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Zinc in PDB 6brm: The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria

Protein crystallography data

The structure of The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria, PDB code: 6brm was solved by K.Tan, T.Van Den Bosch, A.Joachimiak, C.Welte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.84 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 179.163, 79.526, 90.408, 90.00, 89.98, 90.00
R / Rfree (%) 20.6 / 24.3

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria (pdb code 6brm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria, PDB code: 6brm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 6brm

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Zinc binding site 1 out of 16 in the The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:45.6
occ:1.00
O A:HOH401 2.2 42.2 1.0
ND1 A:HIS69 2.2 41.3 1.0
NE2 A:HIS128 2.2 41.8 1.0
NE2 A:HIS67 2.2 41.6 1.0
OD2 A:ASP164 2.2 43.1 1.0
CD2 A:HIS128 2.9 40.1 1.0
CD2 A:HIS67 3.1 42.4 1.0
CE1 A:HIS69 3.1 41.2 1.0
ZN A:ZN302 3.2 47.9 1.0
CG A:ASP164 3.3 43.4 1.0
CG A:HIS69 3.3 42.9 1.0
CE1 A:HIS67 3.3 41.7 1.0
CE1 A:HIS128 3.3 41.6 1.0
CB A:HIS69 3.6 43.0 1.0
CB A:ASP164 3.7 42.2 1.0
NE2 A:HIS72 3.8 45.0 1.0
O A:HOH404 3.8 44.7 1.0
CD2 A:HIS72 4.0 45.6 1.0
CG A:HIS128 4.2 40.3 1.0
NE2 A:HIS69 4.2 41.6 1.0
CG A:HIS67 4.3 42.5 1.0
OD1 A:ASP164 4.3 44.2 1.0
ND1 A:HIS128 4.3 40.1 1.0
ND1 A:HIS67 4.3 41.7 1.0
CD2 A:HIS69 4.4 41.9 1.0
OD1 A:ASP71 4.6 47.2 1.0
O1 A:FMT303 4.7 51.6 1.0
OD2 A:ASP71 4.8 44.6 1.0
CE1 A:HIS72 4.9 45.2 1.0

Zinc binding site 2 out of 16 in 6brm

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Zinc binding site 2 out of 16 in the The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:47.9
occ:1.00
OD2 A:ASP164 2.2 43.1 1.0
O A:HOH401 2.2 42.2 1.0
NE2 A:HIS72 2.2 45.0 1.0
O A:HOH404 2.2 44.7 1.0
OD2 A:ASP71 2.2 44.6 1.0
NE2 A:HIS221 2.2 44.6 1.0
CD2 A:HIS72 3.0 45.6 1.0
CG A:ASP164 3.1 43.4 1.0
CE1 A:HIS221 3.1 45.2 1.0
CG A:ASP71 3.2 46.7 1.0
OD1 A:ASP164 3.2 44.2 1.0
ZN A:ZN301 3.2 45.6 1.0
CD2 A:HIS221 3.3 46.8 1.0
CE1 A:HIS72 3.3 45.2 1.0
OD1 A:ASP71 3.5 47.2 1.0
CG A:HIS72 4.2 45.8 1.0
ND1 A:HIS221 4.3 45.3 1.0
NE2 A:HIS67 4.3 41.6 1.0
ND1 A:HIS72 4.3 45.1 1.0
CG A:HIS221 4.4 46.9 1.0
CB A:ASP164 4.5 42.2 1.0
OD1 A:ASN8 4.5 50.5 1.0
CE1 A:HIS67 4.5 41.7 1.0
CB A:ASP71 4.5 48.3 1.0
NE2 A:HIS128 4.6 41.8 1.0

