Calcium 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:

Zinc (Zn) 12 atoms

Calcium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Calcium 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 Calcium atom.
In total 12 binding sites of Calcium where determined in the Metal Dependent Activation of Plasmodium Falciparum M17 Aminopeptidase (Inactive Form), Spacegroup P22121, PDB code: 7srv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 7srv

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Calcium 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 Calcium with other atoms in the Ca 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:Ca1004

b:33.3
occ:1.00
 OG1 A:THR486 3.0 29.4 1.0
N A:THR486 3.2 25.9 1.0
N A:GLY402 3.2 24.1 1.0
N A:SER401 3.3 28.2 1.0
CD A:LYS374 3.4 27.3 1.0
O A:ASP399 3.5 28.4 1.0
C A:ASP399 3.5 27.4 1.0
O A:LYS374 3.6 23.4 1.0
CB A:LYS374 3.6 28.9 1.0
CG A:LYS374 3.6 26.1 1.0
CG2 A:THR486 3.7 26.9 1.0
CB A:THR486 3.7 27.8 1.0
N A:MET400 3.8 26.4 1.0
CE A:LYS374 3.8 27.0 1.0
C A:MET400 3.9 26.1 1.0
CA A:MET400 3.9 27.1 0.6
CA A:MET400 3.9 26.5 0.4
O A:PHE398 3.9 29.4 1.0
CA A:ALA485 4.0 30.6 1.0
CA A:SER401 4.0 26.6 1.0
CA A:THR486 4.0 27.7 1.0
CA A:ASP399 4.0 27.9 1.0
C A:ALA485 4.1 27.7 1.0
CA A:GLY402 4.1 27.8 1.0
C A:SER401 4.1 22.1 1.0
CB A:SER401 4.1 28.9 1.0
NZ A:LYS374 4.2 30.2 1.0
C A:LYS374 4.2 23.9 1.0
CA A:LYS374 4.4 23.6 1.0
CB A:ALA485 4.6 25.6 1.0
C A:THR486 4.7 23.8 1.0
N A:LYS374 4.8 24.3 1.0
O A:MET400 4.8 26.0 1.0
C A:PHE398 4.8 31.7 1.0
OG A:SER401 4.8 29.1 1.0
O A:THR486 4.8 28.2 1.0
N A:ASP399 4.9 29.3 1.0

Calcium binding site 2 out of 12 in 7srv

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Calcium 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 Calcium with other atoms in the Ca 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
B:Ca1005

b:36.3
occ:1.00
 OG1 B:THR486 3.1 28.8 1.0
N B:GLY402 3.1 33.0 1.0
N B:THR486 3.2 27.7 1.0
N B:SER401 3.2 32.9 1.0
O B:ASP399 3.4 30.2 1.0
C B:ASP399 3.5 30.6 1.0
CB B:LYS374 3.5 28.2 1.0
CD B:LYS374 3.5 28.9 1.0
O B:LYS374 3.6 29.8 1.0
CG B:LYS374 3.7 30.8 1.0
N B:MET400 3.8 31.2 1.0
C B:MET400 3.8 32.6 1.0
CG2 B:THR486 3.8 25.6 1.0
CB B:THR486 3.8 29.7 1.0
CE B:LYS374 3.8 30.8 1.0
CA B:MET400 3.9 37.1 1.0
O B:PHE398 3.9 30.4 1.0
CA B:GLY402 3.9 32.0 1.0
CA B:SER401 3.9 28.2 1.0
CA B:ALA485 3.9 28.8 1.0
C B:SER401 4.0 33.8 1.0
CA B:ASP399 4.0 33.2 1.0
C B:ALA485 4.1 28.9 1.0
CA B:THR486 4.1 28.6 1.0
CB B:SER401 4.1 31.9 1.0
C B:LYS374 4.2 29.2 1.0
NZ B:LYS374 4.2 33.6 1.0
CA B:LYS374 4.4 28.2 1.0
CB B:ALA485 4.6 27.3 1.0
N B:LYS374 4.8 25.8 1.0
O B:MET400 4.8 34.2 1.0
C B:PHE398 4.8 32.0 1.0
C B:THR486 4.8 28.3 1.0
N B:ASP399 4.8 30.3 1.0
OG B:SER401 4.9 32.2 1.0
N B:CYS403 4.9 32.2 1.0
O B:ILE484 4.9 32.8 1.0
O B:THR486 4.9 31.4 1.0

Calcium binding site 3 out of 12 in 7srv

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Calcium 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 Calcium with other atoms in the Ca 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:Ca1006

b:83.6
occ:1.00
 O B:ASN104 2.5 45.0 1.0
OE2 B:GLU102 3.3 60.1 1.0
C B:ASN104 3.7 40.4 1.0
OD1 B:ASN104 3.9 61.1 1.0
CB B:ASN104 4.1 50.6 1.0
CD B:GLU102 4.2 54.3 1.0
CG B:GLU102 4.4 51.0 1.0
CG B:ASN104 4.4 55.5 1.0
CA B:ASN104 4.5 44.4 1.0
O B:HOH1262 4.6 46.7 1.0
N B:THR105 4.7 37.8 1.0
CA B:THR105 4.9 38.5 1.0

