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Magnesium in PDB 6x9d: Structure of Proline Utilization A with Trans-4-Hydroxy-L-Proline Bound in the L-Glutamate-Gamma-Semialdehyde Dehydrogenase Active Site

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

All present enzymatic activity of Structure of Proline Utilization A with Trans-4-Hydroxy-L-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 Trans-4-Hydroxy-L-Proline Bound in the L-Glutamate-Gamma-Semialdehyde Dehydrogenase Active Site, PDB code: 6x9d 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) 48.59 / 1.54
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.32, 102.14, 126.46, 90, 106.42, 90
R / Rfree (%) 17.9 / 21

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Proline Utilization A with Trans-4-Hydroxy-L-Proline Bound in the L-Glutamate-Gamma-Semialdehyde Dehydrogenase Active Site (pdb code 6x9d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Proline Utilization A with Trans-4-Hydroxy-L-Proline Bound in the L-Glutamate-Gamma-Semialdehyde Dehydrogenase Active Site, PDB code: 6x9d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6x9d

Go back to Magnesium Binding Sites List in 6x9d
Magnesium binding site 1 out of 2 in the Structure of Proline Utilization A with Trans-4-Hydroxy-L-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 Trans-4-Hydroxy-L-Proline Bound in the L-Glutamate-Gamma-Semialdehyde Dehydrogenase Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2010

b:29.2
occ:1.00
 O A:HOH2130 2.0 28.9 1.0
O A:HOH2429 2.0 27.6 1.0
O2A A:NAD2005 2.1 26.3 1.0
O A:HOH2275 2.2 26.3 1.0
PA A:NAD2005 3.5 25.3 1.0
O A:HOH2366 3.5 29.0 1.0
O1N A:NAD2005 3.7 28.1 1.0
O5B A:NAD2005 3.9 22.2 1.0
OE1 A:GLU734 4.2 29.8 1.0
O A:HOH3075 4.2 39.2 1.0
OE2 A:GLU733 4.2 29.3 1.0
O3 A:NAD2005 4.3 25.9 1.0
PN A:NAD2005 4.4 27.2 1.0
O1A A:NAD2005 4.5 22.1 1.0
O2N A:NAD2005 4.6 23.1 1.0

Magnesium binding site 2 out of 2 in 6x9d

Go back to Magnesium Binding Sites List in 6x9d
Magnesium binding site 2 out of 2 in the Structure of Proline Utilization A with Trans-4-Hydroxy-L-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 2 of Structure of Proline Utilization A with Trans-4-Hydroxy-L-Proline Bound in the L-Glutamate-Gamma-Semialdehyde Dehydrogenase Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2008

b:25.3
occ:1.00
 O B:HOH2546 2.0 23.9 1.0
O B:HOH2270 2.0 21.5 1.0
O2A B:NAD2005 2.1 16.7 1.0
O B:HOH2993 2.1 26.9 1.0
O B:HOH2739 2.2 30.1 1.0
O B:HOH2846 2.4 29.2 1.0
PA B:NAD2005 3.5 15.3 1.0
O B:HOH2443 3.6 15.0 1.0
O1N B:NAD2005 3.8 16.1 1.0
O5B B:NAD2005 3.8 14.5 1.0
O B:HOH2490 4.0 36.4 1.0
OE2 B:GLU733 4.2 22.3 1.0
O3 B:NAD2005 4.3 12.9 1.0
O B:HOH3009 4.4 39.9 1.0
OE1 B:GLU734 4.4 18.8 1.0
PN B:NAD2005 4.5 15.9 1.0
O B:HOH3059 4.6 30.5 1.0
O1A B:NAD2005 4.6 14.1 1.0
O2N B:NAD2005 4.8 13.7 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: Tue Oct 1 23:28:04 2024

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