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Zinc in PDB 4bg1: Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 1-(3-Carboxypropyl)-1- Methylpyrrolidin-1-Ium Chloride

Enzymatic activity of Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 1-(3-Carboxypropyl)-1- Methylpyrrolidin-1-Ium Chloride

All present enzymatic activity of Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 1-(3-Carboxypropyl)-1- Methylpyrrolidin-1-Ium Chloride:
1.14.11.1;

Protein crystallography data

The structure of Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 1-(3-Carboxypropyl)-1- Methylpyrrolidin-1-Ium Chloride, PDB code: 4bg1 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) 26.92 / 1.89
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 107.630, 107.630, 205.530, 90.00, 90.00, 120.00
R / Rfree (%) 15.597 / 19.906

Zinc Binding Sites:

The binding sites of Zinc atom in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 1-(3-Carboxypropyl)-1- Methylpyrrolidin-1-Ium Chloride (pdb code 4bg1). 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 1-(3-Carboxypropyl)-1- Methylpyrrolidin-1-Ium Chloride, PDB code: 4bg1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4bg1

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Zinc binding site 1 out of 4 in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 1-(3-Carboxypropyl)-1- Methylpyrrolidin-1-Ium Chloride


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 1-(3-Carboxypropyl)-1- Methylpyrrolidin-1-Ium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:18.6
occ:1.00
 O2 A:OGA900 2.0 20.9 1.0
OD1 A:ASP204 2.1 18.0 1.0
NE2 A:HIS202 2.1 18.7 1.0
NE2 A:HIS347 2.2 17.3 1.0
O2' A:OGA900 2.2 19.8 1.0
C1 A:OGA900 2.8 22.6 1.0
C2 A:OGA900 2.8 20.9 1.0
CE1 A:HIS202 3.0 18.4 1.0
CG A:ASP204 3.1 18.3 1.0
CE1 A:HIS347 3.1 18.4 1.0
CD2 A:HIS202 3.1 16.5 1.0
CD2 A:HIS347 3.1 17.4 1.0
OD2 A:ASP204 3.4 18.6 1.0
OE1 A:GLN215 4.0 24.4 1.0
O1 A:OGA900 4.0 21.8 1.0
N1 A:OGA900 4.1 21.4 1.0
ND1 A:HIS347 4.1 16.5 1.0
ND1 A:HIS202 4.1 17.2 1.0
CG A:HIS202 4.2 16.6 1.0
CG A:HIS347 4.2 16.3 1.0
O A:HOH2257 4.4 39.9 1.0
CB A:ASP204 4.4 17.3 1.0
NE2 A:GLN215 4.5 20.7 1.0
CD A:GLN215 4.7 21.5 1.0
CAL A:IVL901 4.8 26.8 1.0
CA A:ASP204 4.9 17.1 1.0
C4 A:OGA900 4.9 21.3 1.0
N A:ASP204 5.0 17.1 1.0

Zinc binding site 2 out of 4 in 4bg1

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Zinc binding site 2 out of 4 in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 1-(3-Carboxypropyl)-1- Methylpyrrolidin-1-Ium Chloride


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 1-(3-Carboxypropyl)-1- Methylpyrrolidin-1-Ium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:16.9
occ:1.00
 NE2 A:HIS82 2.2 18.3 1.0
SG A:CYS40 2.3 19.6 1.0
SG A:CYS38 2.3 18.8 1.0
SG A:CYS43 2.4 17.3 1.0
CE1 A:HIS82 3.0 18.7 1.0
CD2 A:HIS82 3.2 18.0 1.0
CB A:CYS38 3.3 18.8 1.0
CB A:CYS43 3.3 18.9 1.0
CB A:CYS40 3.4 20.3 1.0
O A:HOH2053 3.9 43.6 1.0
NH1 A:ARG35 4.0 16.0 1.0
N A:CYS40 4.1 19.2 1.0
N A:CYS43 4.2 19.3 1.0
ND1 A:HIS82 4.2 19.1 1.0
CA A:CYS40 4.2 20.0 1.0
CG A:HIS82 4.3 18.4 1.0
CA A:CYS43 4.4 19.2 1.0
O A:TYR83 4.4 21.2 1.0
CA A:CYS38 4.5 18.2 1.0
OG A:SER84 4.5 18.0 1.0
C A:CYS38 4.6 17.5 1.0
O A:CYS38 4.6 17.9 1.0
O A:CYS40 4.6 19.7 1.0
C A:CYS40 4.6 20.7 1.0
O A:HOH2040 4.7 27.7 1.0
CZ A:ARG35 4.7 15.2 1.0
CB A:ASP42 4.7 21.1 1.0
NH2 A:ARG35 4.7 15.8 1.0
O A:HOH2054 4.9 49.8 1.0

Zinc binding site 3 out of 4 in 4bg1

Go back to Zinc Binding Sites List in 4bg1
Zinc binding site 3 out of 4 in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 1-(3-Carboxypropyl)-1- Methylpyrrolidin-1-Ium Chloride


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 1-(3-Carboxypropyl)-1- Methylpyrrolidin-1-Ium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn905

b:33.1
occ:0.75
 SG A:CYS267 2.3 37.5 1.0
CB A:CYS267 3.3 29.8 1.0
CA A:CYS267 3.8 27.7 1.0
O A:HOH2320 4.0 54.3 1.0
O A:TYR266 4.2 23.6 1.0
N A:CYS267 4.8 26.0 1.0
N A:ASP268 4.9 23.7 1.0
C A:TYR266 4.9 27.6 1.0
C A:CYS267 4.9 24.5 1.0
OD1 A:ASP268 5.0 25.3 1.0

Zinc binding site 4 out of 4 in 4bg1

Go back to Zinc Binding Sites List in 4bg1
Zinc binding site 4 out of 4 in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 1-(3-Carboxypropyl)-1- Methylpyrrolidin-1-Ium Chloride


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 1-(3-Carboxypropyl)-1- Methylpyrrolidin-1-Ium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn906

b:47.9
occ:0.50
 OD1 A:ASP89 2.0 28.1 0.5
O A:HOH2105 2.2 42.8 1.0
SG A:CYS3 2.3 53.2 1.0
NZ A:LYS72 2.6 39.6 1.0
CG A:ASP89 2.7 25.7 0.5
OD2 A:ASP89 2.8 29.6 0.5
CB A:CYS3 3.2 42.1 1.0
O A:CYS3 3.5 32.8 1.0
CE A:LYS72 3.8 41.2 1.0
C A:CYS3 4.0 34.2 1.0
CB A:ASP89 4.2 24.3 0.5
CA A:CYS3 4.2 38.5 1.0
CB A:ASP89 4.2 24.4 0.5
CA A:ASP89 4.7 23.1 0.5
CA A:ASP89 4.7 23.2 0.5
N A:ASP89 4.9 21.4 1.0
N A:CYS3 5.0 39.3 1.0

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: Wed Aug 20 16:11:33 2025

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