Zinc in PDB 3kr4: Structure of A Protease 3

All present enzymatic activity of Structure of A Protease 3:
3.4.11.1;

The structure of Structure of A Protease 3, PDB code: 3kr4 was solved by S.Mcgowan, J.C.Whisstock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.15 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	173.561, 178.121, 230.479, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 24.2

The structure of Structure of A Protease 3 also contains other interesting chemical elements:

Magnesium

(Mg)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Structure of A Protease 3 (pdb code 3kr4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structure of A Protease 3, PDB code: 3kr4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Protease 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:39.4 occ:1.00 OD2 A:ASP399 2.1 12.5 1.0 OE2 A:GLU461 2.2 10.4 1.0 NZ A:LYS374 2.2 4.3 1.0 O2 A:BES1003 2.3 20.1 1.0 OD2 A:ASP379 2.5 7.4 1.0 N2 A:BES1003 2.6 20.1 1.0 CG A:ASP399 3.0 11.6 1.0 C2 A:BES1003 3.0 27.2 1.0 CE A:LYS374 3.0 6.4 1.0 OD1 A:ASP399 3.2 10.2 1.0 CD A:GLU461 3.2 11.1 1.0 C1 A:BES1003 3.2 26.0 1.0 MG A:MG1004 3.3 24.9 1.0 CG A:ASP379 3.3 8.2 1.0 OE1 A:GLU461 3.4 9.4 1.0 O2 A:CO31002 3.8 14.2 1.0 CB A:ASP379 3.8 7.0 1.0 O A:THR486 4.3 12.2 1.0 OD1 A:ASP379 4.3 9.1 1.0 C3 A:BES1003 4.3 30.6 1.0 CB A:ASP399 4.4 11.1 1.0 CD A:LYS374 4.5 8.2 1.0 CG A:GLU461 4.6 9.2 1.0 C6 A:BES1003 4.6 27.2 1.0 O3 A:BES1003 4.6 29.2 1.0 N A:GLY462 4.7 7.6 1.0 CG1 A:ILE376 4.7 8.8 1.0 O A:ASP459 4.8 11.2 1.0 CB A:ILE376 4.9 10.6 1.0 CG2 A:ILE376 4.9 8.8 1.0 OD1 A:ASP459 5.0 12.2 1.0 CA A:GLY462 5.0 7.1 1.0

Zinc binding site 2 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Protease 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:37.6 occ:1.00 OD2 B:ASP399 2.1 12.1 1.0 OE2 B:GLU461 2.2 11.8 1.0 O2 B:BES1003 2.4 19.9 1.0 OD2 B:ASP379 2.4 8.5 1.0 NZ B:LYS374 2.4 8.2 1.0 N2 B:BES1003 2.5 17.6 1.0 CG B:ASP399 2.9 10.6 1.0 CE B:LYS374 3.1 4.7 1.0 C2 B:BES1003 3.1 25.7 1.0 CD B:GLU461 3.1 11.2 1.0 OD1 B:ASP399 3.2 11.2 1.0 MG B:MG1004 3.2 16.5 1.0 C1 B:BES1003 3.2 24.0 1.0 CG B:ASP379 3.2 9.6 1.0 OE1 B:GLU461 3.4 12.4 1.0 CB B:ASP379 3.7 9.0 1.0 O2 B:CO31002 3.9 11.8 1.0 OD1 B:ASP379 4.2 7.7 1.0 CB B:ASP399 4.3 9.1 1.0 O B:THR486 4.4 13.6 1.0 C3 B:BES1003 4.4 29.2 1.0 CG B:GLU461 4.5 8.4 1.0 C6 B:BES1003 4.5 26.8 1.0 CD B:LYS374 4.5 6.0 1.0 CG1 B:ILE376 4.6 10.2 1.0 CB B:ILE376 4.8 9.4 1.0 N B:GLY462 4.8 10.4 1.0 O3 B:BES1003 4.8 30.4 1.0 OD1 B:ASP459 4.9 11.1 1.0 CG2 B:ILE376 4.9 9.1 1.0 O B:ASP459 4.9 10.6 1.0