Zinc binding site 3 out of 16 in 6brm

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Zinc binding site 3 out of 16 in the The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:48.4
occ:1.00
O B:HOH401 2.2 47.6 1.0
NE2 B:HIS128 2.2 46.0 1.0
ND1 B:HIS69 2.2 44.7 1.0
NE2 B:HIS67 2.2 46.6 1.0
OD2 B:ASP164 2.2 47.3 1.0
CD2 B:HIS128 3.0 46.8 1.0
CD2 B:HIS67 3.1 48.1 1.0
CG B:HIS69 3.2 45.4 1.0
CE1 B:HIS69 3.2 43.0 1.0
CE1 B:HIS67 3.2 47.0 1.0
ZN B:ZN302 3.2 52.8 1.0
CG B:ASP164 3.3 46.6 1.0
CE1 B:HIS128 3.3 46.9 1.0
CB B:HIS69 3.5 45.5 1.0
CB B:ASP164 3.7 45.9 1.0
NE2 B:HIS72 3.7 47.8 1.0
O B:HOH404 3.9 46.8 1.0
CD2 B:HIS72 3.9 47.3 1.0
CG B:HIS128 4.2 47.8 1.0
NE2 B:HIS69 4.3 42.8 1.0
CD2 B:HIS69 4.3 43.0 1.0
CG B:HIS67 4.3 48.0 1.0
ND1 B:HIS67 4.3 47.3 1.0
ND1 B:HIS128 4.3 46.8 1.0
OD1 B:ASP164 4.4 45.5 1.0
OD1 B:ASP71 4.5 55.1 1.0
OD2 B:ASP71 4.8 51.6 1.0
CE1 B:HIS72 4.8 46.8 1.0
CA B:HIS69 4.9 46.4 1.0

Zinc binding site 4 out of 16 in 6brm

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Zinc binding site 4 out of 16 in the The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:52.8
occ:1.00
NE2 B:HIS72 2.2 47.8 1.0
O B:HOH404 2.2 46.8 1.0
OD2 B:ASP164 2.2 47.3 1.0
O B:HOH401 2.2 47.6 1.0
OD2 B:ASP71 2.2 51.6 1.0
NE2 B:HIS221 2.2 47.5 1.0
CE1 B:HIS221 3.0 48.5 1.0
CD2 B:HIS72 3.1 47.3 1.0
CG B:ASP164 3.1 46.6 1.0
CG B:ASP71 3.2 53.1 1.0
ZN B:ZN301 3.2 48.4 1.0
CE1 B:HIS72 3.2 46.8 1.0
OD1 B:ASP164 3.3 45.5 1.0
CD2 B:HIS221 3.3 47.8 1.0
OD1 B:ASP71 3.5 55.1 1.0
ND1 B:HIS221 4.2 48.5 1.0
CG B:HIS72 4.3 45.9 1.0
ND1 B:HIS72 4.3 46.2 1.0
CG B:HIS221 4.4 48.1 1.0
NE2 B:HIS67 4.5 46.6 1.0
CB B:ASP164 4.5 45.9 1.0
NE2 B:HIS128 4.5 46.0 1.0
CB B:ASP71 4.6 52.5 1.0
CE1 B:HIS67 4.6 47.0 1.0
ND2 B:ASN8 4.7 53.1 1.0
CE1 B:HIS128 4.9 46.9 1.0

Zinc binding site 5 out of 16 in 6brm

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Zinc binding site 5 out of 16 in the The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:43.2
occ:1.00
O C:HOH401 2.2 41.8 1.0
ND1 C:HIS69 2.2 41.6 1.0
NE2 C:HIS67 2.2 36.8 1.0
NE2 C:HIS128 2.2 37.5 1.0
OD2 C:ASP164 2.2 41.0 1.0
CD2 C:HIS128 3.0 35.4 1.0
CD2 C:HIS67 3.1 37.4 1.0
CE1 C:HIS69 3.1 41.7 1.0
CG C:HIS69 3.2 44.0 1.0
CG C:ASP164 3.2 41.9 1.0
CE1 C:HIS67 3.3 36.3 1.0
CE1 C:HIS128 3.3 35.9 1.0
ZN C:ZN302 3.3 47.6 1.0
CB C:HIS69 3.5 44.5 1.0
CB C:ASP164 3.7 41.1 1.0
NE2 C:HIS72 3.8 41.7 1.0
CD2 C:HIS72 3.9 42.7 1.0
O C:HOH403 4.0 39.2 1.0
NE2 C:HIS69 4.2 42.7 1.0
CG C:HIS128 4.3 35.6 1.0
CG C:HIS67 4.3 37.8 1.0
OD1 C:ASP164 4.3 43.7 1.0
ND1 C:HIS67 4.3 36.6 1.0
CD2 C:HIS69 4.3 42.6 1.0
ND1 C:HIS128 4.3 34.0 1.0
OD1 C:ASP71 4.4 47.0 1.0
CE1 C:HIS72 4.8 42.1 1.0
OD2 C:ASP71 4.8 43.5 1.0
O1 C:FMT303 4.8 67.4 1.0
CG C:HIS72 5.0 41.8 1.0

