Atomistry » Zinc » PDB 4c6n-4ci1 » 4c8r
Atomistry »
  Zinc »
    PDB 4c6n-4ci1 »
      4c8r »

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: Wed Dec 16 05:08:06 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy