Zinc in PDB 7srv: Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase (Inactive Form), Spacegroup P22121

Enzymatic activity of Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase (Inactive Form), Spacegroup P22121

All present enzymatic activity of Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase (Inactive Form), Spacegroup P22121:
3.4.11.1;

Protein crystallography data

The structure of Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase (Inactive Form), Spacegroup P22121, PDB code: 7srv 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) 49.19 / 2.03
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 111.542, 172.67, 179.395, 90, 90, 90
R / Rfree (%) 18.9 / 21.9

Other elements in 7srv:

The structure of Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase (Inactive Form), Spacegroup P22121 also contains other interesting chemical elements:

Calcium (Ca) 12 atoms

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 (Inactive Form), Spacegroup P22121 (pdb code 7srv). 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 (Inactive Form), Spacegroup P22121, PDB code: 7srv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 7srv

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Zinc binding site 1 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase (Inactive Form), Spacegroup P22121


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 (Inactive Form), Spacegroup P22121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:29.5
occ:0.65
 OD2 A:ASP394 2.3 31.0 1.0
OD2 A:ASP379 2.3 25.8 1.0
O A:ASP459 2.3 28.0 1.0
OD1 A:ASP459 2.4 29.1 1.0
OE1 A:GLU461 2.4 31.4 1.0
O A:HOH1198 2.5 29.9 1.0
O A:HOH1318 2.6 32.4 1.0
CG A:ASP379 3.2 27.5 1.0
CD A:GLU461 3.3 31.5 1.0
CG A:ASP394 3.4 38.6 1.0
C A:ASP459 3.4 29.9 1.0
CG A:ASP459 3.4 35.0 1.0
OE2 A:GLU461 3.5 31.2 1.0
OD1 A:ASP379 3.6 27.8 1.0
ZN A:ZN1006 3.8 34.5 0.5
CB A:ASP394 3.9 38.2 1.0
CA A:ASP459 4.0 26.4 1.0
NZ C:LYS386 4.0 33.7 1.0
CB A:ASP459 4.2 24.5 1.0
O2 A:CO31002 4.3 33.3 1.0
OD2 A:ASP459 4.3 36.0 1.0
OD1 A:ASP394 4.4 33.0 1.0
N A:GLU461 4.5 27.1 1.0
N A:ALA460 4.5 29.4 1.0
CB A:ASP379 4.5 29.5 1.0
O A:HOH1199 4.5 34.1 1.0
O A:HOH1332 4.6 36.0 1.0
O A:HOH1175 4.7 30.0 1.0
O A:HOH1401 4.7 43.3 1.0
CG A:GLU461 4.7 27.6 1.0
CA A:ALA460 4.8 31.9 1.0
CE C:LYS386 4.9 40.7 1.0
O A:HOH1195 4.9 41.2 1.0

Zinc binding site 2 out of 12 in 7srv

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Zinc binding site 2 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase (Inactive Form), Spacegroup P22121


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 (Inactive Form), Spacegroup P22121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1006

b:34.5
occ:0.53
 O A:HOH1175 2.0 30.0 1.0
OD1 A:ASP399 2.3 31.0 1.0
O A:MET396 2.4 32.8 1.0
OD2 A:ASP394 2.4 31.0 1.0
O A:HOH1195 2.5 41.2 1.0
O A:HOH1198 2.5 29.9 1.0
OD1 A:ASP394 2.8 33.0 1.0
OD2 A:ASP399 2.9 33.0 1.0
CG A:ASP399 2.9 30.8 1.0
CG A:ASP394 3.0 38.6 1.0
OD2 A:ASP379 3.1 25.8 1.0
C A:MET396 3.6 37.4 1.0
O A:HOH1332 3.7 36.0 1.0
ZN A:ZN1001 3.8 29.5 0.7
CG A:ASP379 4.1 27.5 1.0
CB A:ASP379 4.3 29.5 1.0
NZ C:LYS386 4.3 33.7 1.0
CB A:ASP399 4.4 28.6 1.0
CB A:ASP394 4.5 38.2 1.0
O A:HOH1318 4.5 32.4 1.0
N A:LYS397 4.5 34.6 1.0
CA A:LYS397 4.5 36.4 1.0
CA A:MET396 4.5 37.8 1.0
NZ A:LYS374 4.5 30.2 1.0
N A:MET396 4.6 38.2 1.0
OE2 A:GLU461 4.7 31.2 1.0
CB A:MET396 4.8 42.1 1.0
O A:HOH1199 4.8 34.1 1.0
O A:HOH1210 4.9 40.6 1.0