Calcium binding site 4 out of 12 in 7srv

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Calcium 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 Calcium with other atoms in the Ca 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
C:Ca1004

b:33.4
occ:1.00
 OG1 C:THR486 3.0 23.8 1.0
N C:GLY402 3.1 24.4 1.0
N C:THR486 3.2 25.9 1.0
N C:SER401 3.3 23.9 1.0
C C:ASP399 3.5 30.7 1.0
O C:ASP399 3.5 27.9 1.0
CD C:LYS374 3.5 27.4 1.0
CB C:LYS374 3.6 26.3 1.0
O C:LYS374 3.6 24.9 1.0
CG C:LYS374 3.7 26.6 1.0
N C:MET400 3.7 23.9 1.0
CB C:THR486 3.8 32.9 1.0
CG2 C:THR486 3.8 24.7 1.0
C C:MET400 3.8 26.6 1.0
CA C:MET400 3.8 30.5 1.0
CE C:LYS374 3.9 29.8 1.0
O C:PHE398 3.9 27.3 1.0
CA C:GLY402 3.9 25.1 1.0
CA C:ALA485 4.0 23.8 1.0
C C:SER401 4.0 29.3 1.0
CA C:SER401 4.0 19.4 1.0
CA C:ASP399 4.0 31.7 1.0
CA C:THR486 4.1 26.6 1.0
C C:ALA485 4.1 25.2 1.0
CB C:SER401 4.2 27.5 1.0
C C:LYS374 4.2 23.7 1.0
NZ C:LYS374 4.3 32.6 1.0
CA C:LYS374 4.4 25.2 1.0
OG C:SER401 4.7 27.2 1.0
CB C:ALA485 4.7 31.0 1.0
O C:MET400 4.7 28.3 1.0
C C:PHE398 4.8 32.4 1.0
N C:LYS374 4.8 24.7 1.0
N C:ASP399 4.8 29.0 1.0
C C:THR486 4.9 24.1 1.0
N C:CYS403 4.9 25.0 1.0
O C:ILE484 5.0 24.9 1.0
O C:THR486 5.0 29.5 1.0

Calcium binding site 5 out of 12 in 7srv

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Calcium 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 Calcium with other atoms in the Ca 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:Ca1005

b:84.9
occ:1.00
 O C:HOH1389 2.6 58.7 1.0
OE1 C:GLU564 3.0 42.9 1.0
OE2 C:GLU564 3.3 45.3 1.0
CD C:GLU564 3.5 35.7 1.0
NH2 C:ARG534 4.2 37.3 1.0
NE C:ARG534 4.7 37.5 1.0
NZ C:LYS451 4.8 34.1 1.0
O C:HOH1357 4.8 43.4 1.0
CZ C:ARG534 4.9 35.4 1.0
O C:HOH1419 5.0 53.7 1.0
O C:HOH1316 5.0 46.1 1.0

Calcium binding site 6 out of 12 in 7srv

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Calcium 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 Calcium with other atoms in the Ca 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:Ca1006

b:60.8
occ:1.00
 O C:HOH1259 2.4 49.4 1.0
O C:HIS606 2.5 52.2 1.0
C1 C:EDO1010 3.0 53.5 1.0
C2 C:EDO1010 3.1 41.7 1.0
C C:HIS606 3.6 55.8 1.0
O1 C:EDO1010 4.0 51.6 1.0
CA C:HIS607 4.3 51.1 1.0
N C:HIS607 4.3 55.8 1.0
CB C:HIS606 4.4 55.2 1.0
O2 C:EDO1010 4.5 43.2 1.0
CA C:HIS606 4.7 53.9 1.0
O C:ASP603 4.8 43.7 1.0
O C:HOH1391 4.9 51.5 1.0

Calcium binding site 7 out of 12 in 7srv

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Calcium 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 Calcium with other atoms in the Ca 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
C:Ca1007

b:75.7
occ:1.00
 O C:HOH1359 2.5 53.9 1.0
OD1 C:ASN133 2.5 59.3 1.0
O C:GLU227 2.6 47.7 1.0
O C:HOH1176 3.0 53.7 1.0
CG C:ASN133 3.6 63.0 1.0
C C:GLU227 3.7 47.1 1.0
ND2 C:ASN133 4.0 66.9 1.0
CA C:ILE228 4.3 48.0 1.0
O C:ASN133 4.4 55.1 1.0
N C:ILE228 4.5 45.8 1.0
N C:ASN133 4.7 50.7 1.0
CA C:GLU227 4.8 45.5 1.0
C C:ASN133 4.9 63.5 1.0
CB C:GLU227 4.9 43.7 1.0
CB C:ASN133 4.9 56.1 1.0
CG2 C:ILE228 4.9 45.5 1.0
O C:HOH1247 5.0 56.9 1.0

