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Zinc in PDB 3qna: Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin

Enzymatic activity of Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin

All present enzymatic activity of Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin:
4.1.2.50;

Protein crystallography data

The structure of Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin, PDB code: 3qna was solved by K.H.Seo, N.N.Zhuang, K.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.85 / 2.50
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 112.714, 115.882, 155.185, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 23

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin (pdb code 3qna). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin, PDB code: 3qna:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3qna

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Zinc binding site 1 out of 6 in the Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn122

b:26.8
occ:1.00
 O9 A:BIO121 2.0 30.5 1.0
NE2 A:HIS32 2.0 16.6 1.0
NE2 A:HIS30 2.0 17.9 1.0
NE2 A:HIS15 2.1 17.6 1.0
C11 A:BIO121 2.5 35.0 1.0
CE1 A:HIS30 3.0 16.2 1.0
CE1 A:HIS32 3.0 18.4 1.0
CE1 A:HIS15 3.0 15.9 1.0
CD2 A:HIS32 3.1 14.1 1.0
CD2 A:HIS30 3.1 18.0 1.0
C9 A:BIO121 3.1 27.1 1.0
CD2 A:HIS15 3.2 15.3 1.0
C10 A:BIO121 3.2 30.8 1.0
CD A:GLU109 3.7 39.7 1.0
OE1 A:GLU109 3.8 40.0 1.0
OE2 A:GLU109 4.0 41.0 1.0
ND1 A:HIS30 4.1 16.9 1.0
ND1 A:HIS32 4.1 17.4 1.0
ND1 A:HIS15 4.2 17.4 1.0
CG A:GLU109 4.2 33.2 1.0
CG A:HIS30 4.2 16.9 1.0
CG A:HIS32 4.2 15.4 1.0
CG A:HIS15 4.3 18.1 1.0
CE1 D:HIS70 4.3 25.8 1.0
C6 A:BIO121 4.4 21.5 1.0
O10 A:BIO121 4.5 40.7 1.0
N5 A:BIO121 4.6 19.1 1.0
ND1 D:HIS70 4.8 22.8 1.0

Zinc binding site 2 out of 6 in 3qna

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Zinc binding site 2 out of 6 in the Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn122

b:29.7
occ:1.00
 NE2 B:HIS30 2.1 18.4 1.0
O9 B:BIO121 2.1 31.3 1.0
NE2 B:HIS32 2.1 14.1 1.0
NE2 B:HIS15 2.2 14.8 1.0
C11 B:BIO121 2.3 37.7 1.0
CD2 B:HIS30 3.0 16.3 1.0
CE1 B:HIS15 3.1 11.3 1.0
CE1 B:HIS32 3.1 13.0 1.0
CD2 B:HIS32 3.1 13.7 1.0
CE1 B:HIS30 3.2 14.4 1.0
C9 B:BIO121 3.2 31.7 1.0
C10 B:BIO121 3.3 37.4 1.0
CD2 B:HIS15 3.3 15.1 1.0
OE1 B:GLU109 3.7 41.4 1.0
CD B:GLU109 3.9 39.9 1.0
O10 B:BIO121 4.2 42.3 1.0
OE2 B:GLU109 4.2 41.5 1.0
CG B:HIS30 4.2 17.4 1.0
ND1 B:HIS32 4.2 13.5 1.0
ND1 B:HIS30 4.2 17.5 1.0
CG B:HIS32 4.3 13.2 1.0
ND1 B:HIS15 4.3 14.3 1.0
CG B:HIS15 4.4 14.9 1.0
CE1 F:HIS70 4.5 24.9 1.0
CG B:GLU109 4.5 32.2 1.0
C6 B:BIO121 4.5 25.6 1.0
N5 B:BIO121 4.8 23.9 1.0
ND1 F:HIS70 4.9 23.8 1.0

Zinc binding site 3 out of 6 in 3qna

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Zinc binding site 3 out of 6 in the Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn122

b:33.0
occ:1.00
 O9 C:BIO121 2.0 44.9 1.0
NE2 C:HIS30 2.2 18.0 1.0
NE2 C:HIS15 2.2 17.6 1.0
NE2 C:HIS32 2.2 19.7 1.0
C11 C:BIO121 2.4 43.8 1.0
C9 C:BIO121 3.0 41.1 1.0
CD2 C:HIS32 3.1 16.1 1.0
CE1 C:HIS15 3.1 13.3 1.0
CD2 C:HIS30 3.1 16.6 1.0
CE1 C:HIS30 3.2 16.1 1.0
CD2 C:HIS15 3.2 18.0 1.0
C10 C:BIO121 3.2 43.8 1.0
CE1 C:HIS32 3.3 14.9 1.0
OE1 C:GLU109 3.9 41.2 1.0
OE2 C:GLU109 4.1 44.0 1.0
CD C:GLU109 4.2 40.3 1.0
O10 C:BIO121 4.2 46.4 1.0
ND1 C:HIS15 4.2 16.5 1.0
ND1 C:HIS30 4.3 18.5 1.0
CG C:HIS32 4.3 16.9 1.0
C6 C:BIO121 4.3 35.2 1.0
CG C:HIS30 4.3 19.2 1.0
CG C:HIS15 4.3 18.0 1.0
ND1 C:HIS32 4.3 19.2 1.0
CE1 E:HIS70 4.6 28.6 1.0
N5 C:BIO121 4.6 32.8 1.0
ND1 E:HIS70 5.0 28.2 1.0