Zinc binding site 3 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Protease 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:39.1 occ:1.00 OD2 C:ASP399 2.1 10.9 1.0 OE2 C:GLU461 2.3 11.6 1.0 NZ C:LYS374 2.3 7.9 1.0 O2 C:BES1003 2.3 22.4 1.0 N2 C:BES1003 2.4 24.3 1.0 OD2 C:ASP379 2.5 9.0 1.0 CG C:ASP399 3.0 12.2 1.0 C2 C:BES1003 3.1 26.8 1.0 CD C:GLU461 3.2 10.2 1.0 C1 C:BES1003 3.2 24.4 1.0 CE C:LYS374 3.2 6.2 1.0 OD1 C:ASP399 3.2 15.1 1.0 CG C:ASP379 3.3 10.6 1.0 MG C:MG1004 3.3 27.1 1.0 OE1 C:GLU461 3.3 8.1 1.0 CB C:ASP379 3.7 8.6 1.0 O1 C:CO31002 4.0 12.9 1.0 OD1 C:ASP379 4.2 10.4 1.0 O C:THR486 4.3 13.2 1.0 CB C:ASP399 4.3 8.8 1.0 C3 C:BES1003 4.3 27.6 1.0 C6 C:BES1003 4.4 23.8 1.0 CG C:GLU461 4.6 8.5 1.0 CD C:LYS374 4.6 4.8 1.0 O3 C:BES1003 4.6 28.2 1.0 CG1 C:ILE376 4.7 9.6 1.0 O C:ASP459 4.8 10.3 1.0 N C:GLY462 4.8 10.4 1.0 CG2 C:ILE376 4.9 9.4 1.0 CB C:ILE376 4.9 8.5 1.0

Zinc binding site 4 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Protease 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:34.2 occ:1.00 OD2 D:ASP399 2.1 9.9 1.0 OE2 D:GLU461 2.3 13.5 1.0 O2 D:BES1003 2.3 13.3 1.0 N2 D:BES1003 2.4 20.8 1.0 OD2 D:ASP379 2.4 9.2 1.0 NZ D:LYS374 2.4 4.4 1.0 CG D:ASP399 2.9 11.9 1.0 CE D:LYS374 3.0 7.1 1.0 OD1 D:ASP399 3.0 11.8 1.0 C2 D:BES1003 3.1 22.8 1.0 MG D:MG1004 3.1 28.2 1.0 C1 D:BES1003 3.2 23.3 1.0 CD D:GLU461 3.3 13.5 1.0 CG D:ASP379 3.3 10.2 1.0 OE1 D:GLU461 3.4 12.2 1.0 CB D:ASP379 3.8 8.5 1.0 O1 D:CO31002 3.8 11.6 1.0 OD1 D:ASP379 4.2 9.0 1.0 O D:THR486 4.3 12.8 1.0 CB D:ASP399 4.3 10.7 1.0 C3 D:BES1003 4.4 23.2 1.0 CD D:LYS374 4.4 6.3 1.0 C6 D:BES1003 4.5 25.7 1.0 CG D:GLU461 4.6 11.1 1.0 CG1 D:ILE376 4.6 9.3 1.0 CB D:ILE376 4.7 8.2 1.0 O3 D:BES1003 4.8 22.8 1.0 O D:ASP459 4.8 9.3 1.0 CG2 D:ILE376 4.8 8.9 1.0 N D:GLY462 4.9 10.5 1.0 OD1 D:ASP459 5.0 12.0 1.0

Zinc binding site 5 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A Protease 3 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1001 b:38.3 occ:1.00 OD2 E:ASP399 2.1 9.7 1.0 O2 E:BES1003 2.2 19.8 1.0 OE2 E:GLU461 2.2 11.9 1.0 OD2 E:ASP379 2.3 10.2 1.0 NZ E:LYS374 2.4 10.3 1.0 N2 E:BES1003 2.5 19.6 1.0 CG E:ASP399 3.0 11.2 1.0 C2 E:BES1003 3.1 24.6 1.0 CD E:GLU461 3.1 12.2 1.0 MG E:MG1004 3.1 26.4 1.0 CG E:ASP379 3.2 10.5 1.0 CE E:LYS374 3.2 10.3 1.0 OD1 E:ASP399 3.3 10.1 1.0 C1 E:BES1003 3.3 24.9 1.0 OE1 E:GLU461 3.3 10.7 1.0 CB E:ASP379 3.6 9.9 1.0 O3 E:CO31002 3.9 17.8 1.0 OD1 E:ASP379 4.1 11.7 1.0 C3 E:BES1003 4.2 27.7 1.0 O E:THR486 4.4 12.4 1.0 CB E:ASP399 4.4 9.2 1.0 O3 E:BES1003 4.5 29.2 1.0 CG E:GLU461 4.5 10.0 1.0 C6 E:BES1003 4.6 27.2 1.0 CD E:LYS374 4.6 8.5 1.0 CG1 E:ILE376 4.7 9.8 1.0 O E:ASP459 4.8 11.6 1.0 OD1 E:ASP459 4.8 12.2 1.0 N E:GLY462 4.8 10.1 1.0 CG2 E:ILE376 4.9 8.7 1.0 CB E:ILE376 4.9 9.5 1.0

