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Zinc in PDB 4ntk: Qued From E. Coli

Enzymatic activity of Qued From E. Coli

All present enzymatic activity of Qued From E. Coli:
4.1.2.50;

Protein crystallography data

The structure of Qued From E. Coli, PDB code: 4ntk was solved by V.Bandarian, S.A.Roberts, Z.D.Miles, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.34 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.070, 112.595, 115.094, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 21.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Qued From E. Coli (pdb code 4ntk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Qued From E. Coli, PDB code: 4ntk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4ntk

Go back to Zinc Binding Sites List in 4ntk
Zinc binding site 1 out of 6 in the Qued From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Qued From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:20.1
occ:1.00
 O05 A:ZSP202 2.0 24.8 1.0
NE2 A:HIS31 2.0 20.1 1.0
NE2 A:HIS33 2.1 20.0 1.0
NE2 A:HIS16 2.1 20.3 1.0
O03 A:ZSP202 2.3 32.7 1.0
C04 A:ZSP202 3.0 25.0 1.0
CD2 A:HIS31 3.0 18.1 1.0
CE1 A:HIS31 3.0 20.5 1.0
CE1 A:HIS16 3.0 19.4 1.0
CE1 A:HIS33 3.0 20.1 1.0
C02 A:ZSP202 3.1 28.1 1.0
CD2 A:HIS33 3.1 16.2 1.0
CD2 A:HIS16 3.1 19.6 1.0
CD A:GLU110 3.9 38.1 1.0
OE2 A:GLU110 3.9 42.5 1.0
OE1 A:GLU110 4.1 45.6 1.0
ND1 A:HIS31 4.1 20.2 1.0
ND1 A:HIS33 4.2 18.1 1.0
ND1 A:HIS16 4.2 20.4 1.0
CG A:HIS31 4.2 19.6 1.0
CG A:HIS33 4.2 16.9 1.0
CG A:HIS16 4.2 19.3 1.0
C06 A:ZSP202 4.3 24.9 1.0
NE2 C:HIS71 4.4 24.6 1.0
CG A:GLU110 4.4 36.2 1.0
C01 A:ZSP202 4.5 33.6 1.0
N07 A:ZSP202 4.7 24.1 1.0
CD2 C:HIS71 4.7 21.8 1.0
O C:HOH373 4.9 33.6 1.0

Zinc binding site 2 out of 6 in 4ntk

Go back to Zinc Binding Sites List in 4ntk
Zinc binding site 2 out of 6 in the Qued From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Qued From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:20.7
occ:1.00
 O05 B:ZSP202 2.0 22.5 1.0
NE2 B:HIS33 2.1 19.5 1.0
NE2 B:HIS31 2.1 19.6 1.0
NE2 B:HIS16 2.1 20.8 1.0
O03 B:ZSP202 2.4 33.1 1.0
C04 B:ZSP202 3.0 26.0 1.0
CD2 B:HIS33 3.0 18.7 1.0
CD2 B:HIS31 3.0 19.1 1.0
CE1 B:HIS33 3.1 21.0 1.0
CE1 B:HIS16 3.1 20.1 1.0
CE1 B:HIS31 3.1 18.6 1.0
C02 B:ZSP202 3.1 28.2 1.0
CD2 B:HIS16 3.1 20.0 1.0
OE1 B:GLU110 3.8 36.4 1.0
CD B:GLU110 4.0 32.3 1.0
ND1 B:HIS33 4.2 18.6 1.0
ND1 B:HIS31 4.2 18.8 1.0
CG B:HIS33 4.2 17.8 1.0
CG B:HIS31 4.2 18.5 1.0
ND1 B:HIS16 4.2 20.1 1.0
CG B:HIS16 4.3 18.8 1.0
OE2 B:GLU110 4.3 34.7 1.0
C06 B:ZSP202 4.3 26.6 1.0
NE2 D:HIS71 4.5 24.8 1.0
C01 B:ZSP202 4.6 34.4 1.0
N07 B:ZSP202 4.6 25.1 1.0
CG B:GLU110 4.7 29.4 1.0
CD2 D:HIS71 4.8 24.9 1.0

