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Zinc in PDB 3ahn: Pz Peptidase A with Inhibitor 1

Protein crystallography data

The structure of Pz Peptidase A with Inhibitor 1, PDB code: 3ahn was solved by H.Nakano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.379, 194.148, 59.924, 90.00, 106.22, 90.00
R / Rfree (%) 18.8 / 20

Zinc Binding Sites:

The binding sites of Zinc atom in the Pz Peptidase A with Inhibitor 1 (pdb code 3ahn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Pz Peptidase A with Inhibitor 1, PDB code: 3ahn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3ahn

Go back to Zinc Binding Sites List in 3ahn
Zinc binding site 1 out of 2 in the Pz Peptidase A with Inhibitor 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pz Peptidase A with Inhibitor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn566

b:16.0
occ:1.00
NE2 A:HIS360 2.1 11.0 1.0
O36 A:3A1565 2.2 13.1 1.0
NE2 A:HIS356 2.2 8.1 1.0
OE2 A:GLU384 2.3 12.4 1.0
OE1 A:GLU384 2.3 11.7 1.0
OP3 A:3A1565 2.6 14.3 1.0
CD A:GLU384 2.6 11.1 1.0
P33 A:3A1565 2.9 14.8 1.0
CD2 A:HIS360 3.1 11.7 1.0
CE1 A:HIS360 3.1 10.3 1.0
CE1 A:HIS356 3.1 11.5 1.0
CD2 A:HIS356 3.2 9.9 1.0
OG A:SER387 3.6 10.2 1.0
CE1 A:TYR490 3.8 11.8 1.0
OH A:TYR486 4.1 11.6 1.0
N13 A:3A1565 4.1 14.7 1.0
CB A:SER387 4.1 11.4 1.0
CG A:GLU384 4.2 10.5 1.0
C37 A:3A1565 4.2 15.7 1.0
ND1 A:HIS360 4.2 10.6 1.0
CG A:HIS360 4.2 10.1 1.0
C15 A:3A1565 4.2 17.1 1.0
ND1 A:HIS356 4.2 10.1 1.0
OH A:TYR490 4.3 12.6 1.0
C39 A:3A1565 4.3 16.8 1.0
CG A:HIS356 4.3 9.4 1.0
CZ A:TYR490 4.5 12.8 1.0
C11 A:3A1565 4.7 16.6 1.0
CD1 A:TYR490 4.7 8.7 1.0
OE1 A:GLU357 4.8 14.5 1.0
C45 A:3A1565 5.0 15.7 1.0
CA A:GLU384 5.0 9.4 1.0
CB A:GLU384 5.0 9.7 1.0

Zinc binding site 2 out of 2 in 3ahn

Go back to Zinc Binding Sites List in 3ahn
Zinc binding site 2 out of 2 in the Pz Peptidase A with Inhibitor 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pz Peptidase A with Inhibitor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn565

b:21.9
occ:1.00
O36 B:3A1566 2.1 19.6 1.0
NE2 B:HIS360 2.2 14.6 1.0
NE2 B:HIS356 2.2 14.4 1.0
OE1 B:GLU384 2.3 14.9 1.0
OE2 B:GLU384 2.4 18.5 1.0
OP3 B:3A1566 2.6 17.8 1.0
CD B:GLU384 2.7 17.9 1.0
P33 B:3A1566 2.9 20.8 1.0
CD2 B:HIS360 3.1 13.3 1.0
CE1 B:HIS356 3.2 16.4 1.0
CD2 B:HIS356 3.2 14.1 1.0
CE1 B:HIS360 3.2 18.3 1.0
OG B:SER387 3.6 15.2 1.0
CE1 B:TYR490 3.8 16.2 1.0
N13 B:3A1566 4.1 25.1 1.0
CB B:SER387 4.1 14.0 1.0
OH B:TYR486 4.2 17.3 1.0
CG B:GLU384 4.2 16.5 1.0
C37 B:3A1566 4.2 22.7 1.0
C39 B:3A1566 4.2 24.8 1.0
C15 B:3A1566 4.2 23.6 1.0
CG B:HIS360 4.3 14.8 1.0
ND1 B:HIS356 4.3 16.4 1.0
OH B:TYR490 4.3 17.8 1.0
ND1 B:HIS360 4.3 15.2 1.0
CG B:HIS356 4.3 16.1 1.0
CZ B:TYR490 4.5 16.9 1.0
CD1 B:TYR490 4.7 14.8 1.0
C11 B:3A1566 4.8 29.9 1.0
CA B:GLU384 4.9 16.2 1.0
OE1 B:GLU357 4.9 19.7 1.0
CB B:GLU384 5.0 15.6 1.0

Reference:

A.Kawasaki, H.Nakano, A.Hosokawa, T.Nakatsu, H.Kato, K.Watanabe. The Exquisite Structure and Reaction Mechanism of Bacterial Pz-Peptidase A Toward Collagenous Peptides: X-Ray Crystallographic Structure Analysis of Pz-Peptidase A Reveals Differences From Mammalian Thimet Oligopeptidase. J.Biol.Chem. V. 285 34972 2010.
ISSN: ISSN 0021-9258
PubMed: 20817732
DOI: 10.1074/JBC.M110.141838
Page generated: Sat Sep 26 05:29:28 2020
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