Zinc binding site 6 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A Protease 3 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1001 b:40.9 occ:1.00 OD2 F:ASP399 2.1 20.6 1.0 OE2 F:GLU461 2.2 9.6 1.0 O2 F:BES1003 2.3 13.3 1.0 NZ F:LYS374 2.3 5.2 1.0 N2 F:BES1003 2.3 19.6 1.0 OD2 F:ASP379 2.4 13.3 1.0 CG F:ASP399 2.9 14.1 1.0 CE F:LYS374 3.0 5.2 1.0 C2 F:BES1003 3.1 22.7 1.0 MG F:MG1004 3.1 37.5 1.0 CD F:GLU461 3.1 11.1 1.0 C1 F:BES1003 3.2 22.4 1.0 OD1 F:ASP399 3.2 16.0 1.0 CG F:ASP379 3.3 12.8 1.0 OE1 F:GLU461 3.4 12.1 1.0 CB F:ASP379 3.7 11.1 1.0 O1 F:CO31002 3.8 12.6 1.0 OD1 F:ASP379 4.3 14.6 1.0 CB F:ASP399 4.3 11.7 1.0 O F:THR486 4.3 13.7 1.0 C3 F:BES1003 4.3 28.1 1.0 C6 F:BES1003 4.4 22.9 1.0 CD F:LYS374 4.5 5.6 1.0 CG F:GLU461 4.5 10.6 1.0 CG1 F:ILE376 4.6 12.9 1.0 O3 F:BES1003 4.7 27.7 1.0 O F:ASP459 4.7 11.1 1.0 N F:GLY462 4.8 7.6 1.0 CB F:ILE376 4.8 10.3 1.0 CG2 F:ILE376 4.8 11.6 1.0 OD1 F:ASP459 4.9 11.5 1.0

Zinc binding site 7 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of A Protease 3 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1001 b:38.2 occ:1.00 OD2 G:ASP399 2.1 12.9 1.0 OE2 G:GLU461 2.2 11.1 1.0 O2 G:BES1003 2.3 13.8 1.0 OD2 G:ASP379 2.4 7.0 1.0 NZ G:LYS374 2.4 4.3 1.0 N2 G:BES1003 2.5 15.9 1.0 CG G:ASP399 3.0 11.9 1.0 C2 G:BES1003 3.1 24.0 1.0 MG G:MG1004 3.1 23.7 1.0 CD G:GLU461 3.1 11.0 1.0 CE G:LYS374 3.1 5.9 1.0 C1 G:BES1003 3.2 22.9 1.0 OD1 G:ASP399 3.2 10.8 1.0 CG G:ASP379 3.2 8.2 1.0 OE1 G:GLU461 3.3 8.5 1.0 CB G:ASP379 3.7 7.4 1.0 O2 G:CO31002 3.9 11.8 1.0 OD1 G:ASP379 4.2 7.9 1.0 C3 G:BES1003 4.3 26.3 1.0 CB G:ASP399 4.4 11.2 1.0 O G:THR486 4.4 12.3 1.0 C6 G:BES1003 4.4 24.5 1.0 CG G:GLU461 4.5 9.8 1.0 O3 G:BES1003 4.6 28.3 1.0 CD G:LYS374 4.7 8.1 1.0 CG1 G:ILE376 4.7 8.9 1.0 O G:ASP459 4.7 11.3 1.0 N G:GLY462 4.8 7.8 1.0 CB G:ILE376 4.9 10.2 1.0 CG2 G:ILE376 4.9 8.7 1.0 OD1 G:ASP459 4.9 11.9 1.0

Zinc binding site 8 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of A Protease 3 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn1001 b:34.8 occ:1.00 OD2 H:ASP399 2.1 11.4 1.0 OE2 H:GLU461 2.2 10.3 1.0 O2 H:BES1003 2.3 16.5 1.0 N2 H:BES1003 2.3 15.8 1.0 OD2 H:ASP379 2.4 8.3 1.0 NZ H:LYS374 2.4 8.1 1.0 CG H:ASP399 2.9 10.4 1.0 OD1 H:ASP399 3.1 11.5 1.0 C2 H:BES1003 3.1 19.6 1.0 CD H:GLU461 3.2 10.8 1.0 C1 H:BES1003 3.2 19.2 1.0 CE H:LYS374 3.2 4.5 1.0 CG H:ASP379 3.2 9.3 1.0 MG H:MG1004 3.2 40.7 1.0 OE1 H:GLU461 3.4 11.3 1.0 CB H:ASP379 3.7 8.8 1.0 O2 H:CO31002 3.9 10.3 1.0 OD1 H:ASP379 4.3 6.6 1.0 CB H:ASP399 4.3 8.1 1.0 C3 H:BES1003 4.3 24.5 1.0 O H:THR486 4.4 13.4 1.0 C6 H:BES1003 4.5 21.8 1.0 CG H:GLU461 4.5 8.0 1.0 O3 H:BES1003 4.6 22.7 1.0 CD H:LYS374 4.7 5.6 1.0 CG1 H:ILE376 4.8 9.8 1.0 CB H:ILE376 4.8 9.2 1.0 OD1 H:ASP459 4.8 11.7 1.0 O H:ASP459 4.9 10.4 1.0 CG2 H:ILE376 4.9 8.1 1.0 N H:GLY462 4.9 10.2 1.0

