Zinc in PDB 7t3v: Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+

Enzymatic activity of Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+

All present enzymatic activity of Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+:
3.4.11.1;

Protein crystallography data

The structure of Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+, PDB code: 7t3v was solved by C.T.Webb, S.Mcgowan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.24 / 2.30
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 111.76, 172.756, 176.922, 90, 90, 90
R / Rfree (%) 21.9 / 26.4

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+ (pdb code 7t3v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+, PDB code: 7t3v:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 7t3v

Go back to Zinc Binding Sites List in 7t3v
Zinc binding site 1 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:48.4
occ:0.88
 OD2 A:ASP379 1.8 36.1 1.0
O A:ASP459 2.1 38.2 1.0
OE1 A:GLU461 2.2 45.9 1.0
OD1 A:ASP459 2.2 44.9 1.0
ZN A:ZN703 2.5 50.3 0.9
CG A:ASP379 2.8 40.7 1.0
CD A:GLU461 2.9 45.7 1.0
OE2 A:GLU461 2.9 43.0 1.0
OD1 A:ASP379 3.1 44.7 1.0
C A:ASP459 3.2 49.7 1.0
CG A:ASP459 3.4 47.5 1.0
CA A:ASP459 3.8 48.4 1.0
OD2 A:ASP399 4.0 32.2 1.0
NZ A:LYS386 4.1 49.9 1.0
CB A:ASP379 4.1 42.3 1.0
CB A:ASP459 4.2 45.7 1.0
OD2 A:ASP459 4.3 47.7 1.0
N A:GLU461 4.3 46.7 1.0
N A:ALA460 4.3 51.8 1.0
CG A:GLU461 4.4 41.2 1.0
CE A:LYS386 4.4 48.5 1.0
O3 A:CO3701 4.6 46.9 1.0
NZ A:LYS374 4.6 41.7 1.0
CA A:ALA460 4.7 44.6 1.0
ND2 A:ASN432 4.8 49.9 1.0
CG A:ASP399 5.0 43.2 1.0

Zinc binding site 2 out of 12 in 7t3v

Go back to Zinc Binding Sites List in 7t3v
Zinc binding site 2 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:50.3
occ:0.95
 OE2 A:GLU461 1.9 43.0 1.0
OD2 A:ASP399 2.0 32.2 1.0
NZ A:LYS374 2.2 41.7 1.0
ZN A:ZN702 2.5 48.4 0.9
OD2 A:ASP379 2.6 36.1 1.0
CD A:GLU461 2.9 45.7 1.0
CG A:ASP399 3.0 43.2 1.0
OE1 A:GLU461 3.2 45.9 1.0
OD1 A:ASP399 3.4 47.7 1.0
CG A:ASP379 3.4 40.7 1.0
CE A:LYS374 3.5 45.3 1.0
O A:ASP459 4.0 38.2 1.0
O3 A:CO3701 4.1 46.9 1.0
CB A:ASP379 4.1 42.3 1.0
OD1 A:ASP379 4.2 44.7 1.0
CG A:GLU461 4.2 41.2 1.0
CB A:ASP399 4.4 45.9 1.0
O A:THR486 4.5 46.8 1.0
N A:GLY462 4.5 45.4 1.0
OD1 A:ASP459 4.6 44.9 1.0
CD A:LYS374 4.7 46.2 1.0
CG1 A:ILE376 4.8 44.5 1.0
N A:GLU461 4.9 46.7 1.0
CA A:GLY462 4.9 46.4 1.0

