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Copper in PDB 7d1n: Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cu Ions Bound to the Active Site

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

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

Protein crystallography data

The structure of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cu Ions Bound to the Active Site, PDB code: 7d1n 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) 25.81 / 2.26
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.839, 73.706, 82.603, 90, 90, 90
R / Rfree (%) 18.6 / 28.1

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cu Ions Bound to the Active Site (pdb code 7d1n). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cu Ions Bound to the Active Site, PDB code: 7d1n:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 7d1n

Go back to Copper Binding Sites List in 7d1n
Copper binding site 1 out of 4 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cu Ions Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cu Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:42.8
occ:1.00
 NE2 A:HIS322 1.9 42.1 1.0
OE2 A:GLU184 1.9 42.4 1.0
O1 A:BCT405 2.1 48.3 1.0
OD2 A:ASP144 2.3 34.3 1.0
CD A:GLU184 2.8 43.8 1.0
CD2 A:HIS322 2.8 37.6 1.0
OE1 A:GLU184 3.0 51.0 1.0
CE1 A:HIS322 3.0 36.2 1.0
CG A:ASP144 3.0 31.3 1.0
C A:BCT405 3.0 53.8 1.0
OD1 A:ASP144 3.1 42.0 1.0
CU A:CU402 3.4 41.3 1.0
O2 A:BCT405 3.6 49.8 1.0
NE1 A:TRP321 3.8 43.6 1.0
O3 A:BCT405 3.9 47.0 1.0
CG A:HIS322 4.0 36.1 1.0
ND1 A:HIS322 4.0 33.5 1.0
CG A:GLU184 4.2 44.9 1.0
O A:HOH560 4.3 19.1 1.0
CB A:ASP144 4.4 29.4 1.0
CD1 A:TRP321 4.4 39.8 1.0
CD2 A:LEU239 4.6 26.1 1.0
CE2 A:TRP321 4.8 38.0 1.0
O A:HOH546 4.8 39.1 1.0
NE2 A:HIS128 5.0 18.9 1.0

Copper binding site 2 out of 4 in 7d1n

Go back to Copper Binding Sites List in 7d1n
Copper binding site 2 out of 4 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cu Ions Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cu Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:41.3
occ:1.00
 NE2 A:HIS128 1.9 18.9 1.0
OD1 A:ASP144 2.0 42.0 1.0
O2 A:BCT405 2.1 49.8 1.0
CE1 A:HIS128 2.8 19.7 1.0
C A:BCT405 2.9 53.8 1.0
CD2 A:HIS128 3.0 17.4 1.0
OE2 A:GLU184 3.0 42.4 1.0
CG A:ASP144 3.2 31.3 1.0
OD2 A:ASP238 3.3 44.5 1.0
O1 A:BCT405 3.3 48.3 1.0
CU A:CU401 3.4 42.8 1.0
OG A:SER145 3.6 31.6 1.0
CD A:GLU184 3.7 43.8 1.0
OD2 A:ASP144 3.8 34.3 1.0
O3 A:BCT405 3.9 47.0 1.0
ND1 A:HIS128 4.0 18.4 1.0
CG A:HIS128 4.1 19.8 1.0
CG A:GLU184 4.2 44.9 1.0
CG A:ASP238 4.3 39.0 1.0
CB A:ASP144 4.4 29.4 1.0
C A:ASP144 4.5 26.8 1.0
CA A:ASP144 4.5 25.6 1.0
O A:HOH560 4.6 19.1 1.0
OE1 A:GLU184 4.6 51.0 1.0
CD2 A:LEU239 4.6 26.1 1.0
O A:ASP144 4.7 23.4 1.0
CB A:SER145 4.8 27.0 1.0
N A:SER145 4.9 25.1 1.0
OD1 A:ASP238 4.9 42.2 1.0
O A:HOH527 4.9 22.3 1.0

Copper binding site 3 out of 4 in 7d1n

Go back to Copper Binding Sites List in 7d1n
Copper binding site 3 out of 4 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cu Ions Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cu Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:59.1
occ:1.00
 NE2 A:HIS40 2.4 26.9 1.0
NZ A:LYS162 2.6 37.7 1.0
OD1 A:ASP41 2.7 60.5 1.0
OD2 A:ASP41 2.8 53.2 1.0
CD2 A:HIS40 2.9 28.2 1.0
CG A:ASP41 3.0 45.3 1.0
CE A:LYS162 3.4 38.2 1.0
CE1 A:HIS40 3.5 33.1 1.0
CG A:HIS40 4.2 26.8 1.0
CB A:ASP41 4.3 38.2 1.0
ND1 A:HIS40 4.4 29.2 1.0
CA A:ASP41 4.6 32.5 1.0
CD A:LYS162 4.7 33.8 1.0
N A:ASP41 4.8 31.9 1.0
OXT A:LEU353 5.0 32.9 1.0

Copper binding site 4 out of 4 in 7d1n

Go back to Copper Binding Sites List in 7d1n
Copper binding site 4 out of 4 in the Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cu Ions Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Ixodes Scapularis Glutaminyl Cyclase with Three Cu Ions Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu404

b:31.6
occ:1.00
 ND1 A:HIS311 1.9 29.0 1.0
OE1 A:GLU296 1.9 38.4 1.0
NE2 A:HIS299 1.9 46.8 1.0
CE1 A:HIS311 2.8 28.0 1.0
O A:HOH554 2.9 36.4 1.0
CE1 A:HIS299 2.9 46.8 1.0
CD2 A:HIS299 2.9 41.8 1.0
CG A:HIS311 2.9 28.4 1.0
CD A:GLU296 3.0 35.3 1.0
CB A:HIS311 3.3 24.3 1.0
CG A:GLU296 3.5 40.8 1.0
NE2 A:HIS311 4.0 28.8 1.0
O A:HOH654 4.0 45.1 1.0
ND1 A:HIS299 4.0 44.3 1.0
OE2 A:GLU296 4.0 35.6 1.0
CD2 A:HIS311 4.0 24.6 1.0
CG A:HIS299 4.0 41.5 1.0
CZ A:PHE251 4.2 27.7 1.0
CE2 A:PHE251 4.3 26.7 1.0
OD1 A:ASP298 4.6 46.1 1.0
CG2 A:ILE313 4.7 18.9 1.0
CB A:GLU296 4.8 34.3 1.0
CA A:HIS311 4.9 21.9 1.0
CB A:TYR250 4.9 24.8 1.0
CG A:TYR250 4.9 24.6 1.0
CA A:GLU296 5.0 35.8 1.0
CD2 A:TYR250 5.0 25.5 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: Wed Jul 31 08:24:59 2024

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