Zinc binding site 9 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of A Protease 3 within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn1001 b:36.9 occ:1.00 OD2 I:ASP399 2.1 10.4 1.0 OE2 I:GLU461 2.2 11.9 1.0 NZ I:LYS374 2.3 8.1 1.0 OD2 I:ASP379 2.3 8.2 1.0 O2 I:BES1003 2.4 11.2 1.0 N2 I:BES1003 2.4 20.4 1.0 CG I:ASP399 3.0 11.7 1.0 CE I:LYS374 3.1 6.6 1.0 MG I:MG1004 3.2 15.1 1.0 CD I:GLU461 3.2 9.5 1.0 OD1 I:ASP399 3.2 15.0 1.0 CG I:ASP379 3.2 10.2 1.0 C2 I:BES1003 3.2 22.5 1.0 C1 I:BES1003 3.3 22.6 1.0 OE1 I:GLU461 3.5 8.1 1.0 CB I:ASP379 3.7 8.2 1.0 O1 I:CO31002 3.9 15.7 1.0 OD1 I:ASP379 4.2 10.4 1.0 CB I:ASP399 4.3 8.4 1.0 O I:THR486 4.3 12.7 1.0 C3 I:BES1003 4.4 24.5 1.0 CG I:GLU461 4.5 8.4 1.0 C6 I:BES1003 4.6 24.6 1.0 CD I:LYS374 4.6 5.0 1.0 CG1 I:ILE376 4.6 9.2 1.0 CG2 I:ILE376 4.7 9.0 1.0 O3 I:BES1003 4.8 25.1 1.0 CB I:ILE376 4.8 7.9 1.0 N I:GLY462 4.8 10.2 1.0 O I:ASP459 4.8 9.6 1.0 OD1 I:ASP459 5.0 11.6 1.0

Zinc binding site 10 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of A Protease 3 within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1001 b:38.0 occ:1.00 OD2 J:ASP399 2.1 9.9 1.0 OE1 J:GLU461 2.2 12.4 1.0 O2 J:BES1003 2.3 11.3 1.0 NZ J:LYS374 2.3 4.5 1.0 OD2 J:ASP379 2.4 8.2 1.0 N2 J:BES1003 2.5 23.6 1.0 CG J:ASP399 2.9 12.3 1.0 C2 J:BES1003 3.1 23.9 1.0 CE J:LYS374 3.1 6.9 1.0 OD1 J:ASP399 3.1 11.4 1.0 C1 J:BES1003 3.2 22.4 1.0 CD J:GLU461 3.2 13.4 1.0 MG J:MG1004 3.3 23.0 1.0 CG J:ASP379 3.3 10.2 1.0 OE2 J:GLU461 3.4 12.9 1.0 CB J:ASP379 3.8 9.1 1.0 O3 J:CO31002 3.9 16.0 1.0 OD1 J:ASP379 4.2 8.6 1.0 CB J:ASP399 4.2 10.7 1.0 O J:THR486 4.3 12.8 1.0 C3 J:BES1003 4.4 26.1 1.0 C6 J:BES1003 4.4 25.2 1.0 CD J:LYS374 4.5 6.5 1.0 CG J:GLU461 4.6 11.0 1.0 CG1 J:ILE376 4.7 9.4 1.0 O3 J:BES1003 4.7 28.9 1.0 CB J:ILE376 4.8 7.6 1.0 CG2 J:ILE376 4.8 9.7 1.0 N J:GLY462 4.9 10.9 1.0 O J:ASP459 4.9 9.7 1.0 OD1 J:ASP459 5.0 11.6 1.0

S.Mcgowan, C.A.Oellig, W.A.Birru, T.T.Caradoc-Davies, C.M.Stack, J.Lowther, T.Skinner-Adams, A.Mucha, P.Kafarski, J.Grembecka, K.R.Trenholme, A.M.Buckle, D.L.Gardiner, J.P.Dalton, J.C.Whisstock. Structure of the Plasmodium Falciparum M17 Aminopeptidase and Significance For the Design of Drugs Targeting the Neutral Exopeptidases Proc.Natl.Acad.Sci.Usa V. 107 2449 2010.
ISSN: ISSN 0027-8424
PubMed: 20133789
DOI: 10.1073/PNAS.0911813107