Zinc in PDB 7f09: Crystal Structure of the Hlh-Lz Domain of Human TFE3

The structure of Crystal Structure of the Hlh-Lz Domain of Human TFE3, PDB code: 7f09 was solved by G.Yang, P.Li, Z.Liu, S.Wu, C.Zhuang, H.Qiao, P.Fang, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.83 / 2.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	27.94, 47.37, 69.96, 85.24, 87.21, 88.32
R / Rfree (%)	22.1 / 24.5

The binding sites of Zinc atom in the Crystal Structure of the Hlh-Lz Domain of Human TFE3 (pdb code 7f09). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Hlh-Lz Domain of Human TFE3, PDB code: 7f09:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Hlh-Lz Domain of Human TFE3


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 Hlh-Lz Domain of Human TFE3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:144.4 occ:1.00 O B:HOH609 2.2 73.4 1.0 O B:HOH601 2.4 75.0 1.0 NE B:ARG365 2.7 82.0 1.0 CG B:ARG365 2.8 57.7 1.0 CD B:ARG365 3.0 73.8 1.0 CZ B:ARG365 3.7 70.0 1.0 O A:GLY386 3.8 54.4 1.0 O B:PHE360 4.1 72.6 1.0 CB B:ARG365 4.1 45.2 1.0 O B:ASN361 4.1 36.8 1.0 NH1 B:ARG365 4.1 78.5 1.0 CA A:GLY386 4.2 48.7 1.0 C B:ASN361 4.3 41.0 1.0 C A:GLY386 4.4 44.9 1.0 CD2 B:PHE360 4.5 48.9 1.0 N B:ILE362 4.6 51.8 1.0 CA B:ILE362 4.7 54.5 1.0 C B:PHE360 4.7 64.7 1.0 NH2 B:ARG365 4.8 66.8 1.0 CB A:LYS390 4.9 54.3 1.0 CA B:ASN361 4.9 50.8 1.0 CG1 B:ILE362 5.0 58.7 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Hlh-Lz Domain of Human TFE3


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 Hlh-Lz Domain of Human TFE3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:51.7 occ:0.79 OE2 B:GLU368 2.1 52.4 1.0 CD B:GLU368 2.9 43.3 1.0 OE1 B:GLU368 3.1 48.6 1.0 NH1 A:ARG397 4.0 79.1 0.9 O A:HOH610 4.3 62.6 1.0 CG B:GLU368 4.4 45.7 1.0 O A:HOH611 4.5 54.9 1.0 NH2 B:ARG365 4.5 66.8 1.0 CZ B:PHE360 4.6 44.1 1.0 O A:HOH607 4.6 78.9 1.0 CE2 B:PHE360 4.8 44.7 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Hlh-Lz Domain of Human TFE3


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 Hlh-Lz Domain of Human TFE3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:64.0 occ:0.68 O B:HOH606 2.2 49.6 1.0 O B:GLY359 2.2 85.0 1.0 N B:GLY359 2.2 53.2 1.0 C B:GLY359 3.0 70.0 1.0 CA B:GLY359 3.2 62.1 1.0 O2 B:EDO505 4.0 80.8 1.0 N B:PHE360 4.3 65.3 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Hlh-Lz Domain of Human TFE3


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 Hlh-Lz Domain of Human TFE3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:164.5 occ:1.00 OE1 C:GLU368 2.5 80.2 1.0 O C:HOH605 2.7 91.2 1.0 NH1 D:ARG397 3.4 74.3 0.9 CD C:GLU368 3.4 81.5 1.0 OE2 C:GLU368 3.5 83.8 1.0 O C:HOH607 3.6 95.2 1.0 NH2 C:ARG365 3.8 116.8 1.0 NH1 C:ARG365 4.0 107.5 1.0 O D:HOH602 4.2 86.7 1.0 CZ D:ARG397 4.3 70.2 0.9 CZ C:ARG365 4.4 110.0 1.0 NH2 D:ARG397 4.4 67.5 0.9 CG C:GLU368 4.8 66.6 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Hlh-Lz Domain of Human TFE3


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 Hlh-Lz Domain of Human TFE3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:57.3 occ:0.82 OD2 C:ASP364 1.9 63.0 0.7 O C:GLY359 2.3 60.1 1.0 N C:GLY359 2.4 61.7 1.0 C C:GLY359 3.0 63.7 1.0 CG C:ASP364 3.0 52.3 0.7 CA C:GLY359 3.1 70.7 1.0 OD1 C:ASP364 3.5 57.6 0.7 N C:PHE360 4.2 56.2 1.0 CB C:ASP364 4.3 46.9 0.7 O C:PHE360 4.7 55.3 1.0 CA C:PHE360 4.9 52.1 1.0 C C:PHE360 4.9 53.6 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the Hlh-Lz Domain of Human TFE3


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 Hlh-Lz Domain of Human TFE3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:79.3 occ:0.80 O D:HOH608 2.1 66.9 1.0 O D:GLY359 2.1 107.0 1.0 N D:GLY359 2.1 114.9 1.0 CA D:GLY359 2.7 111.9 1.0 C D:GLY359 2.7 101.8 1.0 N D:PHE360 4.0 69.7 1.0 O D:HOH610 4.1 83.2 1.0 ND2 D:ASN361 4.2 47.5 0.7 O D:HOH607 4.8 75.6 1.0 CA D:PHE360 4.9 55.2 1.0

G.Yang, P.Li, Z.Liu, S.Wu, C.Zhuang, H.Qiao, L.Zheng, P.Fang, C.Lei, J.Wang. Structural Basis For the Dimerization Mechanism of Human Transcription Factor E3. Biochem.Biophys.Res.Commun. V. 569 41 2021.
ISSN: ESSN 1090-2104
PubMed: 34225079
DOI: 10.1016/J.BBRC.2021.06.091