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Magnesium in PDB 6lk2: Crystal Structure of Providencia Alcalifaciens 3-Dehydroquinate Synthase (Dhqs) in Complex with MG2+, Nad and Chlorogenic Acid

Enzymatic activity of Crystal Structure of Providencia Alcalifaciens 3-Dehydroquinate Synthase (Dhqs) in Complex with MG2+, Nad and Chlorogenic Acid

All present enzymatic activity of Crystal Structure of Providencia Alcalifaciens 3-Dehydroquinate Synthase (Dhqs) in Complex with MG2+, Nad and Chlorogenic Acid:
4.2.3.4;

Protein crystallography data

The structure of Crystal Structure of Providencia Alcalifaciens 3-Dehydroquinate Synthase (Dhqs) in Complex with MG2+, Nad and Chlorogenic Acid, PDB code: 6lk2 was solved by N.Neetu, M.Katiki, P.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.59 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.639, 60.825, 143.069, 90.00, 93.75, 90.00
R / Rfree (%) 20.5 / 25.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Providencia Alcalifaciens 3-Dehydroquinate Synthase (Dhqs) in Complex with MG2+, Nad and Chlorogenic Acid (pdb code 6lk2). 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 Providencia Alcalifaciens 3-Dehydroquinate Synthase (Dhqs) in Complex with MG2+, Nad and Chlorogenic Acid, PDB code: 6lk2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6lk2

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Magnesium binding site 1 out of 4 in the Crystal Structure of Providencia Alcalifaciens 3-Dehydroquinate Synthase (Dhqs) in Complex with MG2+, Nad and Chlorogenic Acid


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 Providencia Alcalifaciens 3-Dehydroquinate Synthase (Dhqs) in Complex with MG2+, Nad and Chlorogenic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:36.3
occ:1.00
 OE1 A:GLU184 2.1 43.3 1.0
NE2 A:HIS248 2.1 42.7 1.0
O A:HOH532 2.3 41.2 1.0
NE2 A:HIS265 2.3 42.9 1.0
OAH A:7LH403 2.3 47.6 1.0
OAJ A:7LH403 2.3 53.5 1.0
CAG A:7LH403 3.0 66.3 1.0
CD A:GLU184 3.0 35.8 1.0
CE1 A:HIS248 3.1 34.3 1.0
CD2 A:HIS248 3.1 44.2 1.0
CAI A:7LH403 3.2 64.0 1.0
CD2 A:HIS265 3.2 38.5 1.0
CE1 A:HIS265 3.3 37.8 1.0
OE2 A:GLU184 3.5 40.5 1.0
OD2 A:ASP136 3.9 41.6 1.0
ND1 A:HIS248 4.2 42.7 1.0
CG A:GLU184 4.2 37.3 1.0
CG A:HIS248 4.3 41.3 1.0
CG2 A:VAL269 4.3 36.7 1.0
CG A:HIS265 4.4 39.5 1.0
O A:HOH519 4.4 46.3 1.0
ND1 A:HIS265 4.4 38.1 1.0
O A:HOH622 4.5 38.8 1.0
CAF A:7LH403 4.5 73.0 1.0
NZ A:LYS187 4.5 38.6 1.0
CAK A:7LH403 4.5 81.9 1.0
OAL A:7LH403 4.6 90.8 1.0

Magnesium binding site 2 out of 4 in 6lk2

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Magnesium binding site 2 out of 4 in the Crystal Structure of Providencia Alcalifaciens 3-Dehydroquinate Synthase (Dhqs) in Complex with MG2+, Nad and Chlorogenic Acid


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 Providencia Alcalifaciens 3-Dehydroquinate Synthase (Dhqs) in Complex with MG2+, Nad and Chlorogenic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:38.2
occ:1.00
 OE1 B:GLU184 2.1 47.6 1.0
OAJ B:7LH403 2.1 63.3 1.0
O B:HOH529 2.1 46.5 1.0
NE2 B:HIS265 2.2 46.1 1.0
NE2 B:HIS248 2.2 42.7 1.0
OAH B:7LH403 2.3 55.0 1.0
CAG B:7LH403 2.9 81.4 1.0
CAI B:7LH403 3.0 75.7 1.0
CD B:GLU184 3.1 40.6 1.0
CD2 B:HIS265 3.1 43.0 1.0
CD2 B:HIS248 3.2 53.2 1.0
CE1 B:HIS248 3.2 40.6 1.0
CE1 B:HIS265 3.2 37.9 1.0
OE2 B:GLU184 3.6 47.3 1.0
OD2 B:ASP136 3.8 48.5 1.0
CG B:GLU184 4.3 44.0 1.0
O B:HOH522 4.3 51.6 1.0
CG B:HIS265 4.3 40.5 1.0
CAK B:7LH403 4.3 87.9 1.0
ND1 B:HIS248 4.3 43.7 1.0
ND1 B:HIS265 4.3 35.9 1.0
CG B:HIS248 4.3 49.1 1.0
CG2 B:VAL269 4.3 35.8 1.0
CAF B:7LH403 4.4 76.7 1.0
OAL B:7LH403 4.5 87.9 1.0
NZ B:LYS187 4.6 37.4 1.0