Zinc binding site 6 out of 16 in 6brm

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Zinc binding site 6 out of 16 in the The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:47.6
occ:1.00
O C:HOH403 2.2 39.2 1.0
NE2 C:HIS72 2.2 41.7 1.0
NE2 C:HIS221 2.2 40.1 1.0
OD2 C:ASP164 2.2 41.0 1.0
OD2 C:ASP71 2.2 43.5 1.0
O C:HOH401 2.6 41.8 1.0
CD2 C:HIS72 3.1 42.7 1.0
CE1 C:HIS221 3.1 40.9 1.0
CG C:ASP164 3.1 41.9 1.0
CG C:ASP71 3.2 44.8 1.0
CE1 C:HIS72 3.3 42.1 1.0
CD2 C:HIS221 3.3 40.8 1.0
ZN C:ZN301 3.3 43.2 1.0
OD1 C:ASP164 3.3 43.7 1.0
OD1 C:ASP71 3.4 47.0 1.0
ND1 C:HIS221 4.2 41.2 1.0
CG C:HIS72 4.3 41.8 1.0
ND1 C:HIS72 4.3 41.0 1.0
CG C:HIS221 4.4 42.1 1.0
NE2 C:HIS67 4.4 36.8 1.0
CB C:ASP164 4.5 41.1 1.0
CB C:ASP71 4.5 45.0 1.0
CE1 C:HIS67 4.6 36.3 1.0
ND2 C:ASN8 4.7 44.4 1.0
NE2 C:HIS128 4.7 37.5 1.0

Zinc binding site 7 out of 16 in 6brm

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Zinc binding site 7 out of 16 in the The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:38.6
occ:1.00
NE2 D:HIS72 2.1 38.7 1.0
OD2 D:ASP164 2.2 37.9 1.0
O D:HOH404 2.2 35.8 1.0
OD2 D:ASP71 2.4 42.2 1.0
NE2 D:HIS221 2.5 40.1 1.0
ZN D:ZN302 2.7 41.4 1.0
CD2 D:HIS72 3.0 40.3 1.0
CG D:ASP164 3.1 38.5 1.0
CE1 D:HIS72 3.2 40.5 1.0
OD1 D:ASP164 3.3 37.5 1.0
CE1 D:HIS221 3.4 40.6 1.0
CD2 D:HIS221 3.5 40.7 1.0
CG D:ASP71 3.6 46.6 1.0
NE2 D:HIS67 4.1 37.2 1.0
CG D:HIS72 4.2 41.0 1.0
OD1 D:ASP71 4.2 49.2 1.0
ND1 D:HIS72 4.3 41.0 1.0
NE2 D:HIS128 4.3 42.7 1.0
CB D:ASP164 4.4 40.3 1.0
CE1 D:HIS67 4.5 37.3 1.0
ND1 D:HIS221 4.6 40.8 1.0
CG D:HIS221 4.6 41.1 1.0
CB D:ASP71 4.7 46.5 1.0
CE1 D:HIS128 4.9 45.3 1.0
ND2 D:ASN8 4.9 47.0 1.0

Zinc binding site 8 out of 16 in 6brm

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Zinc binding site 8 out of 16 in the The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:41.4
occ:1.00
OD2 D:ASP164 2.2 37.9 1.0
NE2 D:HIS128 2.5 42.7 1.0
ND1 D:HIS69 2.6 41.1 1.0
ZN D:ZN301 2.7 38.6 1.0
NE2 D:HIS67 2.7 37.2 1.0
CD2 D:HIS128 3.3 44.0 1.0
CG D:ASP164 3.4 38.5 1.0
O D:HOH404 3.4 35.8 1.0
CG D:HIS69 3.5 41.9 1.0
CD2 D:HIS67 3.5 37.4 1.0
CE1 D:HIS128 3.5 45.3 1.0
NE2 D:HIS72 3.5 38.7 1.0
CE1 D:HIS69 3.6 41.1 1.0
CB D:HIS69 3.6 42.2 1.0
CD2 D:HIS72 3.7 40.3 1.0
CE1 D:HIS67 3.7 37.3 1.0
OD2 D:ASP71 3.9 42.2 1.0
CB D:ASP164 4.0 40.3 1.0
OD1 D:ASP164 4.4 37.5 1.0
OD1 D:ASP71 4.5 49.2 1.0
CG D:HIS128 4.5 43.7 1.0
ND1 D:HIS128 4.6 44.8 1.0
CG D:ASP71 4.6 46.6 1.0
CE1 D:HIS72 4.6 40.5 1.0
CD2 D:HIS69 4.6 40.3 1.0
NE2 D:HIS69 4.7 39.2 1.0
CG D:HIS67 4.7 38.5 1.0
ND1 D:HIS67 4.8 37.1 1.0
CG D:HIS72 4.9 41.0 1.0

