Magnesium in PDB 8upq: Campylobacter Jejuni Ketol-Acid Reductoisomerase in Complex with 2,3- Dihydroxy-3-Isovalerate.

Protein crystallography data

The structure of Campylobacter Jejuni Ketol-Acid Reductoisomerase in Complex with 2,3- Dihydroxy-3-Isovalerate., PDB code: 8upq was solved by X.Lin, T.Lonhienne, L.W.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.19 / 2.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 179.822, 134.127, 126.862, 90, 134.83, 90
R / Rfree (%) 19.3 / 24

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Campylobacter Jejuni Ketol-Acid Reductoisomerase in Complex with 2,3- Dihydroxy-3-Isovalerate. (pdb code 8upq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Campylobacter Jejuni Ketol-Acid Reductoisomerase in Complex with 2,3- Dihydroxy-3-Isovalerate., PDB code: 8upq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8upq

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Magnesium binding site 1 out of 6 in the Campylobacter Jejuni Ketol-Acid Reductoisomerase in Complex with 2,3- Dihydroxy-3-Isovalerate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Campylobacter Jejuni Ketol-Acid Reductoisomerase in Complex with 2,3- Dihydroxy-3-Isovalerate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:27.4
occ:1.00
 O B:HOH587 2.0 26.2 1.0
OE2 A:GLU196 2.0 30.7 1.0
O07 B:XAI402 2.1 25.4 1.0
O A:HOH515 2.1 27.9 1.0
O08 B:XAI402 2.1 33.9 1.0
OD2 A:ASP192 2.2 27.8 1.0
C05 B:XAI402 2.8 26.6 1.0
C04 B:XAI402 2.9 32.0 1.0
CG A:ASP192 3.2 27.5 1.0
CD A:GLU196 3.2 27.2 1.0
OD1 A:ASP192 3.5 26.8 1.0
O A:HOH523 3.9 36.0 1.0
OE1 A:GLU196 3.9 24.1 1.0
O06 B:XAI402 4.0 31.2 1.0
NE2 A:HIS109 4.1 31.1 1.0
CE1 A:HIS109 4.1 31.7 1.0
C02 B:XAI402 4.2 29.9 1.0
CD2 A:HIS109 4.2 28.6 1.0
OG B:SER253 4.3 22.8 1.0
CG A:GLU196 4.3 27.9 1.0
ND1 A:HIS109 4.4 30.6 1.0
CG A:HIS109 4.4 29.0 1.0
CB A:ASP192 4.5 28.7 1.0
C03 B:XAI402 4.5 24.7 1.0
O B:HOH535 4.5 29.1 1.0
O09 B:XAI402 4.7 33.7 1.0
CB B:ALA256 5.0 18.1 1.0

Magnesium binding site 2 out of 6 in 8upq

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Magnesium binding site 2 out of 6 in the Campylobacter Jejuni Ketol-Acid Reductoisomerase in Complex with 2,3- Dihydroxy-3-Isovalerate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Campylobacter Jejuni Ketol-Acid Reductoisomerase in Complex with 2,3- Dihydroxy-3-Isovalerate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:21.9
occ:1.00
 OE2 B:GLU196 1.8 22.3 1.0
O07 A:XAI402 2.0 23.9 1.0
O08 A:XAI402 2.1 21.3 1.0
O B:HOH605 2.1 20.3 1.0
OD2 B:ASP192 2.2 19.9 1.0
O B:HOH513 2.3 22.7 1.0
C05 A:XAI402 2.8 20.6 1.0
C04 A:XAI402 2.9 21.7 1.0
CD B:GLU196 3.0 22.4 1.0
CG B:ASP192 3.2 20.9 1.0
O B:HOH533 3.6 27.7 1.0
OD1 B:ASP192 3.6 22.9 1.0
OE1 B:GLU196 3.8 20.6 1.0
O06 A:XAI402 4.0 22.2 1.0
CE1 B:HIS109 4.0 19.9 1.0
CG B:GLU196 4.1 19.5 1.0
NE2 B:HIS109 4.1 18.6 1.0
C02 A:XAI402 4.1 21.2 1.0
O B:HOH565 4.1 22.7 1.0
O B:HOH541 4.2 23.8 1.0
ND1 B:HIS109 4.3 26.6 1.0
OG A:SER253 4.3 20.4 1.0
C03 A:XAI402 4.3 21.3 1.0
O A:HOH517 4.3 20.0 1.0
CD2 B:HIS109 4.4 17.1 1.0
CB B:ASP192 4.5 14.9 1.0
O09 A:XAI402 4.5 18.9 1.0
CG B:HIS109 4.5 18.6 1.0
CB A:ALA256 4.6 19.1 1.0
O B:ASP192 4.9 21.7 1.0

