Magnesium in PDB 6x9b: Structure of Proline Utilization A with Cis-4-Hydroxy-D-Proline Bound in the L-Glutamate-Gamma-Semialdehyde Dehydrogenase Active Site

Enzymatic activity of Structure of Proline Utilization A with Cis-4-Hydroxy-D-Proline Bound in the L-Glutamate-Gamma-Semialdehyde Dehydrogenase Active Site

All present enzymatic activity of Structure of Proline Utilization A with Cis-4-Hydroxy-D-Proline Bound in the L-Glutamate-Gamma-Semialdehyde Dehydrogenase Active Site:
1.2.1.88; 1.5.5.2;

Protein crystallography data

The structure of Structure of Proline Utilization A with Cis-4-Hydroxy-D-Proline Bound in the L-Glutamate-Gamma-Semialdehyde Dehydrogenase Active Site, PDB code: 6x9b was solved by J.J.Tanner, A.C.Campbell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	48.38 / 1.46
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	100.89, 101.92, 126.2, 90, 106.44, 90
*R / R_free (%)*	19.4 / 22

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Proline Utilization A with Cis-4-Hydroxy-D-Proline Bound in the L-Glutamate-Gamma-Semialdehyde Dehydrogenase Active Site (pdb code 6x9b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Structure of Proline Utilization A with Cis-4-Hydroxy-D-Proline Bound in the L-Glutamate-Gamma-Semialdehyde Dehydrogenase Active Site, PDB code: 6x9b:

Magnesium binding site 1 out of 1 in 6x9b

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Magnesium Binding Sites List in 6x9b

Magnesium binding site 1 out of 1 in the Structure of Proline Utilization A with Cis-4-Hydroxy-D-Proline Bound in the L-Glutamate-Gamma-Semialdehyde Dehydrogenase Active Site

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Proline Utilization A with Cis-4-Hydroxy-D-Proline Bound in the L-Glutamate-Gamma-Semialdehyde Dehydrogenase Active Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg2005 b:30.5 occ:1.00	O2A	A:NAD2003	2.0	28.0	1.0
	O	A:HOH2103	2.0	19.7	1.0
	O	A:HOH2797	2.0	29.4	1.0
	O1N	A:NAD2003	2.5	25.5	1.0
	PA	A:NAD2003	3.3	23.7	1.0
	O3	A:NAD2003	3.6	24.2	1.0
	PN	A:NAD2003	3.7	24.9	1.0
	O	A:HOH2938	3.7	36.4	1.0
	O	A:HOH2481	4.1	31.3	1.0
	O1A	A:NAD2003	4.1	20.9	1.0
	O5B	A:NAD2003	4.3	22.3	1.0
	O2N	A:NAD2003	4.4	22.7	1.0
	O	A:HOH2774	4.5	39.5	1.0
	O	A:HOH2426	4.6	27.6	1.0
	O5D	A:NAD2003	4.9	23.7	1.0

Reference:

A.C.Campbell, A.N.Bogner, Y.Mao, D.F.Becker, J.J.Tanner. Structural Analysis of Prolines and Hydroxyprolines Binding to the L-Glutamate-Gamma-Semialdehyde Dehydrogenase Active Site of Bifunctional Proline Utilization A. Arch.Biochem.Biophys. V. 698 08727 2020.
ISSN: ESSN 1096-0384
PubMed: 33333077
DOI: 10.1016/J.ABB.2020.108727

Page generated: Wed Aug 13 20:06:47 2025

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