0 39.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Apo Xczur


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 Apo Xczur within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:28.5 occ:1.00 SG C:CYS124 2.3 25.0 1.0 SG C:CYS167 2.4 34.0 1.0 SG C:CYS127 2.5 35.0 1.0 SG C:CYS164 2.7 43.8 1.0 CB C:CYS167 3.1 25.5 1.0 CB C:CYS164 3.1 32.6 1.0 CB C:CYS127 3.2 24.5 1.0 CB C:CYS124 3.2 24.6 1.0 N C:CYS127 3.6 22.8 1.0 O C:HOH376 3.9 30.5 1.0 CA C:CYS127 4.0 25.0 1.0 N C:CYS164 4.0 27.0 1.0 CA C:CYS164 4.1 30.4 1.0 N C:CYS167 4.1 29.0 1.0 CA C:CYS167 4.2 33.6 1.0 O C:HOH374 4.2 30.9 1.0 CB C:ARG126 4.6 25.2 1.0 CA C:CYS124 4.6 23.5 1.0 C C:ARG126 4.7 23.8 1.0 C C:CYS164 4.8 31.4 1.0 O C:CYS164 4.9 31.6 1.0 C C:CYS127 5.0 22.2 1.0 O C:HOH349 5.0 42.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Apo Xczur


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 Apo Xczur within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:35.0 occ:1.00 SG D:CYS124 2.3 27.7 1.0 SG D:CYS167 2.4 34.0 1.0 SG D:CYS164 2.6 33.4 1.0 CB D:CYS127 2.7 36.9 1.0 SG D:CYS127 2.7 60.8 1.0 CB D:CYS164 3.1 33.4 1.0 CB D:CYS167 3.2 30.8 1.0 CB D:CYS124 3.2 28.4 1.0 N D:CYS127 3.4 28.8 1.0 CA D:CYS127 3.6 33.1 1.0 N D:CYS164 4.0 31.4 1.0 CA D:CYS164 4.0 33.5 1.0 N D:CYS167 4.2 33.1 1.0 CA D:CYS167 4.3 33.5 1.0 C D:ARG126 4.6 29.0 1.0 CA D:CYS124 4.7 27.2 1.0 C D:CYS164 4.8 36.2 1.0 C D:CYS127 4.8 25.4 1.0 CB D:ARG126 4.8 37.6 1.0 O D:CYS164 4.9 33.7 1.0

F.Liu, Z.Su, P.Chen, X.Tian, L.Wu, D.J.Tang, P.Li, H.Deng, P.Ding, Q.Fu, J.L.Tang, Z.Ming. Structural Basis For Zinc-Induced Activation of A Zinc Uptake Transcriptional Regulator. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 34048589
DOI: 10.1093/NAR/GKAB432