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Zinc in PDB 7cm0: Crystal Structure of A Glutaminyl Cyclase in Complex with Nhv-1009

Enzymatic activity of Crystal Structure of A Glutaminyl Cyclase in Complex with Nhv-1009

All present enzymatic activity of Crystal Structure of A Glutaminyl Cyclase in Complex with Nhv-1009:
2.3.2.5;

Protein crystallography data

The structure of Crystal Structure of A Glutaminyl Cyclase in Complex with Nhv-1009, PDB code: 7cm0 was solved by J.W.Lee, J.Y.Song, T.H.Jang, J.H.Ha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.74 / 2.20
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 116.896, 116.896, 99.459, 90, 90, 120
R / Rfree (%) 29 / 33.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Glutaminyl Cyclase in Complex with Nhv-1009 (pdb code 7cm0). 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 A Glutaminyl Cyclase in Complex with Nhv-1009, PDB code: 7cm0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7cm0

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Zinc binding site 1 out of 4 in the Crystal Structure of A Glutaminyl Cyclase in Complex with Nhv-1009


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 A Glutaminyl Cyclase in Complex with Nhv-1009 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:43.0
occ:1.00
NE2 A:HIS330 1.9 33.6 1.0
N20 A:G5R701 2.0 31.8 1.0
OD2 A:ASP159 2.1 32.8 1.0
OE2 A:GLU202 2.4 34.4 1.0
CD2 A:HIS330 2.6 37.1 1.0
CG A:ASP159 2.8 44.3 1.0
OE1 A:GLU202 2.9 55.5 1.0
C19 A:G5R701 2.9 29.3 1.0
OD1 A:ASP159 2.9 44.0 1.0
CD A:GLU202 3.0 42.6 1.0
CE1 A:HIS330 3.0 36.1 1.0
C21 A:G5R701 3.2 31.0 1.0
NE1 A:TRP329 3.8 32.6 1.0
CG A:HIS330 3.8 36.6 1.0
ND1 A:HIS330 4.0 32.3 1.0
CB A:ASP159 4.1 45.1 1.0
N18 A:G5R701 4.1 34.1 1.0
C22 A:G5R701 4.3 34.9 1.0
CE2 A:TRP329 4.4 31.0 1.0
CD1 A:TRP329 4.5 32.5 1.0
CG A:GLU202 4.5 39.7 1.0
OE1 A:GLU201 4.6 32.1 1.0
CZ2 A:TRP329 4.6 40.4 1.0
O A:HOH812 5.0 38.8 1.0

Zinc binding site 2 out of 4 in 7cm0

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Zinc binding site 2 out of 4 in the Crystal Structure of A Glutaminyl Cyclase in Complex with Nhv-1009


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 A Glutaminyl Cyclase in Complex with Nhv-1009 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:47.1
occ:1.00
NE2 B:HIS330 1.9 34.2 1.0
OD2 B:ASP159 2.0 36.5 1.0
N20 B:G5R401 2.0 47.8 1.0
OE2 B:GLU202 2.1 37.8 1.0
C21 B:G5R401 2.5 40.4 1.0
CD2 B:HIS330 2.7 33.0 1.0
CD B:GLU202 2.8 38.0 1.0
OE1 B:GLU202 2.8 42.7 1.0
CE1 B:HIS330 2.9 32.2 1.0
CG B:ASP159 3.0 42.4 1.0
OD1 B:ASP159 3.3 57.0 1.0
C19 B:G5R401 3.4 38.9 1.0
NE1 B:TRP329 3.6 30.3 1.0
C22 B:G5R401 3.8 39.2 1.0
CG B:HIS330 3.9 34.6 1.0
ND1 B:HIS330 3.9 31.7 1.0
CE2 B:TRP329 4.2 28.2 1.0
N18 B:G5R401 4.2 39.2 1.0
CG B:GLU202 4.2 32.0 1.0
CB B:ASP159 4.3 48.4 1.0
OE1 B:GLU201 4.3 36.1 1.0
CZ2 B:TRP329 4.4 34.8 1.0
CD1 B:TRP329 4.4 36.2 1.0