Zinc binding site 9 out of 16 in 6brm

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Zinc binding site 9 out of 16 in the The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:49.2
occ:1.00
O E:HOH401 2.2 47.1 1.0
NE2 E:HIS67 2.2 43.8 1.0
NE2 E:HIS128 2.2 43.4 1.0
ND1 E:HIS69 2.2 45.8 1.0
OD2 E:ASP164 2.2 47.3 1.0
CD2 E:HIS128 3.0 41.6 1.0
CE1 E:HIS69 3.1 44.4 1.0
CD2 E:HIS67 3.1 44.7 1.0
CE1 E:HIS67 3.2 43.2 1.0
ZN E:ZN302 3.2 51.5 1.0
CG E:HIS69 3.2 46.2 1.0
CG E:ASP164 3.3 46.3 1.0
CE1 E:HIS128 3.3 42.2 1.0
NE2 E:HIS72 3.6 47.6 1.0
CB E:HIS69 3.6 46.2 1.0
CB E:ASP164 3.8 45.7 1.0
CD2 E:HIS72 3.8 47.8 1.0
O E:HOH405 4.0 47.4 1.0
CG E:HIS128 4.2 41.4 1.0
NE2 E:HIS69 4.2 44.2 1.0
CG E:HIS67 4.3 44.0 1.0
ND1 E:HIS67 4.3 43.0 1.0
CD2 E:HIS69 4.3 44.3 1.0
ND1 E:HIS128 4.3 40.7 1.0
OD1 E:ASP164 4.4 46.3 1.0
OD1 E:ASP71 4.4 45.8 1.0
CE1 E:HIS72 4.7 48.6 1.0
OD2 E:ASP71 4.7 48.4 1.0
CG E:HIS72 4.9 47.5 1.0
CG E:ASP71 5.0 46.2 1.0

Zinc binding site 10 out of 16 in 6brm

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Zinc binding site 10 out of 16 in the The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Crystal Structure of Isothiocyanate Hydrolase From Delia Radicum Gut Bacteria within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn302

b:51.5
occ:1.00
NE2 E:HIS72 2.2 47.6 1.0
O E:HOH405 2.2 47.4 1.0
O E:HOH401 2.2 47.1 1.0
OD2 E:ASP164 2.2 47.3 1.0
OD2 E:ASP71 2.2 48.4 1.0
NE2 E:HIS221 2.2 49.0 1.0
CE1 E:HIS221 3.0 51.1 1.0
CG E:ASP164 3.1 46.3 1.0
CD2 E:HIS72 3.1 47.8 1.0
CE1 E:HIS72 3.2 48.6 1.0
CG E:ASP71 3.2 46.2 1.0
ZN E:ZN301 3.2 49.2 1.0
OD1 E:ASP164 3.3 46.3 1.0
CD2 E:HIS221 3.3 51.0 1.0
OD1 E:ASP71 3.5 45.8 1.0
ND1 E:HIS221 4.2 51.4 1.0
ND1 E:HIS72 4.3 47.9 1.0
CG E:HIS72 4.3 47.5 1.0
CG E:HIS221 4.4 51.1 1.0
NE2 E:HIS67 4.4 43.8 1.0
CB E:ASP164 4.5 45.7 1.0
CB E:ASP71 4.5 47.0 1.0
NE2 E:HIS128 4.6 43.4 1.0
CE1 E:HIS67 4.6 43.2 1.0
ND2 E:ASN8 4.9 52.4 1.0
ND1 E:HIS69 5.0 45.8 1.0
CE1 E:HIS128 5.0 42.2 1.0

Reference:

T.J.M.Van Den Bosch, K.Tan, A.Joachimiak, C.U.Welte. Functional Profiling and Crystal Structures of Isothiocyanate Hydrolases Found in Gut-Associated and Plant-Pathogenic Bacteria. Appl. Environ. Microbiol. V. 84 2018.
ISSN: ESSN 1098-5336
PubMed: 29752272
DOI: 10.1128/AEM.00478-18
Page generated: Wed Dec 16 11:33:08 2020

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