Zinc in PDB 6oiu: X-Ray Crystal Structure of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350)

Enzymatic activity of X-Ray Crystal Structure of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350)

All present enzymatic activity of X-Ray Crystal Structure of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350):
3.4.11.2;

Protein crystallography data

The structure of X-Ray Crystal Structure of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350), PDB code: 6oiu was solved by S.Mcgowan, N.Drinkwater, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.54 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.930, 207.874, 102.867, 90.00, 94.34, 90.00
R / Rfree (%) 19 / 23.6

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Crystal Structure of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350) (pdb code 6oiu). 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 of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350), PDB code: 6oiu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6oiu

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Zinc binding site 1 out of 8 in the X-Ray Crystal Structure of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350)


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 of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:16.7
occ:1.00
 OE2 A:GLU858 2.0 19.3 1.0
NE2 A:HIS839 2.1 17.6 1.0
NE2 A:HIS835 2.1 23.3 1.0
ZN A:ZN2002 2.3 56.4 1.0
CD A:GLU858 2.8 15.8 1.0
CD2 A:HIS839 2.9 17.5 1.0
OE1 A:GLU858 3.0 22.0 1.0
CE1 A:HIS835 3.0 18.1 1.0
CE1 A:HIS839 3.1 22.4 1.0
CD2 A:HIS835 3.2 20.2 1.0
O A:HOH2134 3.9 19.6 1.0
CE2 A:TYR919 3.9 16.6 1.0
OH A:TYR919 4.0 17.3 1.0
CG A:HIS839 4.1 19.6 1.0
ND1 A:HIS835 4.2 18.0 1.0
ND1 A:HIS839 4.2 19.5 1.0
CG A:GLU858 4.3 15.7 1.0
CG A:HIS835 4.3 20.3 1.0
CZ A:TYR919 4.3 20.1 1.0
OE1 A:GLU802 4.5 20.9 1.0
CA A:GLU858 4.7 14.0 1.0
CB A:GLU858 4.8 15.1 1.0
OE2 A:GLU836 4.8 23.2 1.0
CG2 A:THR861 4.8 18.0 1.0
OE2 A:GLU802 4.8 22.2 1.0
CD2 A:TYR919 4.9 16.8 1.0
CB A:THR861 4.9 17.0 1.0
CD A:GLU802 4.9 22.9 1.0

Zinc binding site 2 out of 8 in 6oiu

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Zinc binding site 2 out of 8 in the X-Ray Crystal Structure of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350)


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 of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:56.4
occ:1.00
 ZN A:ZN2001 2.3 16.7 1.0
O A:HOH2134 2.9 19.6 1.0
NE2 A:HIS835 3.4 23.3 1.0
OE2 A:GLU836 3.6 23.2 1.0
OH A:TYR919 3.6 17.3 1.0
OE1 A:GLU802 3.7 20.9 1.0
NE2 A:HIS839 3.7 17.6 1.0
OE2 A:GLU858 3.7 19.3 1.0
CD2 A:HIS835 3.8 20.2 1.0
C1 A:GOL2005 3.8 37.5 1.0
O A:ALA800 3.9 23.1 1.0
CD2 A:HIS839 4.0 17.5 1.0
CE A:MET798 4.0 40.4 1.0
OE1 A:GLU858 4.0 22.0 1.0
O1 A:GOL2005 4.1 41.5 1.0
OE1 A:GLU836 4.2 20.0 1.0
CD A:GLU858 4.3 15.8 1.0
CD A:GLU836 4.3 19.9 1.0
CE2 A:TYR919 4.3 16.6 1.0
C2 A:GOL2005 4.4 39.8 1.0
CZ A:TYR919 4.5 20.1 1.0
CE1 A:HIS835 4.5 18.1 1.0
CD A:GLU802 4.6 22.9 1.0
C3 A:GOL2005 4.7 39.6 1.0
OE2 A:GLU802 4.8 22.2 1.0
CE1 A:HIS839 4.9 22.4 1.0
C A:ALA800 5.0 20.4 1.0

Zinc binding site 3 out of 8 in 6oiu

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Zinc binding site 3 out of 8 in the X-Ray Crystal Structure of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350)


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 of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1501

b:18.7
occ:1.00
 NE2 B:HIS839 2.0 12.8 1.0
OE2 B:GLU858 2.0 17.3 1.0
NE2 B:HIS835 2.1 23.7 1.0
ZN B:ZN1502 2.3 62.7 1.0
CD B:GLU858 2.9 18.5 1.0
CD2 B:HIS839 2.9 16.4 1.0
OE1 B:GLU858 3.0 15.9 1.0
CE1 B:HIS839 3.0 16.9 1.0
CD2 B:HIS835 3.0 19.7 1.0
CE1 B:HIS835 3.1 19.4 1.0
O B:HOH1666 3.7 20.2 1.0
CE2 B:TYR919 3.9 26.1 1.0
CG B:HIS839 4.1 13.9 1.0
ND1 B:HIS839 4.1 12.2 1.0
OH B:TYR919 4.1 23.2 1.0
ND1 B:HIS835 4.2 19.9 1.0
CG B:HIS835 4.2 20.7 1.0
CG B:GLU858 4.3 19.0 1.0
CZ B:TYR919 4.4 22.5 1.0
OE1 B:GLU802 4.5 16.4 1.0
OE2 B:GLU802 4.6 21.5 1.0
CA B:GLU858 4.7 17.2 1.0
CG2 B:THR861 4.7 16.8 1.0
OE2 B:GLU836 4.7 21.7 1.0
CD B:GLU802 4.8 18.4 1.0
CD2 B:TYR919 4.8 19.3 1.0
CB B:THR861 4.8 18.1 1.0
CB B:GLU858 4.9 15.3 1.0

Zinc binding site 4 out of 8 in 6oiu

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Zinc binding site 4 out of 8 in the X-Ray Crystal Structure of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350)


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 of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1502

b:62.7
occ:1.00
 ZN B:ZN1501 2.3 18.7 1.0
O B:HOH1666 2.9 20.2 1.0
OH B:TYR919 3.4 23.2 1.0
NE2 B:HIS835 3.4 23.7 1.0
OE2 B:GLU858 3.5 17.3 1.0
NE2 B:HIS839 3.7 12.8 1.0
CD2 B:HIS835 3.8 19.7 1.0
OE2 B:GLU836 3.8 21.7 1.0
C1 B:GOL1505 3.9 42.5 1.0
CE2 B:TYR919 3.9 26.1 1.0
OE1 B:GLU802 3.9 16.4 1.0
OE1 B:GLU858 4.0 15.9 1.0
CZ B:TYR919 4.1 22.5 1.0
CD B:GLU858 4.1 18.5 1.0
CD2 B:HIS839 4.2 16.4 1.0
O B:ALA800 4.2 25.9 1.0
O1 B:GOL1505 4.3 39.5 1.0
C3 B:GOL1505 4.3 36.6 1.0
C2 B:GOL1505 4.3 44.1 1.0
OE1 B:GLU836 4.4 23.8 1.0
CE1 B:HIS835 4.5 19.4 1.0
CD B:GLU836 4.5 23.1 1.0
CD B:GLU802 4.7 18.4 1.0
OE2 B:GLU802 4.8 21.5 1.0
CE1 B:HIS839 4.9 16.9 1.0

Zinc binding site 5 out of 8 in 6oiu

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Zinc binding site 5 out of 8 in the X-Ray Crystal Structure of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350)


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 of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1501

b:16.2
occ:1.00
 OE2 C:GLU858 2.0 16.2 1.0
NE2 C:HIS839 2.0 16.8 1.0
NE2 C:HIS835 2.1 14.9 1.0
ZN C:ZN1502 2.2 51.1 1.0
CD C:GLU858 2.8 16.7 1.0
CD2 C:HIS839 2.9 14.3 1.0
OE1 C:GLU858 3.0 13.0 1.0
CE1 C:HIS835 3.0 17.8 1.0
CE1 C:HIS839 3.1 16.5 1.0
CD2 C:HIS835 3.1 14.9 1.0
O C:HOH1763 3.7 10.7 1.0
CE2 C:TYR919 3.9 18.3 1.0
OH C:TYR919 4.1 19.9 1.0
CG C:HIS839 4.1 13.9 1.0
ND1 C:HIS839 4.1 12.3 1.0
ND1 C:HIS835 4.2 13.5 1.0
CG C:HIS835 4.2 16.0 1.0
CG C:GLU858 4.3 16.5 1.0
CZ C:TYR919 4.4 21.0 1.0
OE1 C:GLU802 4.4 11.4 1.0
O2 C:GOL1503 4.6 32.7 1.0
CA C:GLU858 4.6 12.9 1.0
CG2 C:THR861 4.7 13.3 1.0
CB C:THR861 4.7 16.0 1.0
CB C:GLU858 4.8 13.3 1.0
OE2 C:GLU802 4.8 14.0 1.0
CD C:GLU802 4.9 13.7 1.0
OE2 C:GLU836 4.9 12.4 1.0
CD2 C:TYR919 4.9 15.3 1.0

Zinc binding site 6 out of 8 in 6oiu

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Zinc binding site 6 out of 8 in the X-Ray Crystal Structure of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350)


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 of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1502

b:51.1
occ:1.00
 ZN C:ZN1501 2.2 16.2 1.0
O C:HOH1763 2.8 10.7 1.0
NE2 C:HIS835 3.4 14.9 1.0
OH C:TYR919 3.5 19.9 1.0
OE2 C:GLU858 3.5 16.2 1.0
O2 C:GOL1503 3.5 32.7 1.0
NE2 C:HIS839 3.7 16.8 1.0
OE1 C:GLU802 3.7 11.4 1.0
OE2 C:GLU836 3.8 12.4 1.0
C3 C:GOL1503 3.8 31.3 1.0
CD2 C:HIS835 3.8 14.9 1.0
OE1 C:GLU858 3.9 13.0 1.0
CD2 C:HIS839 4.0 14.3 1.0
CD C:GLU858 4.1 16.7 1.0
CE2 C:TYR919 4.1 18.3 1.0
C2 C:GOL1503 4.2 32.7 1.0
OE1 C:GLU836 4.2 15.1 1.0
O C:ALA800 4.2 16.5 1.0
CZ C:TYR919 4.3 21.0 1.0
CD C:GLU836 4.4 16.0 1.0
CE1 C:HIS835 4.5 17.8 1.0
CD C:GLU802 4.6 13.7 1.0
C1 C:GOL1503 4.8 34.6 1.0
O C:HOH1603 4.9 32.3 1.0
OE2 C:GLU802 4.9 14.0 1.0
CE1 C:HIS839 4.9 16.5 1.0

Zinc binding site 7 out of 8 in 6oiu

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Zinc binding site 7 out of 8 in the X-Ray Crystal Structure of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350)


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 of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1501

b:32.6
occ:1.00
 OE1 D:GLU858 2.0 34.5 1.0
NE2 D:HIS839 2.0 31.6 1.0
NE2 D:HIS835 2.2 26.9 1.0
ZN D:ZN1502 2.4 78.3 1.0
CD D:GLU858 2.8 34.2 1.0
CE1 D:HIS839 2.9 27.7 1.0
OE2 D:GLU858 2.9 30.2 1.0
CE1 D:HIS835 3.1 30.2 1.0
CD2 D:HIS839 3.1 26.5 1.0
CD2 D:HIS835 3.2 25.9 1.0
CE2 D:TYR919 3.8 33.0 1.0
OH D:TYR919 3.8 35.8 1.0
O D:HOH1609 4.0 27.9 1.0
ND1 D:HIS839 4.1 28.3 1.0
CG D:HIS839 4.2 27.4 1.0
CZ D:TYR919 4.2 34.5 1.0
ND1 D:HIS835 4.2 24.1 1.0
CG D:GLU858 4.2 34.3 1.0
CG D:HIS835 4.3 26.4 1.0
OE1 D:GLU802 4.4 30.1 1.0
CA D:GLU858 4.7 26.1 1.0
CB D:GLU858 4.7 26.8 1.0
CD2 D:TYR919 4.8 28.5 1.0
OE2 D:GLU836 4.8 30.2 1.0
CG2 D:THR861 4.9 26.7 1.0
CB D:THR861 4.9 29.3 1.0
CD D:GLU802 4.9 30.8 1.0
OE2 D:GLU802 4.9 24.3 1.0

Zinc binding site 8 out of 8 in 6oiu

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Zinc binding site 8 out of 8 in the X-Ray Crystal Structure of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350)


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 of the Ectodomain of the Toxoplasma Gondii ME49 Aminopeptidase N (TGME49_224350) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1502

b:78.3
occ:1.00
 ZN D:ZN1501 2.4 32.6 1.0
O D:HOH1609 3.0 27.9 1.0
OH D:TYR919 3.4 35.8 1.0
NE2 D:HIS835 3.5 26.9 1.0
OE2 D:GLU836 3.7 30.2 1.0
NE2 D:HIS839 3.7 31.6 1.0
OE1 D:GLU802 3.7 30.1 1.0
OE1 D:GLU858 3.7 34.5 1.0
CD2 D:HIS835 4.0 25.9 1.0
OE2 D:GLU858 4.0 30.2 1.0
O D:ALA800 4.0 34.5 1.0
CE D:MET798 4.0 39.7 1.0
CD2 D:HIS839 4.1 26.5 1.0
CE2 D:TYR919 4.2 33.0 1.0
OE1 D:GLU836 4.2 33.3 1.0
CD D:GLU858 4.2 34.2 1.0
CZ D:TYR919 4.3 34.5 1.0
CD D:GLU836 4.4 28.0 1.0
O D:HOH1924 4.4 39.4 1.0
O D:HOH1979 4.5 38.3 1.0
CE1 D:HIS835 4.7 30.2 1.0
CD D:GLU802 4.7 30.8 1.0
CE1 D:HIS839 4.9 27.7 1.0

Reference:

E.M.Marijanovic, K.Weronika Swiderska, J.Andersen, J.C.Aschenbrenner, C.T.Webb, M.Drag, N.Drinkwater, S.Mcgowan. X-Ray Crystal Structure and Specificity of the Toxoplasma Gondii ME49 TGAPN2. Biochem.J. V. 477 3819 2020.
ISSN: ESSN 1470-8728
PubMed: 32926129
DOI: 10.1042/BCJ20200569
Page generated: Wed Dec 16 12:26:50 2020

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