Atomistry » Zinc » PDB 5thi-5tt8 » 5thw
Atomistry »
  Zinc »
    PDB 5thi-5tt8 »
      5thw »

Zinc in PDB 5thw: Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans

Enzymatic activity of Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans

All present enzymatic activity of Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans:
3.5.1.87;

Protein crystallography data

The structure of Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans, PDB code: 5thw was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.39 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.460, 88.510, 126.440, 90.00, 90.21, 90.00
R / Rfree (%) 15.5 / 21.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans (pdb code 5thw). 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 Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans, PDB code: 5thw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5thw

Go back to Zinc Binding Sites List in 5thw
Zinc binding site 1 out of 6 in the Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans


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 Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:56.4
occ:0.68
N3 A:URP503 2.0 52.7 1.0
NE2 A:HIS96 2.3 43.0 1.0
O A:HOH622 2.3 28.8 1.0
NE2 A:HIS203 2.3 39.3 1.0
OD1 A:ASP107 2.4 32.9 1.0
C2 A:URP503 3.1 43.8 1.0
CE1 A:HIS203 3.2 38.6 1.0
CE1 A:HIS96 3.2 41.6 1.0
CD2 A:HIS96 3.3 40.9 1.0
CD2 A:HIS203 3.4 41.2 1.0
CG A:ASP107 3.6 37.1 1.0
OE1 A:GLU141 3.7 46.0 1.0
O2 A:URP503 3.7 47.2 1.0
N1 A:URP503 3.9 47.7 1.0
N A:GLY108 3.9 33.9 1.0
ND1 A:HIS371 3.9 42.2 1.0
ZN A:ZN502 4.0 35.3 0.8
OE2 A:GLU141 4.0 44.3 1.0
CD A:GLU141 4.1 41.2 1.0
OD2 A:ASP107 4.1 44.4 1.0
CA A:GLY108 4.2 31.7 1.0
CE1 A:HIS371 4.3 42.7 1.0
NE2 A:GLN206 4.3 25.7 1.0
ND1 A:HIS203 4.3 42.4 1.0
ND1 A:HIS96 4.4 42.9 1.0
CG A:HIS96 4.4 43.2 1.0
CG A:HIS203 4.4 40.7 1.0
C A:ASP107 4.5 36.5 1.0
OE2 A:GLU142 4.6 45.4 1.0
OE1 A:GLN206 4.6 34.0 1.0
O A:HOH603 4.7 49.7 1.0
CD A:GLN206 4.8 35.6 1.0
CB A:ASP107 4.8 35.4 1.0
CA A:ASP107 4.9 36.0 1.0
OG A:SER95 4.9 48.5 1.0
O A:GLY370 4.9 56.3 1.0
C6 A:URP503 5.0 48.7 1.0

Zinc binding site 2 out of 6 in 5thw

Go back to Zinc Binding Sites List in 5thw
Zinc binding site 2 out of 6 in the Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans


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 Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:35.3
occ:0.79
OD2 A:ASP107 2.0 44.4 1.0
OE2 A:GLU142 2.1 45.4 1.0
NE2 A:HIS395 2.1 41.4 1.0
O2 A:URP503 2.3 47.2 1.0
OE1 A:GLU142 2.6 41.5 1.0
N3 A:URP503 2.6 52.7 1.0
CD A:GLU142 2.7 39.5 1.0
C2 A:URP503 2.7 43.8 1.0
CG A:ASP107 3.0 37.1 1.0
CD2 A:HIS395 3.0 34.0 1.0
CE1 A:HIS395 3.2 37.0 1.0
OD1 A:ASP107 3.2 32.9 1.0
NE2 A:GLN206 3.7 25.7 1.0
N1 A:URP503 3.8 47.7 1.0
O A:HOH652 3.9 30.1 1.0
ZN A:ZN501 4.0 56.4 0.7
NE2 B:HIS239 4.1 39.1 1.0
CG A:GLU142 4.2 38.5 1.0
CG A:HIS395 4.2 38.3 1.0
ND1 A:HIS395 4.2 34.4 1.0
C6 A:URP503 4.3 48.7 1.0
CB A:ASP107 4.3 35.4 1.0
CD2 B:HIS239 4.3 40.9 1.0
CG A:GLN100 4.5 24.5 1.0
CE1 A:HIS96 4.5 41.6 1.0
NE2 A:HIS96 4.7 43.0 1.0
OE1 A:GLU141 4.7 46.0 1.0
NE2 A:GLN100 4.7 33.5 1.0
O A:HOH655 4.8 36.2 1.0
CD A:GLN206 4.9 35.6 1.0

