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Zinc in PDB 4eme: X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase

Enzymatic activity of X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase

All present enzymatic activity of X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase:
3.4.11.21;

Protein crystallography data

The structure of X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase, PDB code: 4eme was solved by S.Mcgowan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.58 / 2.60
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 200.384, 200.384, 200.384, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.6

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase (pdb code 4eme). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase, PDB code: 4eme:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4eme

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Zinc binding site 1 out of 8 in the X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:42.2
occ:1.00
 OD1 A:ASP435 2.1 32.1 1.0
OD1 A:ASP325 2.2 31.8 1.0
NE2 A:HIS87 2.3 25.5 1.0
OD2 A:ASP435 2.5 37.1 1.0
CG A:ASP435 2.6 32.3 1.0
CG A:ASP325 3.2 30.2 1.0
ZN A:ZN1002 3.2 40.2 1.0
CE1 A:HIS87 3.3 24.4 1.0
CD2 A:HIS87 3.3 26.1 1.0
OD2 A:ASP325 3.5 38.1 1.0
OE1 A:GLU380 3.5 35.1 1.0
CB A:ASN326 4.0 24.5 1.0
OE2 A:GLU381 4.1 24.4 1.0
CD A:GLU380 4.1 55.0 1.0
CB A:ASP435 4.1 24.9 1.0
OE2 A:GLU380 4.4 56.4 1.0
ND1 A:HIS87 4.4 25.0 1.0
CG A:HIS87 4.4 24.4 1.0
CG A:ASN326 4.5 33.8 1.0
CB A:ASP325 4.5 23.6 1.0
N A:MET436 4.8 28.0 1.0
CD A:GLU381 4.8 41.0 1.0
ND2 A:ASN326 4.8 20.9 1.0
CA A:ASP435 4.9 24.2 1.0
CA A:ASP325 4.9 23.9 1.0
C A:ASP325 5.0 29.3 1.0
CA A:ASN326 5.0 27.7 1.0
CG A:GLU380 5.0 35.9 1.0
N A:ASN326 5.0 27.7 1.0

Zinc binding site 2 out of 8 in 4eme

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Zinc binding site 2 out of 8 in the X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:40.2
occ:1.00
 OD2 A:ASP325 2.2 38.1 1.0
NE2 A:HIS535 2.2 31.2 1.0
OE2 A:GLU381 2.2 24.4 1.0
OE1 A:GLU381 2.5 34.5 1.0
CD A:GLU381 2.7 41.0 1.0
CE1 A:HIS535 3.1 30.7 1.0
CG A:ASP325 3.1 30.2 1.0
ZN A:ZN1001 3.2 42.2 1.0
CD2 A:HIS535 3.3 31.3 1.0
OD1 A:ASP325 3.3 31.8 1.0
OE1 A:GLU380 3.8 35.1 1.0
O A:HOH1149 4.0 26.8 1.0
CG A:GLU381 4.2 30.1 1.0
ND1 A:HIS535 4.3 31.5 1.0
CG A:HIS535 4.3 29.9 1.0
NE2 A:HIS87 4.4 25.5 1.0
CE1 A:HIS87 4.5 24.4 1.0
CB A:ASP325 4.5 23.6 1.0
O A:HOH1231 4.8 61.5 1.0
O A:HOH1229 4.8 31.9 1.0
SD A:MET534 4.8 40.3 1.0
CD A:GLU380 4.9 55.0 1.0

Zinc binding site 3 out of 8 in 4eme

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Zinc binding site 3 out of 8 in the X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:36.8
occ:1.00
 OD1 B:ASP325 2.1 28.6 1.0
NE2 B:HIS87 2.2 27.2 1.0
OD1 B:ASP435 2.2 32.9 1.0
OD2 B:ASP435 2.4 38.5 1.0
CG B:ASP435 2.6 32.8 1.0
CE1 B:HIS87 3.1 26.8 1.0
CG B:ASP325 3.1 27.6 1.0
ZN B:ZN1002 3.2 41.3 1.0
CD2 B:HIS87 3.3 27.8 1.0
OD2 B:ASP325 3.4 31.4 1.0
OE1 B:GLU380 3.5 54.3 1.0
CD B:GLU380 3.8 57.9 1.0
OE2 B:GLU380 3.9 56.8 1.0
OE2 B:GLU381 4.0 31.0 1.0
CB B:ASN326 4.1 18.5 1.0
CB B:ASP435 4.1 24.6 1.0
ND1 B:HIS87 4.3 28.1 1.0
CG B:HIS87 4.3 26.8 1.0
CB B:ASP325 4.4 24.1 1.0
CG B:ASN326 4.7 28.6 1.0
CD B:GLU381 4.7 42.6 1.0
CG B:GLU380 4.8 36.9 1.0
N B:MET436 4.8 28.7 1.0
O B:HOH1146 4.9 28.4 1.0
CA B:ASP325 4.9 23.7 1.0
CA B:ASP435 4.9 23.8 1.0
C B:ASP325 4.9 27.4 1.0
OE1 B:GLU381 4.9 26.8 1.0