Zinc binding site 3 out of 12 in 7t3v

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Zinc binding site 3 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:51.6
occ:0.97
 OE2 B:GLU461 2.1 42.5 1.0
OD2 B:ASP399 2.1 47.2 1.0
OD2 B:ASP379 2.2 48.0 1.0
NZ B:LYS374 2.3 39.3 1.0
ZN B:ZN703 2.4 52.2 1.0
CD B:GLU461 3.0 47.8 1.0
CG B:ASP399 3.1 51.5 1.0
CG B:ASP379 3.1 47.9 1.0
OE1 B:GLU461 3.2 50.9 1.0
CE B:LYS374 3.3 48.6 1.0
OD1 B:ASP399 3.4 45.1 1.0
CB B:ASP379 3.8 48.4 1.0
OD1 B:ASP379 4.0 47.1 1.0
OD1 B:ASP459 4.3 42.3 1.0
CG B:GLU461 4.4 51.3 1.0
CB B:ASP399 4.4 44.7 1.0
O B:ASP459 4.5 45.8 1.0
N B:GLY462 4.5 49.0 1.0
O B:THR486 4.6 53.7 1.0
CD B:LYS374 4.6 49.5 1.0
CG1 B:ILE376 4.7 49.7 1.0
CG2 B:ILE376 4.8 46.5 1.0
CB B:ILE376 4.9 41.6 1.0
CA B:GLY462 4.9 45.8 1.0

Zinc binding site 4 out of 12 in 7t3v

Go back to Zinc Binding Sites List in 7t3v
Zinc binding site 4 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:52.2
occ:1.00
 OD1 B:ASP459 2.0 42.3 1.0
OD2 B:ASP379 2.1 48.0 1.0
OE1 B:GLU461 2.3 50.9 1.0
ZN B:ZN702 2.4 51.6 1.0
O B:ASP459 2.4 45.8 1.0
CG B:ASP379 3.0 47.9 1.0
CD B:GLU461 3.0 47.8 1.0
OE2 B:GLU461 3.1 42.5 1.0
CG B:ASP459 3.1 50.7 1.0
OD1 B:ASP379 3.3 47.1 1.0
C B:ASP459 3.4 49.2 1.0
CA B:ASP459 3.9 42.4 1.0
OD2 B:ASP459 3.9 45.5 1.0
CB B:ASP459 4.1 43.5 1.0
OD2 B:ASP399 4.1 47.2 1.0
CB B:ASP379 4.4 48.4 1.0
N B:GLU461 4.4 49.2 1.0
NZ B:LYS386 4.4 49.5 1.0
NZ B:LYS374 4.4 39.3 1.0
CG B:GLU461 4.5 51.3 1.0
CE B:LYS386 4.5 45.5 1.0
N B:ALA460 4.5 47.9 1.0
CA B:ALA460 4.9 50.8 1.0
ND2 B:ASN432 4.9 47.9 1.0
N B:GLY462 5.0 49.0 1.0

Zinc binding site 5 out of 12 in 7t3v

Go back to Zinc Binding Sites List in 7t3v
Zinc binding site 5 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn703

b:49.4
occ:1.00
 OD2 C:ASP399 1.8 51.9 1.0
OE2 C:GLU461 2.1 41.3 1.0
NZ C:LYS374 2.1 39.0 1.0
ZN C:ZN704 2.5 50.5 1.0
CG C:ASP399 2.9 52.7 1.0
CG C:ASP379 3.0 47.0 1.0
CD C:GLU461 3.0 46.6 1.0
CE C:LYS374 3.1 51.6 1.0
OD1 C:ASP399 3.3 46.2 1.0
OE1 C:GLU461 3.3 46.2 1.0
CB C:ASP379 3.6 47.3 1.0
OD1 C:ASP379 3.9 49.0 1.0
CB C:ASP399 4.2 47.9 1.0
OD1 C:ASP459 4.3 40.4 1.0
CG C:GLU461 4.4 42.1 1.0
CD C:LYS374 4.5 46.0 1.0
O C:THR486 4.7 49.0 1.0
O C:ASP459 4.7 40.3 1.0
O1 C:CO3702 4.7 58.0 1.0
CG1 C:ILE376 4.7 44.3 1.0
N C:GLY462 4.7 43.3 1.0
CG2 C:ILE376 4.8 42.2 1.0
CB C:ILE376 4.9 51.5 1.0

