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Magnesium in PDB 7nuj: Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1

Protein crystallography data

The structure of Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1, PDB code: 7nuj was solved by J.Laustsen, I.Justo, S.R.Marsden, U.Hanefeld, I.Bento, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.36 / 1.90
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 71.102, 71.102, 223.196, 90, 90, 120
R / Rfree (%) 16.5 / 20.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 (pdb code 7nuj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1, PDB code: 7nuj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7nuj

Go back to Magnesium Binding Sites List in 7nuj
Magnesium binding site 1 out of 2 in the Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:27.1
occ:1.00
O A:HOH482 2.0 23.5 1.0
OD2 A:ASP171 2.1 26.1 1.0
OE1 A:GLU145 2.1 25.9 1.0
O A:HOH497 2.1 28.9 1.0
O A:HOH423 2.1 27.1 1.0
CD A:GLU145 3.0 27.0 1.0
CG A:ASP171 3.0 24.3 1.0
OE2 A:GLU145 3.4 28.6 1.0
HE2 A:HIS44 3.4 19.7 0.0
HE21 A:GLN43 3.7 21.5 1.0
OD1 A:ASP171 3.8 26.5 1.0
HB2 A:ASP171 3.8 24.1 1.0
CB A:ASP171 3.9 24.5 1.0
NE2 A:GLN43 3.9 21.2 1.0
HB3 A:ASP171 4.0 24.1 1.0
OE1 A:GLN43 4.2 20.0 1.0
HE22 A:GLN43 4.2 21.5 1.0
NE2 A:HIS44 4.2 19.5 1.0
HB2 A:GLU145 4.2 27.0 1.0
CG A:GLU145 4.3 29.2 1.0
CD A:GLN43 4.4 22.0 1.0
HG2 A:MET93 4.4 34.0 1.0
HE1 A:MET143 4.4 28.8 1.0
O A:HOH489 4.5 32.5 1.0
O A:HOH559 4.6 33.9 1.0
HB3 A:PRO92 4.7 26.9 1.0
HB2 A:PRO92 4.7 26.9 1.0
HG3 A:GLU145 4.7 28.3 1.0
CB A:GLU145 4.8 27.7 1.0
HD2 A:HIS44 4.8 20.4 1.0
HE2 A:MET143 4.9 28.8 1.0
CD2 A:HIS44 4.9 20.6 1.0
HB3 A:GLU145 5.0 27.0 1.0

Magnesium binding site 2 out of 2 in 7nuj

Go back to Magnesium Binding Sites List in 7nuj
Magnesium binding site 2 out of 2 in the Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Holo-Swhpa-Mg (Hydroxy Ketone Aldolase) From Sphingomonas Wittichii RW1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:32.2
occ:1.00
OD2 B:ASP171 2.1 35.3 1.0
O B:HOH508 2.1 30.6 1.0
O B:HOH454 2.1 32.9 1.0
OE1 B:GLU145 2.1 28.1 1.0
O B:HOH465 2.1 25.7 1.0
CG B:ASP171 3.0 39.0 1.0
CD B:GLU145 3.0 31.1 1.0
HE2 B:HIS44 3.4 23.8 0.0
OE2 B:GLU145 3.4 34.0 1.0
HE21 B:GLN43 3.7 22.8 1.0
OD1 B:ASP171 3.7 31.7 1.0
HB2 B:ASP171 3.8 34.5 1.0
CB B:ASP171 3.8 34.4 1.0
HB3 B:ASP171 3.9 34.5 1.0
NE2 B:GLN43 4.0 22.0 1.0
OE1 B:GLN43 4.2 25.2 1.0
HB2 B:GLU145 4.2 29.9 1.0
HE22 B:GLN43 4.2 22.8 1.0
NE2 B:HIS44 4.2 23.5 1.0
O B:HOH527 4.3 33.3 1.0
CG B:GLU145 4.3 30.4 1.0
CD B:GLN43 4.4 24.6 1.0
HG2 B:MET93 4.4 36.3 1.0
HE1 B:MET143 4.5 29.8 1.0
O B:HOH560 4.5 33.4 1.0
HG3 B:GLU145 4.6 30.7 1.0
HB3 B:PRO92 4.7 27.3 1.0
HB2 B:PRO92 4.7 27.3 1.0
CB B:GLU145 4.7 30.8 1.0
O B:HOH525 4.7 37.4 1.0
HE2 B:MET143 4.8 29.8 1.0
HD2 B:HIS44 4.8 22.6 1.0
HB3 B:GLU145 4.9 29.9 1.0
CD2 B:HIS44 5.0 22.5 1.0

Reference:

S.R.Marsden, H.J.Wijma, M.K.F.Mohr, I.Justo, P.L.Hagedoorn, J.Laustsen, C.M.Jeffries, D.Svergun, L.Mestrom, D.G.G.Mcmillan, I.Bento, U.Hanefeld. Substrate Induced Movement of the Metal Cofactor Between Active and Resting State. Angew.Chem.Int.Ed.Engl. V. 61 13338 2022.
ISSN: ESSN 1521-3773
PubMed: 36214476
DOI: 10.1002/ANIE.202213338
Page generated: Thu Oct 3 02:14:25 2024

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