Zinc binding site 4 out of 8 in 4eme

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Zinc binding site 4 out of 8 in the X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:41.3
occ:1.00
 NE2 B:HIS535 2.2 29.6 1.0
OD2 B:ASP325 2.2 31.4 1.0
OE2 B:GLU381 2.2 31.0 1.0
OE1 B:GLU381 2.5 26.8 1.0
CD B:GLU381 2.7 42.6 1.0
CE1 B:HIS535 3.1 28.9 1.0
CG B:ASP325 3.2 27.6 1.0
ZN B:ZN1001 3.2 36.8 1.0
CD2 B:HIS535 3.3 29.6 1.0
OD1 B:ASP325 3.4 28.6 1.0
OE1 B:GLU380 3.6 54.3 1.0
O B:HOH1177 3.9 28.8 1.0
CG B:GLU381 4.2 29.0 1.0
ND1 B:HIS535 4.3 29.4 1.0
CG B:HIS535 4.4 27.9 1.0
CE1 B:HIS87 4.4 26.8 1.0
NE2 B:HIS87 4.4 27.2 1.0
CB B:ASP325 4.5 24.1 1.0
CD B:GLU380 4.5 57.9 1.0
OE2 B:GLU380 4.6 56.8 1.0
O B:HOH1196 4.8 23.7 1.0
SD B:MET534 4.9 32.8 1.0

Zinc binding site 5 out of 8 in 4eme

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Zinc binding site 5 out of 8 in the X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:44.5
occ:1.00
 OD1 C:ASP435 2.1 35.7 1.0
OD1 C:ASP325 2.1 41.5 1.0
NE2 C:HIS87 2.3 29.9 1.0
OD2 C:ASP435 2.3 41.5 1.0
CG C:ASP435 2.5 37.0 1.0
CG C:ASP325 3.2 39.8 1.0
CD2 C:HIS87 3.2 30.2 1.0
ZN C:ZN1002 3.3 47.2 1.0
CE1 C:HIS87 3.3 29.3 1.0
OE1 C:GLU380 3.6 53.8 1.0
OD2 C:ASP325 3.6 41.5 1.0
CB C:ASP435 4.0 32.0 1.0
CD C:GLU380 4.1 60.8 1.0
CB C:ASN326 4.1 28.9 1.0
OE2 C:GLU381 4.2 39.4 1.0
OE2 C:GLU380 4.4 67.8 1.0
CG C:HIS87 4.4 28.6 1.0
ND1 C:HIS87 4.4 29.8 1.0
CB C:ASP325 4.5 32.2 1.0
CG C:ASN326 4.6 45.5 1.0
N C:MET436 4.7 34.2 1.0
CA C:ASP435 4.8 31.2 1.0
CD C:GLU381 4.8 50.2 1.0
C C:ASP325 4.9 34.1 1.0
O C:HOH1178 4.9 32.1 1.0
CA C:ASP325 4.9 30.7 1.0
OE1 C:GLU381 4.9 31.8 1.0
N C:ASN326 4.9 31.1 1.0
ND2 C:ASN326 5.0 31.6 1.0

Zinc binding site 6 out of 8 in 4eme

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Zinc binding site 6 out of 8 in the X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1002

