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Zinc in PDB 3kqx: Structure of A Protease 1

Enzymatic activity of Structure of A Protease 1

All present enzymatic activity of Structure of A Protease 1:
3.4.11.1;

Protein crystallography data

The structure of Structure of A Protease 1, PDB code: 3kqx 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) 56.08 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 173.404, 176.809, 224.246, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 23.2

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Structure of A Protease 1 (pdb code 3kqx). 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 1, PDB code: 3kqx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 3kqx

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


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:77.4
occ:1.00
 OD2 A:ASP399 2.2 11.1 1.0
OE2 A:GLU461 2.3 15.0 1.0
NZ A:LYS374 2.4 5.9 1.0
O A:HOH4267 2.4 33.5 1.0
OD2 A:ASP379 2.6 8.4 1.0
O A:HOH4274 2.6 23.3 1.0
CG A:ASP399 3.1 18.0 1.0
CE A:LYS374 3.2 6.9 1.0
CD A:GLU461 3.3 14.3 1.0
OD1 A:ASP399 3.4 13.8 1.0
CG A:ASP379 3.4 13.0 1.0
OE1 A:GLU461 3.5 15.4 1.0
O2 A:CO31002 3.9 17.2 1.0
CB A:ASP379 3.9 7.8 1.0
CB A:ASP399 4.4 8.9 1.0
OD1 A:ASP379 4.4 10.5 1.0
O A:THR486 4.4 16.0 1.0
CG A:GLU461 4.7 5.5 1.0
CD A:LYS374 4.7 6.9 1.0
N A:GLY462 4.8 8.8 1.0
CG1 A:ILE376 4.9 8.4 1.0
O A:ASP459 4.9 10.9 1.0
OD1 A:ASP459 4.9 9.3 1.0

Zinc binding site 2 out of 12 in 3kqx

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Zinc binding site 2 out of 12 in the Structure of A Protease 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:60.3
occ:1.00
 OE2 B:GLU461 2.2 12.7 1.0
OD2 B:ASP399 2.3 17.6 1.0
OD2 B:ASP379 2.3 9.9 1.0
NZ B:LYS374 2.5 12.7 1.0
O B:HOH4281 2.8 41.2 1.0
CG B:ASP399 3.1 11.4 1.0
CD B:GLU461 3.1 15.7 1.0
CG B:ASP379 3.2 8.5 1.0
OD1 B:ASP399 3.3 15.9 1.0
OE1 B:GLU461 3.3 13.8 1.0
CE B:LYS374 3.3 11.0 1.0
O2 B:CO31002 3.8 17.6 1.0
CB B:ASP379 3.8 6.1 1.0
OD1 B:ASP379 4.2 8.9 1.0
CB B:ASP399 4.5 9.4 1.0
O B:THR486 4.5 15.2 1.0
CG B:GLU461 4.6 6.5 1.0
O B:ASP459 4.6 13.2 1.0
OD1 B:ASP459 4.7 14.5 1.0
CD B:LYS374 4.8 9.0 1.0
CG1 B:ILE376 4.8 11.0 1.0
N B:GLY462 4.8 9.4 1.0

Zinc binding site 3 out of 12 in 3kqx

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


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:59.6
occ:1.00
 OD2 C:ASP399 2.2 13.5 1.0
OE2 C:GLU461 2.3 10.6 1.0
O C:HOH4276 2.5 23.9 1.0
OD2 C:ASP379 2.6 6.9 1.0
NZ C:LYS374 2.6 9.6 1.0
CG C:ASP399 3.1 18.5 1.0
CD C:GLU461 3.3 9.7 1.0
OD1 C:ASP399 3.3 16.9 1.0
CE C:LYS374 3.4 5.8 1.0
OE1 C:GLU461 3.4 11.0 1.0
CG C:ASP379 3.4 7.0 1.0
O1 C:CO31002 3.8 20.8 1.0
CB C:ASP379 3.9 6.0 1.0
OD1 C:ASP379 4.3 9.2 1.0
O C:THR486 4.4 12.5 1.0
CB C:ASP399 4.5 7.8 1.0
OD1 C:ASP459 4.6 15.5 1.0
O C:ASP459 4.6 9.0 1.0
CG C:GLU461 4.7 6.3 1.0
CD C:LYS374 4.8 9.4 1.0
N C:GLY462 4.9 9.1 1.0
CG1 C:ILE376 4.9 5.3 1.0

Zinc binding site 4 out of 12 in 3kqx

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Zinc binding site 4 out of 12 in the Structure of A Protease 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1001

b:71.8
occ:1.00
 OE2 D:GLU461 2.3 16.1 1.0
OD2 D:ASP399 2.4 15.8 1.0
OD2 D:ASP379 2.4 13.0 1.0
NZ D:LYS374 2.6 7.7 1.0
O D:HOH4275 2.7 19.8 1.0
CD D:GLU461 3.2 8.3 1.0
CG D:ASP399 3.3 18.2 1.0
OE1 D:GLU461 3.3 10.4 1.0
CG D:ASP379 3.4 9.1 1.0
OD1 D:ASP399 3.5 14.1 1.0
CE D:LYS374 3.5 5.0 1.0
O1 D:CO31002 3.8 18.0 1.0
CB D:ASP379 3.9 6.9 1.0
OD1 D:ASP379 4.3 11.3 1.0
O D:ASP459 4.4 9.3 1.0
O D:THR486 4.5 13.6 1.0
OD1 D:ASP459 4.5 9.5 1.0
CB D:ASP399 4.6 9.2 1.0
CG D:GLU461 4.6 8.2 1.0
C15 D:1PE23 4.6 65.8 1.0
N D:GLY462 4.8 8.9 1.0
CD D:LYS374 4.9 10.5 1.0
C25 D:1PE23 5.0 58.9 1.0
CG1 D:ILE376 5.0 8.2 1.0

Zinc binding site 5 out of 12 in 3kqx

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Zinc binding site 5 out of 12 in the Structure of A Protease 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1001

b:67.1
occ:1.00
 OD2 E:ASP399 2.1 14.7 1.0
OE2 E:GLU461 2.2 16.3 1.0
O E:HOH4272 2.4 20.4 1.0
OD2 E:ASP379 2.5 11.0 1.0
NZ E:LYS374 2.6 7.2 1.0
O E:HOH4271 2.7 26.8 1.0
CG E:ASP399 3.1 13.3 1.0
CD E:GLU461 3.1 11.6 1.0
OE1 E:GLU461 3.2 8.5 1.0
CE E:LYS374 3.3 8.0 1.0
OD1 E:ASP399 3.3 15.3 1.0
CG E:ASP379 3.4 7.8 1.0
CB E:ASP379 3.9 10.4 1.0
O3 E:CO31002 3.9 23.0 1.0
OD1 E:ASP379 4.3 10.8 1.0
CB E:ASP399 4.4 12.5 1.0
O E:THR486 4.5 11.5 1.0
CG E:GLU461 4.5 7.7 1.0
OD1 E:ASP459 4.6 11.4 1.0
CG1 E:ILE376 4.7 9.2 1.0
N E:GLY462 4.7 8.4 1.0
O E:ASP459 4.7 11.6 1.0
CD E:LYS374 4.8 5.7 1.0
CB E:ILE376 5.0 10.4 1.0
NZ E:LYS386 5.0 6.3 1.0

Zinc binding site 6 out of 12 in 3kqx

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Zinc binding site 6 out of 12 in the Structure of A Protease 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1001

b:82.1
occ:1.00
 OD2 F:ASP399 2.1 17.7 1.0
OD2 F:ASP379 2.4 8.5 1.0
OE2 F:GLU461 2.5 15.0 1.0
NZ F:LYS374 2.6 6.0 1.0
CG F:ASP399 3.0 3.8 1.0
CG F:ASP379 3.2 7.9 1.0
OD1 F:ASP399 3.2 11.3 1.0
CD F:GLU461 3.3 15.0 1.0
OE1 F:GLU461 3.4 16.4 1.0
CB F:ASP379 3.6 11.2 1.0
CE F:LYS374 3.6 13.6 1.0
O1 F:CO31002 4.2 23.9 1.0
OD1 F:ASP379 4.3 14.2 1.0
CB F:ASP399 4.3 5.0 1.0
OD1 F:ASP459 4.5 14.8 1.0
O F:THR486 4.6 16.0 1.0
O F:ASP459 4.6 10.8 1.0
CG F:GLU461 4.7 16.2 1.0
CG1 F:ILE376 4.8 11.7 1.0
NZ F:LYS386 4.9 10.9 1.0
N F:GLY462 5.0 9.5 1.0
CB F:ILE376 5.0 11.5 1.0
CD F:LYS374 5.0 10.4 1.0

Zinc binding site 7 out of 12 in 3kqx

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Zinc binding site 7 out of 12 in the Structure of A Protease 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1001

b:74.1
occ:1.00
 OD2 G:ASP399 2.1 11.8 1.0
OE2 G:GLU461 2.2 14.5 1.0
OD2 G:ASP379 2.4 7.9 1.0
NZ G:LYS374 2.4 6.7 1.0
O G:HOH4257 2.4 17.8 1.0
O G:HOH4256 2.6 23.7 1.0
CG G:ASP399 3.0 18.3 1.0
CD G:GLU461 3.2 13.4 1.0
CG G:ASP379 3.2 13.8 1.0
OD1 G:ASP399 3.3 13.7 1.0
CE G:LYS374 3.3 7.5 1.0
OE1 G:GLU461 3.5 15.3 1.0
CB G:ASP379 3.7 7.0 1.0
O2 G:CO31002 3.9 22.3 1.0
OD1 G:ASP379 4.3 11.1 1.0
CB G:ASP399 4.3 8.2 1.0
O G:THR486 4.5 16.3 1.0
CG G:GLU461 4.6 5.4 1.0
OH3 G:1PE16 4.6 41.4 1.0
CD G:LYS374 4.8 5.8 1.0
CG1 G:ILE376 4.8 8.7 1.0
OD1 G:ASP459 4.8 9.3 1.0
CB G:ILE376 4.9 7.3 1.0
O G:ASP459 4.9 10.2 1.0
N G:GLY462 4.9 8.1 1.0
CG2 G:ILE376 4.9 5.0 1.0

