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Zinc in PDB 6yi1: Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala

Enzymatic activity of Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala

All present enzymatic activity of Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala:
2.3.2.5;

Protein crystallography data

The structure of Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala, PDB code: 6yi1 was solved by O.Kupski, V.Sautner, K.Tittmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 88.28 / 1.92
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 120.380, 120.380, 331.910, 90.00, 90.00, 120.00
R / Rfree (%) 15.9 / 18.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala (pdb code 6yi1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala, PDB code: 6yi1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 6yi1

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Zinc binding site 1 out of 10 in the Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala


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 Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:18.3
occ:1.00
 OD2 A:ASP159 2.0 21.5 1.0
OE2 A:GLU202 2.1 20.6 1.0
NE2 A:HIS330 2.1 19.1 1.0
N2 A:ORT419 2.1 19.8 1.0
O3 A:ORT419 2.3 18.8 1.0
CD A:GLU202 2.8 19.1 1.0
OE1 A:GLU202 2.8 16.3 1.0
CG A:ASP159 2.8 20.9 1.0
N1 A:ORT419 3.0 16.0 1.0
C5 A:ORT419 3.0 17.3 1.0
OD1 A:ASP159 3.0 20.8 1.0
CD2 A:HIS330 3.0 16.9 1.0
CE1 A:HIS330 3.1 17.1 1.0
NE1 A:TRP329 4.1 18.8 1.0
ND1 A:HIS330 4.2 16.2 1.0
CG A:HIS330 4.2 17.4 1.0
CG A:GLU202 4.2 17.7 1.0
O A:HOH518 4.3 18.6 1.0
OE1 A:GLU201 4.3 16.1 1.0
CB A:ASP159 4.3 17.2 1.0
N4 A:ORT419 4.3 17.0 1.0
CD2 A:LEU249 4.3 15.5 1.0
C4 A:ORT419 4.5 15.8 1.0
O A:HOH572 4.6 17.2 1.0
CD1 A:TRP329 4.7 16.9 1.0
NE2 A:HIS140 4.7 18.1 1.0

Zinc binding site 2 out of 10 in 6yi1

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Zinc binding site 2 out of 10 in the Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala


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 Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:20.2
occ:0.39
 OD1 A:ASP107 1.8 29.4 1.0
NE2 A:HIS218 2.0 25.4 1.0
NZ A:LYS222 2.3 44.1 1.0
O A:HOH699 2.4 58.3 1.0
CG A:ASP107 2.9 26.2 1.0
CE1 A:HIS218 3.0 25.1 1.0
CD2 A:HIS218 3.0 24.6 1.0
OD2 A:ASP107 3.3 27.3 1.0
CE A:LYS222 3.5 41.3 1.0
CD A:LYS222 3.8 33.2 1.0
O B:HOH650 4.1 32.1 1.0
ND1 A:HIS218 4.1 24.9 1.0
CG A:HIS218 4.1 22.8 1.0
CB A:ASP107 4.1 22.3 1.0
O A:THR108 4.1 21.4 1.0
CB A:PHE109 4.2 22.3 1.0
C A:ASP107 4.4 22.5 1.0
CA A:ASP107 4.5 25.0 1.0
N A:THR108 4.5 22.2 1.0
CD2 A:PHE109 4.6 22.2 1.0
C A:THR108 4.6 23.5 1.0
O A:ASP107 4.7 19.5 1.0
CG A:LYS222 4.7 29.0 1.0
CG A:PHE109 4.8 22.3 1.0
O A:HOH688 4.9 38.7 1.0
CB A:LYS222 5.0 24.0 1.0

Zinc binding site 3 out of 10 in 6yi1

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Zinc binding site 3 out of 10 in the Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala


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 Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:26.5
occ:0.59
 OD1 A:ASP286 1.9 49.3 1.0
O A:HOH677 2.1 30.4 1.0
O A:HOH505 2.2 28.8 1.0
N2 A:ORT422 2.2 21.7 0.8
O3 A:ORT422 2.3 59.2 1.0
O A:HOH711 2.4 34.0 1.0
CG A:ASP286 3.0 48.4 1.0
C5 A:ORT422 3.0 70.8 1.0
N1 A:ORT422 3.0 75.6 1.0
OD2 A:ASP286 3.5 50.5 1.0
N A:ASP286 3.9 26.5 1.0
CB A:ASP286 4.1 39.8 1.0
CA A:ASP286 4.2 33.0 1.0
C4 A:ORT422 4.5 65.9 1.0
CB A:LYS285 4.7 32.7 1.0
C A:LYS285 4.7 26.2 1.0
O A:HOH708 4.8 47.5 1.0
CA A:LYS285 4.9 28.0 1.0

Zinc binding site 4 out of 10 in 6yi1

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Zinc binding site 4 out of 10 in the Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala


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 Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:32.8
occ:1.00
 OE2 A:GLU280 2.0 44.9 1.0
NE2 A:HIS276 2.1 36.5 1.0
CD A:GLU280 2.4 47.1 1.0
OE1 A:GLU280 2.6 53.4 1.0
O A:HOH501 2.8 32.5 1.0
CE1 A:HIS276 3.1 35.4 1.0
CD2 A:HIS276 3.1 34.5 1.0
CG A:GLU280 3.5 43.5 1.0
CD1 A:LEU289 3.9 42.5 1.0
ND1 A:HIS276 4.2 33.9 1.0
CG A:HIS276 4.3 32.0 1.0
CB A:GLU280 4.9 34.3 1.0
O4 A:PG4413 5.0 53.2 1.0

Zinc binding site 5 out of 10 in 6yi1

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Zinc binding site 5 out of 10 in the Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:26.6
occ:0.32
 O A:HOH535 1.9 33.2 1.0
OE2 A:GLU76 2.0 33.0 1.0
NE2 A:HIS148 2.0 53.4 1.0
O A:HOH703 2.1 38.2 1.0
CD A:GLU76 2.7 31.5 1.0
OE1 A:GLU76 2.7 32.2 1.0
CD2 A:HIS148 2.9 52.2 1.0
O A:HOH692 3.0 40.2 1.0
CE1 A:HIS148 3.0 56.2 1.0
O A:HOH664 3.9 61.4 1.0
CG A:HIS148 4.0 55.8 1.0
ND1 A:HIS148 4.0 58.3 1.0
CE2 A:TYR78 4.1 24.2 1.0
CG A:GLU76 4.1 26.7 1.0
O A:HOH521 4.1 21.6 1.0
O A:PHE146 4.2 29.4 1.0
O A:HOH712 4.2 41.4 1.0
O A:HOH580 4.6 61.0 1.0
O A:HOH634 4.7 23.3 1.0
OH A:TYR78 4.8 29.7 1.0
CD2 A:TYR78 4.9 22.9 1.0
CZ A:TYR78 5.0 27.2 1.0
CE1 A:TYR145 5.0 34.5 1.0

Zinc binding site 6 out of 10 in 6yi1

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Zinc binding site 6 out of 10 in the Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:20.8
occ:1.00
 OE2 B:GLU202 2.0 22.4 1.0
OD2 B:ASP159 2.0 19.7 1.0
NE2 B:HIS330 2.1 21.5 1.0
N2 B:ORT422 2.2 20.2 1.0
O3 B:ORT422 2.3 22.6 1.0
CD B:GLU202 2.8 20.7 1.0
CG B:ASP159 2.8 21.2 1.0
OE1 B:GLU202 2.9 19.4 1.0
OD1 B:ASP159 2.9 17.5 1.0
C5 B:ORT422 3.0 21.4 1.0
N1 B:ORT422 3.0 21.3 1.0
CD2 B:HIS330 3.0 21.3 1.0
CE1 B:HIS330 3.1 23.5 1.0
NE1 B:TRP329 4.0 19.0 1.0
O B:HOH532 4.1 20.1 1.0
ND1 B:HIS330 4.1 22.0 1.0
CG B:HIS330 4.2 20.5 1.0
CG B:GLU202 4.2 16.2 1.0
CB B:ASP159 4.3 18.2 1.0
OE1 B:GLU201 4.3 21.1 1.0
CD2 B:LEU249 4.4 21.1 1.0
N4 B:ORT422 4.4 21.2 1.0
C4 B:ORT422 4.5 20.6 1.0
CD1 B:TRP329 4.6 19.9 1.0
O B:HOH548 4.6 18.8 1.0
NE2 B:HIS140 4.7 18.9 1.0
CE2 B:TRP329 4.9 23.2 1.0

Zinc binding site 7 out of 10 in 6yi1

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Zinc binding site 7 out of 10 in the Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:21.5
occ:1.00
 O B:HOH664 1.9 19.4 0.5
NE2 B:HIS148 2.0 25.7 1.0
OE2 B:GLU76 2.1 22.9 1.0
O B:HOH510 2.1 22.2 1.0
OE1 B:GLU76 2.7 24.9 1.0
CD B:GLU76 2.7 23.0 1.0
CE1 B:HIS148 2.9 24.4 1.0
CD2 B:HIS148 3.0 23.7 1.0
O3 B:SO4401 4.0 33.3 0.5
ND1 B:HIS148 4.0 25.3 1.0
CG B:HIS148 4.1 24.4 1.0
CG B:GLU76 4.2 21.9 1.0
O B:HOH529 4.2 18.1 1.0
O B:PHE146 4.3 21.6 1.0
CE2 B:TYR78 4.4 16.4 1.0
O B:HOH636 4.6 20.7 1.0
O2 B:SO4401 4.7 33.3 0.5
CG1 B:VAL153 4.8 24.5 1.0
O B:HOH673 4.9 36.7 0.5
S B:SO4401 4.9 33.5 0.5

Zinc binding site 8 out of 10 in 6yi1

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Zinc binding site 8 out of 10 in the Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:24.5
occ:0.66
 NZ B:LYS40 2.2 36.8 1.0
O2 B:SO4409 2.4 28.5 1.0
O B:HOH604 2.4 35.7 1.0
CE B:LYS40 3.0 32.2 1.0
S B:SO4409 3.3 28.6 1.0
O3 B:SO4409 3.4 29.8 1.0
O B:HOH545 3.8 27.1 1.0
O1 B:SO4409 3.9 29.4 1.0
O B:PRO37 4.0 27.6 1.0
O B:HOH561 4.3 25.2 1.0
CD B:LYS40 4.4 28.6 1.0
O4 B:SO4409 4.6 30.8 1.0
O B:HOH517 4.6 39.8 1.0
O B:GLY314 4.9 26.2 1.0

Zinc binding site 9 out of 10 in 6yi1

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Zinc binding site 9 out of 10 in the Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn405

b:21.4
occ:0.52
 OD2 B:ASP107 1.9 28.2 1.0
O B:HOH652 2.0 30.1 1.0
NE2 B:HIS218 2.0 24.4 1.0
NZ B:LYS222 2.2 40.0 1.0
CE1 B:HIS218 2.9 25.9 1.0
CE B:LYS222 2.9 34.2 1.0
CG B:ASP107 3.0 26.6 1.0
CD2 B:HIS218 3.1 22.4 1.0
OD1 B:ASP107 3.4 26.0 1.0
O A:HOH674 3.7 39.4 1.0
ND1 B:HIS218 4.0 24.2 1.0
CG B:HIS218 4.2 21.7 1.0
O B:THR108 4.2 20.5 1.0
CB B:ASP107 4.2 23.8 1.0
CB B:PHE109 4.3 19.8 1.0
O B:HOH678 4.3 38.1 1.0
CD B:LYS222 4.3 32.4 1.0
C B:ASP107 4.5 22.1 1.0
CA B:ASP107 4.6 21.1 1.0
N B:THR108 4.6 21.2 1.0
CD2 B:PHE109 4.6 20.0 1.0
C B:THR108 4.6 22.6 1.0
O B:ASP107 4.8 21.5 1.0
CG B:PHE109 4.8 20.8 1.0
CG B:LYS222 4.9 27.5 1.0

Zinc binding site 10 out of 10 in 6yi1

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Zinc binding site 10 out of 10 in the Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Human Glutaminyl Cyclase in Complex with Glu(Gamma-Hydrazide)-Phe-Ala within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn406

b:48.7
occ:0.35
 OE2 B:GLU280 2.0 86.8 1.0
O B:HOH682 2.2 50.9 1.0
O B:HOH504 2.2 54.4 1.0
CE1 B:HIS276 2.3 46.4 1.0
NE2 B:HIS276 2.3 47.9 1.0
CD B:GLU280 3.1 79.9 1.0
ND1 B:HIS276 3.6 44.6 1.0
CD2 B:HIS276 3.7 44.0 1.0
OE1 B:GLU280 3.8 85.5 1.0
CG B:GLU280 4.2 64.9 1.0
CG B:HIS276 4.3 41.7 1.0
CD1 B:LEU289 4.6 58.8 1.0

Reference:

O.Kupski, L.M.Funk, V.Sautner, F.Seifert, B.Worbs, D.Ramsbeck, F.Meyer, U.Diederichsen, M.Buchholz, S.Schilling, H.U.Demuth, K.Tittmann. Hydrazides Are Potent Transition-State Analogues For Glutaminyl Cyclase Implicated in the Pathogenesis of Alzheimer'S Disease. Biochemistry V. 59 2585 2020.
ISSN: ISSN 0006-2960
PubMed: 32551535
DOI: 10.1021/ACS.BIOCHEM.0C00337
Page generated: Tue Oct 29 15:07:12 2024

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