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Magnesium in PDB 6ubz: Crystal Structure of D678A Goxa Bound to Glycine at pH 5.5

Protein crystallography data

The structure of Crystal Structure of D678A Goxa Bound to Glycine at pH 5.5, PDB code: 6ubz was solved by E.T.Yukl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.35 / 1.83
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 110.325, 93.403, 187.987, 90.00, 95.20, 90.00
R / Rfree (%) 16.2 / 18.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of D678A Goxa Bound to Glycine at pH 5.5 (pdb code 6ubz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of D678A Goxa Bound to Glycine at pH 5.5, PDB code: 6ubz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6ubz

Go back to Magnesium Binding Sites List in 6ubz
Magnesium binding site 1 out of 4 in the Crystal Structure of D678A Goxa Bound to Glycine at pH 5.5


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 D678A Goxa Bound to Glycine at pH 5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg901

b:17.0
occ:1.00
O B:ALA699 2.3 16.6 1.0
O B:ILE365 2.3 12.2 1.0
O B:ALA362 2.3 12.2 1.0
OD1 B:ASN700 2.4 14.9 1.0
O B:HOH1079 2.6 19.5 1.0
OD1 B:ASP360 2.8 14.6 1.0
C B:ALA699 3.2 17.6 1.0
C B:ALA362 3.3 14.4 1.0
OD2 B:ASP360 3.4 19.2 1.0
CG B:ASP360 3.5 19.1 1.0
C B:ILE365 3.5 13.8 1.0
CG B:ASN700 3.5 17.1 1.0
CA B:ASN700 3.8 12.5 1.0
N B:ASN700 3.8 15.1 1.0
CA B:ALA362 4.1 16.5 1.0
N B:ILE365 4.1 13.2 1.0
N B:PRO363 4.1 13.3 1.0
CB B:ALA362 4.1 13.7 1.0
CB B:ALA699 4.1 10.2 1.0
CA B:PRO363 4.2 15.5 1.0
CA B:ALA699 4.2 11.0 1.0
CA B:ILE365 4.2 11.8 1.0
CB B:ASN700 4.2 11.8 1.0
N B:ALA362 4.3 15.8 1.0
CB B:ILE365 4.3 12.8 1.0
C B:PRO363 4.4 17.3 1.0
O B:HOH1459 4.4 23.7 1.0
ND2 B:ASN700 4.5 17.0 1.0
N B:GLU366 4.5 12.3 1.0
O B:PRO363 4.5 14.8 1.0
CA B:GLU366 4.8 12.5 1.0
CD B:PRO367 4.8 10.5 1.0
N B:GLN364 4.9 15.3 1.0
CB B:ASP360 4.9 15.8 1.0

Magnesium binding site 2 out of 4 in 6ubz

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Magnesium binding site 2 out of 4 in the Crystal Structure of D678A Goxa Bound to Glycine at pH 5.5


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 D678A Goxa Bound to Glycine at pH 5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:22.2
occ:1.00
O A:ILE365 2.3 22.2 1.0
O A:ALA699 2.4 19.2 1.0
O A:ALA362 2.4 23.0 1.0
OD1 A:ASN700 2.4 22.7 1.0
O A:HOH1063 2.5 24.9 1.0
OD1 A:ASP360 2.8 23.0 1.0
C A:ALA699 3.2 20.6 1.0
C A:ALA362 3.3 21.7 1.0
OD2 A:ASP360 3.4 26.5 1.0
CG A:ASP360 3.5 26.4 1.0
C A:ILE365 3.5 23.4 1.0
CG A:ASN700 3.5 24.2 1.0
CA A:ASN700 3.8 19.8 1.0
N A:ASN700 3.9 18.6 1.0
N A:PRO363 4.1 17.9 1.0
CA A:ALA362 4.1 21.5 1.0
N A:ILE365 4.1 17.2 1.0
CA A:PRO363 4.2 19.6 1.0
CB A:ALA362 4.2 23.1 1.0
CB A:ALA699 4.2 18.1 1.0
CA A:ILE365 4.2 20.0 1.0
CA A:ALA699 4.2 17.4 1.0
O A:HOH1411 4.3 26.7 1.0
CB A:ASN700 4.3 21.1 1.0
N A:ALA362 4.3 21.9 1.0
CB A:ILE365 4.3 20.8 1.0
C A:PRO363 4.4 25.5 1.0
ND2 A:ASN700 4.5 23.0 1.0
N A:GLU366 4.5 22.9 1.0
O A:PRO363 4.6 22.7 1.0
CA A:GLU366 4.8 20.4 1.0
CD A:PRO367 4.9 18.6 1.0
CB A:ASP360 4.9 20.1 1.0
N A:GLN364 5.0 21.0 1.0

Magnesium binding site 3 out of 4 in 6ubz

Go back to Magnesium Binding Sites List in 6ubz
Magnesium binding site 3 out of 4 in the Crystal Structure of D678A Goxa Bound to Glycine at pH 5.5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of D678A Goxa Bound to Glycine at pH 5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg901

b:16.1
occ:1.00
O C:ALA362 2.3 14.1 1.0
O C:ALA699 2.3 18.6 1.0
O C:ILE365 2.3 13.9 1.0
OD1 C:ASN700 2.4 14.4 1.0
O C:HOH1210 2.5 20.0 1.0
OD1 C:ASP360 2.7 16.0 1.0
C C:ALA362 3.2 15.5 1.0
C C:ALA699 3.2 14.1 1.0
OD2 C:ASP360 3.4 21.4 1.0
CG C:ASP360 3.4 19.4 1.0
C C:ILE365 3.5 13.2 1.0
CG C:ASN700 3.5 16.4 1.0
CA C:ASN700 3.8 11.0 1.0
N C:ASN700 3.9 12.3 1.0
N C:PRO363 4.0 11.8 1.0
CA C:ALA362 4.1 12.5 1.0
N C:ILE365 4.1 14.0 1.0
CA C:PRO363 4.1 12.6 1.0
CB C:ALA362 4.1 14.2 1.0
CA C:ILE365 4.2 12.4 1.0
CB C:ALA699 4.2 10.7 1.0
CA C:ALA699 4.2 10.5 1.0
N C:ALA362 4.2 12.4 1.0
CB C:ASN700 4.3 14.7 1.0
O C:HOH1475 4.3 22.4 1.0
CB C:ILE365 4.3 14.2 1.0
C C:PRO363 4.3 18.1 1.0
ND2 C:ASN700 4.5 15.0 1.0
N C:GLU366 4.5 14.0 1.0
O C:PRO363 4.6 14.3 1.0
CA C:GLU366 4.8 11.7 1.0
CD C:PRO367 4.8 13.9 1.0
N C:GLN364 4.9 17.8 1.0
CB C:ASP360 4.9 14.2 1.0
O C:ALA576 5.0 22.2 1.0

Magnesium binding site 4 out of 4 in 6ubz

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Magnesium binding site 4 out of 4 in the Crystal Structure of D678A Goxa Bound to Glycine at pH 5.5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of D678A Goxa Bound to Glycine at pH 5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg901

b:22.9
occ:1.00
O D:ILE365 2.3 20.4 1.0
O D:ALA699 2.3 19.4 1.0
O D:ALA362 2.3 20.6 1.0
OD1 D:ASN700 2.4 19.1 1.0
O D:HOH1026 2.5 27.3 1.0
OD1 D:ASP360 2.8 21.8 1.0
C D:ALA699 3.2 19.1 1.0
C D:ALA362 3.3 19.8 1.0
C D:ILE365 3.5 17.4 1.0
OD2 D:ASP360 3.5 26.1 1.0
CG D:ASN700 3.5 24.3 1.0
CG D:ASP360 3.6 23.5 1.0
CA D:ASN700 3.8 20.3 1.0
N D:ASN700 3.9 19.0 1.0
CA D:ALA362 4.1 17.9 1.0
CB D:ALA362 4.1 19.6 1.0
N D:ILE365 4.1 20.3 1.0
N D:PRO363 4.1 18.0 1.0
CA D:ILE365 4.2 20.4 1.0
CA D:PRO363 4.2 23.1 1.0
CB D:ALA699 4.2 15.8 1.0
CA D:ALA699 4.2 14.4 1.0
O D:HOH1323 4.2 31.7 1.0
CB D:ILE365 4.3 20.2 1.0
CB D:ASN700 4.3 18.8 1.0
N D:ALA362 4.3 18.4 1.0
C D:PRO363 4.4 24.3 1.0
ND2 D:ASN700 4.5 21.5 1.0
N D:GLU366 4.5 18.4 1.0
O D:PRO363 4.6 27.4 1.0
CA D:GLU366 4.7 19.2 1.0
CD D:PRO367 4.8 17.9 1.0
N D:GLN364 4.9 20.8 1.0
O D:ALA576 5.0 28.9 1.0

Reference:

K.J.Mamounis, D.Avalos, E.T.Yukl, V.L.Davidson. Kinetic and Structural Evidence That Asp-678 Plays Multiple Roles in Catalysis By the Quinoprotein Glycine Oxidase. J.Biol.Chem. V. 294 17463 2019.
ISSN: ESSN 1083-351X
PubMed: 31615898
DOI: 10.1074/JBC.RA119.011255
Page generated: Tue Oct 1 20:54:07 2024

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