Zinc binding site 3 out of 12 in 7srv

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Zinc binding site 3 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase (Inactive Form), Spacegroup P22121


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 (Inactive Form), Spacegroup P22121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:34.1
occ:0.71
 O B:ASP459 2.2 28.1 1.0
OD2 B:ASP379 2.3 27.8 1.0
OE1 B:GLU461 2.3 28.8 1.0
OD2 B:ASP394 2.3 32.0 1.0
OD1 B:ASP459 2.4 31.6 1.0
O B:HOH1213 2.5 32.4 1.0
O B:HOH1157 2.7 28.9 1.0
CD B:GLU461 3.2 30.7 1.0
CG B:ASP379 3.3 27.6 1.0
C B:ASP459 3.3 29.1 1.0
CG B:ASP459 3.4 31.5 1.0
OE2 B:GLU461 3.4 29.9 1.0
CG B:ASP394 3.4 38.4 1.0
OD1 B:ASP379 3.6 27.8 1.0
NZ A:LYS386 3.7 39.7 1.0
CA B:ASP459 3.9 29.1 1.0
ZN B:ZN1007 3.9 39.1 0.7
CB B:ASP394 4.0 39.1 1.0
CB B:ASP459 4.2 29.3 1.0
OD2 B:ASP459 4.2 37.2 1.0
O1 B:CO31002 4.2 32.3 1.0
N B:ALA460 4.4 29.0 1.0
N B:GLU461 4.4 25.4 1.0
OD1 B:ASP394 4.4 39.2 1.0
O B:HOH1203 4.5 29.3 1.0
O B:HOH1133 4.6 32.6 1.0
CB B:ASP379 4.6 31.0 1.0
O B:HOH1239 4.6 34.9 1.0
CG B:GLU461 4.6 23.8 1.0
O B:HOH1305 4.7 42.9 1.0
O A:HOH1133 4.7 32.4 1.0
CA B:ALA460 4.7 30.8 1.0
CE A:LYS386 4.7 38.9 1.0

Zinc binding site 4 out of 12 in 7srv

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Zinc binding site 4 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase (Inactive Form), Spacegroup P22121


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 (Inactive Form), Spacegroup P22121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1007

b:39.1
occ:0.67
 O B:HOH1203 2.1 29.3 1.0
O B:MET396 2.3 34.1 1.0
OD1 B:ASP399 2.4 30.1 1.0
OD2 B:ASP394 2.4 32.0 1.0
O B:HOH1157 2.5 28.9 1.0
O A:HOH1133 2.5 32.4 1.0
OD1 B:ASP394 2.7 39.2 1.0
OD2 B:ASP399 2.8 31.3 1.0
CG B:ASP394 2.9 38.4 1.0
CG B:ASP399 2.9 32.0 1.0
OD2 B:ASP379 3.2 27.8 1.0
C B:MET396 3.6 35.6 1.0
ZN B:ZN1001 3.9 34.1 0.7
NZ A:LYS386 4.0 39.7 1.0
O B:HOH1239 4.1 34.9 1.0
CG B:ASP379 4.2 27.6 1.0
O B:HOH1304 4.2 42.8 1.0
O B:HOH1234 4.2 38.1 1.0
CB B:ASP379 4.4 31.0 1.0
CB B:ASP399 4.4 30.1 1.0
CB B:ASP394 4.4 39.1 1.0
N B:LYS397 4.4 34.5 1.0
O B:HOH1213 4.4 32.4 1.0
CA B:LYS397 4.5 40.6 1.0
CA B:MET396 4.5 38.4 1.0
N B:MET396 4.5 38.5 1.0
NZ B:LYS374 4.6 33.6 1.0
OE2 B:GLU461 4.8 29.9 1.0
CB B:MET396 4.8 44.1 1.0
O B:HOH1133 4.8 32.6 1.0