Zinc binding site 3 out of 6 in 5thw

Go back to Zinc Binding Sites List in 5thw
Zinc binding site 3 out of 6 in the Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans


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 Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:55.4
occ:1.00
OD1 B:ASP107 2.2 57.7 1.0
NE2 B:HIS203 2.3 35.4 1.0
NE2 B:HIS96 2.4 39.0 1.0
O B:HOH738 2.9 52.1 1.0
CE1 B:HIS203 3.1 32.9 1.0
CD2 B:HIS203 3.3 35.0 1.0
CG B:ASP107 3.3 50.7 1.0
CD2 B:HIS96 3.3 36.5 1.0
CE1 B:HIS96 3.4 40.9 1.0
OD2 B:ASP107 3.8 59.4 1.0
O B:HOH601 3.8 41.9 1.0
CD2 B:HIS371 3.8 41.1 1.0
OE1 B:GLU141 3.9 58.2 1.0
N B:GLY108 3.9 32.6 1.0
CD B:GLU141 4.0 46.4 1.0
OE2 B:GLU141 4.0 44.5 1.0
ND1 B:HIS203 4.3 40.2 1.0
CA B:GLY108 4.3 27.6 1.0
O B:HOH606 4.4 39.3 1.0
CG B:HIS203 4.4 36.4 1.0
NE2 B:HIS371 4.4 44.6 1.0
C B:ASP107 4.5 36.7 1.0
ND1 B:HIS96 4.5 41.3 1.0
CG B:HIS96 4.5 40.4 1.0
CB B:ASP107 4.6 39.5 1.0
OE2 B:GLU142 4.7 55.2 1.0
NE2 B:GLN206 4.7 38.0 1.0
CA B:ASP107 4.8 36.8 1.0
CG B:GLU141 4.9 38.9 1.0
OE1 B:GLN206 4.9 51.7 1.0
OG B:SER95 4.9 43.8 1.0

Zinc binding site 4 out of 6 in 5thw

Go back to Zinc Binding Sites List in 5thw
Zinc binding site 4 out of 6 in the Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans


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 Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:62.0
occ:0.65
N3 C:URP503 2.3 53.9 1.0
NE2 C:HIS96 2.3 42.7 1.0
NE2 C:HIS203 2.3 53.0 1.0
OD1 C:ASP107 2.5 44.7 1.0
C2 C:URP503 3.0 51.7 1.0
CE1 C:HIS203 3.2 47.8 1.0
CE1 C:HIS96 3.2 41.1 1.0
CD2 C:HIS96 3.3 39.3 1.0
CD2 C:HIS203 3.4 53.6 1.0
O2 C:URP503 3.5 46.8 1.0
CG C:ASP107 3.6 44.6 1.0
OE1 C:GLU141 3.7 39.9 1.0
N1 C:URP503 3.8 53.9 1.0
ND1 C:HIS371 3.8 49.2 1.0
N C:GLY108 4.0 37.7 1.0
OD2 C:ASP107 4.1 43.3 1.0
CE1 C:HIS371 4.1 44.3 1.0
ZN C:ZN502 4.1 23.3 0.6
CD C:GLU141 4.2 36.6 1.0
OE2 C:GLU141 4.2 43.1 1.0
O C:HOH622 4.3 55.6 1.0
CA C:GLY108 4.3 38.9 1.0
NE2 C:GLN206 4.3 27.2 1.0
ND1 C:HIS203 4.3 56.9 1.0
ND1 C:HIS96 4.4 43.5 1.0
CG C:HIS96 4.4 43.1 1.0
CG C:HIS203 4.4 55.3 1.0
OE1 C:GLN206 4.5 42.2 1.0
OE2 C:GLU142 4.6 36.3 1.0
C C:ASP107 4.6 41.8 1.0
CD C:GLN206 4.7 31.7 1.0
OG C:SER95 4.8 55.1 1.0
O C:GLY370 4.8 41.6 1.0
CB C:ASP107 4.9 41.7 1.0
C6 C:URP503 4.9 47.0 1.0
CA C:ASP107 5.0 35.3 1.0

Zinc binding site 5 out of 6 in 5thw

Go back to Zinc Binding Sites List in 5thw
Zinc binding site 5 out of 6 in the Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans


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 Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:23.3
occ:0.58
OD2 C:ASP107 2.0 43.3 1.0
OE2 C:GLU142 2.1 36.3 1.0
NE2 C:HIS395 2.1 44.8 1.0
O2 C:URP503 2.2 46.8 1.0
OE1 C:GLU142 2.4 41.1 1.0
N3 C:URP503 2.5 53.9 1.0
CD C:GLU142 2.6 39.1 1.0
C2 C:URP503 2.6 51.7 1.0
CD2 C:HIS395 2.9 38.7 1.0
CG C:ASP107 3.1 44.6 1.0
CE1 C:HIS395 3.2 43.3 1.0
OD1 C:ASP107 3.4 44.7 1.0
O C:HOH623 3.7 38.6 1.0
N1 C:URP503 3.7 53.9 1.0
NE2 C:GLN206 3.7 27.2 1.0
CG C:GLU142 4.1 39.4 1.0
ZN C:ZN501 4.1 62.0 0.7
CG C:HIS395 4.1 42.6 1.0
NE2 D:HIS239 4.2 46.3 1.0
ND1 C:HIS395 4.2 43.3 1.0
C6 C:URP503 4.2 47.0 1.0
CG C:GLN100 4.3 34.1 1.0
CD2 D:HIS239 4.4 42.5 1.0
CB C:ASP107 4.4 41.7 1.0
CE1 C:HIS96 4.5 41.1 1.0
NE2 C:GLN100 4.5 31.0 1.0
NE2 C:HIS96 4.8 42.7 1.0
OE1 C:GLU141 4.8 39.9 1.0
CD C:GLN206 4.9 31.7 1.0
CD C:GLN100 4.9 30.2 1.0
CB C:GLU142 5.0 35.7 1.0

Zinc binding site 6 out of 6 in 5thw

Go back to Zinc Binding Sites List in 5thw
Zinc binding site 6 out of 6 in the Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans


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 Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:57.7
occ:1.00
OD1 D:ASP107 2.2 76.5 1.0
NE2 D:HIS203 2.3 54.2 1.0
NE2 D:HIS96 2.5 42.7 1.0
O D:HOH636 2.8 42.0 1.0
CE1 D:HIS203 3.1 54.3 1.0
CG D:ASP107 3.3 70.3 1.0
CD2 D:HIS203 3.4 51.3 1.0
O D:HOH601 3.4 34.7 1.0
CE1 D:HIS96 3.5 36.2 1.0
CD2 D:HIS96 3.5 40.8 1.0
OD2 D:ASP107 3.8 71.2 1.0
N D:GLY108 3.9 38.1 1.0
OE1 D:GLU141 3.9 51.0 1.0
OE2 D:GLU141 4.0 56.7 1.0
ND1 D:HIS371 4.0 39.5 1.0
CD D:GLU141 4.1 46.2 1.0
CA D:GLY108 4.2 29.8 1.0
ND1 D:HIS203 4.3 55.2 1.0
CE1 D:HIS371 4.4 39.2 1.0
C D:ASP107 4.4 42.8 1.0
CG D:HIS203 4.4 49.0 1.0
NE2 D:GLN206 4.5 42.6 1.0
CB D:ASP107 4.6 58.5 1.0
OE2 D:GLU142 4.6 58.9 1.0
ND1 D:HIS96 4.6 38.3 1.0
CG D:HIS96 4.7 39.9 1.0
CA D:ASP107 4.7 45.8 1.0
OE1 D:GLN206 4.7 56.9 1.0
O D:HOH608 4.8 33.2 1.0
CD D:GLN206 4.9 48.5 1.0
OG D:SER95 5.0 37.2 1.0

Reference:

J.Abendroth, S.L.Delker, D.D.Lorimer, T.E.Edwards. Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Multivorans To Be Published.
Page generated: Mon Oct 28 08:33:25 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy