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Nickel 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:

Zinc (Zn) 6 atoms

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 6 binding sites of Nickel 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 Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 4c8r

Go back to Nickel Binding Sites List in 4c8r
Nickel 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 Nickel with other atoms in the Ni 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:Ni501

b:76.8
occ:1.00
 OAB A:6YT601 2.0 99.2 1.0
NE2 A:HIS347 2.3 52.8 1.0
OD1 A:ASP204 2.4 58.9 1.0
NAO A:6YT601 2.5 0.2 1.0
NE2 A:HIS202 2.6 47.0 1.0
CAS A:6YT601 2.7 99.7 1.0
OD2 A:ASP204 2.8 60.0 1.0
CG A:ASP204 2.9 57.4 1.0
CAV A:6YT601 3.0 0.3 1.0
CD2 A:HIS347 3.0 51.5 1.0
CE1 A:HIS347 3.2 53.4 1.0
CE1 A:HIS202 3.4 48.1 1.0
CD2 A:HIS202 3.5 45.1 1.0
CAI A:6YT601 3.7 0.3 1.0
N A:6YT601 3.8 99.9 1.0
CG A:HIS347 4.1 50.9 1.0
ND1 A:HIS347 4.1 52.0 1.0
CB A:6YT601 4.2 0.8 1.0
CAT A:6YT601 4.3 0.6 1.0
SAQ A:6YT601 4.4 0.7 1.0
CB A:ASP204 4.5 51.5 1.0
CA A:6YT601 4.5 0.0 1.0
ND1 A:HIS202 4.6 48.4 1.0
CG A:HIS202 4.6 45.9 1.0
NE2 A:GLN215 4.7 55.2 1.0
OE1 A:GLN215 4.7 55.6 1.0
CAG A:6YT601 4.9 0.8 1.0
O A:HOH2064 4.9 40.7 1.0

Nickel binding site 2 out of 6 in 4c8r

Go back to Nickel Binding Sites List in 4c8r
Nickel 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 Nickel with other atoms in the Ni 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:Ni501

b:71.0
occ:1.00
 OAB B:6YT601 2.2 99.2 1.0
OD1 B:ASP204 2.3 53.0 1.0
NE2 B:HIS347 2.3 54.6 1.0
NE2 B:HIS202 2.5 33.9 1.0
NAO B:6YT601 2.5 0.2 1.0
CAS B:6YT601 2.8 99.7 1.0
CAV B:6YT601 3.0 0.3 1.0
CG B:ASP204 3.1 50.4 1.0
CE1 B:HIS202 3.2 33.0 1.0
CE1 B:HIS347 3.2 54.8 1.0
CD2 B:HIS347 3.2 55.2 1.0
OD2 B:ASP204 3.2 50.1 1.0
CD2 B:HIS202 3.5 34.0 1.0
CAI B:6YT601 3.6 0.3 1.0
N B:6YT601 3.9 99.9 1.0
ND1 B:HIS347 4.3 54.2 1.0
CG B:HIS347 4.3 54.1 1.0
ND1 B:HIS202 4.3 35.8 1.0
CB B:6YT601 4.4 0.8 1.0
CAT B:6YT601 4.4 0.6 1.0
OE1 B:GLN215 4.4 66.5 1.0
SAQ B:6YT601 4.5 0.7 1.0
CG B:HIS202 4.5 34.4 1.0
CB B:ASP204 4.6 45.3 1.0
NE2 B:GLN215 4.6 65.6 1.0
CA B:6YT601 4.6 0.0 1.0
CAG B:6YT601 4.8 0.8 1.0
CD B:GLN215 5.0 64.6 1.0

Nickel binding site 3 out of 6 in 4c8r

Go back to Nickel Binding Sites List in 4c8r
Nickel 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 Nickel with other atoms in the Ni 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:Ni501

b:67.5
occ:1.00
 OAB C:6YT601 2.0 99.9 1.0
NE2 C:HIS347 2.2 48.0 1.0
OD1 C:ASP204 2.3 54.7 1.0
NAO C:6YT601 2.4 0.1 1.0
NE2 C:HIS202 2.6 43.7 1.0
CAS C:6YT601 2.8 0.8 1.0
CD2 C:HIS347 2.9 48.1 1.0
CG C:ASP204 3.0 54.4 1.0
OD2 C:ASP204 3.0 57.1 1.0
CAV C:6YT601 3.1 0.0 1.0
CE1 C:HIS347 3.2 47.5 1.0
CE1 C:HIS202 3.5 44.1 1.0
CD2 C:HIS202 3.5 45.1 1.0
CAI C:6YT601 3.6 0.0 1.0
NAN C:6YT601 3.9 0.2 1.0
CG C:HIS347 4.1 47.1 1.0
N C:6YT601 4.1 0.3 1.0
ND1 C:HIS347 4.2 47.0 1.0
CAU C:6YT601 4.4 0.9 1.0
CAL C:6YT601 4.4 0.8 1.0
NE2 C:GLN215 4.4 64.2 1.0
CAT C:6YT601 4.4 0.7 1.0
CB C:ASP204 4.4 51.2 1.0
CAH C:6YT601 4.5 0.7 1.0
ND1 C:HIS202 4.6 44.0 1.0
CG C:HIS202 4.6 44.9 1.0
CB C:6YT601 4.7 0.4 1.0
OE1 C:GLN215 4.7 61.8 1.0
CA C:6YT601 4.7 99.9 1.0
CAG C:6YT601 4.8 0.3 1.0
CA C:ASP204 4.9 49.2 1.0

Nickel binding site 4 out of 6 in 4c8r

Go back to Nickel Binding Sites List in 4c8r
Nickel 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 Nickel with other atoms in the Ni 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:Ni501

b:54.5
occ:1.00
 OAB D:6YT601 2.0 83.4 1.0
NAO D:6YT601 2.2 82.7 1.0
NE2 D:HIS347 2.3 53.1 1.0
O D:HOH2037 2.3 64.0 1.0
OD1 D:ASP204 2.3 52.9 1.0
NE2 D:HIS202 2.3 38.0 1.0
CAS D:6YT601 2.8 83.5 1.0
CAV D:6YT601 2.9 84.2 1.0
CE1 D:HIS202 3.1 39.9 1.0
CG D:ASP204 3.1 52.3 1.0
CD2 D:HIS347 3.2 50.8 1.0
CAI D:6YT601 3.2 81.6 1.0
CE1 D:HIS347 3.2 52.0 1.0
OD2 D:ASP204 3.3 54.5 1.0
CD2 D:HIS202 3.4 40.1 1.0
N D:6YT601 4.2 83.0 1.0
ND1 D:HIS202 4.2 42.5 1.0
CAT D:6YT601 4.2 84.5 1.0
ND1 D:HIS347 4.3 52.8 1.0
CG D:HIS347 4.3 51.2 1.0
CG D:HIS202 4.4 42.2 1.0
CAG D:6YT601 4.5 83.2 1.0
NAN D:6YT601 4.5 91.8 1.0
CB D:ASP204 4.5 49.4 1.0
CAH D:6YT601 4.8 91.6 1.0
CA D:6YT601 4.8 83.0 1.0
CAJ D:6YT601 4.9 84.0 1.0
OE1 D:GLN215 4.9 66.9 1.0
CA D:ASP204 4.9 46.6 1.0
CB D:6YT601 5.0 84.9 1.0

Nickel binding site 5 out of 6 in 4c8r

Go back to Nickel Binding Sites List in 4c8r
Nickel 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 Nickel with other atoms in the Ni 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:Ni501

b:81.0
occ:1.00
 OAB E:6YT601 2.0 94.8 1.0
NE2 E:HIS347 2.1 57.0 1.0
OD1 E:ASP204 2.3 60.1 1.0
NE2 E:HIS202 2.5 51.1 1.0
NAO E:6YT601 2.5 96.0 1.0
CAS E:6YT601 2.9 96.3 1.0
CE1 E:HIS347 2.9 55.5 1.0
CAV E:6YT601 3.1 96.4 1.0
CG E:ASP204 3.2 58.0 1.0
CD2 E:HIS347 3.2 55.6 1.0
CE1 E:HIS202 3.3 50.9 1.0
OD2 E:ASP204 3.4 60.4 1.0
CD2 E:HIS202 3.4 52.0 1.0
CAI E:6YT601 3.6 95.2 1.0
CAL E:6YT601 3.8 0.2 1.0
ND1 E:HIS347 4.1 55.1 1.0
CAU E:6YT601 4.1 0.1 1.0
NAN E:6YT601 4.1 0.2 1.0
N E:6YT601 4.1 97.0 1.0
CG E:HIS347 4.2 54.7 1.0
ND1 E:HIS202 4.4 53.0 1.0
OE1 E:GLN215 4.5 57.5 1.0
CAT E:6YT601 4.5 96.6 1.0
CG E:HIS202 4.5 52.1 1.0
CB E:ASP204 4.6 53.7 1.0
CB E:6YT601 4.6 98.8 1.0
NE2 E:GLN215 4.7 60.6 1.0
CA E:6YT601 4.7 97.5 1.0
CAG E:6YT601 4.9 95.2 1.0
CAK E:6YT601 4.9 0.7 1.0
CAH E:6YT601 4.9 0.9 1.0

Nickel binding site 6 out of 6 in 4c8r

Go back to Nickel Binding Sites List in 4c8r
Nickel 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 Nickel with other atoms in the Ni 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:Ni501

b:49.8
occ:1.00
 OAB F:6YT601 1.9 97.2 1.0
O F:HOH2035 2.1 66.9 1.0
NE2 F:HIS347 2.3 51.0 1.0
OD1 F:ASP204 2.3 55.7 1.0
NE2 F:HIS202 2.5 49.5 1.0
CAS F:6YT601 3.0 96.5 1.0
CG F:ASP204 3.0 52.9 1.0
OD2 F:ASP204 3.0 53.8 1.0
CE1 F:HIS347 3.0 52.7 1.0
NAO F:6YT601 3.1 94.1 1.0
CE1 F:HIS202 3.1 49.7 1.0
CD2 F:HIS347 3.2 51.5 1.0
CAV F:6YT601 3.5 95.2 1.0
CD2 F:HIS202 3.6 50.2 1.0
CB F:6YT601 4.0 98.5 1.0
N F:6YT601 4.0 97.6 1.0
ND1 F:HIS347 4.1 53.8 1.0
CG F:HIS347 4.2 51.3 1.0
SAQ F:6YT601 4.2 99.0 1.0
CAI F:6YT601 4.3 95.0 1.0
ND1 F:HIS202 4.3 51.5 1.0
CA F:6YT601 4.4 97.6 1.0
CB F:ASP204 4.4 51.8 1.0
CG F:HIS202 4.5 50.0 1.0
OE1 F:GLN215 4.7 66.0 1.0
CAT F:6YT601 4.9 95.4 1.0
NE2 F:GLN215 4.9 67.5 1.0
CA F:ASP204 5.0 50.8 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 Oct 9 18:02:42 2024

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