Zinc binding site 5 out of 12 in 7srv

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Zinc binding site 5 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase (Inactive Form), Spacegroup P22121


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 (Inactive Form), Spacegroup P22121 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:44.9
occ:1.00
 O C:ASP459 2.2 28.7 1.0
OD2 C:ASP379 2.4 28.8 1.0
OE1 C:GLU461 2.5 28.5 1.0
OD2 C:ASP394 2.5 31.5 1.0
O C:HOH1339 2.5 31.3 1.0
OD1 C:ASP459 2.5 28.4 1.0
O C:HOH1217 2.6 27.8 1.0
CG C:ASP379 3.3 29.2 1.0
C C:ASP459 3.3 25.0 1.0
CD C:GLU461 3.4 33.7 1.0
CG C:ASP459 3.4 30.9 1.0
OE2 C:GLU461 3.5 33.7 1.0
CG C:ASP394 3.5 38.9 1.0
OD1 C:ASP379 3.6 25.4 1.0
NZ B:LYS386 3.7 39.0 1.0
ZN C:ZN1012 3.8 31.3 0.5
CA C:ASP459 3.9 26.1 1.0
CB C:ASP394 4.1 41.3 1.0
OD2 C:ASP459 4.2 32.6 1.0
CB C:ASP459 4.2 29.3 1.0
O2 C:CO31002 4.3 34.4 1.0
N C:ALA460 4.4 25.7 1.0
N C:GLU461 4.5 27.5 1.0
OD1 C:ASP394 4.5 40.1 1.0
CB C:ASP379 4.6 28.5 1.0
O C:HOH1136 4.6 34.3 1.0
O C:HOH1320 4.6 31.5 1.0
O C:HOH1426 4.6 46.9 1.0
O B:HOH1196 4.7 35.7 1.0
CA C:ALA460 4.7 27.5 1.0
CG C:GLU461 4.8 27.4 1.0
O C:HOH1309 4.9 44.8 1.0

Zinc binding site 6 out of 12 in 7srv

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Zinc binding site 6 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase (Inactive Form), Spacegroup P22121


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 (Inactive Form), Spacegroup P22121 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1012

b:31.3
occ:0.53
 OD1 C:ASP399 2.2 35.0 1.0
O C:MET396 2.4 38.9 1.0
O C:HOH1217 2.4 27.8 1.0
OD2 C:ASP394 2.4 31.5 1.0
O B:HOH1196 2.5 35.7 1.0
O C:HOH1320 2.6 31.5 1.0
OD2 C:ASP399 2.8 28.6 1.0
CG C:ASP399 2.8 32.9 1.0
OD1 C:ASP394 2.9 40.1 1.0
CG C:ASP394 3.1 38.9 1.0
OD2 C:ASP379 3.1 28.8 1.0
C C:MET396 3.6 42.1 1.0
ZN C:ZN1001 3.8 44.9 1.0
O C:HOH1308 4.0 39.0 1.0
O C:HOH1399 4.1 44.5 1.0
CG C:ASP379 4.1 29.2 1.0
NZ B:LYS386 4.2 39.0 1.0
CB C:ASP399 4.3 31.3 1.0
O C:HOH1339 4.4 31.3 1.0
CB C:ASP379 4.4 28.5 1.0
O C:HOH1309 4.4 44.8 1.0
N C:LYS397 4.5 36.6 1.0
CA C:LYS397 4.5 38.8 1.0
NZ C:LYS374 4.5 32.6 1.0
CB C:ASP394 4.6 41.3 1.0
CA C:MET396 4.6 43.4 1.0
N C:MET396 4.6 44.7 1.0
CB C:MET396 4.7 42.9 1.0
OE2 C:GLU461 4.8 33.7 1.0
O C:HOH1136 4.9 34.3 1.0
O C:HOH1165 4.9 38.9 1.0

