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Zinc in PDB 6hkj: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 2-19-1

Enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 2-19-1

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 2-19-1:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 2-19-1, PDB code: 6hkj 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) 47.30 / 2.09
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.296, 131.658, 160.019, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 20.4

Other elements in 6hkj:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 2-19-1 also contains other interesting chemical elements:

Fluorine (F) 1 atom
Calcium (Ca) 1 atom
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 2-19-1 (pdb code 6hkj). 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 Inhibitor Rna 2-19-1, PDB code: 6hkj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6hkj

Go back to Zinc Binding Sites List in 6hkj
Zinc binding site 1 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 2-19-1


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 Inhibitor Rna 2-19-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn813

b:46.3
occ:1.00
OD2 A:ASP387 2.0 47.8 1.0
OE2 A:GLU425 2.1 46.6 1.0
NE2 A:HIS553 2.1 45.4 1.0
O A:HOH1024 2.1 39.9 1.0
OBD A:G8W818 2.5 46.4 1.0
OE1 A:GLU425 2.6 46.2 1.0
CD A:GLU425 2.7 47.2 1.0
CG A:ASP387 3.0 49.9 1.0
CE1 A:HIS553 3.0 45.1 1.0
CD2 A:HIS553 3.1 43.6 1.0
ZN A:ZN814 3.3 45.2 1.0
OD1 A:ASP387 3.3 53.0 1.0
CAA A:G8W818 3.3 52.7 1.0
NAS A:G8W818 3.9 49.6 1.0
OE1 A:GLU424 4.0 40.1 1.0
CAT A:G8W818 4.0 47.5 1.0
CE1 A:TYR552 4.2 45.6 1.0
ND1 A:HIS553 4.2 45.8 1.0
CG A:GLU425 4.2 43.9 1.0
O A:HOH953 4.2 43.2 1.0
CG A:HIS553 4.3 44.6 1.0
N A:G8W818 4.3 47.3 1.0
CB A:ASP387 4.3 48.2 1.0
OH A:TYR552 4.4 43.2 1.0
NE2 A:HIS377 4.5 44.5 1.0
CA A:G8W818 4.6 49.3 1.0
CAU A:G8W818 4.6 48.7 1.0
CZ A:TYR552 4.7 46.6 1.0
CE1 A:HIS377 4.8 49.5 1.0
OD2 A:ASP453 4.9 43.2 1.0
CD1 A:TRP381 4.9 49.7 1.0
OAW A:G8W818 4.9 45.6 1.0
CD A:GLU424 4.9 45.0 1.0

Zinc binding site 2 out of 2 in 6hkj

Go back to Zinc Binding Sites List in 6hkj
Zinc binding site 2 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 2-19-1


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 Inhibitor Rna 2-19-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn814

b:45.2
occ:1.00
O A:HOH1024 1.8 39.9 1.0
OD1 A:ASP387 2.0 53.0 1.0
OD2 A:ASP453 2.0 43.2 1.0
NE2 A:HIS377 2.1 44.5 1.0
CG A:ASP453 2.7 45.0 1.0
OD1 A:ASP453 2.8 43.1 1.0
CG A:ASP387 2.9 49.9 1.0
CE1 A:HIS377 3.1 49.5 1.0
CD2 A:HIS377 3.1 47.1 1.0
OD2 A:ASP387 3.2 47.8 1.0
ZN A:ZN813 3.3 46.3 1.0
OE2 A:GLU425 3.5 46.6 1.0
OE1 A:GLU424 3.7 40.1 1.0
CD A:GLU424 4.0 45.0 1.0
ND1 A:HIS377 4.2 44.7 1.0
CB A:ASP453 4.2 44.1 1.0
CG A:HIS377 4.2 45.3 1.0
OE2 A:GLU424 4.2 43.8 1.0
CB A:ASP387 4.3 48.2 1.0
ND2 A:ASN519 4.3 41.8 1.0
CB A:PRO388 4.4 44.9 1.0
CD A:GLU425 4.4 47.2 1.0
OBD A:G8W818 4.5 46.4 1.0
CAA A:G8W818 4.5 52.7 1.0
CA A:PRO388 4.7 44.8 1.0
CA A:ASP387 4.7 45.4 1.0
C A:ASP387 4.7 47.2 1.0
N A:G8W818 4.7 47.3 1.0
N A:PRO388 4.7 42.2 1.0
OG A:SER454 4.8 47.1 1.0
O A:HOH1018 4.8 52.1 1.0
OE1 A:GLU425 4.8 46.2 1.0
CA A:G8W818 4.9 49.3 1.0
NAS A:G8W818 4.9 49.6 1.0
CG A:GLU424 5.0 45.0 1.0

Reference:

R.Nakajima, Z.Novakova, W.Tueckmantel, L.Motlova, C.Barinka, A.P.Kozikowski. 2-Aminoadipic Acid-C(O)-Glutamate Based Prostate-Specific Membrane Antigen Ligands For Potential Use As Theranostics. Acs Med Chem Lett V. 9 1099 2018.
ISSN: ISSN 1948-5875
PubMed: 30429952
DOI: 10.1021/ACSMEDCHEMLETT.8B00318
Page generated: Wed Dec 16 11:57:18 2020

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