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Zinc in PDB 1z8l: Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase

Enzymatic activity of Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase

All present enzymatic activity of Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase:
3.4.17.21;

Protein crystallography data

The structure of Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase, PDB code: 1z8l was solved by M.I.Davis, M.J.Bennett, L.M.Thomas, P.J.Bjorkman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.865, 157.765, 133.839, 90.00, 93.24, 90.00
R / Rfree (%) 25.2 / 28.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase (pdb code 1z8l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase, PDB code: 1z8l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1z8l

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Zinc binding site 1 out of 8 in the Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:52.4
occ:1.00
 NE2 A:HIS377 2.1 46.2 1.0
OD1 A:ASP387 2.2 12.2 1.0
O A:HOH1753 2.2 0.0 1.0
OD2 A:ASP453 2.3 23.9 1.0
OD1 A:ASP453 2.3 23.9 1.0
CG A:ASP453 2.5 23.9 1.0
CG A:ASP387 3.0 12.2 1.0
CD2 A:HIS377 3.1 46.2 1.0
CE1 A:HIS377 3.1 46.2 1.0
ZN A:ZN1752 3.2 52.4 1.0
OE1 A:GLU424 3.3 30.4 1.0
OD2 A:ASP387 3.4 12.2 1.0
ND2 A:ASN519 3.5 65.7 1.0
CB A:ASP453 3.9 23.9 1.0
CD A:GLU424 4.0 30.4 1.0
ND1 A:HIS377 4.2 46.2 1.0
CB A:ASP387 4.2 12.2 1.0
CG A:HIS377 4.2 46.2 1.0
OE2 A:GLU424 4.3 30.4 1.0
OD1 A:ASN519 4.3 65.7 1.0
CG A:ASN519 4.3 65.7 1.0
CB A:PRO388 4.5 15.5 1.0
OE2 A:GLU425 4.5 14.1 1.0
OE1 A:GLU425 4.5 14.1 1.0
CD A:GLU425 4.6 14.1 1.0
CA A:ASP387 4.8 46.9 1.0
CA A:PRO388 5.0 27.8 1.0

Zinc binding site 2 out of 8 in 1z8l

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Zinc binding site 2 out of 8 in the Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:52.4
occ:1.00
 O A:HOH1753 2.0 0.0 1.0
NE2 A:HIS553 2.2 17.2 1.0
OE1 A:GLU425 2.2 14.1 1.0
OD2 A:ASP387 2.3 12.2 1.0
CE1 A:HIS553 2.7 17.2 1.0
CD A:GLU425 3.0 14.1 1.0
CG A:ASP387 3.2 12.2 1.0
OE2 A:GLU425 3.2 14.1 1.0
ZN A:ZN1751 3.2 52.4 1.0
OH A:TYR552 3.3 56.1 1.0
OD1 A:ASP387 3.5 12.2 1.0
CD2 A:HIS553 3.5 17.2 1.0
ND1 A:HIS553 4.0 17.2 1.0
OE1 A:GLU424 4.0 30.4 1.0
CZ A:TYR552 4.1 56.1 1.0
CE1 A:TYR552 4.3 56.1 1.0
OE2 A:GLU424 4.4 30.4 1.0
CG A:HIS553 4.4 17.2 1.0
CG A:GLU425 4.4 14.1 1.0
CB A:ASP387 4.5 12.2 1.0
NE2 A:HIS377 4.5 46.2 1.0
CE1 A:HIS377 4.6 46.2 1.0
CD A:GLU424 4.7 30.4 1.0
OD2 A:ASP453 4.9 23.9 1.0

Zinc binding site 3 out of 8 in 1z8l

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Zinc binding site 3 out of 8 in the Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2751

b:52.4
occ:1.00
 NE2 B:HIS377 2.1 46.2 1.0
OD1 B:ASP387 2.2 12.2 1.0
O B:HOH2753 2.2 0.0 1.0
OD2 B:ASP453 2.3 23.9 1.0
OD1 B:ASP453 2.3 23.9 1.0
CG B:ASP453 2.5 23.9 1.0
CG B:ASP387 3.0 12.2 1.0
CD2 B:HIS377 3.1 46.2 1.0
CE1 B:HIS377 3.1 46.2 1.0
ZN B:ZN2752 3.2 52.4 1.0
OE1 B:GLU424 3.3 30.4 1.0
OD2 B:ASP387 3.4 12.2 1.0
ND2 B:ASN519 3.5 65.7 1.0
CB B:ASP453 3.9 23.9 1.0
CD B:GLU424 4.0 30.4 1.0
ND1 B:HIS377 4.2 46.2 1.0
CB B:ASP387 4.2 12.2 1.0
CG B:HIS377 4.2 46.2 1.0
OE2 B:GLU424 4.3 30.4 1.0
OD1 B:ASN519 4.3 65.7 1.0
CG B:ASN519 4.3 65.7 1.0
CB B:PRO388 4.5 15.5 1.0
OE2 B:GLU425 4.5 14.1 1.0
OE1 B:GLU425 4.5 14.1 1.0
CD B:GLU425 4.6 14.1 1.0
CA B:ASP387 4.8 46.9 1.0
CA B:PRO388 5.0 27.8 1.0

