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Zinc in PDB 2xef: Human Glutamate Carboxypeptidase II in Complex with Antibody-Recruiting Molecule Arm-P8

Enzymatic activity of Human Glutamate Carboxypeptidase II in Complex with Antibody-Recruiting Molecule Arm-P8

All present enzymatic activity of Human Glutamate Carboxypeptidase II in Complex with Antibody-Recruiting Molecule Arm-P8:
3.4.17.21;

Protein crystallography data

The structure of Human Glutamate Carboxypeptidase II in Complex with Antibody-Recruiting Molecule Arm-P8, PDB code: 2xef was solved by A.X.Zhang, R.P.Murelli, C.Barinka, J.Michel, A.Cocleaza, W.L.Jorgensen, J.Lubkowski, D.A.Spiegel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.59
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.844, 130.026, 158.741, 90.00, 90.00, 90.00
R / Rfree (%) 16.075 / 18.266

Other elements in 2xef:

The structure of Human Glutamate Carboxypeptidase II in Complex with Antibody-Recruiting Molecule Arm-P8 also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Glutamate Carboxypeptidase II in Complex with Antibody-Recruiting Molecule Arm-P8 (pdb code 2xef). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Glutamate Carboxypeptidase II in Complex with Antibody-Recruiting Molecule Arm-P8, PDB code: 2xef:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2xef

Go back to Zinc Binding Sites List in 2xef
Zinc binding site 1 out of 2 in the Human Glutamate Carboxypeptidase II in Complex with Antibody-Recruiting Molecule Arm-P8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Glutamate Carboxypeptidase II in Complex with Antibody-Recruiting Molecule Arm-P8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:6.2
occ:1.00
O A:HOH2562 2.0 15.8 1.0
NE2 A:HIS553 2.1 14.8 1.0
OD2 A:ASP387 2.1 21.1 1.0
OE2 A:GLU425 2.1 17.8 1.0
OE1 A:GLU425 2.4 15.8 1.0
OAD A:AR81770 2.6 16.7 0.7
CD A:GLU425 2.6 16.4 1.0
OAD A:AR81770 2.7 18.4 0.3
CE1 A:HIS553 2.9 16.5 1.0
CG A:ASP387 3.0 17.8 1.0
CD2 A:HIS553 3.2 15.6 1.0
ZN A:ZN1752 3.3 6.0 1.0
OD1 A:ASP387 3.3 15.8 1.0
CCC A:AR81770 3.5 19.1 0.7
CCC A:AR81770 3.5 20.1 0.3
NBQ A:AR81770 4.0 17.1 0.7
CCI A:AR81770 4.0 19.3 0.3
CCI A:AR81770 4.0 18.5 0.7
NBQ A:AR81770 4.0 19.3 0.3
CE1 A:TYR552 4.1 17.6 1.0
OE1 A:GLU424 4.1 15.8 1.0
ND1 A:HIS553 4.1 16.1 1.0
CG A:GLU425 4.2 15.7 1.0
O A:HOH2283 4.2 17.9 1.0
CG A:HIS553 4.2 14.8 1.0
CB A:ASP387 4.3 16.2 1.0
N A:AR81770 4.3 18.2 0.7
N A:AR81770 4.3 20.0 0.3
OH A:TYR552 4.4 16.9 1.0
CCB A:AR81770 4.5 20.9 0.3
NE2 A:HIS377 4.5 14.8 1.0
CCB A:AR81770 4.6 21.5 0.7
CZ A:TYR552 4.6 16.8 1.0
CA A:AR81770 4.6 20.4 0.7
CD1 A:TRP381 4.6 16.9 1.0
CA A:AR81770 4.6 21.4 0.3
OAI A:AR81770 4.7 20.2 0.3
CE1 A:HIS377 4.7 13.8 1.0
NE1 A:TRP381 4.8 16.8 1.0
OAI A:AR81770 4.8 20.3 0.7
OD2 A:ASP453 4.9 17.3 1.0
CD1 A:TYR552 5.0 18.7 1.0

Zinc binding site 2 out of 2 in 2xef

Go back to Zinc Binding Sites List in 2xef
Zinc binding site 2 out of 2 in the Human Glutamate Carboxypeptidase II in Complex with Antibody-Recruiting Molecule Arm-P8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Glutamate Carboxypeptidase II in Complex with Antibody-Recruiting Molecule Arm-P8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:6.0
occ:1.00
O A:HOH2562 1.9 15.8 1.0
OD2 A:ASP453 2.0 17.3 1.0
OD1 A:ASP387 2.0 15.8 1.0
NE2 A:HIS377 2.0 14.8 1.0
CG A:ASP453 2.7 17.5 1.0
OD1 A:ASP453 2.7 19.9 1.0
CG A:ASP387 2.9 17.8 1.0
CE1 A:HIS377 3.0 13.8 1.0
CD2 A:HIS377 3.0 17.5 1.0
OD2 A:ASP387 3.2 21.1 1.0
ZN A:ZN1751 3.3 6.2 1.0
OE2 A:GLU425 3.6 17.8 1.0
OE1 A:GLU424 3.6 15.8 1.0
CD A:GLU424 4.1 15.4 1.0
ND1 A:HIS377 4.1 13.6 1.0
OE2 A:GLU424 4.1 16.9 1.0
CG A:HIS377 4.2 15.1 1.0
CB A:ASP453 4.2 16.2 1.0
CB A:ASP387 4.2 16.2 1.0
ND2 A:ASN519 4.3 15.7 1.0
CB A:PRO388 4.3 16.1 1.0
CD A:GLU425 4.3 16.4 1.0
OAD A:AR81770 4.5 16.7 0.7
CA A:ASP387 4.5 16.4 1.0
CA A:PRO388 4.6 15.1 1.0
CCC A:AR81770 4.6 19.1 0.7
C A:ASP387 4.6 17.9 1.0
CCC A:AR81770 4.6 20.1 0.3
OAD A:AR81770 4.6 18.4 0.3
N A:PRO388 4.6 15.9 1.0
OE1 A:GLU425 4.7 15.8 1.0
N A:AR81770 4.7 18.2 0.7
N A:AR81770 4.7 20.0 0.3
O A:HOH2317 4.8 31.1 1.0
OG A:SER454 4.8 19.7 1.0
NBQ A:AR81770 4.9 17.1 0.7
CA A:AR81770 4.9 20.4 0.7
CA A:AR81770 4.9 21.4 0.3
OXT A:AR81770 5.0 24.1 0.7
NBQ A:AR81770 5.0 19.3 0.3

Reference:

A.X.Zhang, R.P.Murelli, C.Barinka, J.Michel, A.Cocleaza, W.L.Jorgensen, J.Lubkowski, D.A.Spiegel. A Remote Arene-Binding Site on Prostate Specific Membrane Antigen Revealed By Antibody-Recruiting Small Molecules. J.Am.Chem.Soc. V. 132 12711 2010.
ISSN: ISSN 0002-7863
PubMed: 20726553
DOI: 10.1021/JA104591M
Page generated: Wed Dec 16 03:59:48 2020

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