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Zinc in PDB 7lzp: Lc/A-Jpu-B9-Jpu-A11-Jpu-G11

Enzymatic activity of Lc/A-Jpu-B9-Jpu-A11-Jpu-G11

All present enzymatic activity of Lc/A-Jpu-B9-Jpu-A11-Jpu-G11:
3.4.24.69;

Protein crystallography data

The structure of Lc/A-Jpu-B9-Jpu-A11-Jpu-G11, PDB code: 7lzp was solved by K.Lam, R.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.06 / 2.86
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 132.604, 132.604, 413.03, 90, 90, 120
R / Rfree (%) 23.5 / 27.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Lc/A-Jpu-B9-Jpu-A11-Jpu-G11 (pdb code 7lzp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Lc/A-Jpu-B9-Jpu-A11-Jpu-G11, PDB code: 7lzp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7lzp

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Zinc binding site 1 out of 4 in the Lc/A-Jpu-B9-Jpu-A11-Jpu-G11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Lc/A-Jpu-B9-Jpu-A11-Jpu-G11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:60.2
occ:1.00
OG1 A:THR176 3.2 59.0 1.0
CG2 A:THR176 4.2 46.3 1.0
N A:LEU175 4.2 62.7 1.0
N A:THR176 4.3 47.6 1.0
CB A:THR176 4.3 48.8 1.0
CA A:ASN174 4.3 52.1 1.0
O D:LYS438 4.5 71.3 1.0
C A:ASN174 4.5 55.4 1.0
OD1 A:ASN174 4.5 68.7 1.0
CB A:ASN174 4.6 52.2 1.0
OG A:SER167 4.6 64.2 1.0
NH1 A:ARG177 4.8 49.2 1.0
C D:LYS438 4.8 64.4 1.0
CA A:THR176 4.9 46.0 1.0
CG A:ASN174 4.9 58.4 1.0
CA A:GLY169 4.9 64.5 1.0

Zinc binding site 2 out of 4 in 7lzp

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Zinc binding site 2 out of 4 in the Lc/A-Jpu-B9-Jpu-A11-Jpu-G11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Lc/A-Jpu-B9-Jpu-A11-Jpu-G11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:48.3
occ:1.00
NE2 A:HIS227 1.9 63.4 1.0
OE1 A:GLU262 1.9 78.9 1.0
OE2 A:GLU262 2.2 68.3 1.0
CD A:GLU262 2.3 65.9 1.0
NE2 A:HIS223 2.4 63.0 1.0
CE1 A:HIS223 2.5 66.2 1.0
CD2 A:HIS227 2.8 55.5 1.0
CE1 A:HIS227 3.0 53.7 1.0
O A:HOH601 3.0 47.5 1.0
CD2 A:HIS223 3.5 62.3 1.0
ND1 A:HIS223 3.6 66.5 1.0
CG A:GLU262 3.8 57.7 1.0
CG A:HIS227 3.9 53.5 1.0
ND1 A:HIS227 4.0 53.2 1.0
CG A:HIS223 4.1 55.1 1.0
OE2 A:GLU224 4.2 64.5 1.0
OH A:TYR366 4.2 43.8 1.0
CE1 A:TYR366 4.4 48.8 1.0
CB A:GLU262 4.6 43.9 1.0
CZ A:TYR366 4.6 53.4 1.0
CA A:GLU262 4.7 43.0 1.0
CD A:GLU224 4.8 60.2 1.0
OE1 A:GLU224 4.8 62.7 1.0

Zinc binding site 3 out of 4 in 7lzp

Go back to Zinc Binding Sites List in 7lzp
Zinc binding site 3 out of 4 in the Lc/A-Jpu-B9-Jpu-A11-Jpu-G11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Lc/A-Jpu-B9-Jpu-A11-Jpu-G11 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:56.6
occ:1.00
OG1 D:THR176 3.2 72.8 1.0
CA D:ASN174 4.1 50.6 1.0
N D:LEU175 4.1 52.4 1.0
N D:THR176 4.2 51.6 1.0
CG2 D:THR176 4.2 46.3 1.0
CB D:THR176 4.3 59.1 1.0
C D:ASN174 4.4 50.6 1.0
CB D:ASN174 4.4 59.5 1.0
OD1 D:ASN174 4.4 64.0 1.0
NH1 D:ARG177 4.7 56.4 1.0
O A:LYS438 4.8 63.3 1.0
CG D:ASN174 4.8 63.4 1.0
OG D:SER167 4.8 62.9 1.0
CA D:THR176 4.9 54.5 1.0
CA D:GLY169 4.9 56.2 1.0

Zinc binding site 4 out of 4 in 7lzp

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Zinc binding site 4 out of 4 in the Lc/A-Jpu-B9-Jpu-A11-Jpu-G11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Lc/A-Jpu-B9-Jpu-A11-Jpu-G11 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:47.5
occ:1.00
OE1 D:GLU262 2.0 82.5 1.0
OE2 D:GLU262 2.3 71.6 1.0
NE2 D:HIS227 2.3 59.4 1.0
CD D:GLU262 2.4 69.4 1.0
NE2 D:HIS223 2.5 57.1 1.0
CE1 D:HIS223 2.5 60.0 1.0
O D:HOH601 2.7 47.5 1.0
CD2 D:HIS227 3.0 62.5 1.0
CE1 D:HIS227 3.4 62.3 1.0
ND1 D:HIS223 3.6 60.2 1.0
CD2 D:HIS223 3.6 58.2 1.0
CG D:GLU262 3.9 67.0 1.0
OE2 D:GLU224 4.0 57.8 1.0
CG D:HIS223 4.1 56.0 1.0
CG D:HIS227 4.1 57.0 1.0
ND1 D:HIS227 4.3 61.8 1.0
OH D:TYR366 4.5 50.1 1.0
CE1 D:TYR366 4.6 50.7 1.0
CB D:GLU262 4.7 55.6 1.0
CD D:GLU224 4.7 60.1 1.0
OE1 D:GLU224 4.8 61.0 1.0
CZ D:TYR366 4.9 52.5 1.0
CA D:GLU262 5.0 55.4 1.0

Reference:

K.Lam, R.Jin. Probing the Structure and Function of the Protease Domain of Botulinum Neurotoxins Using Single-Domain Antibodies. Plos Pathog. 2021.
ISSN: ESSN 1553-7374
Page generated: Fri Dec 24 10:38:50 2021

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