Zinc binding site 8 out of 12 in 3kqx

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Zinc binding site 8 out of 12 in the Structure of A Protease 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1001

b:73.3
occ:1.00
 OD2 H:ASP399 2.2 18.0 1.0
OD2 H:ASP379 2.4 10.2 1.0
OE2 H:GLU461 2.4 14.0 1.0
NZ H:LYS374 2.7 12.0 1.0
O H:HOH4259 2.8 33.7 1.0
CG H:ASP399 3.1 11.9 1.0
CD H:GLU461 3.2 17.0 1.0
CG H:ASP379 3.3 8.6 1.0
OE1 H:GLU461 3.3 13.1 1.0
OD1 H:ASP399 3.4 16.5 1.0
CE H:LYS374 3.5 10.9 1.0
CB H:ASP379 3.8 6.3 1.0
O2 H:CO31002 3.9 16.1 1.0
OD1 H:ASP379 4.3 10.2 1.0
CB H:ASP399 4.5 9.6 1.0
O H:THR486 4.5 15.8 1.0
O H:ASP459 4.6 13.1 1.0
OD1 H:ASP459 4.6 14.9 1.0
CG H:GLU461 4.7 6.4 1.0
CD H:LYS374 4.9 8.2 1.0
NZ H:LYS386 4.9 9.5 1.0
N H:GLY462 5.0 9.9 1.0
CG1 H:ILE376 5.0 11.6 1.0

Zinc binding site 9 out of 12 in 3kqx

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Zinc binding site 9 out of 12 in the Structure of A Protease 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1001

b:64.7
occ:1.00
 OD2 I:ASP399 2.2 14.8 1.0
OE2 I:GLU461 2.3 8.9 1.0
O I:HOH4261 2.3 21.3 1.0
OD2 I:ASP379 2.5 6.2 1.0
NZ I:LYS374 2.6 9.7 1.0
O I:HOH4260 2.8 20.5 1.0
CG I:ASP399 3.1 18.3 1.0
CD I:GLU461 3.2 11.4 1.0
OD1 I:ASP399 3.3 17.2 1.0
CE I:LYS374 3.3 6.5 1.0
CG I:ASP379 3.3 7.8 1.0
OE1 I:GLU461 3.4 10.1 1.0
CB I:ASP379 3.8 5.7 1.0
O1 I:CO31002 3.9 13.2 1.0
OD1 I:ASP379 4.3 10.0 1.0
CB I:ASP399 4.4 8.0 1.0
O I:THR486 4.5 13.2 1.0
CG I:GLU461 4.6 6.0 1.0
OD1 I:ASP459 4.7 12.8 1.0
O I:ASP459 4.7 9.6 1.0
CD I:LYS374 4.8 8.7 1.0
N I:GLY462 4.8 9.5 1.0
CG1 I:ILE376 4.9 6.6 1.0
CG2 I:ILE376 4.9 5.8 1.0
CB I:ILE376 5.0 7.1 1.0

Zinc binding site 10 out of 12 in 3kqx

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Zinc binding site 10 out of 12 in the Structure of A Protease 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1001

b:92.0
occ:1.00
 OE2 J:GLU461 2.3 16.1 1.0
OD2 J:ASP379 2.4 10.2 1.0
OD2 J:ASP399 2.4 14.5 1.0
NZ J:LYS374 2.5 7.0 1.0
OH6 J:1PE15 2.9 37.8 1.0
CD J:GLU461 3.1 7.1 1.0
OE1 J:GLU461 3.1 9.1 1.0
CG J:ASP399 3.3 18.0 1.0
CG J:ASP379 3.4 8.4 1.0
OD1 J:ASP399 3.5 14.6 1.0
CE J:LYS374 3.5 2.8 1.0
O1 J:CO31002 3.6 15.1 1.0
C15 J:1PE15 4.0 41.2 1.0
CB J:ASP379 4.0 5.3 1.0
OD1 J:ASP379 4.3 11.6 1.0
O J:THR486 4.4 14.2 1.0
O J:ASP459 4.4 10.7 1.0
OD1 J:ASP459 4.6 10.3 1.0
CG J:GLU461 4.6 8.4 1.0
N J:GLY462 4.6 8.3 1.0
CB J:ASP399 4.7 9.8 1.0
C J:CO31002 4.9 13.5 1.0
CD J:LYS374 4.9 8.7 1.0
CG1 J:ILE376 4.9 8.3 1.0

Reference:

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
Page generated: Sat Oct 26 07:59:04 2024

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