Calcium binding site 8 out of 12 in 7srv

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Calcium 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 Calcium with other atoms in the Ca 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:Ca1004

b:34.1
occ:1.00
 OG1 D:THR486 3.0 27.9 1.0
N D:GLY402 3.1 26.3 1.0
N D:THR486 3.2 25.2 1.0
N D:SER401 3.3 29.3 1.0
O D:ASP399 3.5 27.6 1.0
C D:ASP399 3.5 30.1 1.0
CD D:LYS374 3.6 27.8 1.0
CB D:LYS374 3.6 26.0 1.0
O D:LYS374 3.6 24.5 1.0
CG D:LYS374 3.6 30.4 1.0
CG2 D:THR486 3.7 28.1 1.0
CB D:THR486 3.8 31.4 1.0
N D:MET400 3.8 30.0 1.0
C D:MET400 3.8 30.9 1.0
CA D:MET400 3.9 30.7 0.3
CA D:MET400 3.9 30.5 0.7
O D:PHE398 3.9 33.1 1.0
CA D:GLY402 3.9 28.6 1.0
CE D:LYS374 3.9 29.3 1.0
CA D:ALA485 4.0 26.5 1.0
CA D:SER401 4.0 28.9 1.0
C D:SER401 4.0 27.1 1.0
C D:ALA485 4.1 26.7 1.0
CA D:ASP399 4.1 27.9 1.0
CA D:THR486 4.1 29.5 1.0
CB D:SER401 4.1 28.8 1.0
NZ D:LYS374 4.2 34.7 1.0
C D:LYS374 4.2 30.1 1.0
CA D:LYS374 4.4 28.6 1.0
CB D:ALA485 4.7 23.2 1.0
O D:MET400 4.7 27.6 1.0
OG D:SER401 4.8 31.6 1.0
N D:LYS374 4.8 26.2 1.0
C D:PHE398 4.8 35.0 1.0
N D:ASP399 4.9 32.5 1.0
C D:THR486 4.9 29.7 1.0
O D:ILE484 4.9 26.8 1.0
N D:CYS403 5.0 30.5 1.0

Calcium binding site 9 out of 12 in 7srv

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Calcium 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 Calcium with other atoms in the Ca 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:Ca1004

b:33.1
occ:1.00
 N E:GLY402 3.1 27.1 1.0
OG1 E:THR486 3.1 29.3 1.0
N E:SER401 3.2 25.6 1.0
N E:THR486 3.3 28.4 1.0
O E:ASP399 3.4 28.4 1.0
CB E:LYS374 3.5 24.0 1.0
C E:ASP399 3.5 30.2 1.0
O E:LYS374 3.6 30.2 1.0
CD E:LYS374 3.6 26.4 1.0
CG E:LYS374 3.6 27.1 1.0
N E:MET400 3.8 27.8 1.0
C E:MET400 3.8 26.1 1.0
CG2 E:THR486 3.9 28.9 1.0
CB E:THR486 3.9 29.3 1.0
CA E:MET400 3.9 30.9 1.0
CA E:SER401 3.9 27.6 1.0
CA E:GLY402 3.9 25.6 1.0
O E:PHE398 3.9 32.5 1.0
CA E:ALA485 3.9 30.3 1.0
C E:SER401 4.0 26.5 1.0
CE E:LYS374 4.0 27.7 1.0
CA E:ASP399 4.0 28.7 1.0
C E:ALA485 4.1 24.2 1.0
CB E:SER401 4.1 26.1 1.0
CA E:THR486 4.1 29.6 1.0
C E:LYS374 4.2 27.8 1.0
NZ E:LYS374 4.3 27.7 1.0
CA E:LYS374 4.3 26.0 1.0
CB E:ALA485 4.6 28.7 1.0
N E:LYS374 4.7 28.6 1.0
O E:MET400 4.8 25.3 1.0
C E:PHE398 4.8 36.2 1.0
OG E:SER401 4.8 28.8 1.0
N E:ASP399 4.8 30.5 1.0
O E:ILE484 4.9 26.7 1.0
C E:THR486 4.9 29.6 1.0
N E:CYS403 4.9 27.2 1.0

Calcium binding site 10 out of 12 in 7srv

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Calcium 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 Calcium with other atoms in the Ca 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:Ca1005

b:48.4
occ:1.00
 OE2 E:GLU124 2.5 53.4 1.0
OD1 E:ASN181 2.5 40.5 1.0
O E:HOH1113 2.6 36.6 1.0
OE1 E:GLU124 2.6 41.4 1.0
O E:HOH1148 2.7 51.1 1.0
CD E:GLU124 2.9 49.3 1.0
CG E:ASN181 3.5 37.6 1.0
ND2 E:ASN181 3.8 35.6 1.0
OD2 E:ASP150 4.0 43.7 1.0
O E:HOH1200 4.1 45.8 1.0
CG E:GLU124 4.4 42.9 1.0
O E:VAL123 4.4 50.2 1.0
ND2 E:ASN179 4.5 37.4 1.0
O E:ASN149 4.6 56.4 1.0
CB E:ASP180 4.6 38.8 1.0
O E:HOH1237 4.7 35.5 1.0
N E:ASN181 4.9 33.4 1.0
CB E:ASN181 4.9 32.4 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: Fri Jul 19 04:10:47 2024

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