Zinc binding site 4 out of 8 in 1z8l

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Zinc binding site 4 out of 8 in the Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2752

b:52.4
occ:1.00
 O B:HOH2753 2.0 0.0 1.0
NE2 B:HIS553 2.2 17.2 1.0
OE1 B:GLU425 2.2 14.1 1.0
OD2 B:ASP387 2.3 12.2 1.0
CE1 B:HIS553 2.7 17.2 1.0
CD B:GLU425 3.0 14.1 1.0
CG B:ASP387 3.2 12.2 1.0
ZN B:ZN2751 3.2 52.4 1.0
OE2 B:GLU425 3.2 14.1 1.0
OH B:TYR552 3.3 56.1 1.0
OD1 B:ASP387 3.5 12.2 1.0
CD2 B:HIS553 3.5 17.2 1.0
ND1 B:HIS553 4.0 17.2 1.0
OE1 B:GLU424 4.0 30.4 1.0
CZ B:TYR552 4.1 56.1 1.0
CE1 B:TYR552 4.3 56.1 1.0
OE2 B:GLU424 4.4 30.4 1.0
CG B:HIS553 4.4 17.2 1.0
CG B:GLU425 4.4 14.1 1.0
CB B:ASP387 4.5 12.2 1.0
NE2 B:HIS377 4.5 46.2 1.0
CE1 B:HIS377 4.6 46.2 1.0
CD B:GLU424 4.7 30.4 1.0
OD2 B:ASP453 4.9 23.9 1.0

Zinc binding site 5 out of 8 in 1z8l

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Zinc binding site 5 out of 8 in the Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3751

b:52.4
occ:1.00
 NE2 C:HIS377 2.1 46.2 1.0
OD1 C:ASP387 2.2 12.2 1.0
O C:HOH3753 2.2 0.0 1.0
OD2 C:ASP453 2.3 23.9 1.0
OD1 C:ASP453 2.3 23.9 1.0
CG C:ASP453 2.5 23.9 1.0
CG C:ASP387 3.0 12.2 1.0
CD2 C:HIS377 3.1 46.2 1.0
CE1 C:HIS377 3.1 46.2 1.0
ZN C:ZN3752 3.2 52.4 1.0
OE1 C:GLU424 3.3 30.4 1.0
OD2 C:ASP387 3.4 12.2 1.0
ND2 C:ASN519 3.5 65.7 1.0
CB C:ASP453 3.9 23.9 1.0
CD C:GLU424 4.0 30.4 1.0
ND1 C:HIS377 4.2 46.2 1.0
CB C:ASP387 4.2 12.2 1.0
CG C:HIS377 4.2 46.2 1.0
OE2 C:GLU424 4.3 30.4 1.0
OD1 C:ASN519 4.3 65.7 1.0
CG C:ASN519 4.3 65.7 1.0
CB C:PRO388 4.5 15.5 1.0
OE2 C:GLU425 4.5 14.1 1.0
OE1 C:GLU425 4.5 14.1 1.0
CD C:GLU425 4.6 14.1 1.0
CA C:ASP387 4.8 46.9 1.0
CA C:PRO388 5.0 27.8 1.0

