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Zinc in PDB 4c5w: Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Ethyldimethylammonio)Butanoate

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

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

Protein crystallography data

The structure of Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Ethyldimethylammonio)Butanoate, PDB code: 4c5w 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) 28.85 / 1.70
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 107.140, 107.140, 205.290, 90.00, 90.00, 120.00
R / Rfree (%) 16.363 / 19.978

Zinc Binding Sites:

The binding sites of Zinc atom in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Ethyldimethylammonio)Butanoate (pdb code 4c5w). 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-(Ethyldimethylammonio)Butanoate, PDB code: 4c5w:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4c5w

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Zinc binding site 1 out of 4 in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Ethyldimethylammonio)Butanoate


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-(Ethyldimethylammonio)Butanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:18.3
occ:1.00
 O2 A:OGA400 2.0 25.4 1.0
OD1 A:ASP204 2.0 16.9 1.0
NE2 A:HIS347 2.1 16.1 1.0
NE2 A:HIS202 2.1 17.2 1.0
O2' A:OGA400 2.3 22.1 1.0
C1 A:OGA400 2.8 25.8 1.0
C2 A:OGA400 2.9 25.3 1.0
CE1 A:HIS347 3.0 18.3 1.0
CE1 A:HIS202 3.0 17.1 1.0
CD2 A:HIS347 3.0 18.1 1.0
CG A:ASP204 3.1 18.0 1.0
CD2 A:HIS202 3.1 17.5 1.0
OD2 A:ASP204 3.4 19.3 1.0
O1 A:OGA400 4.0 27.2 1.0
ND1 A:HIS347 4.1 16.9 1.0
ND1 A:HIS202 4.1 17.2 1.0
CG A:HIS347 4.1 16.3 1.0
OE1 A:GLN215 4.1 24.3 1.0
CG A:HIS202 4.2 16.0 1.0
N1 A:OGA400 4.2 24.4 1.0
O A:HOH2271 4.3 41.2 1.0
CB A:ASP204 4.4 18.1 1.0
NE2 A:GLN215 4.5 19.1 1.0
C6 A:NM3401 4.6 22.8 1.0
C3 A:NM3401 4.7 23.9 1.0
CD A:GLN215 4.8 21.0 1.0
CA A:ASP204 4.8 17.1 1.0
C4 A:OGA400 4.9 22.6 1.0
N A:ASP204 4.9 17.4 1.0
CD1 A:LEU199 5.0 19.8 1.0

Zinc binding site 2 out of 4 in 4c5w

Go back to Zinc Binding Sites List in 4c5w
Zinc binding site 2 out of 4 in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Ethyldimethylammonio)Butanoate


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-(Ethyldimethylammonio)Butanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:17.8
occ:1.00
 NE2 A:HIS82 2.1 19.8 1.0
SG A:CYS40 2.3 19.8 1.0
SG A:CYS38 2.3 18.9 1.0
SG A:CYS43 2.3 16.9 1.0
CE1 A:HIS82 3.0 19.4 1.0
CB A:CYS38 3.2 17.6 1.0
CD2 A:HIS82 3.2 18.9 1.0
CB A:CYS43 3.3 18.5 1.0
CB A:CYS40 3.4 20.1 1.0
O A:HOH2056 3.9 35.5 1.0
N A:CYS43 4.1 18.8 1.0
N A:CYS40 4.1 19.8 1.0
NH1 A:ARG35 4.1 17.3 1.0
ND1 A:HIS82 4.1 19.5 1.0
CA A:CYS40 4.2 19.8 1.0
CG A:HIS82 4.3 18.0 1.0
CA A:CYS43 4.3 18.4 1.0
O A:TYR83 4.4 18.8 1.0
CA A:CYS38 4.5 17.1 1.0
OG A:SER84 4.5 17.6 1.0
C A:CYS38 4.6 17.0 1.0
CB A:ASP42 4.6 20.9 1.0
O A:CYS38 4.6 16.6 1.0
O A:CYS40 4.6 18.5 1.0
C A:CYS40 4.7 19.9 1.0
O A:HOH2041 4.7 23.6 1.0
CZ A:ARG35 4.7 16.7 1.0
NH2 A:ARG35 4.8 16.5 1.0
C A:ASP42 5.0 20.4 1.0

Zinc binding site 3 out of 4 in 4c5w

Go back to Zinc Binding Sites List in 4c5w
Zinc binding site 3 out of 4 in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Ethyldimethylammonio)Butanoate


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-(Ethyldimethylammonio)Butanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:39.5
occ:0.80
 SG A:CYS267 2.3 36.6 1.0
CB A:CYS267 3.4 29.9 1.0
CA A:CYS267 3.9 26.3 1.0
O A:TYR266 4.2 25.8 1.0
N A:CYS267 4.8 25.4 1.0
C A:TYR266 4.9 27.0 1.0
N A:ASP268 5.0 23.0 1.0
OD1 A:ASP268 5.0 25.7 1.0
C A:CYS267 5.0 24.0 1.0

Zinc binding site 4 out of 4 in 4c5w

Go back to Zinc Binding Sites List in 4c5w
Zinc binding site 4 out of 4 in the Three Dimensional Structure of Human Gamma-Butyrobetaine Hydroxylase in Complex with 4-(Ethyldimethylammonio)Butanoate


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-(Ethyldimethylammonio)Butanoate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:44.0
occ:0.50
 OD1 A:ASP89 2.1 26.9 0.5
SG A:CYS3 2.2 49.4 1.0
NZ A:LYS72 2.6 42.7 1.0
CG A:ASP89 2.9 26.3 0.5
OD2 A:ASP89 3.0 28.6 0.5
CB A:CYS3 3.1 38.9 1.0
O A:CYS3 3.7 31.9 1.0
CE A:LYS72 3.9 40.8 1.0
C A:CYS3 4.1 32.3 1.0
CB A:ASP89 4.2 24.4 0.5
CA A:CYS3 4.2 35.8 1.0
CB A:ASP89 4.3 24.1 0.5
CA A:ASP89 4.7 22.9 0.5
CA A:ASP89 4.7 22.8 0.5
O A:HOH2109 4.8 33.0 1.0
N A:ASP89 4.9 21.3 1.0
N A:CYS3 5.0 35.8 1.0
OD2 A:ASP89 5.0 26.9 0.5
CG A:ASP89 5.0 26.1 0.5
N A:THR4 5.0 26.6 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 20:27:48 2024

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