Magnesium binding site 3 out of 4 in 6lk2

Go back to Magnesium Binding Sites List in 6lk2
Magnesium binding site 3 out of 4 in the Crystal Structure of Providencia Alcalifaciens 3-Dehydroquinate Synthase (Dhqs) in Complex with MG2+, Nad and Chlorogenic Acid


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 Providencia Alcalifaciens 3-Dehydroquinate Synthase (Dhqs) in Complex with MG2+, Nad and Chlorogenic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:75.6
occ:1.00
 O C:HOH505 2.0 67.7 1.0
NE2 C:HIS248 2.1 88.6 1.0
NE2 C:HIS265 2.3 70.9 1.0
OE1 C:GLU184 2.4 79.7 1.0
OAJ C:7LH403 2.8 0.8 1.0
CD2 C:HIS248 3.0 91.7 1.0
CE1 C:HIS248 3.2 90.1 1.0
CD2 C:HIS265 3.3 66.6 1.0
CE1 C:HIS265 3.3 66.0 1.0
CD C:GLU184 3.5 74.9 1.0
OAH C:7LH403 3.6 0.5 1.0
OD2 C:ASP136 3.8 75.3 1.0
CAI C:7LH403 3.9 0.7 1.0
OE2 C:GLU184 4.1 78.2 1.0
CG C:HIS248 4.2 95.1 1.0
CAG C:7LH403 4.3 0.8 1.0
ND1 C:HIS248 4.3 93.5 1.0
CG C:HIS265 4.4 64.7 1.0
ND1 C:HIS265 4.4 62.8 1.0
CG C:GLU184 4.6 70.0 1.0
CG2 C:VAL269 4.8 87.3 1.0

Magnesium binding site 4 out of 4 in 6lk2

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Magnesium binding site 4 out of 4 in the Crystal Structure of Providencia Alcalifaciens 3-Dehydroquinate Synthase (Dhqs) in Complex with MG2+, Nad and Chlorogenic Acid


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 Providencia Alcalifaciens 3-Dehydroquinate Synthase (Dhqs) in Complex with MG2+, Nad and Chlorogenic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:0.2
occ:1.00
 OAJ D:7LH403 1.9 0.9 1.0
O D:HOH501 2.0 0.6 1.0
NE2 D:HIS248 2.1 0.9 1.0
NE2 D:HIS265 2.1 90.7 1.0
OAH D:7LH403 2.5 0.1 1.0
OE1 D:GLU184 2.6 1.0 1.0
CD2 D:HIS248 2.9 0.7 1.0
CAI D:7LH403 2.9 0.7 1.0
OE2 D:GLU184 3.0 0.3 1.0
CD D:GLU184 3.0 0.9 1.0
CE1 D:HIS265 3.1 89.4 1.0
CD2 D:HIS265 3.1 90.7 1.0
CE1 D:HIS248 3.2 0.6 1.0
CAG D:7LH403 3.3 0.7 1.0
OD2 D:ASP136 4.0 98.6 1.0
CG D:HIS248 4.1 0.6 1.0
ND1 D:HIS265 4.2 83.7 1.0
ND1 D:HIS248 4.2 0.7 1.0
CG D:HIS265 4.3 86.7 1.0
CAK D:7LH403 4.3 0.9 1.0
CG D:GLU184 4.4 98.4 1.0
CAF D:7LH403 4.5 0.5 1.0
OAL D:7LH403 4.8 0.3 1.0

Reference:

N.Neetu, M.Katiki, A.Dev, S.Gaur, S.Tomar, P.Kumar. Structural and Biochemical Analyses Reveal That Chlorogenic Acid Inhibits the Shikimate Pathway. J.Bacteriol. V. 202 2020.
ISSN: ESSN 1098-5530
PubMed: 32661075
DOI: 10.1128/JB.00248-20
Page generated: Tue Oct 1 10:27:58 2024

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