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Zinc in PDB 5o5r: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1023

Enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1023

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1023:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1023, PDB code: 5o5r was solved by L.Motlova, Z.Novakova, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.13 / 1.65
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.512, 130.203, 159.160, 90.00, 90.00, 90.00
R / Rfree (%) 12.4 / 16

Other elements in 5o5r:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1023 also contains other interesting chemical elements:

Fluorine (F) 1 atom
Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1023 (pdb code 5o5r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1023, PDB code: 5o5r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5o5r

Go back to Zinc Binding Sites List in 5o5r
Zinc binding site 1 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1023


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1023 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn817

b:25.1
occ:1.00
 O A:HOH1215 2.0 25.0 1.0
OD2 A:ASP387 2.1 25.2 1.0
NE2 A:HIS553 2.1 24.3 1.0
OE2 A:GLU425 2.1 23.7 1.0
OE1 A:GLU425 2.4 25.0 1.0
OBA A:9OQ801 2.5 26.1 1.0
CD A:GLU425 2.6 24.3 1.0
CE1 A:HIS553 3.0 26.0 1.0
CG A:ASP387 3.0 26.2 1.0
CD2 A:HIS553 3.1 25.4 1.0
ZN A:ZN818 3.3 26.5 1.0
OD1 A:ASP387 3.3 23.8 1.0
CAW A:9OQ801 3.3 27.1 1.0
NAX A:9OQ801 3.9 23.1 1.0
CAY A:9OQ801 4.0 25.7 1.0
CE1 A:TYR552 4.1 25.1 1.0
OE1 A:GLU424 4.1 22.7 1.0
CG A:GLU425 4.1 23.1 1.0
ND1 A:HIS553 4.1 24.2 1.0
O A:HOH1056 4.2 24.6 1.0
NAV A:9OQ801 4.2 23.6 1.0
CG A:HIS553 4.2 24.3 1.0
CB A:ASP387 4.3 24.1 1.0
OH A:TYR552 4.3 25.5 1.0
CAU A:9OQ801 4.4 25.8 1.0
CAZ A:9OQ801 4.5 28.5 1.0
NE2 A:HIS377 4.6 25.5 1.0
CZ A:TYR552 4.6 24.2 1.0
CD1 A:TRP381 4.7 25.5 1.0
CE1 A:HIS377 4.7 25.1 1.0
OBF A:9OQ801 4.8 29.1 1.0
NE1 A:TRP381 4.9 25.2 1.0
OD2 A:ASP453 4.9 27.0 1.0
CD1 A:TYR552 5.0 26.6 1.0
CD A:GLU424 5.0 24.7 1.0

Zinc binding site 2 out of 2 in 5o5r

Go back to Zinc Binding Sites List in 5o5r
Zinc binding site 2 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1023


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1023 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn818

b:26.5
occ:1.00
 O A:HOH1215 1.9 25.0 1.0
OD1 A:ASP387 2.0 23.8 1.0
OD2 A:ASP453 2.0 27.0 1.0
NE2 A:HIS377 2.0 25.5 1.0
CG A:ASP453 2.7 30.9 1.0
OD1 A:ASP453 2.8 29.6 1.0
CG A:ASP387 2.9 26.2 1.0
CE1 A:HIS377 3.0 25.1 1.0
CD2 A:HIS377 3.0 23.1 1.0
OD2 A:ASP387 3.2 25.2 1.0
ZN A:ZN817 3.3 25.1 1.0
OE1 A:GLU424 3.6 22.7 1.0
OE2 A:GLU425 3.6 23.7 1.0
CD A:GLU424 4.0 24.7 1.0
ND1 A:HIS377 4.1 23.8 1.0
CG A:HIS377 4.1 23.2 1.0
ND2 A:ASN519 4.1 23.3 1.0
CB A:ASP453 4.2 27.1 1.0
CB A:ASP387 4.2 24.1 1.0
OE2 A:GLU424 4.2 25.6 1.0
CD A:GLU425 4.3 24.3 1.0
CB A:PRO388 4.3 24.5 1.0
CA A:PRO388 4.5 23.8 1.0
CAW A:9OQ801 4.5 27.1 1.0
OBA A:9OQ801 4.5 26.1 1.0
CA A:ASP387 4.6 25.2 1.0
C A:ASP387 4.6 25.1 1.0
OE1 A:GLU425 4.6 25.0 1.0
N A:PRO388 4.6 23.6 1.0
NAV A:9OQ801 4.6 23.6 1.0
OG A:SER454 4.7 28.6 1.0
CAU A:9OQ801 4.7 25.8 1.0
O A:HOH1133 4.8 32.0 1.0
CAT A:9OQ801 4.9 28.8 1.0
NAX A:9OQ801 4.9 23.1 1.0
CG A:GLU424 5.0 22.9 1.0

Reference:

L.Motlova, Z.Novakova, C.Barinka. X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1023 To Be Published.
Page generated: Wed Dec 16 06:37:12 2020

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