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Zinc in PDB 4c8r: Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B)

Enzymatic activity of Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B)

All present enzymatic activity of Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B):
1.14.11.1;

Protein crystallography data

The structure of Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B), PDB code: 4c8r was solved by R.Chowdhury, A.M.Rydzik, G.T.Kochan, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.42 / 2.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 195.744, 91.659, 167.132, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 24.4

Other elements in 4c8r:

The structure of Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B) also contains other interesting chemical elements:

Nickel (Ni) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B) (pdb code 4c8r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B), PDB code: 4c8r:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4c8r

Go back to Zinc Binding Sites List in 4c8r
Zinc binding site 1 out of 6 in the Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:52.3
occ:1.00
 NE2 A:HIS82 2.3 58.1 1.0
SG A:CYS43 2.4 52.5 1.0
SG A:CYS40 2.4 59.2 1.0
SG A:CYS38 2.4 42.3 1.0
CB A:CYS40 3.0 56.0 1.0
CB A:CYS38 3.2 42.2 1.0
CB A:CYS43 3.2 55.5 1.0
CD2 A:HIS82 3.3 59.9 1.0
CE1 A:HIS82 3.3 58.7 1.0
NH1 A:ARG35 3.9 31.0 1.0
CA A:CYS40 4.1 54.0 1.0
O A:TYR83 4.2 59.1 1.0
N A:CYS43 4.2 58.8 1.0
N A:CYS40 4.2 51.0 1.0
O A:CYS40 4.3 55.5 1.0
CA A:CYS43 4.3 56.9 1.0
CG A:HIS82 4.4 59.7 1.0
ND1 A:HIS82 4.4 58.8 1.0
O A:CYS38 4.5 41.9 1.0
CA A:CYS38 4.5 42.4 1.0
NH2 A:ARG35 4.5 24.8 1.0
C A:CYS40 4.5 55.7 1.0
OG A:SER84 4.5 55.5 1.0
C A:CYS38 4.6 42.6 1.0
CZ A:ARG35 4.6 30.9 1.0
C A:ASP42 5.0 59.5 1.0
CB A:ASP42 5.0 62.0 1.0

Zinc binding site 2 out of 6 in 4c8r

Go back to Zinc Binding Sites List in 4c8r
Zinc binding site 2 out of 6 in the Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:55.0
occ:1.00
 NE2 B:HIS82 2.2 55.0 1.0
SG B:CYS38 2.4 49.7 1.0
SG B:CYS43 2.5 57.9 1.0
SG B:CYS40 2.5 52.5 1.0
CB B:CYS40 2.8 48.1 1.0
CE1 B:HIS82 3.1 55.3 1.0
CB B:CYS38 3.2 47.6 1.0
CD2 B:HIS82 3.2 55.7 1.0
CB B:CYS43 3.5 52.9 1.0
CA B:CYS40 4.0 46.9 1.0
NH1 B:ARG35 4.1 44.0 1.0
O B:TYR83 4.2 53.2 1.0
N B:CYS40 4.2 47.1 1.0
ND1 B:HIS82 4.3 55.2 1.0
N B:CYS43 4.3 52.4 1.0
CG B:HIS82 4.4 56.6 1.0
O B:CYS40 4.5 48.7 1.0
C B:CYS40 4.5 48.1 1.0
CA B:CYS38 4.5 44.1 1.0
CA B:CYS43 4.6 53.0 1.0
O B:CYS38 4.6 44.9 1.0
NH2 B:ARG35 4.6 39.6 1.0
C B:CYS38 4.6 43.6 1.0
CZ B:ARG35 4.6 42.3 1.0
CB B:ASP42 4.9 57.9 1.0

Zinc binding site 3 out of 6 in 4c8r

Go back to Zinc Binding Sites List in 4c8r
Zinc binding site 3 out of 6 in the Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:63.4
occ:1.00
 NE2 C:HIS82 2.2 66.2 1.0
SG C:CYS43 2.4 74.2 1.0
SG C:CYS38 2.5 58.8 1.0
SG C:CYS40 2.7 67.1 1.0
CB C:CYS40 2.7 64.2 1.0
CE1 C:HIS82 3.0 66.7 1.0
CB C:CYS43 3.3 78.4 1.0
CB C:CYS38 3.3 56.0 1.0
CD2 C:HIS82 3.4 68.0 1.0
N C:CYS43 3.8 78.4 1.0
CA C:CYS40 3.8 64.7 1.0
N C:CYS40 4.0 62.7 1.0
O C:CYS40 4.1 67.5 1.0
C C:CYS40 4.2 66.4 1.0
CA C:CYS43 4.2 78.5 1.0
O C:CYS38 4.2 53.3 1.0
ND1 C:HIS82 4.2 68.3 1.0
NH1 C:ARG35 4.2 38.6 1.0
CB C:ASP42 4.3 79.7 1.0
C C:CYS38 4.4 55.2 1.0
CG C:HIS82 4.4 68.9 1.0
C C:ASP42 4.5 78.2 1.0
O C:TYR83 4.5 63.6 1.0
CA C:CYS38 4.5 54.5 1.0
N C:ASP42 4.6 75.1 1.0
OG C:SER84 4.6 62.5 1.0
CA C:ASP42 4.7 77.5 1.0
CZ C:ARG35 5.0 44.7 1.0

Zinc binding site 4 out of 6 in 4c8r

Go back to Zinc Binding Sites List in 4c8r
Zinc binding site 4 out of 6 in the Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:67.4
occ:1.00
 NE2 D:HIS82 2.2 83.0 1.0
SG D:CYS38 2.3 58.0 1.0
SG D:CYS43 2.4 70.4 1.0
SG D:CYS40 2.5 54.4 1.0
CB D:CYS38 3.1 59.6 1.0
CD2 D:HIS82 3.1 83.2 1.0
CE1 D:HIS82 3.2 83.6 1.0
CB D:CYS43 3.3 68.6 1.0
CB D:CYS40 3.4 57.9 1.0
OG D:SER84 4.1 74.8 1.0
O D:TYR83 4.1 80.1 1.0
N D:CYS43 4.2 68.9 1.0
NH1 D:ARG35 4.3 60.8 1.0
CG D:HIS82 4.3 84.6 1.0
ND1 D:HIS82 4.3 85.0 1.0
CA D:CYS43 4.4 69.1 1.0
CA D:CYS40 4.4 58.8 1.0
N D:CYS40 4.5 58.8 1.0
CA D:CYS38 4.5 58.7 1.0
O D:CYS38 4.6 58.0 1.0
NH2 D:ARG35 4.7 61.1 1.0
C D:CYS38 4.7 58.4 1.0
CZ D:ARG35 4.8 62.3 1.0
CB D:ASP42 4.9 72.1 1.0
O D:CYS40 4.9 59.4 1.0
C D:CYS40 4.9 60.6 1.0
CB D:SER84 5.0 76.0 1.0

Zinc binding site 5 out of 6 in 4c8r

Go back to Zinc Binding Sites List in 4c8r
Zinc binding site 5 out of 6 in the Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn502

b:95.2
occ:1.00
 SG E:CYS38 2.3 91.7 1.0
NE2 E:HIS82 2.4 98.3 1.0
SG E:CYS40 2.6 78.4 1.0
SG E:CYS43 2.7 85.3 1.0
CB E:CYS40 2.7 82.9 1.0
CD2 E:HIS82 3.2 98.2 1.0
CB E:CYS38 3.3 87.7 1.0
CE1 E:HIS82 3.5 97.8 1.0
CB E:CYS43 3.7 88.6 1.0
O E:TYR83 4.0 99.4 1.0
CA E:CYS40 4.0 85.2 1.0
O E:HOH2002 4.2 33.7 1.0
N E:CYS40 4.3 85.4 1.0
CG E:HIS82 4.4 98.5 1.0
ND1 E:HIS82 4.5 98.3 1.0
C E:CYS40 4.6 86.9 1.0
CA E:CYS38 4.7 86.4 1.0
NE E:ARG35 4.7 82.5 1.0
O E:CYS40 4.7 88.3 1.0
N E:CYS43 4.7 91.8 1.0
C E:CYS38 4.8 86.2 1.0
O E:CYS38 4.9 86.0 1.0
CA E:CYS43 4.9 91.1 1.0
CB E:SER84 5.0 98.1 1.0

Zinc binding site 6 out of 6 in 4c8r

Go back to Zinc Binding Sites List in 4c8r
Zinc binding site 6 out of 6 in the Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Gamma-Butyrobetaine Dioxygenase (BBOX1) in Complex with Ni(II) and N-(3-Hydroxypicolinoyl)-S-(Pyridin-2-Ylmethyl)-L-Cysteine (AR692B) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn502

b:63.6
occ:1.00
 NE2 F:HIS82 2.1 51.7 1.0
SG F:CYS38 2.3 52.0 1.0
SG F:CYS40 2.4 57.1 1.0
SG F:CYS43 2.6 59.2 1.0
CE1 F:HIS82 2.8 50.7 1.0
CB F:CYS40 3.0 58.2 1.0
CB F:CYS38 3.1 52.6 1.0
CD2 F:HIS82 3.4 54.3 1.0
CB F:CYS43 3.6 63.2 1.0
NH1 F:ARG35 3.8 43.6 1.0
ND1 F:HIS82 4.1 53.5 1.0
CA F:CYS40 4.1 60.3 1.0
N F:CYS40 4.1 59.8 1.0
O F:TYR83 4.3 61.5 1.0
CG F:HIS82 4.3 55.6 1.0
CA F:CYS38 4.4 53.2 1.0
O F:CYS38 4.4 53.4 1.0
C F:CYS38 4.5 54.8 1.0
CZ F:ARG35 4.5 44.9 1.0
N F:CYS43 4.6 67.9 1.0
NH2 F:ARG35 4.6 44.9 1.0
C F:CYS40 4.6 61.6 1.0
CA F:CYS43 4.7 65.4 1.0
CB F:SER84 4.8 60.0 1.0
O F:CYS40 4.9 62.3 1.0

Reference:

A.M.Rydzik, R.Chowdhury, G.T.Kochan, S.T.Williams, M.A.Mcdonough, A.Kawamura, C.J.Schofield. Modulating Carnitine Levels By Targeting Its Biosynthesis - Selective Inhibition of Gamma-Butyrobetaine Hydroxylase Chem.Sci. V. 5 1765 2014.
ISSN: ISSN 2041-6520
DOI: 10.1039/C4SC00020J
Page generated: Sat Oct 26 20:40:58 2024

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