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Zinc in PDB 6bvd: Structure of Botulinum Neurotoxin Serotype Ha Light Chain

Protein crystallography data

The structure of Structure of Botulinum Neurotoxin Serotype Ha Light Chain, PDB code: 6bvd was solved by R.Jin, K.Lam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.05 / 2.09
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 76.249, 160.745, 219.099, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 19.1

Other elements in 6bvd:

The structure of Structure of Botulinum Neurotoxin Serotype Ha Light Chain also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Botulinum Neurotoxin Serotype Ha Light Chain (pdb code 6bvd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Botulinum Neurotoxin Serotype Ha Light Chain, PDB code: 6bvd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6bvd

Go back to Zinc Binding Sites List in 6bvd
Zinc binding site 1 out of 2 in the Structure of Botulinum Neurotoxin Serotype Ha Light Chain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Botulinum Neurotoxin Serotype Ha Light Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:71.9
occ:0.37
OE1 A:GLU264 2.0 34.1 1.0
OXT A:ACT502 2.0 57.6 1.0
NE2 A:HIS230 2.1 23.1 1.0
NE2 A:HIS226 2.2 24.4 1.0
CE1 A:HIS230 2.9 30.5 1.0
CD A:GLU264 3.1 32.2 1.0
C A:ACT502 3.1 46.9 1.0
CD2 A:HIS226 3.1 30.4 1.0
CE1 A:HIS226 3.2 34.0 1.0
CD2 A:HIS230 3.2 16.8 1.0
OE2 A:GLU264 3.5 41.8 1.0
O A:ACT502 3.7 50.1 1.0
CH3 A:ACT502 4.1 41.3 1.0
ND1 A:HIS230 4.1 24.6 1.0
CE1 A:TYR366 4.2 34.5 1.0
ND1 A:HIS226 4.2 30.3 1.0
CG A:HIS230 4.3 17.2 1.0
CG A:HIS226 4.3 28.5 1.0
O A:HOH805 4.3 25.8 1.0
CG A:GLU264 4.4 24.1 1.0
OE2 A:GLU227 4.4 28.6 1.0
CG2 A:THR267 4.6 19.6 1.0
O A:HOH647 4.6 37.1 1.0
CB A:GLU264 4.7 20.9 1.0
CA A:GLU264 4.8 25.5 1.0
OH A:TYR366 4.8 48.7 1.0
O A:HOH601 4.8 31.5 1.0
CB A:THR267 4.9 26.3 1.0
CZ A:TYR366 4.9 41.6 1.0
CD1 A:TYR366 5.0 31.3 1.0

Zinc binding site 2 out of 2 in 6bvd

Go back to Zinc Binding Sites List in 6bvd
Zinc binding site 2 out of 2 in the Structure of Botulinum Neurotoxin Serotype Ha Light Chain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Botulinum Neurotoxin Serotype Ha Light Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:67.6
occ:0.39
O B:ACT501 1.9 48.8 1.0
OE1 B:GLU264 2.0 49.3 1.0
NE2 B:HIS230 2.2 40.5 1.0
NE2 B:HIS226 2.4 42.7 1.0
O B:HOH604 2.8 34.3 1.0
CE1 B:HIS230 2.9 35.7 1.0
CD B:GLU264 3.0 44.5 1.0
C B:ACT501 3.0 43.7 1.0
CE1 B:HIS226 3.3 37.9 1.0
OE2 B:GLU264 3.3 48.6 1.0
CD2 B:HIS226 3.3 37.5 1.0
CD2 B:HIS230 3.3 32.4 1.0
OXT B:ACT501 3.7 59.5 1.0
ND1 B:HIS230 4.1 37.4 1.0
CH3 B:ACT501 4.1 43.6 1.0
CE1 B:TYR366 4.2 36.8 1.0
CG B:HIS230 4.4 33.6 1.0
CG B:GLU264 4.4 31.2 1.0
O B:HOH745 4.4 40.3 1.0
ND1 B:HIS226 4.4 39.3 1.0
CG B:HIS226 4.4 33.0 1.0
CG2 B:THR267 4.5 28.0 1.0
O B:HOH640 4.5 36.4 1.0
CB B:GLU264 4.7 21.5 1.0
OE2 B:GLU227 4.7 33.0 1.0
CA B:GLU264 4.7 30.1 1.0
CB B:THR267 4.8 23.9 1.0
CD1 B:TYR366 4.9 36.8 1.0
OH B:TYR366 5.0 51.2 1.0
CZ B:TYR366 5.0 39.8 1.0

Reference:

K.H.Lam, S.Sikorra, J.Weisemann, H.Maatsch, K.Perry, A.Rummel, T.Binz, R.Jin. Structural and Biochemical Characterization of the Protease Domain of the Mosaic Botulinum Neurotoxin Type Ha. Pathog Dis V. 76 2018.
ISSN: ISSN 2049-632X
PubMed: 29688327
DOI: 10.1093/FEMSPD/FTY044
Page generated: Wed Dec 16 11:33:32 2020

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