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Zinc in PDB 4bgm: Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 3-Carboxy-N-(2-Fluoroethyl)-N, N-Dimethylpropan-1-Aminium Chloride

Enzymatic activity of Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 3-Carboxy-N-(2-Fluoroethyl)-N, N-Dimethylpropan-1-Aminium Chloride

All present enzymatic activity of Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 3-Carboxy-N-(2-Fluoroethyl)-N, N-Dimethylpropan-1-Aminium Chloride:
1.14.11.1;

Protein crystallography data

The structure of Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 3-Carboxy-N-(2-Fluoroethyl)-N, N-Dimethylpropan-1-Aminium Chloride, PDB code: 4bgm 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) 45.27 / 2.40
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 107.182, 107.182, 205.171, 90.00, 90.00, 120.00
R / Rfree (%) 15.647 / 22.811

Other elements in 4bgm:

The structure of Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 3-Carboxy-N-(2-Fluoroethyl)-N, N-Dimethylpropan-1-Aminium Chloride also contains other interesting chemical elements:

Fluorine (F) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 4bgm

Go back to Zinc Binding Sites List in 4bgm
Zinc binding site 1 out of 2 in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 3-Carboxy-N-(2-Fluoroethyl)-N, N-Dimethylpropan-1-Aminium 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 3-Carboxy-N-(2-Fluoroethyl)-N, N-Dimethylpropan-1-Aminium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:23.1
occ:1.00
 O1 A:OGA400 1.9 30.8 1.0
OD1 A:ASP204 2.1 19.8 1.0
NE2 A:HIS347 2.1 18.0 1.0
NE2 A:HIS202 2.2 19.7 1.0
O2' A:OGA400 2.2 28.4 1.0
C1 A:OGA400 2.7 32.0 1.0
C2 A:OGA400 2.8 29.4 1.0
CG A:ASP204 3.0 19.6 1.0
CE1 A:HIS347 3.0 18.0 1.0
CD2 A:HIS347 3.1 17.9 1.0
CE1 A:HIS202 3.2 19.8 1.0
CD2 A:HIS202 3.2 20.4 1.0
OD2 A:ASP204 3.3 19.2 1.0
O2 A:OGA400 3.9 35.9 1.0
OE1 A:GLN215 4.0 27.1 1.0
N1 A:OGA400 4.1 25.5 1.0
ND1 A:HIS347 4.1 17.4 1.0
CG A:HIS347 4.2 17.8 1.0
O A:HOH2170 4.2 34.5 1.0
ND1 A:HIS202 4.3 20.0 1.0
CG A:HIS202 4.3 19.3 1.0
CB A:ASP204 4.4 18.6 1.0
NE2 A:GLN215 4.4 23.3 1.0
CD A:GLN215 4.7 24.9 1.0
CAL A:DLT401 4.8 28.0 1.0
C4 A:OGA400 4.8 24.9 1.0
CAK A:DLT401 4.9 30.1 1.0
CA A:ASP204 4.9 17.9 1.0

Zinc binding site 2 out of 2 in 4bgm

Go back to Zinc Binding Sites List in 4bgm
Zinc binding site 2 out of 2 in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 3-Carboxy-N-(2-Fluoroethyl)-N, N-Dimethylpropan-1-Aminium 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 3-Carboxy-N-(2-Fluoroethyl)-N, N-Dimethylpropan-1-Aminium Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:25.2
occ:1.00
 NE2 A:HIS82 2.1 23.8 1.0
SG A:CYS40 2.3 28.9 1.0
SG A:CYS38 2.3 22.2 1.0
SG A:CYS43 2.4 24.0 1.0
CE1 A:HIS82 2.9 24.4 1.0
CB A:CYS40 3.1 28.1 1.0
CB A:CYS38 3.2 22.5 1.0
CD2 A:HIS82 3.3 23.9 1.0
CB A:CYS43 3.3 24.5 1.0
N A:CYS40 4.0 25.4 1.0
CA A:CYS40 4.1 26.8 1.0
ND1 A:HIS82 4.1 22.9 1.0
NH1 A:ARG35 4.1 18.0 1.0
N A:CYS43 4.1 24.9 1.0
CG A:HIS82 4.3 23.6 1.0
O A:TYR83 4.3 24.2 1.0
CA A:CYS43 4.4 24.4 1.0
O A:CYS38 4.4 22.5 1.0
CA A:CYS38 4.4 21.4 1.0
OG A:SER84 4.4 21.6 1.0
C A:CYS38 4.5 21.3 1.0
C A:CYS40 4.6 26.4 1.0
O A:CYS40 4.6 26.7 1.0
O A:HOH2018 4.7 26.9 1.0
CZ A:ARG35 4.7 16.6 1.0
CB A:ASP42 4.8 27.2 1.0
NH2 A:ARG35 4.9 16.4 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: Sat Oct 26 19:45:45 2024

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