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Zinc in PDB 3e6u: Crystal Structure of Human LANCL1

Protein crystallography data

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

Zinc Binding Sites:

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 3e6u

Go back to Zinc Binding Sites List in 3e6u
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 3e6u

Go back to Zinc Binding Sites List in 3e6u
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 3e6u

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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 3e6u

Go back to Zinc Binding Sites List in 3e6u
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

Reference:

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
Page generated: Wed Dec 16 04:15:02 2020

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