Zinc binding site 3 out of 6 in 4ntk

Go back to Zinc Binding Sites List in 4ntk
Zinc binding site 3 out of 6 in the Qued From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Qued From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:20.0
occ:1.00
 O05 C:ZSP202 1.9 24.3 1.0
NE2 C:HIS33 2.1 17.9 1.0
NE2 C:HIS31 2.1 16.8 1.0
NE2 C:HIS16 2.1 19.6 1.0
O03 C:ZSP202 2.3 34.3 1.0
C04 C:ZSP202 2.9 26.3 1.0
CE1 C:HIS31 3.0 19.8 1.0
CD2 C:HIS33 3.0 17.6 1.0
C02 C:ZSP202 3.0 28.3 1.0
CE1 C:HIS33 3.0 17.4 1.0
CE1 C:HIS16 3.1 19.1 1.0
CD2 C:HIS31 3.1 19.1 1.0
CD2 C:HIS16 3.1 19.4 1.0
OE2 C:GLU110 3.9 37.7 1.0
CD C:GLU110 4.0 31.9 1.0
OE1 C:GLU110 4.0 36.3 1.0
ND1 C:HIS31 4.1 17.7 1.0
ND1 C:HIS33 4.1 16.7 1.0
CG C:HIS33 4.2 15.6 1.0
ND1 C:HIS16 4.2 20.1 1.0
C06 C:ZSP202 4.2 24.4 1.0
CG C:HIS31 4.2 17.2 1.0
CG C:HIS16 4.3 20.3 1.0
NE2 A:HIS71 4.4 23.1 1.0
C01 C:ZSP202 4.5 32.7 1.0
N07 C:ZSP202 4.6 24.2 1.0
O C:HOH379 4.8 35.4 1.0
CG C:GLU110 4.8 29.4 1.0
CD2 A:HIS71 4.9 23.2 1.0
CB C:ALA27 4.9 24.3 1.0

Zinc binding site 4 out of 6 in 4ntk

Go back to Zinc Binding Sites List in 4ntk
Zinc binding site 4 out of 6 in the Qued From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Qued From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:18.6
occ:1.00
 O05 D:ZSP202 2.0 21.5 1.0
NE2 D:HIS31 2.1 18.4 1.0
NE2 D:HIS33 2.1 16.7 1.0
NE2 D:HIS16 2.1 18.1 1.0
O03 D:ZSP202 2.2 33.5 1.0
C04 D:ZSP202 2.9 23.1 1.0
C02 D:ZSP202 3.0 26.9 1.0
CE1 D:HIS31 3.0 18.2 1.0
CE1 D:HIS16 3.0 16.1 1.0
CE1 D:HIS33 3.1 18.1 1.0
CD2 D:HIS33 3.1 17.4 1.0
CD2 D:HIS31 3.1 17.7 1.0
CD2 D:HIS16 3.1 18.4 1.0
OE2 D:GLU110 3.7 33.6 1.0
ND1 D:HIS31 4.1 18.6 1.0
ND1 D:HIS33 4.2 17.3 1.0
ND1 D:HIS16 4.2 18.0 1.0
CD D:GLU110 4.2 33.5 1.0
CG D:HIS31 4.2 16.6 1.0
CG D:HIS33 4.2 16.6 1.0
CG D:HIS16 4.2 17.8 1.0
C06 D:ZSP202 4.3 22.3 1.0
NE2 B:HIS71 4.4 23.7 1.0
OE1 D:GLU110 4.4 33.0 1.0
C01 D:ZSP202 4.4 32.1 1.0
N07 D:ZSP202 4.6 20.6 1.0
O D:HOH372 4.7 26.5 1.0
CD2 B:HIS71 4.8 21.7 1.0