Zinc binding site 3 out of 4 in 7cm0

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Zinc binding site 3 out of 4 in the Crystal Structure of A Glutaminyl Cyclase in Complex with Nhv-1009


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 A Glutaminyl Cyclase in Complex with Nhv-1009 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:47.9
occ:1.00
OE2 C:GLU202 2.0 40.6 1.0
N20 C:G5R401 2.0 40.2 1.0
NE2 C:HIS330 2.2 32.9 1.0
C21 C:G5R401 2.3 33.9 1.0
OD1 C:ASP159 2.3 54.4 1.0
CD2 C:HIS330 2.8 35.2 1.0
CD C:GLU202 2.8 44.6 1.0
OD2 C:ASP159 3.0 51.1 1.0
OE1 C:GLU202 3.0 48.6 1.0
CG C:ASP159 3.0 52.9 1.0
CE1 C:HIS330 3.3 35.9 1.0
C19 C:G5R401 3.4 48.0 1.0
C22 C:G5R401 3.7 36.6 1.0
NE1 C:TRP329 3.7 29.8 1.0
CG C:HIS330 4.0 35.4 1.0
N18 C:G5R401 4.2 37.3 1.0
ND1 C:HIS330 4.3 38.5 1.0
CG C:GLU202 4.3 39.8 1.0
CE2 C:TRP329 4.4 34.4 1.0
CD1 C:TRP329 4.4 27.6 1.0
CB C:ASP159 4.4 50.0 1.0
OE1 C:GLU201 4.6 35.9 1.0
CZ2 C:TRP329 4.7 42.7 1.0
C23 C:G5R401 4.8 27.9 1.0
CA C:ASP159 5.0 48.8 1.0
O C:HOH516 5.0 33.7 1.0

Zinc binding site 4 out of 4 in 7cm0

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Zinc binding site 4 out of 4 in the Crystal Structure of A Glutaminyl Cyclase in Complex with Nhv-1009


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 A Glutaminyl Cyclase in Complex with Nhv-1009 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:42.4
occ:1.00
NE2 D:HIS330 1.8 39.0 1.0
OD2 D:ASP159 2.0 36.1 1.0
OE2 D:GLU202 2.1 29.3 1.0
N20 D:G5R401 2.2 31.8 1.0
CD2 D:HIS330 2.6 37.4 1.0
CG D:ASP159 2.7 44.1 1.0
OD1 D:ASP159 2.9 43.2 1.0
CD D:GLU202 2.9 38.0 1.0
C19 D:G5R401 2.9 37.0 1.0
CE1 D:HIS330 2.9 35.3 1.0
OE1 D:GLU202 3.0 41.0 1.0
C21 D:G5R401 3.4 34.3 1.0
NE1 D:TRP329 3.8 34.0 1.0
CG D:HIS330 3.8 36.0 1.0
ND1 D:HIS330 3.9 37.4 1.0
CB D:ASP159 4.0 40.0 1.0
N18 D:G5R401 4.2 35.6 1.0
CG D:GLU202 4.3 32.4 1.0
CE2 D:TRP329 4.4 34.3 1.0
C22 D:G5R401 4.4 42.0 1.0
CD1 D:TRP329 4.5 34.2 1.0
OE1 D:GLU201 4.6 34.8 1.0
CZ2 D:TRP329 4.7 40.5 1.0
CD2 D:LEU249 4.9 33.8 1.0

Reference:

N.Van Manh, V.H.Hoang, V.T.H.Ngo, J.Ann, T.H.Jang, J.H.Ha, J.Y.Song, H.J.Ha, H.Kim, Y.H.Kim, J.Lee, J.Lee. Discovery of Highly Potent Human Glutaminyl Cyclase (Qc) Inhibitors As Anti-Alzheimer'S Agents By the Combination of Pharmacophore-Based and Structure-Based Design. Eur.J.Med.Chem. V. 226 13819 2021.
ISSN: ISSN 0223-5234
PubMed: 34536669
DOI: 10.1016/J.EJMECH.2021.113819
Page generated: Fri Dec 24 10:37:50 2021

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