Calcium in PDB 3vl7: 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 650 Mpa

Enzymatic activity of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 650 Mpa

All present enzymatic activity of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 650 Mpa:
1.1.1.85;

Protein crystallography data

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 650 Mpa, PDB code: 3vl7 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)*	48.57 / 2.20
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	103.135, 57.561, 75.067, 90.00, 118.67, 90.00
*R / R_free (%)*	16.6 / 24.4

Other elements in 3vl7:

The structure of 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 650 Mpa 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 650 Mpa (pdb code 3vl7). 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 650 Mpa, PDB code: 3vl7:

Calcium binding site 1 out of 1 in 3vl7

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Calcium Binding Sites List in 3vl7

Calcium binding site 1 out of 1 in the 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis Mr-1 at 650 Mpa

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 650 Mpa within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca402 b:16.8 occ:1.00	OD1	A:ASP249	2.1	13.4	1.0
	O3	A:IPM401	2.2	10.8	1.0
	OD2	A:ASP253	2.5	12.9	1.0
	O	A:HOH518	2.5	7.5	1.0
	O	A:HOH600	2.5	22.3	1.0
	O1	A:IPM401	2.6	13.7	1.0
	C1	A:IPM401	3.1	19.2	1.0
	C2	A:IPM401	3.3	17.4	1.0
	CG	A:ASP249	3.3	13.3	1.0
	CG	A:ASP253	3.5	10.7	1.0
	OD1	A:ASP253	3.8	11.3	1.0
	O	A:ASP249	3.9	6.9	1.0
	OD2	A:ASP249	4.0	17.4	1.0
	O2	A:IPM401	4.3	21.9	1.0
	CB	A:ASP249	4.4	9.3	1.0
	C	A:ASP249	4.5	7.6	1.0
	CA	A:ASP249	4.5	8.0	1.0
	C4	A:IPM401	4.5	17.1	1.0
	O5	A:IPM401	4.5	16.5	1.0
	O	A:HOH664	4.6	24.1	1.0
	C3	A:IPM401	4.6	16.8	1.0
	CB	A:ASP253	4.7	8.4	1.0
	NH1	A:ARG107	4.7	18.9	1.0
	NH1	A:ARG136	4.8	4.1	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: Tue Jul 8 17:38:46 2025

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