Magnesium binding site 3 out of 6 in 8upq

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Magnesium binding site 3 out of 6 in the Campylobacter Jejuni Ketol-Acid Reductoisomerase in Complex with 2,3- Dihydroxy-3-Isovalerate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Campylobacter Jejuni Ketol-Acid Reductoisomerase in Complex with 2,3- Dihydroxy-3-Isovalerate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:24.7
occ:1.00
 OD2 C:ASP192 2.0 18.9 1.0
O C:HOH507 2.0 27.5 1.0
O08 D:XAI402 2.1 20.6 1.0
O C:HOH582 2.2 22.3 1.0
O06 D:XAI402 2.3 21.2 1.0
OE1 C:GLU196 2.3 23.2 1.0
C05 D:XAI402 3.0 24.1 1.0
C04 D:XAI402 3.1 24.2 1.0
CG C:ASP192 3.1 20.3 1.0
CD C:GLU196 3.2 21.9 1.0
OE2 C:GLU196 3.4 23.2 1.0
OD1 C:ASP192 3.7 20.6 1.0
O C:HOH523 3.7 31.0 1.0
CE1 C:HIS109 4.0 21.7 1.0
NE2 C:HIS109 4.1 21.5 1.0
O D:HOH545 4.2 20.0 1.0
OG D:SER253 4.2 20.5 1.0
O C:HOH565 4.2 22.9 1.0
O07 D:XAI402 4.2 26.8 1.0
ND1 C:HIS109 4.3 27.5 1.0
C02 D:XAI402 4.3 24.2 1.0
CB C:ASP192 4.3 19.2 1.0
CB D:ALA256 4.4 19.6 1.0
C03 D:XAI402 4.5 20.0 1.0
CD2 C:HIS109 4.5 19.9 1.0
O C:HOH547 4.6 22.5 1.0
CG C:GLU196 4.6 18.1 1.0
CG C:HIS109 4.6 23.9 1.0
O C:ASP192 4.6 22.7 1.0
C C:ASP192 4.7 22.8 1.0
O09 D:XAI402 4.8 20.1 1.0
N D:ALA256 5.0 21.1 1.0

Magnesium binding site 4 out of 6 in 8upq

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Magnesium binding site 4 out of 6 in the Campylobacter Jejuni Ketol-Acid Reductoisomerase in Complex with 2,3- Dihydroxy-3-Isovalerate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Campylobacter Jejuni Ketol-Acid Reductoisomerase in Complex with 2,3- Dihydroxy-3-Isovalerate. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:28.7
occ:1.00
 OD2 F:ASP192 1.9 24.7 1.0
O08 F:XAI402 2.0 29.0 1.0
O F:HOH516 2.0 25.0 1.0
O F:HOH558 2.1 28.0 1.0
O06 F:XAI402 2.2 24.1 1.0
OE1 F:GLU196 2.3 24.4 1.0
C05 F:XAI402 3.0 25.1 1.0
CG F:ASP192 3.0 25.5 1.0
C04 F:XAI402 3.0 28.8 1.0
CD F:GLU196 3.2 23.1 1.0
OD1 F:ASP192 3.4 27.2 1.0
OE2 F:GLU196 3.4 25.6 1.0
C02 F:XAI402 4.1 30.6 1.0
O07 F:XAI402 4.2 25.8 1.0
O F:HOH505 4.2 30.5 1.0
O F:HOH515 4.3 28.9 1.0
CE1 F:HIS109 4.3 28.6 1.0
CB F:ASP192 4.3 23.7 1.0
NE2 F:HIS109 4.3 27.7 1.0
C03 F:XAI402 4.3 25.5 1.0
O F:ASP192 4.4 27.5 1.0
O09 F:XAI402 4.4 32.4 1.0
O F:HOH524 4.5 30.3 1.0
ND1 F:HIS109 4.5 27.6 1.0
CG F:GLU196 4.6 23.2 1.0
CD2 F:HIS109 4.6 27.3 1.0
C F:ASP192 4.7 25.0 1.0
CG F:HIS109 4.7 28.8 1.0
CB F:GLU196 5.0 23.5 1.0