Zinc binding site 6 out of 12 in 7t3v

Go back to Zinc Binding Sites List in 7t3v
Zinc binding site 6 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn704

b:50.5
occ:0.98
 OD1 C:ASP459 1.9 40.4 1.0
OE1 C:GLU461 2.0 46.2 1.0
O C:ASP459 2.4 40.3 1.0
ZN C:ZN703 2.5 49.4 1.0
CD C:GLU461 2.8 46.6 1.0
OE2 C:GLU461 2.9 41.3 1.0
CG C:ASP379 2.9 47.0 1.0
CG C:ASP459 3.1 48.7 1.0
OD1 C:ASP379 3.1 49.0 1.0
C C:ASP459 3.4 39.5 1.0
CA C:ASP459 3.8 34.9 1.0
OD2 C:ASP459 3.9 39.3 1.0
CB C:ASP459 4.0 35.6 1.0
NZ C:LYS374 4.1 39.0 1.0
OD2 C:ASP399 4.1 51.9 1.0
NZ C:LYS386 4.2 47.4 1.0
CG C:GLU461 4.2 42.1 1.0
CE C:LYS386 4.3 44.6 1.0
CB C:ASP379 4.3 47.3 1.0
N C:GLU461 4.3 42.0 1.0
N C:ALA460 4.5 40.6 1.0
ND2 C:ASN432 4.8 44.6 1.0
CA C:ALA460 4.8 42.6 1.0
O1 C:CO3702 4.9 58.0 1.0
N C:GLY462 5.0 43.3 1.0
CB C:GLU461 5.0 43.6 1.0

Zinc binding site 7 out of 12 in 7t3v

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Zinc binding site 7 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn703

b:49.5
occ:0.96
 OE2 D:GLU461 2.0 49.1 1.0
OD2 D:ASP399 2.1 48.0 1.0
NZ D:LYS374 2.1 37.1 1.0
O D:HOH835 2.3 56.3 1.0
ZN D:ZN704 2.4 52.9 1.0
OD2 D:ASP379 2.4 50.0 1.0
CD D:GLU461 3.0 53.1 1.0
CG D:ASP399 3.1 50.9 1.0
CE D:LYS374 3.2 44.5 1.0
CG D:ASP379 3.3 48.1 1.0
OE1 D:GLU461 3.3 51.2 1.0
OD1 D:ASP399 3.4 44.5 1.0
CB D:ASP379 3.9 54.7 1.0
OD1 D:ASP379 4.1 46.1 1.0
O1 D:CO3702 4.1 63.0 1.0
O D:ASP459 4.3 45.2 1.0
CG D:GLU461 4.4 41.5 1.0
N D:GLY462 4.4 42.3 1.0
CB D:ASP399 4.4 47.1 1.0
OD1 D:ASP459 4.5 49.0 1.0
CG1 D:ILE376 4.5 45.7 1.0
O D:THR486 4.5 44.0 1.0
CD D:LYS374 4.6 42.3 1.0
CA D:GLY462 4.8 43.9 1.0
CB D:ILE376 4.9 41.2 1.0

Zinc binding site 8 out of 12 in 7t3v

Go back to Zinc Binding Sites List in 7t3v
Zinc binding site 8 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn704

b:52.9
occ:1.00
 OD2 D:ASP379 2.0 50.0 1.0
O D:HOH835 2.1 56.3 1.0
OD1 D:ASP459 2.1 49.0 1.0
OE1 D:GLU461 2.2 51.2 1.0
O D:ASP459 2.4 45.2 1.0
ZN D:ZN703 2.4 49.5 1.0
OE2 D:GLU461 2.9 49.1 1.0
CD D:GLU461 2.9 53.1 1.0
CG D:ASP379 3.0 48.1 1.0
CG D:ASP459 3.2 51.5 1.0
OD1 D:ASP379 3.3 46.1 1.0
C D:ASP459 3.4 44.4 1.0
NZ D:LYS386 3.7 61.1 1.0
CA D:ASP459 3.8 46.5 1.0
OD2 D:ASP399 4.0 48.0 1.0
OD2 D:ASP459 4.0 49.3 1.0
CB D:ASP459 4.1 48.7 1.0
CE D:LYS386 4.2 51.7 1.0
O1 D:CO3702 4.2 63.0 1.0
CB D:ASP379 4.3 54.7 1.0
CG D:GLU461 4.4 41.5 1.0
N D:GLU461 4.4 47.9 1.0
NZ D:LYS374 4.4 37.1 1.0
N D:ALA460 4.5 49.2 1.0
ND2 D:ASN432 4.7 46.2 1.0
CA D:ALA460 4.9 52.5 1.0
N D:GLY462 5.0 42.3 1.0