Zinc binding site 4 out of 6 in 3qna

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Zinc binding site 4 out of 6 in the Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn122

b:32.4
occ:1.00
 O9 D:BIO121 1.9 38.3 1.0
NE2 D:HIS30 2.1 18.4 1.0
NE2 D:HIS15 2.1 17.7 1.0
NE2 D:HIS32 2.2 17.0 1.0
C11 D:BIO121 2.4 37.2 1.0
C9 D:BIO121 2.9 35.6 1.0
CE1 D:HIS30 3.0 19.1 1.0
CE1 D:HIS15 3.1 14.9 1.0
CD2 D:HIS30 3.1 18.1 1.0
C10 D:BIO121 3.1 36.9 1.0
CE1 D:HIS32 3.1 13.2 1.0
CD2 D:HIS32 3.2 11.8 1.0
CD2 D:HIS15 3.2 17.7 1.0
OE1 D:GLU109 3.8 42.6 1.0
CD D:GLU109 3.9 42.1 1.0
OE2 D:GLU109 4.0 46.2 1.0
O10 D:BIO121 4.1 41.7 1.0
ND1 D:HIS30 4.1 18.8 1.0
CG D:HIS30 4.2 20.4 1.0
ND1 D:HIS15 4.2 16.6 1.0
C6 D:BIO121 4.2 34.4 1.0
ND1 D:HIS32 4.3 17.2 1.0
CG D:HIS32 4.3 15.6 1.0
CG D:HIS15 4.3 17.9 1.0
NE2 A:HIS70 4.5 29.0 1.0
N5 D:BIO121 4.6 31.8 1.0
CD2 A:HIS70 4.8 27.4 1.0
CG D:GLU109 4.8 33.7 1.0

Zinc binding site 5 out of 6 in 3qna

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Zinc binding site 5 out of 6 in the Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn122

b:30.0
occ:1.00
 O9 E:BIO121 1.8 33.7 1.0
NE2 E:HIS32 2.0 20.9 1.0
NE2 E:HIS30 2.1 16.3 1.0
NE2 E:HIS15 2.2 17.7 1.0
C11 E:BIO121 2.7 38.0 1.0
CD2 E:HIS32 2.9 17.1 1.0
C9 E:BIO121 2.9 34.8 1.0
CD2 E:HIS30 3.0 19.4 1.0
CE1 E:HIS32 3.1 18.6 1.0
CE1 E:HIS15 3.1 15.1 1.0
CE1 E:HIS30 3.2 17.8 1.0
CD2 E:HIS15 3.2 17.8 1.0
C10 E:BIO121 3.3 36.2 1.0
OE1 E:GLU109 3.8 42.0 1.0
OE2 E:GLU109 3.9 45.0 1.0
CD E:GLU109 4.0 42.1 1.0
CG E:HIS32 4.1 16.6 1.0
ND1 E:HIS32 4.1 19.4 1.0
CG E:HIS30 4.2 18.3 1.0
ND1 E:HIS30 4.2 20.3 1.0
ND1 E:HIS15 4.3 18.4 1.0
C6 E:BIO121 4.3 32.7 1.0
O10 E:BIO121 4.3 42.6 1.0
CG E:HIS15 4.3 18.8 1.0
CE1 C:HIS70 4.4 24.6 1.0
N5 E:BIO121 4.7 32.4 1.0
ND1 C:HIS70 4.9 26.9 1.0

Zinc binding site 6 out of 6 in 3qna

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Zinc binding site 6 out of 6 in the Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A 6-Pyruvoyltetrahydropterin Synthase Homologue From Esherichia Coli Complexed Sepiapterin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn122

b:27.3
occ:1.00
 NE2 F:HIS32 2.0 15.0 1.0
O9 F:BIO121 2.0 33.3 1.0
NE2 F:HIS30 2.1 14.7 1.0
NE2 F:HIS15 2.2 13.3 1.0
C11 F:BIO121 2.4 40.1 1.0
CD2 F:HIS32 2.9 13.8 1.0
CE1 F:HIS30 3.0 16.1 1.0
CE1 F:HIS32 3.1 12.2 1.0
C9 F:BIO121 3.1 35.3 1.0
CD2 F:HIS30 3.1 15.4 1.0
CE1 F:HIS15 3.2 13.3 1.0
CD2 F:HIS15 3.2 15.2 1.0
C10 F:BIO121 3.2 37.9 1.0
OE2 F:GLU109 3.6 42.8 1.0
OE1 F:GLU109 3.7 41.4 1.0
CD F:GLU109 3.8 40.7 1.0
CG F:HIS32 4.1 14.4 1.0
ND1 F:HIS32 4.1 14.0 1.0
ND1 F:HIS30 4.1 17.4 1.0
CG F:HIS30 4.2 17.1 1.0
ND1 F:HIS15 4.3 15.1 1.0
CG F:HIS15 4.4 17.3 1.0
O10 F:BIO121 4.4 44.0 1.0
C6 F:BIO121 4.4 32.5 1.0
NE2 B:HIS70 4.4 25.6 1.0
N5 F:BIO121 4.7 28.1 1.0
CD2 B:HIS70 4.7 24.6 1.0
CG F:GLU109 4.8 34.4 1.0

Reference:

K.H.Seo, N.Zhuang, Y.S.Park, K.H.Park, K.H.Lee. Structural Basis of A Novel Activity of Bacterial 6-Pyruvoyltetrahydropterin Synthase Homologues Distinct From Mammalian 6-Pyruvoyltetrahydropterin Synthase Activity. Acta Crystallogr.,Sect.D V. 70 1212 2014.
ISSN: ISSN 0907-4449
PubMed: 24816091
DOI: 10.1107/S1399004714002016
Page generated: Sat Oct 26 12:14:34 2024

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