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Zinc in PDB 5lpe: Kallikrein-Related Peptidase 10 Complex with ZN2+

Protein crystallography data

The structure of Kallikrein-Related Peptidase 10 Complex with ZN2+, PDB code: 5lpe was solved by P.Goettig, M.Debela, V.Magdolen, W.Bode, H.Brandstetter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.57 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.914, 67.037, 57.768, 90.00, 104.37, 90.00
R / Rfree (%) 22 / 27.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Kallikrein-Related Peptidase 10 Complex with ZN2+ (pdb code 5lpe). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Kallikrein-Related Peptidase 10 Complex with ZN2+, PDB code: 5lpe:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5lpe

Go back to Zinc Binding Sites List in 5lpe
Zinc binding site 1 out of 2 in the Kallikrein-Related Peptidase 10 Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Kallikrein-Related Peptidase 10 Complex with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:46.4
occ:1.00
OD2 A:ASP99 1.9 43.0 1.0
OD2 A:ASP102 2.1 31.9 1.0
ND1 A:HIS57 2.1 40.7 1.0
CG A:ASP99 2.6 46.0 1.0
CG A:HIS57 2.9 34.9 1.0
CB A:ASP99 3.1 43.3 1.0
CB A:HIS57 3.1 32.5 1.0
CE1 A:HIS57 3.1 39.2 1.0
CG A:ASP102 3.2 36.9 1.0
OD1 A:ASP99 3.5 52.8 1.0
O A:SER214 3.6 29.1 1.0
OG A:SER214 3.7 31.1 1.0
CB A:ASP102 3.7 33.0 1.0
CD2 A:HIS57 4.1 34.9 1.0
NE2 A:HIS57 4.2 36.5 1.0
OD1 A:ASP102 4.2 45.5 1.0
C A:SER214 4.3 26.8 1.0
CA A:HIS57 4.4 28.3 1.0
CA A:ASP99 4.4 43.2 1.0
N A:HIS57 4.4 31.4 1.0
CA A:SER214 4.4 26.4 1.0
N A:ASP99 4.7 46.5 1.0
CB A:SER214 4.7 27.0 1.0
CB A:ALA55 4.7 22.5 1.0
O A:ASP99 4.8 46.8 1.0
OH A:TYR94 4.8 33.2 1.0
NH1 B:ARG97 4.9 47.1 1.0
C A:ASP99 5.0 44.9 1.0

Zinc binding site 2 out of 2 in 5lpe

Go back to Zinc Binding Sites List in 5lpe
Zinc binding site 2 out of 2 in the Kallikrein-Related Peptidase 10 Complex with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Kallikrein-Related Peptidase 10 Complex with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:44.5
occ:1.00
OD2 B:ASP99 2.0 54.2 1.0
OD2 B:ASP102 2.0 32.0 1.0
ND1 B:HIS57 2.1 30.9 1.0
CG B:ASP99 2.9 45.0 1.0
CG B:HIS57 2.9 31.2 1.0
CG B:ASP102 3.0 35.0 1.0
CB B:HIS57 3.0 33.0 1.0
CB B:ASP99 3.1 39.4 1.0
CE1 B:HIS57 3.2 27.1 1.0
OD1 B:ASP102 3.4 37.0 1.0
O B:SER214 3.6 27.1 1.0
OG B:SER214 3.9 27.2 1.0
OD1 B:ASP99 4.0 51.9 1.0
CD2 B:HIS57 4.1 31.0 1.0
CB B:ASP102 4.1 36.2 1.0
NE2 B:HIS57 4.2 27.8 1.0
CA B:HIS57 4.3 33.1 1.0
CA B:ASP99 4.4 45.8 1.0
C B:SER214 4.4 26.5 1.0
N B:HIS57 4.5 34.7 1.0
N B:ASP99 4.7 47.5 1.0
CA B:SER214 4.7 26.0 1.0
O B:HOH444 4.8 38.1 1.0
O B:ASP99 4.9 53.0 1.0
CB B:SER214 5.0 21.6 1.0
OH B:TYR94 5.0 43.1 1.0

Reference:

M.Debela, V.Magdolen, W.Bode, H.Brandstetter, P.Goettig. Structural Basis For the ZN2+ Inhibition of the Zymogen-Like Kallikrein-Related Peptidase 10. Biol.Chem. V. 397 1251 2016.
ISSN: ISSN 1431-6730
PubMed: 27611765
DOI: 10.1515/HSZ-2016-0205
Page generated: Wed Dec 16 06:30:21 2020

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