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Zinc in PDB 7d21: Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Two Zn Ions Bound to the Active Site

Enzymatic activity of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Two Zn Ions Bound to the Active Site

All present enzymatic activity of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Two Zn Ions Bound to the Active Site:
2.3.2.5;

Protein crystallography data

The structure of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Two Zn Ions Bound to the Active Site, PDB code: 7d21 was solved by K.-F.Huang, J.-S.Huang, M.-L.Wu, W.-L.Hsieh, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.84 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.646, 70.932, 80.556, 90, 90, 90
R / Rfree (%) 18.9 / 22.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Two Zn Ions Bound to the Active Site (pdb code 7d21). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Two Zn Ions Bound to the Active Site, PDB code: 7d21:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 7d21

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Zinc binding site 1 out of 5 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Two Zn Ions Bound to the Active Site


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 Ixodes Scapularis Glutaminyl Cyclase with Two Zn Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:29.4
occ:1.00
 OD2 A:ASP144 2.0 26.5 1.0
OE2 A:GLU184 2.0 32.5 1.0
NE2 A:HIS322 2.1 31.0 1.0
O8 A:EPE406 2.3 52.7 1.0
CD A:GLU184 2.8 28.5 1.0
CG A:ASP144 2.8 24.6 1.0
OE1 A:GLU184 2.8 28.8 1.0
OD1 A:ASP144 3.0 26.4 1.0
CD2 A:HIS322 3.0 32.1 1.0
CE1 A:HIS322 3.2 33.7 1.0
ZN A:ZN402 3.2 31.8 1.0
C8 A:EPE406 3.4 52.6 1.0
O A:HOH510 3.9 26.2 1.0
NE1 A:TRP321 4.1 29.7 1.0
CG A:HIS322 4.2 32.0 1.0
CB A:ASP144 4.2 26.5 1.0
OE1 A:GLU183 4.2 58.7 1.0
ND1 A:HIS322 4.3 32.3 1.0
CG A:GLU184 4.3 30.2 1.0
NE2 A:HIS128 4.6 27.0 1.0
C7 A:EPE406 4.7 59.5 1.0
O A:HOH520 4.7 25.1 1.0
CE1 A:HIS128 4.7 27.6 1.0
C3 A:EPE406 4.7 70.4 1.0
CD2 A:LEU239 4.8 28.7 1.0
CE2 A:TRP321 4.8 31.7 1.0
CD1 A:TRP321 4.8 30.8 1.0
OD2 A:ASP238 4.9 29.6 1.0

Zinc binding site 2 out of 5 in 7d21

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Zinc binding site 2 out of 5 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Two Zn Ions Bound to the Active Site


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 Ixodes Scapularis Glutaminyl Cyclase with Two Zn Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:31.8
occ:1.00
 OD1 A:ASP144 2.0 26.4 1.0
OD2 A:ASP238 2.0 29.6 1.0
NE2 A:HIS128 2.1 27.0 1.0
O8 A:EPE406 2.4 52.7 1.0
OE1 A:GLU183 2.7 58.7 1.0
CG A:ASP238 2.9 32.4 1.0
CE1 A:HIS128 3.1 27.6 1.0
CG A:ASP144 3.1 24.6 1.0
CD2 A:HIS128 3.1 27.2 1.0
OD1 A:ASP238 3.2 30.9 1.0
ZN A:ZN401 3.2 29.4 1.0
CD A:GLU183 3.5 53.7 1.0
OE2 A:GLU183 3.5 62.1 1.0
C8 A:EPE406 3.5 52.6 1.0
OD2 A:ASP144 3.5 26.5 1.0
OE2 A:GLU184 3.6 32.5 1.0
OG A:SER145 3.7 35.9 1.0
C7 A:EPE406 4.1 59.5 1.0
CD2 A:LEU239 4.2 28.7 1.0
ND1 A:HIS128 4.2 25.3 1.0
CG A:HIS128 4.2 25.4 1.0
CD A:GLU184 4.3 28.5 1.0
CB A:ASP144 4.3 26.5 1.0
CB A:ASP238 4.4 29.9 1.0
CA A:ASP144 4.6 26.9 1.0
O A:HOH535 4.7 31.1 1.0
OE1 A:GLU184 4.7 28.8 1.0
C A:ASP144 4.7 28.4 1.0
O A:ASP144 4.9 27.6 1.0
CG A:GLU183 4.9 44.1 1.0

Zinc binding site 3 out of 5 in 7d21

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Zinc binding site 3 out of 5 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Two Zn Ions Bound to the Active Site


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 Ixodes Scapularis Glutaminyl Cyclase with Two Zn Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:51.8
occ:1.00
 NE2 A:HIS26 2.5 77.5 1.0
CD2 A:HIS26 3.1 77.0 1.0
CE1 A:HIS26 3.7 77.4 1.0
CG A:HIS26 4.3 76.7 1.0
ND1 A:HIS26 4.6 76.7 1.0

Zinc binding site 4 out of 5 in 7d21

Go back to Zinc Binding Sites List in 7d21
Zinc binding site 4 out of 5 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Two Zn Ions Bound to the Active Site


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 Ixodes Scapularis Glutaminyl Cyclase with Two Zn Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:50.2
occ:1.00
 OD1 A:ASP95 1.8 45.3 1.0
NE2 A:HIS200 2.1 39.8 1.0
NZ A:LYS204 2.4 67.4 1.0
CG A:ASP95 2.7 41.5 1.0
CD2 A:HIS200 3.0 37.6 1.0
OD2 A:ASP95 3.1 41.8 1.0
CE1 A:HIS200 3.2 40.8 1.0
CD A:LYS204 3.4 62.9 1.0
CE A:LYS204 3.5 65.4 1.0
CB A:ASP95 4.1 41.2 1.0
CG A:HIS200 4.2 39.5 1.0
ND1 A:HIS200 4.2 41.2 1.0
O A:CYS96 4.5 49.4 1.0
C A:ASP95 4.5 43.5 1.0
O A:ASP95 4.6 35.6 1.0
CA A:ASP95 4.6 40.4 1.0
CD1 A:PHE97 4.6 47.6 1.0
CG A:LYS204 4.7 56.5 1.0
CB A:PHE97 4.8 45.7 1.0
CB A:LYS204 5.0 50.6 1.0
N A:CYS96 5.0 47.0 1.0

Zinc binding site 5 out of 5 in 7d21

Go back to Zinc Binding Sites List in 7d21
Zinc binding site 5 out of 5 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Two Zn Ions Bound to the Active Site


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 Ixodes Scapularis Glutaminyl Cyclase with Two Zn Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:57.4
occ:1.00
 ND1 A:HIS311 2.0 33.9 1.0
NE2 A:HIS299 2.4 55.3 1.0
CE1 A:HIS311 2.9 34.3 1.0
O A:HOH616 3.0 44.8 1.0
CG A:HIS311 3.1 30.0 1.0
CE1 A:HIS299 3.1 52.3 1.0
CD2 A:HIS299 3.2 54.8 1.0
O A:ILE295 3.4 79.1 1.0
CB A:ILE295 3.5 81.1 1.0
CB A:HIS311 3.5 29.3 1.0
CD1 A:ILE295 4.0 76.5 1.0
NE2 A:HIS311 4.0 33.8 1.0
ND1 A:HIS299 4.1 55.5 1.0
CG A:HIS299 4.1 55.5 1.0
CD2 A:HIS311 4.1 32.8 1.0
CG2 A:ILE295 4.2 81.4 1.0
CA A:ILE295 4.2 80.3 1.0
CG1 A:ILE295 4.2 79.5 1.0
C A:ILE295 4.2 80.6 1.0
N A:ILE295 4.2 80.0 1.0
CZ A:PHE251 4.5 41.7 1.0
CE2 A:PHE251 4.5 40.9 1.0
CB A:ASP297 4.6 55.9 1.0
CG2 A:ILE313 4.8 27.5 1.0

Reference:

K.F.Huang, J.S.Huang, M.L.Wu, W.L.Hsieh, K.C.Hsu, H.L.Hsu, T.P.Ko, A.H-J Wang. A Unique Carboxylic-Acid Hydrogen-Bond Network (Cahbn) Confers Glutaminyl Cyclase Activity on M28 Family Enzymes. J.Mol.Biol. 66960 2021.
ISSN: ESSN 1089-8638
PubMed: 33774034
DOI: 10.1016/J.JMB.2021.166960
Page generated: Tue Oct 29 18:36:22 2024

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