Zinc binding site 5 out of 6 in 4ntk

Go back to Zinc Binding Sites List in 4ntk
Zinc binding site 5 out of 6 in the Qued From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Qued From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:19.5
occ:1.00
 O05 E:ZSP202 2.0 21.1 1.0
NE2 E:HIS33 2.1 18.0 1.0
NE2 E:HIS31 2.1 16.5 1.0
NE2 E:HIS16 2.1 18.2 1.0
O03 E:ZSP202 2.3 31.4 1.0
C04 E:ZSP202 2.9 24.8 1.0
CE1 E:HIS31 3.0 18.6 1.0
CE1 E:HIS33 3.0 17.8 1.0
CE1 E:HIS16 3.1 18.9 1.0
CD2 E:HIS33 3.1 16.1 1.0
CD2 E:HIS31 3.1 18.3 1.0
C02 E:ZSP202 3.1 27.9 1.0
CD2 E:HIS16 3.2 19.6 1.0
OE2 E:GLU110 3.9 36.0 1.0
OE1 E:GLU110 3.9 36.6 1.0
CD E:GLU110 3.9 33.8 1.0
ND1 E:HIS33 4.1 16.6 1.0
ND1 E:HIS31 4.1 17.9 1.0
CG E:HIS33 4.2 17.6 1.0
CG E:HIS31 4.2 17.2 1.0
ND1 E:HIS16 4.2 18.2 1.0
C06 E:ZSP202 4.3 23.8 1.0
CG E:HIS16 4.3 16.7 1.0
NE2 F:HIS71 4.4 24.4 1.0
N07 E:ZSP202 4.5 22.4 1.0
C01 E:ZSP202 4.5 32.4 1.0
CD2 F:HIS71 4.8 23.3 1.0
CG E:GLU110 4.8 33.0 1.0
O E:HOH368 4.9 32.6 1.0
CB E:ALA27 5.0 24.8 1.0

Zinc binding site 6 out of 6 in 4ntk

Go back to Zinc Binding Sites List in 4ntk
Zinc binding site 6 out of 6 in the Qued From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Qued From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:18.0
occ:1.00
 O05 F:ZSP202 1.9 21.5 1.0
NE2 F:HIS31 2.1 18.2 1.0
NE2 F:HIS33 2.1 16.8 1.0
O03 F:ZSP202 2.1 33.8 1.0
NE2 F:HIS16 2.1 17.2 1.0
C04 F:ZSP202 2.9 24.0 1.0
C02 F:ZSP202 3.0 23.2 1.0
CE1 F:HIS31 3.0 16.9 1.0
CD2 F:HIS33 3.0 18.1 1.0
CE1 F:HIS33 3.1 18.3 1.0
CD2 F:HIS31 3.1 16.7 1.0
CD2 F:HIS16 3.1 15.2 1.0
CE1 F:HIS16 3.1 15.7 1.0
OE2 F:GLU110 4.0 38.2 1.0
OE1 F:GLU110 4.1 38.7 1.0
CD F:GLU110 4.1 36.9 1.0
ND1 F:HIS31 4.2 16.6 1.0
ND1 F:HIS33 4.2 16.5 1.0
CG F:HIS33 4.2 16.0 1.0
CG F:HIS31 4.2 16.4 1.0
C06 F:ZSP202 4.2 23.4 1.0
ND1 F:HIS16 4.2 17.9 1.0
CG F:HIS16 4.3 16.0 1.0
NE2 E:HIS71 4.3 25.7 1.0
C01 F:ZSP202 4.4 32.1 1.0
N07 F:ZSP202 4.6 23.5 1.0
CD2 E:HIS71 4.7 24.5 1.0
O E:HOH324 4.8 31.0 1.0
CG F:GLU110 4.9 31.9 1.0

Reference:

Z.D.Miles, S.A.Roberts, R.M.Mccarty, V.Bandarian. Biochemical and Structural Studies of 6-Carboxy-5,6,7,8-Tetrahydropterin Synthase Reveal the Molecular Basis of Catalytic Promiscuity Within the Tunnel-Fold Superfamily. J.Biol.Chem. V. 289 23641 2014.
ISSN: ISSN 0021-9258
PubMed: 24990950
DOI: 10.1074/JBC.M114.555680
Page generated: Sun Oct 27 03:21:05 2024

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