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Magnesium in PDB 4xiy: Crystal Structure of Ketol-Acid Reductoisomerase From Azotobacter

Enzymatic activity of Crystal Structure of Ketol-Acid Reductoisomerase From Azotobacter

All present enzymatic activity of Crystal Structure of Ketol-Acid Reductoisomerase From Azotobacter:
1.1.1.86;

Protein crystallography data

The structure of Crystal Structure of Ketol-Acid Reductoisomerase From Azotobacter, PDB code: 4xiy was solved by T.Spatzal, J.K.B.Cahn, J.A.Wiig, O.Einsle, Y.Hu, M.W.Ribbe, F.H.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.79 / 2.50
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 185.050, 185.050, 185.050, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.4

Other elements in 4xiy:

The structure of Crystal Structure of Ketol-Acid Reductoisomerase From Azotobacter also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Ketol-Acid Reductoisomerase From Azotobacter (pdb code 4xiy). 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 Ketol-Acid Reductoisomerase From Azotobacter, PDB code: 4xiy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4xiy

Go back to Magnesium Binding Sites List in 4xiy
Magnesium binding site 1 out of 4 in the Crystal Structure of Ketol-Acid Reductoisomerase From Azotobacter


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 Ketol-Acid Reductoisomerase From Azotobacter within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:54.8
occ:1.00
 OD1 B:ASP190 1.9 41.4 1.0
O B:HOH507 2.1 61.6 1.0
OE1 A:GLU226 2.2 59.2 1.0
OE1 A:GLU230 2.4 61.3 1.0
O B:HOH506 2.4 53.1 1.0
CD A:GLU226 3.1 60.0 1.0
CG B:ASP190 3.2 36.1 1.0
CD A:GLU230 3.2 61.2 1.0
OE2 A:GLU226 3.3 79.7 1.0
OE2 A:GLU230 3.3 70.1 1.0
O B:HOH501 3.5 49.8 1.0
O B:HOH508 3.6 39.8 1.0
OD2 B:ASP190 4.0 40.1 1.0
CB B:ASP190 4.0 31.3 1.0
NZ B:LYS130 4.1 75.7 1.0
CA B:ASP190 4.3 30.8 1.0
CG A:GLU226 4.5 52.1 1.0
CG A:GLU230 4.7 51.1 1.0
FE B:FE402 4.8 56.7 1.0
O B:ASP190 4.9 27.2 1.0

Magnesium binding site 2 out of 4 in 4xiy

Go back to Magnesium Binding Sites List in 4xiy
Magnesium binding site 2 out of 4 in the Crystal Structure of Ketol-Acid Reductoisomerase From Azotobacter


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 Ketol-Acid Reductoisomerase From Azotobacter within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:56.0
occ:1.00
 OD1 A:ASP190 2.2 44.8 1.0
OE1 B:GLU230 2.6 86.3 1.0
OE2 B:GLU226 2.6 59.9 1.0
OE1 B:GLU226 3.1 59.0 1.0
O A:HOH503 3.2 43.8 1.0
CD B:GLU226 3.2 50.1 1.0
CG A:ASP190 3.5 36.1 1.0
CD B:GLU230 3.6 71.0 1.0
OE2 B:GLU230 3.9 66.3 1.0
NZ A:LYS130 4.0 69.1 1.0
OD2 A:ASP190 4.2 37.8 1.0
CB A:ASP190 4.5 32.6 1.0
CG B:GLU226 4.7 41.4 1.0
CG B:GLU230 4.8 58.0 1.0

Magnesium binding site 3 out of 4 in 4xiy

Go back to Magnesium Binding Sites List in 4xiy
Magnesium binding site 3 out of 4 in the Crystal Structure of Ketol-Acid Reductoisomerase From Azotobacter


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 Ketol-Acid Reductoisomerase From Azotobacter within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:54.4
occ:1.00
 OE2 C:GLU230 2.2 71.2 1.0
O D:HOH509 2.2 55.4 1.0
OD1 D:ASP190 2.2 45.4 1.0
OE2 C:GLU226 2.4 53.2 1.0
O C:HOH506 2.4 48.4 1.0
OE1 C:GLU226 2.7 64.8 1.0
CD C:GLU226 2.9 51.7 1.0
CD C:GLU230 3.0 69.9 1.0
O D:HOH503 3.2 44.2 1.0
OE1 C:GLU230 3.2 71.1 1.0
CG D:ASP190 3.5 34.6 1.0
NZ D:LYS130 4.1 79.2 1.0
OD2 D:ASP190 4.3 35.0 1.0
CB D:ASP190 4.4 28.1 1.0
CG C:GLU226 4.4 45.4 1.0
CG C:GLU230 4.5 55.3 1.0
FE D:FE402 4.6 59.8 1.0
CA D:ASP190 4.6 26.8 1.0
CD2 D:LEU198 4.9 26.7 1.0
O D:ASP190 4.9 24.7 1.0
O D:HOH508 5.0 48.2 1.0

Magnesium binding site 4 out of 4 in 4xiy

Go back to Magnesium Binding Sites List in 4xiy
Magnesium binding site 4 out of 4 in the Crystal Structure of Ketol-Acid Reductoisomerase From Azotobacter


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 Ketol-Acid Reductoisomerase From Azotobacter within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:58.5
occ:1.00
 OD1 C:ASP190 2.1 56.4 1.0
OE1 D:GLU230 2.6 87.3 1.0
OE2 D:GLU226 2.8 53.1 1.0
OE1 D:GLU226 3.2 51.9 1.0
O C:HOH501 3.3 41.8 1.0
CG C:ASP190 3.3 43.2 1.0
CD D:GLU226 3.4 45.7 1.0
CD D:GLU230 3.5 79.6 1.0
OE2 D:GLU230 3.9 86.6 1.0
OD2 C:ASP190 4.1 47.4 1.0
NZ C:LYS130 4.2 60.3 1.0
CB C:ASP190 4.3 36.8 1.0
FE C:FE401 4.4 74.2 1.0
CG D:GLU230 4.5 65.3 1.0
CA C:ASP190 4.7 31.5 1.0
CG D:GLU226 4.9 38.8 1.0

Reference:

J.K.Cahn, S.Brinkmann-Chen, T.Spatzal, J.A.Wiig, A.R.Buller, O.Einsle, Y.Hu, M.W.Ribbe, F.H.Arnold. Cofactor Specificity Motifs and the Induced Fit Mechanism in Class I Ketol-Acid Reductoisomerases. Biochem.J. 2015.
ISSN: ESSN 1470-8728
PubMed: 25849365
DOI: 10.1042/BJ20150183
Page generated: Mon Dec 14 19:46:45 2020

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