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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy