Atomistry » Zinc » PDB 6fdw-6fjk » 6fei
Atomistry »
  Zinc »
    PDB 6fdw-6fjk »
      6fei »

Zinc in PDB 6fei: Phosphotriesterase PTE_A53_1

Protein crystallography data

The structure of Phosphotriesterase PTE_A53_1, PDB code: 6fei was solved by O.Dym, N.Aggarwal, S.Albeck, T.Unger, S.Hamer Rogotner, I.Silman, H.Leader, Y.Ashani, M.Goldsmith, P.Greisen, D.Tawfik, L.J.Sussman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.18 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.230, 81.249, 70.666, 90.00, 94.80, 90.00
R / Rfree (%) 15.5 / 18.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Phosphotriesterase PTE_A53_1 (pdb code 6fei). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Phosphotriesterase PTE_A53_1, PDB code: 6fei:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6fei

Go back to Zinc Binding Sites List in 6fei
Zinc binding site 1 out of 4 in the Phosphotriesterase PTE_A53_1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase PTE_A53_1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:20.2
occ:1.00
OAF A:D6K404 2.0 27.2 1.0
NE2 A:HIS57 2.0 16.3 1.0
O1 A:FMT401 2.1 19.6 1.0
NE2 A:HIS55 2.1 18.5 1.0
OD1 A:ASP301 2.3 18.9 1.0
CE1 A:HIS57 3.0 17.0 1.0
CD2 A:HIS55 3.0 17.9 1.0
CAL A:D6K404 3.0 22.2 1.0
CD2 A:HIS57 3.0 18.6 1.0
C A:FMT401 3.1 17.9 1.0
CG A:ASP301 3.1 18.8 1.0
CE1 A:HIS55 3.2 20.2 1.0
CAH A:D6K404 3.3 21.7 1.0
OD2 A:ASP301 3.4 19.9 1.0
O2 A:FMT401 3.5 17.3 1.0
CAI A:D6K404 3.8 31.7 1.0
ZN A:ZN403 3.8 20.6 1.0
CG2 A:VAL101 4.1 17.8 1.0
CE1 A:HIS230 4.1 19.4 1.0
ND1 A:HIS57 4.1 17.2 1.0
CG A:HIS57 4.2 16.9 1.0
CG A:HIS55 4.2 17.5 1.0
ND1 A:HIS55 4.2 16.0 1.0
OAJ A:D6K404 4.2 27.3 1.0
NE2 A:HIS230 4.4 19.0 1.0
NZ A:LYS169 4.4 22.5 1.0
CB A:ASP301 4.4 19.1 1.0
CAE A:D6K404 4.5 29.6 1.0
CAK A:D6K404 4.6 28.8 1.0
CAA A:D6K404 4.8 26.8 1.0
OAG A:D6K404 4.8 38.5 1.0
CA A:ASP301 4.9 17.0 1.0

Zinc binding site 2 out of 4 in 6fei

Go back to Zinc Binding Sites List in 6fei
Zinc binding site 2 out of 4 in the Phosphotriesterase PTE_A53_1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase PTE_A53_1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:20.6
occ:1.00
O2 A:FMT401 2.0 17.3 1.0
NE2 A:HIS230 2.0 19.0 1.0
ND1 A:HIS201 2.1 24.2 1.0
CAL A:D6K404 2.8 22.2 1.0
CD2 A:HIS230 3.0 18.4 1.0
CE1 A:HIS230 3.0 19.4 1.0
CE1 A:HIS201 3.0 26.9 1.0
C A:FMT401 3.0 17.9 1.0
OAF A:D6K404 3.1 27.2 1.0
CG A:HIS201 3.1 21.0 1.0
O1 A:FMT401 3.4 19.6 1.0
CB A:HIS201 3.5 18.6 1.0
OAJ A:D6K404 3.8 27.3 1.0
CAH A:D6K404 3.8 21.7 1.0
ZN A:ZN402 3.8 20.2 1.0
NE1 A:TRP131 3.9 24.3 1.0
ND1 A:HIS230 4.1 18.8 1.0
CG A:HIS230 4.1 18.3 1.0
NE2 A:HIS201 4.2 26.1 1.0
CD2 A:HIS201 4.2 23.2 1.0
CE1 A:HIS55 4.2 20.2 1.0
NE2 A:HIS55 4.3 18.5 1.0
O A:HOH542 4.3 30.6 1.0
CA A:HIS201 4.4 18.0 1.0
NZ A:LYS169 4.5 22.5 1.0
CD1 A:TRP131 4.5 21.9 1.0
OD2 A:ASP301 4.7 19.9 1.0
CE A:LYS169 4.8 18.4 1.0

Zinc binding site 3 out of 4 in 6fei

Go back to Zinc Binding Sites List in 6fei
Zinc binding site 3 out of 4 in the Phosphotriesterase PTE_A53_1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase PTE_A53_1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:23.6
occ:1.00
NE2 B:HIS57 2.0 21.0 1.0
O B:HOH629 2.1 25.7 1.0
O1 B:FMT401 2.1 22.3 1.0
NE2 B:HIS55 2.2 18.7 1.0
OD1 B:ASP301 2.2 22.4 1.0
CE1 B:HIS57 3.0 21.3 1.0
CD2 B:HIS55 3.0 19.8 1.0
CD2 B:HIS57 3.0 20.7 1.0
CG B:ASP301 3.1 24.1 1.0
C B:FMT401 3.2 24.4 1.0
CE1 B:HIS55 3.2 22.0 1.0
OD2 B:ASP301 3.4 22.9 1.0
O2 B:FMT401 3.6 21.4 1.0
ZN B:ZN403 3.8 24.9 1.0
O B:HOH701 4.0 29.8 1.0
CE1 B:HIS230 4.1 24.6 1.0
ND1 B:HIS57 4.1 19.4 1.0
CG2 B:VAL101 4.1 19.8 1.0
CG B:HIS57 4.1 18.7 1.0
CG B:HIS55 4.2 19.5 1.0
ND1 B:HIS55 4.3 20.0 1.0
NE2 B:HIS230 4.3 21.7 1.0
CB B:ASP301 4.4 19.9 1.0
NZ B:LYS169 4.5 25.7 1.0
CA B:ASP301 4.9 19.2 1.0

Zinc binding site 4 out of 4 in 6fei

Go back to Zinc Binding Sites List in 6fei
Zinc binding site 4 out of 4 in the Phosphotriesterase PTE_A53_1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase PTE_A53_1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:24.9
occ:1.00
O2 B:FMT401 2.0 21.4 1.0
NE2 B:HIS230 2.0 21.7 1.0
ND1 B:HIS201 2.1 27.2 1.0
O B:HOH701 2.2 29.8 1.0
O B:HOH629 2.5 25.7 1.0
CE1 B:HIS201 2.9 27.0 1.0
CD2 B:HIS230 3.0 23.1 1.0
C B:FMT401 3.0 24.4 1.0
CE1 B:HIS230 3.0 24.6 1.0
CG B:HIS201 3.1 24.9 1.0
O1 B:FMT401 3.3 22.3 1.0
CB B:HIS201 3.5 22.3 1.0
ZN B:ZN402 3.8 23.6 1.0
NE1 B:TRP131 3.9 24.6 1.0
NE2 B:HIS201 4.1 30.3 1.0
ND1 B:HIS230 4.1 23.8 1.0
CG B:HIS230 4.1 20.7 1.0
CD2 B:HIS201 4.2 27.3 1.0
CE1 B:HIS55 4.3 22.0 1.0
NE2 B:HIS55 4.3 18.7 1.0
CA B:HIS201 4.4 22.3 1.0
NZ B:LYS169 4.5 25.7 1.0
CD1 B:TRP131 4.5 22.3 1.0
OD2 B:ASP301 4.8 22.9 1.0
CE B:LYS169 4.8 22.6 1.0

Reference:

O.Dym, N.Aggarwal, J.L.Sussman, I.Silman. Crystal Structures of Bacterail Phosphotriesterase Variant with High Catalytic Activity Towards Organophosphate Nerve Agents Developed By Use of Structure-Based Design and Molecular Evolution To Be Published.
Page generated: Wed Dec 16 11:47:37 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy