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

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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

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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

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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

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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

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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

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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: Wed Dec 16 10:56:01 2020

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