Magnesium binding site 5 out of 6 in 8upq

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Magnesium binding site 5 out of 6 in the Campylobacter Jejuni Ketol-Acid Reductoisomerase in Complex with 2,3- Dihydroxy-3-Isovalerate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Campylobacter Jejuni Ketol-Acid Reductoisomerase in Complex with 2,3- Dihydroxy-3-Isovalerate. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:27.7
occ:1.00
 O08 E:XAI402 1.9 28.1 1.0
O06 E:XAI402 2.0 32.6 1.0
O E:HOH521 2.0 29.8 1.0
O E:HOH567 2.0 33.4 1.0
OD1 E:ASP192 2.1 24.6 1.0
OE1 E:GLU196 2.5 26.2 1.0
C05 E:XAI402 2.7 27.3 1.0
C04 E:XAI402 2.8 30.6 1.0
CG E:ASP192 3.2 28.4 1.0
CD E:GLU196 3.4 24.6 1.0
OD2 E:ASP192 3.6 28.4 1.0
OE2 E:GLU196 3.6 25.3 1.0
O E:HOH514 3.6 23.1 1.0
O07 E:XAI402 3.9 28.1 1.0
C02 E:XAI402 4.0 34.7 1.0
C01 E:XAI402 4.1 33.6 1.0
NE2 E:HIS109 4.4 27.6 1.0
O09 E:XAI402 4.4 30.2 1.0
CE1 E:HIS109 4.5 28.7 1.0
CB E:ASP192 4.5 25.5 1.0
CD2 E:HIS109 4.5 31.3 1.0
ND1 E:HIS109 4.6 32.6 1.0
O E:ASP192 4.6 27.0 1.0
CG E:HIS109 4.7 30.1 1.0
CG E:GLU196 4.8 21.6 1.0
C E:ASP192 4.9 29.6 1.0

Magnesium binding site 6 out of 6 in 8upq

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Magnesium binding site 6 out of 6 in the Campylobacter Jejuni Ketol-Acid Reductoisomerase in Complex with 2,3- Dihydroxy-3-Isovalerate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Campylobacter Jejuni Ketol-Acid Reductoisomerase in Complex with 2,3- Dihydroxy-3-Isovalerate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:24.5
occ:1.00
 O06 C:XAI402 1.9 26.3 1.0
O D:HOH525 2.0 27.4 1.0
O08 C:XAI402 2.1 28.9 1.0
O D:HOH529 2.1 23.9 1.0
OD1 D:ASP192 2.1 30.3 1.0
OE1 D:GLU196 2.2 22.7 1.0
C05 C:XAI402 2.7 23.3 1.0
C04 C:XAI402 2.9 25.6 1.0
CG D:ASP192 3.0 29.8 1.0
OD2 D:ASP192 3.2 31.9 1.0
CD D:GLU196 3.3 23.2 1.0
OE2 D:GLU196 3.6 24.1 1.0
O D:HOH558 3.8 33.1 1.0
O07 C:XAI402 3.9 22.2 1.0
C02 C:XAI402 4.0 29.9 1.0
C03 C:XAI402 4.1 22.9 1.0
O D:HOH544 4.1 20.1 1.0
OG C:SER253 4.3 22.7 1.0
O D:ASP192 4.3 25.8 1.0
CB D:ASP192 4.4 28.2 1.0
CB C:ALA256 4.4 18.0 1.0
O09 C:XAI402 4.5 34.1 1.0
CG D:GLU196 4.6 24.2 1.0
CE1 D:HIS109 4.6 29.8 1.0
NE2 D:HIS109 4.6 28.7 1.0
C D:ASP192 4.7 24.6 1.0
ND1 D:HIS109 4.9 28.9 1.0
CB D:GLU196 4.9 18.4 1.0
CD2 D:HIS109 5.0 27.7 1.0

Reference:

X.Lin, T.Lonhienne, Y.Lv, J.Kurz, R.Mcgeary, G.Schenk, L.W.Guddat. Mapping of the Reaction Trajectory Catalyzed By Class I Ketol-Acid Reductoisomerase Acs Catalysis 2024.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.4C00958
Page generated: Fri Oct 4 21:25:37 2024

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