Chlorine in PDB 3vdr: Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+)

Enzymatic activity of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+)

All present enzymatic activity of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+):
1.1.1.30;

Protein crystallography data

The structure of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+), PDB code: 3vdr was solved by M.M.Hoque, S.Shimizu, E.C.M.Juan, Y.Sato, M.T.Hossain, T.Yamamoto, S.Imamura, H.Amano, K.Suzuki, T.Sekiguchi, M.Tsunoda, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	43.00 / 3.00
*Space group*	P 4₁ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	91.100, 91.100, 262.000, 90.00, 90.00, 90.00
*R / R_free (%)*	17.6 / 24.1

Other elements in 3vdr:

The structure of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+) also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+) (pdb code 3vdr). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+), PDB code: 3vdr:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 3vdr

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Chlorine Binding Sites List in 3vdr

Chlorine binding site 1 out of 3 in the Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+)

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl302 b:81.8 occ:1.00	NZ	A:LYS219	2.9	50.0	1.0
	O	C:HOH410	3.1	23.2	1.0
	CG2	A:VAL150	3.2	31.2	1.0
	N	A:VAL150	3.5	30.8	1.0
	CE	A:LYS219	3.8	47.3	1.0
	CA	A:SER149	3.9	29.0	1.0
	CB	A:VAL150	4.1	31.6	1.0
	OE2	A:GLU218	4.1	61.4	1.0
	OG	A:SER149	4.1	27.9	1.0
	CB	A:SER149	4.2	28.3	1.0
	C	A:SER149	4.2	30.1	1.0
	CA	A:VAL150	4.4	32.6	1.0
	O	A:ALA148	4.9	28.0	1.0

Chlorine binding site 2 out of 3 in 3vdr

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Chlorine Binding Sites List in 3vdr

Chlorine binding site 2 out of 3 in the Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+)

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Cl302 b:69.8 occ:1.00	CG1	B:VAL150	3.3	34.9	1.0
	N	B:VAL150	3.5	35.6	1.0
	NZ	B:LYS219	3.7	46.8	1.0
	CG2	B:VAL150	3.9	34.5	1.0
	CB	B:VAL150	4.0	34.6	1.0
	CA	B:SER149	4.1	35.3	1.0
	C	B:SER149	4.3	35.5	1.0
	CA	B:VAL150	4.4	34.4	1.0
	CB	B:SER149	4.5	35.2	1.0
	CD1	C:LEU171	4.6	30.9	1.0
	CE	B:LYS219	4.6	44.3	1.0
	OG	B:SER149	4.6	30.2	1.0
	NH1	D:ARG260	4.7	43.9	1.0
	CD	D:ARG260	4.9	45.9	1.0
	CB	C:LEU171	5.0	31.7	1.0

Chlorine binding site 3 out of 3 in 3vdr

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Chlorine Binding Sites List in 3vdr

Chlorine binding site 3 out of 3 in the Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+)

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase, Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad(+) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Cl301 b:54.5 occ:1.00	NZ	D:LYS219	3.0	47.8	1.0
	N	D:VAL150	3.4	34.1	1.0
	CG1	D:VAL150	3.7	34.0	1.0
	CG2	D:VAL150	3.8	34.9	1.0
	CA	D:SER149	4.0	33.8	1.0
	CE	D:LYS219	4.0	48.2	1.0
	CB	D:VAL150	4.2	34.2	1.0
	C	D:SER149	4.2	34.6	1.0
	CD1	A:LEU171	4.3	26.3	1.0
	CB	D:SER149	4.4	34.2	1.0
	CA	D:VAL150	4.4	35.2	1.0
	NH1	B:ARG260	4.7	48.6	1.0
	OG	D:SER149	4.7	34.4	1.0
	CD	B:ARG260	4.8	47.0	1.0

Reference:

M.M.Hoque, S.Shimizu, E.C.M.Juan, Y.Sato, M.T.Hossain, T.Yamamoto, S.Imamura, K.Suzuki, H.Amano, T.Sekiguchi, M.Tsunoda, A.Takenaka. Structure of D-3-Hydroxybutyrate Dehydrogenase Prepared in the Presence of the Substrate D-3-Hydroxybutyrate and Nad+. Acta Crystallogr.,Sect.F V. 65 331 2009.
ISSN: ESSN 1744-3091
PubMed: 19342772
DOI: 10.1107/S1744309109008537

Page generated: Fri Jul 11 11:38:48 2025

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