Calcium in PDB 3vkz: 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at Atmospheric Pressure

Enzymatic activity of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at Atmospheric Pressure

All present enzymatic activity of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at Atmospheric Pressure:
1.1.1.85;

Protein crystallography data

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at Atmospheric Pressure, PDB code: 3vkz was solved by T.Nagae, N.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	22.15 / 1.84
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	104.797, 59.003, 76.754, 90.00, 119.07, 90.00
*R / R_free (%)*	14.2 / 18.5

Other elements in 3vkz:

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at Atmospheric Pressure also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at Atmospheric Pressure (pdb code 3vkz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at Atmospheric Pressure, PDB code: 3vkz:

Calcium binding site 1 out of 1 in 3vkz

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Calcium Binding Sites List in 3vkz

Calcium binding site 1 out of 1 in the 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at Atmospheric Pressure

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at Atmospheric Pressure within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca402 b:15.8 occ:1.00	OD1	A:ASP249	2.2	16.4	1.0
	O3	A:IPM401	2.3	17.4	1.0
	O	A:HOH539	2.4	27.4	1.0
	OD2	A:ASP253	2.4	19.8	1.0
	O1	A:IPM401	2.5	15.0	1.0
	O	A:HOH501	2.5	15.9	1.0
	C1	A:IPM401	3.2	21.1	1.0
	C2	A:IPM401	3.4	16.8	1.0
	CG	A:ASP253	3.4	18.2	1.0
	CG	A:ASP249	3.4	18.1	1.0
	OD1	A:ASP253	3.9	16.3	1.0
	O	A:ASP249	4.0	13.7	1.0
	OD2	A:ASP249	4.1	19.4	1.0
	O2	A:IPM401	4.3	19.4	1.0
	C4	A:IPM401	4.4	16.6	1.0
	O	A:HOH636	4.5	43.5	1.0
	O5	A:IPM401	4.5	17.5	1.0
	CB	A:ASP249	4.5	14.0	1.0
	C3	A:IPM401	4.5	15.6	1.0
	C	A:ASP249	4.5	12.6	1.0
	CA	A:ASP249	4.5	12.1	1.0
	CB	A:ASP253	4.7	14.0	1.0
	NH2	A:ARG107	4.8	22.4	1.0
	NH1	A:ARG136	4.9	17.0	1.0
	O4	A:IPM401	4.9	18.6	1.0

Reference:

T.Nagae, T.Kawamura, L.M.G.Chavas, K.Niwa, M.Hasegawa, C.Kato, N.Watanabe. High-Pressure-Induced Water Penetration Into 3-Isopropylmalate Dehydrogenase Acta Crystallogr.,Sect.D V. 68 300 2012.
ISSN: ISSN 0907-4449
PubMed: 22349232
DOI: 10.1107/S0907444912001862

Page generated: Sat Jul 13 20:40:50 2024

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