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Zinc in PDB 6s1x: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii)-E424M Inactive Mutant, in Complex with A Inhibitor KB1160

Enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii)-E424M Inactive Mutant, in Complex with A Inhibitor KB1160

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii)-E424M Inactive Mutant, in Complex with A Inhibitor KB1160:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii)-E424M Inactive Mutant, in Complex with A Inhibitor KB1160, PDB code: 6s1x was solved by C.Barinka, Z.Kutil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 1.76
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.404, 130.150, 159.268, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 19.4

Other elements in 6s1x:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii)-E424M Inactive Mutant, in Complex with A Inhibitor KB1160 also contains other interesting chemical elements:

Iodine (I) 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)-E424M Inactive Mutant, in Complex with A Inhibitor KB1160 (pdb code 6s1x). 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)-E424M Inactive Mutant, in Complex with A Inhibitor KB1160, PDB code: 6s1x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6s1x

Go back to Zinc Binding Sites List in 6s1x
Zinc binding site 1 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii)-E424M Inactive Mutant, in Complex with A Inhibitor KB1160


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)-E424M Inactive Mutant, in Complex with A Inhibitor KB1160 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn816

b:27.2
occ:1.00
OD2 A:ASP387 2.0 29.2 1.0
O A:HOH1225 2.1 23.2 1.0
NE2 A:HIS553 2.1 25.1 1.0
OE2 A:GLU425 2.1 26.2 1.0
OE1 A:GLU425 2.4 26.9 1.0
O3 A:KRZ820 2.4 30.3 1.0
CD A:GLU425 2.6 25.7 1.0
CG A:ASP387 3.0 30.2 1.0
CE1 A:HIS553 3.0 27.6 1.0
CD2 A:HIS553 3.1 24.9 1.0
C8 A:KRZ820 3.2 32.3 1.0
OD1 A:ASP387 3.4 29.4 1.0
ZN A:ZN817 3.4 26.4 1.0
N4 A:KRZ820 3.9 27.9 1.0
N3 A:KRZ820 3.9 31.8 1.0
CE1 A:TYR552 4.0 25.9 1.0
C9 A:KRZ820 4.1 27.5 1.0
CG A:GLU425 4.1 25.9 1.0
O A:HOH1002 4.1 25.4 1.0
C7 A:KRZ820 4.1 31.9 1.0
ND1 A:HIS553 4.1 24.9 1.0
CG A:HIS553 4.2 25.3 1.0
OH A:TYR552 4.3 27.3 1.0
CB A:ASP387 4.4 29.0 1.0
NE2 A:HIS377 4.4 21.4 1.0
CZ A:TYR552 4.6 26.5 1.0
CD1 A:TRP381 4.6 28.8 1.0
CE1 A:HIS377 4.6 25.4 1.0
C13 A:KRZ820 4.6 26.7 1.0
NE1 A:TRP381 4.8 27.6 1.0
SD A:MET424 4.8 25.4 1.0
O6 A:KRZ820 4.9 29.1 1.0
CD1 A:TYR552 5.0 27.8 1.0
OD2 A:ASP453 5.0 27.7 1.0

Zinc binding site 2 out of 2 in 6s1x

Go back to Zinc Binding Sites List in 6s1x
Zinc binding site 2 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii)-E424M Inactive Mutant, in Complex with A Inhibitor KB1160


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)-E424M Inactive Mutant, in Complex with A Inhibitor KB1160 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn817

b:26.4
occ:1.00
O A:HOH1225 1.7 23.2 1.0
NE2 A:HIS377 2.0 21.4 1.0
OD1 A:ASP387 2.0 29.4 1.0
OD2 A:ASP453 2.0 27.7 1.0
OD1 A:ASP453 2.6 28.5 1.0
CG A:ASP453 2.6 26.6 1.0
CD2 A:HIS377 2.9 23.5 1.0
CG A:ASP387 3.0 30.2 1.0
CE1 A:HIS377 3.0 25.4 1.0
OD2 A:ASP387 3.3 29.2 1.0
ZN A:ZN816 3.4 27.2 1.0
CE A:MET424 3.7 24.2 1.0
OE2 A:GLU425 3.8 26.2 1.0
CG A:HIS377 4.1 23.3 1.0
ND1 A:HIS377 4.1 24.9 1.0
SD A:MET424 4.1 25.4 1.0
N3 A:KRZ820 4.1 31.8 1.0
CB A:ASP453 4.1 24.2 1.0
C7 A:KRZ820 4.2 31.9 1.0
CB A:PRO388 4.2 25.7 1.0
CB A:ASP387 4.3 29.0 1.0
C8 A:KRZ820 4.3 32.3 1.0
ND2 A:ASN519 4.4 25.4 1.0
O3 A:KRZ820 4.5 30.3 1.0
CD A:GLU425 4.5 25.7 1.0
CA A:PRO388 4.5 25.9 1.0
N A:PRO388 4.6 27.0 1.0
CA A:ASP387 4.6 29.1 1.0
C A:ASP387 4.6 27.2 1.0
O A:HOH1065 4.7 54.1 1.0
OE1 A:GLU425 4.7 26.9 1.0
OG A:SER454 4.8 30.7 1.0
N4 A:KRZ820 4.9 27.9 1.0

Reference:

K.Kim, H.Kwon, C.Barinka, L.Motlova, S.Nam, D.Choi, H.Ha, H.Nam, S.H.Son, I.Minn, M.G.Pomper, X.Yang, Z.Kutil, Y.Byun. Novel Beta- and Gamma-Amino Acid-Derived Inhibitors of Prostate-Specific Membrane Antigen. J.Med.Chem. V. 63 3261 2020.
ISSN: ISSN 0022-2623
PubMed: 32097010
DOI: 10.1021/ACS.JMEDCHEM.9B02022
Page generated: Wed Dec 16 12:44:37 2020

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