Zinc in PDB 3e6u: Crystal Structure of Human LANCL1

The structure of Crystal Structure of Human LANCL1, PDB code: 3e6u was solved by W.Zhang, G.Zhu, X.Li, Z.Rao, C.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.58 / 2.60
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	194.278, 194.278, 211.829, 90.00, 90.00, 120.00
R / Rfree (%)	24.6 / 27.5

The binding sites of Zinc atom in the Crystal Structure of Human LANCL1 (pdb code 3e6u). 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 Human LANCL1, PDB code: 3e6u:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Human LANCL1


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 Human LANCL1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:64.8 occ:1.00 ND1 A:HIS323 2.0 61.4 1.0 NE2 C:HIS-7 2.1 76.9 1.0 CD2 C:HIS-7 2.3 81.0 1.0 SG A:CYS322 2.4 61.8 1.0 SG A:CYS276 2.4 60.7 1.0 CE1 A:HIS323 2.9 60.7 1.0 CG A:HIS323 3.0 60.4 1.0 CB A:CYS276 3.2 59.8 1.0 CE1 C:HIS-7 3.4 80.0 1.0 CB A:CYS322 3.4 60.1 1.0 CB A:HIS323 3.5 60.3 1.0 CG C:HIS-7 3.6 83.3 1.0 C A:CYS322 3.7 60.2 1.0 O A:CYS322 3.7 60.2 1.0 N A:HIS323 4.0 60.3 1.0 NE2 A:HIS323 4.0 60.0 1.0 ND1 C:HIS-7 4.1 81.5 1.0 OH A:TYR62 4.1 58.5 1.0 CA A:CYS322 4.1 60.1 1.0 CD2 A:HIS323 4.1 60.2 1.0 CA A:HIS323 4.3 60.3 1.0 CA A:CYS276 4.5 59.8 1.0 N A:CYS276 4.7 59.5 1.0 CB C:HIS-7 4.8 85.4 1.0 ND1 A:HIS274 4.8 57.5 1.0 CD1 A:TRP275 4.9 57.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Human LANCL1


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 Human LANCL1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:66.7 occ:1.00 ND1 C:HIS323 2.0 61.3 1.0 NE2 A:HIS-7 2.1 78.2 1.0 SG C:CYS322 2.3 60.8 1.0 SG C:CYS276 2.4 62.5 1.0 CE1 C:HIS323 2.9 60.2 1.0 CD2 A:HIS-7 2.9 82.0 1.0 CE1 A:HIS-7 3.1 81.2 1.0 CG C:HIS323 3.2 60.0 1.0 CB C:CYS276 3.2 62.6 1.0 CB C:CYS322 3.4 59.4 1.0 CB C:HIS323 3.6 59.4 1.0 C C:CYS322 3.7 59.3 1.0 O C:CYS322 3.8 59.4 1.0 N C:HIS323 4.0 59.3 1.0 NE2 C:HIS323 4.1 59.8 1.0 CA C:CYS322 4.1 59.3 1.0 CG A:HIS-7 4.1 84.0 1.0 ND1 A:HIS-7 4.1 82.3 1.0 CD2 C:HIS323 4.2 59.9 1.0 OH C:TYR62 4.3 53.3 1.0 CA C:HIS323 4.4 59.4 1.0 CA C:CYS276 4.6 62.6 1.0 ND1 C:HIS274 4.6 60.0 1.0 N C:CYS276 4.8 62.3 1.0 O C:HOH508 4.8 43.6 1.0 CB C:HIS274 5.0 61.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Human LANCL1


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 Human LANCL1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:65.2 occ:1.00 ND1 B:HIS323 2.1 62.3 1.0 SG B:CYS276 2.4 60.3 1.0 SG B:CYS322 2.4 62.1 1.0 CE1 B:HIS323 2.6 61.3 1.0 O B:HOH572 2.7 46.4 1.0 CB B:CYS276 3.3 58.7 1.0 CG B:HIS323 3.3 61.0 1.0 CB B:CYS322 3.6 61.0 1.0 O B:CYS322 3.7 60.6 1.0 OH B:TYR62 3.7 68.9 1.0 C B:CYS322 3.8 60.8 1.0 NE2 B:HIS323 3.9 60.8 1.0 CB B:HIS323 4.0 60.5 1.0 N B:HIS323 4.2 60.5 1.0 CD2 B:HIS323 4.2 60.9 1.0 O B:HOH573 4.2 59.8 1.0 CA B:CYS322 4.3 61.0 1.0 O B:HOH561 4.4 61.8 1.0 CA B:CYS276 4.6 58.7 1.0 CA B:HIS323 4.7 60.3 1.0 N B:CYS276 4.9 58.8 1.0 CZ B:TYR62 5.0 69.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Human LANCL1


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 Human LANCL1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn504 b:67.7 occ:1.00 ND1 D:HIS323 2.0 64.1 1.0 SG D:CYS276 2.3 66.0 1.0 SG D:CYS322 2.4 63.8 1.0 O D:HOH548 2.6 51.6 1.0 CE1 D:HIS323 2.7 63.5 1.0 CG D:HIS323 3.2 62.3 1.0 CB D:CYS276 3.5 64.9 1.0 CB D:CYS322 3.5 63.0 1.0 OH D:TYR62 3.6 66.9 1.0 CB D:HIS323 3.8 61.2 1.0 C D:CYS322 3.8 62.3 1.0 O D:CYS322 3.9 62.1 1.0 NE2 D:HIS323 3.9 63.5 1.0 CD2 D:HIS323 4.1 62.9 1.0 N D:HIS323 4.2 61.5 1.0 O D:HOH549 4.2 59.5 1.0 CA D:CYS322 4.3 62.9 1.0 CA D:HIS323 4.6 60.9 1.0 CA D:CYS276 4.8 65.0 1.0 ND1 D:HIS274 4.8 66.2 1.0 N D:CYS276 4.9 65.0 1.0 CZ D:TYR62 4.9 67.2 1.0

W.Zhang, L.Wang, Y.Liu, J.Xu, G.Zhu, H.Cang, X.Li, M.Bartlam, K.Hensley, G.Li, Z.Rao, X.C.Zhang. Structure of Human Lanthionine Synthetase C-Like Protein 1 and Its Interaction with EPS8 and Glutathione Genes Dev. V. 23 1387 2009.
ISSN: ISSN 0890-9369
PubMed: 19528316
DOI: 10.1101/GAD.1789209