b:47.2
occ:1.00
 NE2 C:HIS535 2.1 37.9 1.0
OE2 C:GLU381 2.2 39.4 1.0
OD2 C:ASP325 2.3 41.5 1.0
OE1 C:GLU381 2.4 31.8 1.0
CD C:GLU381 2.6 50.2 1.0
CD2 C:HIS535 3.1 38.3 1.0
CE1 C:HIS535 3.1 37.2 1.0
CG C:ASP325 3.1 39.8 1.0
OD1 C:ASP325 3.3 41.5 1.0
ZN C:ZN1001 3.3 44.5 1.0
OE1 C:GLU380 3.9 53.8 1.0
O C:HOH1147 4.0 34.8 1.0
NE2 D:HIS161 4.1 42.1 1.0
CG C:GLU381 4.1 40.9 1.0
CG C:HIS535 4.2 36.7 1.0
ND1 C:HIS535 4.2 38.0 1.0
NE2 C:HIS87 4.4 29.9 1.0
CE1 C:HIS87 4.5 29.3 1.0
CB C:ASP325 4.6 32.2 1.0
O C:HOH1203 4.7 24.0 1.0
CE1 D:HIS161 4.7 41.8 1.0
CD C:GLU380 4.9 60.8 1.0
SD C:MET534 4.9 43.6 1.0

Zinc binding site 7 out of 8 in 4eme

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Zinc binding site 7 out of 8 in the X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1001

b:57.8
occ:1.00
 OD1 D:ASP325 2.1 48.6 1.0
OD1 D:ASP435 2.2 48.6 1.0
NE2 D:HIS87 2.2 46.9 1.0
OD2 D:ASP435 2.4 54.1 1.0
CG D:ASP435 2.6 49.8 1.0
CE1 D:HIS87 3.1 46.4 1.0
CG D:ASP325 3.2 47.5 1.0
ZN D:ZN1002 3.2 54.2 1.0
CD2 D:HIS87 3.4 47.4 1.0
OD2 D:ASP325 3.5 55.9 1.0
OE1 D:GLU380 3.6 65.5 1.0
CB D:ASN326 4.0 34.4 1.0
CB D:ASP435 4.1 42.6 1.0
OE2 D:GLU381 4.2 49.8 1.0
CD D:GLU380 4.2 82.7 1.0
ND1 D:HIS87 4.3 47.5 1.0
CG D:HIS87 4.4 46.2 1.0
CB D:ASP325 4.5 38.5 1.0
CG D:ASN326 4.5 47.3 1.0
OE1 D:GLU381 4.6 41.7 1.0
OE2 D:GLU380 4.7 83.4 1.0
CD D:GLU381 4.7 58.2 1.0
ND2 D:ASN326 4.7 35.0 1.0
N D:MET436 4.7 43.5 1.0
C D:ASP325 4.9 42.5 1.0
N D:ASN326 4.9 38.9 1.0
CA D:ASP325 4.9 38.0 1.0
CA D:ASP435 4.9 41.5 1.0
CA D:ASN326 5.0 37.8 1.0

Zinc binding site 8 out of 8 in 4eme

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Zinc binding site 8 out of 8 in the X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1002

b:54.2
occ:1.00
 NE2 D:HIS535 2.2 42.8 1.0
OE1 D:GLU381 2.3 41.7 1.0
OD2 D:ASP325 2.3 55.9 1.0
OE2 D:GLU381 2.6 49.8 1.0
CD D:GLU381 2.8 58.2 1.0
CE1 D:HIS535 3.1 42.3 1.0
CG D:ASP325 3.2 47.5 1.0
CD2 D:HIS535 3.2 42.6 1.0
ZN D:ZN1001 3.2 57.8 1.0
OD1 D:ASP325 3.4 48.6 1.0
OE1 D:GLU380 3.9 65.5 1.0
NE2 C:HIS161 4.1 50.4 1.0
ND1 D:HIS535 4.3 42.5 1.0
CG D:GLU381 4.3 49.4 1.0
CG D:HIS535 4.3 41.2 1.0
O D:HOH1129 4.4 33.3 1.0
CE1 D:HIS87 4.5 46.4 1.0
NE2 D:HIS87 4.6 46.9 1.0
CB D:ASP325 4.6 38.5 1.0
SD D:MET534 4.8 53.7 1.0
CE1 C:HIS161 4.8 49.0 1.0
CD D:GLU380 5.0 82.7 1.0

Reference:

K.K.Sivaraman, C.A.Oellig, K.Huynh, S.C.Atkinson, M.Poreba, M.A.Perugini, K.R.Trenholme, D.L.Gardiner, G.Salvesen, M.Drag, J.P.Dalton, J.C.Whisstock, S.Mcgowan. X-Ray Crystal Structure and Specificity of the Plasmodium Falciparum Malaria Aminopeptidase PFM18AAP. J.Mol.Biol. V. 422 495 2012.
ISSN: ISSN 0022-2836
PubMed: 22709581
DOI: 10.1016/J.JMB.2012.06.006
Page generated: Wed Dec 16 05:16:12 2020

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