Zinc binding site 9 out of 12 in 7t3v

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Zinc binding site 9 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn702

b:51.0
occ:1.00
 OD2 E:ASP399 1.9 47.0 1.0
OD2 E:ASP379 2.1 58.4 1.0
NZ E:LYS374 2.2 29.1 1.0
OE2 E:GLU461 2.2 45.9 1.0
ZN E:ZN703 2.5 47.8 0.9
CG E:ASP399 3.0 48.4 1.0
CG E:ASP379 3.1 51.5 1.0
CD E:GLU461 3.1 51.4 1.0
CE E:LYS374 3.2 46.2 1.0
OE1 E:GLU461 3.3 44.0 1.0
OD1 E:ASP399 3.4 47.9 1.0
CB E:ASP379 3.6 47.5 1.0
OD1 E:ASP379 4.0 53.5 1.0
O E:ASP459 4.2 46.9 1.0
OD1 E:ASP459 4.3 38.7 1.0
CB E:ASP399 4.3 49.8 1.0
O3 E:CO3701 4.3 56.9 1.0
O E:THR486 4.5 47.3 1.0
CG E:GLU461 4.5 45.0 1.0
CE E:MET396 4.6 48.8 1.0
CD E:LYS374 4.6 43.9 1.0
N E:GLY462 4.7 51.1 1.0
CG2 E:ILE376 4.8 44.3 1.0
CG1 E:ILE376 4.9 44.7 1.0
CB E:ILE376 4.9 51.5 1.0

Zinc binding site 10 out of 12 in 7t3v

Go back to Zinc Binding Sites List in 7t3v
Zinc binding site 10 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase, Spacegroup P22121 After Crystals Soaked with ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn703

b:47.8
occ:0.94
 OD2 E:ASP379 2.0 58.4 1.0
O E:ASP459 2.0 46.9 1.0
OD1 E:ASP459 2.0 38.7 1.0
OE1 E:GLU461 2.1 44.0 1.0
ZN E:ZN702 2.5 51.0 1.0
CG E:ASP379 2.9 51.5 1.0
CD E:GLU461 2.9 51.4 1.0
OE2 E:GLU461 3.0 45.9 1.0
C E:ASP459 3.1 48.2 1.0
CG E:ASP459 3.2 53.8 1.0
OD1 E:ASP379 3.2 53.5 1.0
CA E:ASP459 3.5 47.6 1.0
CB E:ASP459 3.9 46.1 1.0
OD2 E:ASP459 4.1 46.8 1.0
NZ E:LYS374 4.2 29.1 1.0
N E:GLU461 4.2 48.4 1.0
OD2 E:ASP399 4.2 47.0 1.0
N E:ALA460 4.2 50.3 1.0
CB E:ASP379 4.3 47.5 1.0
CG E:GLU461 4.4 45.0 1.0
O3 E:CO3701 4.4 56.9 1.0
NZ E:LYS386 4.5 44.3 1.0
CE E:LYS386 4.7 43.3 1.0
CA E:ALA460 4.7 53.3 1.0
ND2 E:ASN432 4.9 46.5 1.0
CB E:GLU461 4.9 40.9 1.0
N E:ASP459 4.9 51.2 1.0
N E:GLY462 4.9 51.1 1.0
C E:ALA460 4.9 53.1 1.0

Reference:

C.T.Webb, W.Yang, B.T.Riley, B.K.Hayes, K.K.Sivaraman, T.R.Malcolm, S.Harrop, S.C.Atkinson, I.Kass, A.M.Buckle, N.Drinkwater, S.Mcgowan. A Metal Ion-Dependent Conformational Switch Modulates Activity of the Plasmodium M17 Aminopeptidase. J.Biol.Chem. V. 298 02119 2022.
ISSN: ESSN 1083-351X
PubMed: 35691342
DOI: 10.1016/J.JBC.2022.102119
Page generated: Wed Oct 30 11:26:16 2024

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