Zinc binding site 7 out of 12 in 7srv

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Zinc binding site 7 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase (Inactive Form), Spacegroup P22121


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 (Inactive Form), Spacegroup P22121 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1001

b:33.9
occ:0.62
 O D:ASP459 2.2 30.3 1.0
OD2 D:ASP379 2.3 30.9 1.0
OD2 D:ASP394 2.3 32.8 1.0
OE1 D:GLU461 2.4 28.9 1.0
OD1 D:ASP459 2.5 33.2 1.0
O D:HOH1129 2.6 31.9 1.0
O D:HOH1262 2.6 34.9 1.0
CD D:GLU461 3.3 31.3 1.0
CG D:ASP379 3.3 30.4 1.0
C D:ASP459 3.3 29.4 1.0
CG D:ASP459 3.4 33.5 1.0
OE2 D:GLU461 3.4 35.8 1.0
CG D:ASP394 3.5 42.0 1.0
OD1 D:ASP379 3.6 29.1 1.0
NZ F:LYS386 3.7 43.5 1.0
ZN D:ZN1007 3.8 37.7 0.6
CA D:ASP459 3.9 32.7 1.0
CB D:ASP394 4.1 41.9 1.0
OD2 D:ASP459 4.2 43.2 1.0
CB D:ASP459 4.2 32.7 1.0
O2 D:CO31002 4.3 37.0 1.0
N D:GLU461 4.4 31.1 1.0
N D:ALA460 4.4 26.2 1.0
OD1 D:ASP394 4.5 41.1 1.0
O D:HOH1112 4.5 34.1 1.0
CB D:ASP379 4.6 31.4 1.0
CG D:GLU461 4.7 25.1 1.0
CA D:ALA460 4.7 32.6 1.0
O D:HOH1339 4.8 35.1 1.0
O F:HOH1181 4.8 40.4 1.0
CE F:LYS386 4.8 40.9 1.0
O D:HOH1317 4.8 47.3 1.0
OD1 D:ASP399 5.0 31.4 1.0

Zinc binding site 8 out of 12 in 7srv

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Zinc binding site 8 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase (Inactive Form), Spacegroup P22121


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 (Inactive Form), Spacegroup P22121 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1007

b:37.7
occ:0.55
 OD1 D:ASP399 2.3 31.4 1.0
O D:MET396 2.3 42.0 1.0
OD2 D:ASP394 2.5 32.8 1.0
O F:HOH1181 2.5 40.4 1.0
O D:HOH1339 2.6 35.1 1.0
O D:HOH1129 2.7 31.9 1.0
OD1 D:ASP394 2.7 41.1 1.0
OD2 D:ASP399 2.9 36.7 1.0
CG D:ASP394 2.9 42.0 1.0
CG D:ASP399 3.0 33.8 1.0
OD2 D:ASP379 3.3 30.9 1.0
C D:MET396 3.6 43.2 1.0
ZN D:ZN1001 3.8 33.9 0.6
NZ F:LYS386 4.0 43.5 1.0
O D:HOH1317 4.2 47.3 1.0
O D:HOH1333 4.2 39.4 1.0
CG D:ASP379 4.3 30.4 1.0
CB D:ASP399 4.4 31.6 1.0
CB D:ASP394 4.5 41.9 1.0
N D:LYS397 4.5 37.6 1.0
O D:HOH1262 4.5 34.9 1.0
CA D:MET396 4.5 47.8 1.0
CA D:LYS397 4.5 39.9 1.0
CB D:ASP379 4.5 31.4 1.0
N D:MET396 4.6 45.9 1.0
NZ D:LYS374 4.6 34.7 1.0
CB D:MET396 4.7 50.3 1.0
OE2 D:GLU461 4.8 35.8 1.0
O D:HOH1112 4.9 34.1 1.0
O D:HOH1252 4.9 39.3 1.0

