Atomistry » Zinc » PDB 4ngq-4ntm » 4ntk
Atomistry »
  Zinc »
    PDB 4ngq-4ntm »
      4ntk »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy