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Zinc in PDB 4bhf: Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Trimethylammonio)Pentanoate

Enzymatic activity of Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Trimethylammonio)Pentanoate

All present enzymatic activity of Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Trimethylammonio)Pentanoate:
1.14.11.1;

Protein crystallography data

The structure of Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Trimethylammonio)Pentanoate, PDB code: 4bhf was solved by K.Tars, J.Leitans, A.Kazaks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.72 / 2.05
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 107.450, 107.450, 205.280, 90.00, 90.00, 120.00
R / Rfree (%) 15.373 / 20.883

Zinc Binding Sites:

The binding sites of Zinc atom in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Trimethylammonio)Pentanoate (pdb code 4bhf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Trimethylammonio)Pentanoate, PDB code: 4bhf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4bhf

Go back to Zinc Binding Sites List in 4bhf
Zinc binding site 1 out of 4 in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Trimethylammonio)Pentanoate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Trimethylammonio)Pentanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:21.1
occ:1.00
 O1 A:OGA400 2.0 27.1 1.0
OD1 A:ASP204 2.1 16.7 1.0
NE2 A:HIS202 2.2 16.8 1.0
O2' A:OGA400 2.2 21.2 1.0
NE2 A:HIS347 2.2 20.6 1.0
C1 A:OGA400 2.8 26.6 1.0
C2 A:OGA400 2.8 26.3 1.0
CE1 A:HIS347 3.1 20.5 1.0
CD2 A:HIS202 3.1 16.2 1.0
CE1 A:HIS202 3.1 17.4 1.0
CG A:ASP204 3.1 15.9 1.0
CD2 A:HIS347 3.2 19.1 1.0
OD2 A:ASP204 3.5 17.0 1.0
O2 A:OGA400 4.0 27.1 1.0
N1 A:OGA400 4.1 24.7 1.0
OE1 A:GLN215 4.2 26.3 1.0
ND1 A:HIS347 4.2 19.5 1.0
ND1 A:HIS202 4.2 17.2 1.0
CG A:HIS202 4.2 15.9 1.0
CG A:HIS347 4.3 19.2 1.0
O A:HOH2255 4.3 39.3 1.0
CB A:ASP204 4.5 16.4 1.0
NE2 A:GLN215 4.5 22.6 1.0
C6 A:MZT401 4.5 20.4 1.0
C3 A:MZT401 4.7 20.3 1.0
CD A:GLN215 4.8 22.8 1.0
CA A:ASP204 4.9 15.7 1.0
C4 A:OGA400 4.9 24.6 1.0
N A:ASP204 4.9 16.6 1.0

Zinc binding site 2 out of 4 in 4bhf

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Zinc binding site 2 out of 4 in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Trimethylammonio)Pentanoate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Trimethylammonio)Pentanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:19.5
occ:1.00
 NE2 A:HIS82 2.1 19.1 1.0
SG A:CYS40 2.3 20.6 1.0
SG A:CYS38 2.3 21.2 1.0
SG A:CYS43 2.4 20.6 1.0
CE1 A:HIS82 2.9 20.2 1.0
CD2 A:HIS82 3.2 18.8 1.0
CB A:CYS43 3.3 20.1 1.0
CB A:CYS38 3.3 20.5 1.0
CB A:CYS40 3.4 21.1 1.0
NH1 A:ARG35 4.0 19.5 1.0
ND1 A:HIS82 4.1 20.0 1.0
N A:CYS40 4.1 19.5 1.0
N A:CYS43 4.2 19.6 1.0
CG A:HIS82 4.2 19.8 1.0
CA A:CYS40 4.3 19.6 1.0
O A:TYR83 4.4 22.3 1.0
CA A:CYS43 4.4 18.6 1.0
CA A:CYS38 4.5 20.0 1.0
C A:CYS38 4.5 20.5 1.0
O A:CYS38 4.6 20.7 1.0
O A:HOH2038 4.6 29.5 1.0
CB A:ASP42 4.6 22.3 1.0
O A:CYS40 4.6 18.8 1.0
CZ A:ARG35 4.6 18.2 1.0
NH2 A:ARG35 4.6 19.0 1.0
OG A:SER84 4.7 18.9 1.0
C A:CYS40 4.7 20.9 1.0

Zinc binding site 3 out of 4 in 4bhf

Go back to Zinc Binding Sites List in 4bhf
Zinc binding site 3 out of 4 in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Trimethylammonio)Pentanoate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Trimethylammonio)Pentanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:45.5
occ:0.75
 SG A:CYS267 2.5 45.3 1.0
CB A:CYS267 3.5 30.4 1.0
CA A:CYS267 3.9 29.3 1.0
O A:TYR266 4.2 25.4 1.0
N A:CYS267 4.8 26.8 1.0
C A:TYR266 4.9 28.3 1.0
N A:ASP268 5.0 24.6 1.0

Zinc binding site 4 out of 4 in 4bhf

Go back to Zinc Binding Sites List in 4bhf
Zinc binding site 4 out of 4 in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Trimethylammonio)Pentanoate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Trimethylammonio)Pentanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:59.1
occ:0.50
 SG A:CYS3 2.2 53.1 1.0
OD1 A:ASP89 2.2 24.9 0.5
CG A:ASP89 3.0 23.7 0.5
OD2 A:ASP89 3.1 23.8 0.5
CB A:CYS3 3.4 43.3 1.0
O A:CYS3 3.7 37.3 1.0
C A:CYS3 4.2 37.6 1.0
CA A:CYS3 4.3 41.3 1.0
CB A:ASP89 4.4 22.6 0.5
CB A:ASP89 4.5 22.4 0.5
CA A:ASP89 4.9 21.6 0.5
CA A:ASP89 4.9 21.7 0.5

Reference:

K.Tars, J.Leitans, A.Kazaks, D.Zelencova, E.Liepinsh, J.Kuka, M.Makrecka, D.Lola, V.Andrianovs, D.Gustina, S.Grinberga, E.Liepinsh, I.Kalvinsh, M.Dambrova, E.Loza, O.Pugovics. Targeting Carnitine Biosynthesis: Discovery of New Inhibitors Against Gamma-Butyrobetaine Hydroxylase. J.Med.Chem. V. 57 2213 2014.
ISSN: ISSN 0022-2623
PubMed: 24571165
DOI: 10.1021/JM401603E
Page generated: Sat Oct 26 19:45:45 2024

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