Zinc binding site 9 out of 12 in 7srv

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Zinc binding site 9 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase (Inactive Form), Spacegroup P22121


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 (Inactive Form), Spacegroup P22121 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1001

b:32.1
occ:0.62
 OD2 E:ASP394 2.0 43.3 1.0
O E:ASP459 2.3 34.4 1.0
OD2 E:ASP379 2.3 34.5 1.0
OE1 E:GLU461 2.4 28.9 1.0
OD1 E:ASP459 2.5 34.1 1.0
O E:HOH1140 2.7 33.7 1.0
O E:HOH1289 2.8 37.8 1.0
CG E:ASP394 3.1 50.3 1.0
CG E:ASP379 3.3 31.3 1.0
CD E:GLU461 3.3 33.0 1.0
C E:ASP459 3.4 29.9 1.0
CG E:ASP459 3.4 37.2 1.0
OE2 E:GLU461 3.6 34.6 1.0
OD1 E:ASP379 3.6 28.6 1.0
ZN E:ZN1008 3.9 34.5 0.5
CB E:ASP394 3.9 46.0 1.0
NZ D:LYS386 3.9 44.9 1.0
CA E:ASP459 3.9 32.4 1.0
OD1 E:ASP394 4.1 46.1 1.0
OD2 E:ASP459 4.2 44.5 1.0
CB E:ASP459 4.2 36.1 1.0
O2 E:CO31002 4.3 40.3 1.0
N E:GLU461 4.4 27.1 1.0
N E:ALA460 4.4 29.3 1.0
O E:HOH1273 4.5 41.1 1.0
O E:HOH1154 4.6 35.4 1.0
CB E:ASP379 4.6 30.4 1.0
O E:HOH1349 4.6 37.8 1.0
CE D:LYS386 4.7 39.9 1.0
CG E:GLU461 4.7 26.4 1.0
CA E:ALA460 4.7 30.7 1.0
O E:HOH1390 5.0 37.0 1.0

Zinc binding site 10 out of 12 in 7srv

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Zinc binding site 10 out of 12 in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase (Inactive Form), Spacegroup P22121


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 (Inactive Form), Spacegroup P22121 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1008

b:34.5
occ:0.50
 O E:HOH1273 2.2 41.1 1.0
OD1 E:ASP399 2.3 32.6 1.0
O E:MET396 2.5 47.8 1.0
O E:HOH1390 2.5 37.0 1.0
O E:HOH1140 2.7 33.7 1.0
OD2 E:ASP399 2.8 33.4 1.0
OD1 E:ASP394 2.8 46.1 1.0
CG E:ASP399 2.9 33.0 1.0
OD2 E:ASP394 2.9 43.3 1.0
CG E:ASP394 3.2 50.3 1.0
OD2 E:ASP379 3.3 34.5 1.0
C E:MET396 3.6 48.5 1.0
ZN E:ZN1001 3.9 32.1 0.6
O E:HOH1338 3.9 42.2 1.0
O E:HOH1349 4.0 37.8 1.0
NZ D:LYS386 4.3 44.9 1.0
CG E:ASP379 4.3 31.3 1.0
CB E:ASP399 4.4 30.6 1.0
O E:HOH1289 4.4 37.8 1.0
N E:LYS397 4.5 48.1 1.0
N E:MET396 4.5 67.0 1.0
CB E:ASP379 4.5 30.4 1.0
NZ E:LYS374 4.6 27.7 1.0
CA E:LYS397 4.6 45.5 1.0
CA E:MET396 4.6 62.8 1.0
CB E:ASP394 4.8 46.0 1.0
O E:HOH1278 4.8 41.0 1.0
OE2 E:GLU461 4.9 34.6 1.0
O E:HOH1154 4.9 35.4 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 11:16:45 2024

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