Zinc binding site 6 out of 8 in 1z8l

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Zinc binding site 6 out of 8 in the Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3752

b:52.4
occ:1.00
 O C:HOH3753 2.0 0.0 1.0
NE2 C:HIS553 2.2 17.2 1.0
OE1 C:GLU425 2.2 14.1 1.0
OD2 C:ASP387 2.3 12.2 1.0
CE1 C:HIS553 2.7 17.2 1.0
CD C:GLU425 3.0 14.1 1.0
CG C:ASP387 3.2 12.2 1.0
OE2 C:GLU425 3.2 14.1 1.0
ZN C:ZN3751 3.2 52.4 1.0
OH C:TYR552 3.3 56.1 1.0
OD1 C:ASP387 3.5 12.2 1.0
CD2 C:HIS553 3.5 17.2 1.0
ND1 C:HIS553 4.0 17.2 1.0
OE1 C:GLU424 4.0 30.4 1.0
CZ C:TYR552 4.1 56.1 1.0
CE1 C:TYR552 4.3 56.1 1.0
OE2 C:GLU424 4.4 30.4 1.0
CG C:HIS553 4.4 17.2 1.0
CG C:GLU425 4.4 14.1 1.0
CB C:ASP387 4.5 12.2 1.0
NE2 C:HIS377 4.5 46.2 1.0
CE1 C:HIS377 4.6 46.2 1.0
CD C:GLU424 4.7 30.4 1.0
OD2 C:ASP453 4.9 23.9 1.0

Zinc binding site 7 out of 8 in 1z8l

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Zinc binding site 7 out of 8 in the Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4751

b:52.4
occ:1.00
 NE2 D:HIS377 2.1 46.2 1.0
OD1 D:ASP387 2.2 12.2 1.0
O D:HOH4753 2.2 0.0 1.0
OD2 D:ASP453 2.3 23.9 1.0
OD1 D:ASP453 2.3 23.9 1.0
CG D:ASP453 2.5 23.9 1.0
CG D:ASP387 3.0 12.2 1.0
CD2 D:HIS377 3.1 46.2 1.0
CE1 D:HIS377 3.1 46.2 1.0
ZN D:ZN4752 3.2 52.4 1.0
OE1 D:GLU424 3.3 30.4 1.0
OD2 D:ASP387 3.4 12.2 1.0
ND2 D:ASN519 3.5 65.7 1.0
CB D:ASP453 3.9 23.9 1.0
CD D:GLU424 4.0 30.4 1.0
ND1 D:HIS377 4.2 46.2 1.0
CB D:ASP387 4.2 12.2 1.0
CG D:HIS377 4.2 46.2 1.0
OE2 D:GLU424 4.3 30.4 1.0
OD1 D:ASN519 4.3 65.7 1.0
CG D:ASN519 4.3 65.7 1.0
CB D:PRO388 4.5 15.5 1.0
OE2 D:GLU425 4.5 14.1 1.0
OE1 D:GLU425 4.5 14.1 1.0
CD D:GLU425 4.6 14.1 1.0
CA D:ASP387 4.8 46.9 1.0
CA D:PRO388 5.0 27.8 1.0

Zinc binding site 8 out of 8 in 1z8l

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Zinc binding site 8 out of 8 in the Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4752

b:52.4
occ:1.00
 O D:HOH4753 2.0 0.0 1.0
NE2 D:HIS553 2.2 17.2 1.0
OE1 D:GLU425 2.2 14.1 1.0
OD2 D:ASP387 2.3 12.2 1.0
CE1 D:HIS553 2.7 17.2 1.0
CD D:GLU425 3.0 14.1 1.0
CG D:ASP387 3.2 12.2 1.0
OE2 D:GLU425 3.2 14.1 1.0
ZN D:ZN4751 3.2 52.4 1.0
OH D:TYR552 3.3 56.1 1.0
OD1 D:ASP387 3.5 12.2 1.0
CD2 D:HIS553 3.5 17.2 1.0
ND1 D:HIS553 4.0 17.2 1.0
OE1 D:GLU424 4.0 30.4 1.0
CZ D:TYR552 4.1 56.1 1.0
CE1 D:TYR552 4.3 56.1 1.0
OE2 D:GLU424 4.4 30.4 1.0
CG D:HIS553 4.4 17.2 1.0
CG D:GLU425 4.4 14.1 1.0
CB D:ASP387 4.5 12.2 1.0
NE2 D:HIS377 4.5 46.2 1.0
CE1 D:HIS377 4.6 46.2 1.0
CD D:GLU424 4.7 30.4 1.0
OD2 D:ASP453 4.9 23.9 1.0

Reference:

M.I.Davis, M.J.Bennett, L.M.Thomas, P.J.Bjorkman. Crystal Structure of Prostate-Specific Membrane Antigen, A Tumor Marker and Peptidase Proc.Natl.Acad.Sci.Usa V. 102 5981 2005.
ISSN: ISSN 0027-8424
PubMed: 15837926
DOI: 10.1073/PNAS.0502101102
Page generated: Wed Oct 16 21:09:30 2024

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