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

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

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

Protein crystallography data

The structure of Crystal Structure of Providencia Alcalifaciens 3-Dehydroquinate Synthase (Dhqs) in Complex with MG2+ and Nad, PDB code: 6lla 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) 143.46 / 1.88
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.390, 59.920, 143.800, 90.00, 93.95, 90.00
R / Rfree (%) 17.3 / 23.8

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 6lla

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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+ and Nad


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+ and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:20.3
occ:1.00
 O A:HOH667 2.1 23.7 1.0
OE1 A:GLU184 2.1 26.8 1.0
O A:HOH585 2.2 22.7 1.0
NE2 A:HIS265 2.2 19.2 1.0
NE2 A:HIS248 2.2 22.9 1.0
O A:HOH552 2.3 21.7 1.0
CD A:GLU184 3.1 25.1 1.0
CD2 A:HIS248 3.1 18.6 1.0
CD2 A:HIS265 3.1 20.9 1.0
CE1 A:HIS265 3.3 26.2 1.0
CE1 A:HIS248 3.3 24.1 1.0
OE2 A:GLU184 3.6 27.3 1.0
OD2 A:ASP136 3.7 25.9 1.0
O A:HOH665 4.2 31.6 1.0
CG A:GLU184 4.2 21.8 1.0
O A:HOH746 4.2 24.8 1.0
CG A:HIS265 4.3 20.7 1.0
CG A:HIS248 4.3 19.5 1.0
ND1 A:HIS265 4.4 23.1 1.0
ND1 A:HIS248 4.4 23.6 1.0
CG2 A:VAL269 4.5 26.5 1.0
NZ A:LYS187 4.6 20.6 1.0
O A:HOH787 4.7 63.0 1.0
O A:HOH621 4.9 51.6 1.0
CG A:ASP136 4.9 28.3 1.0

Magnesium binding site 2 out of 4 in 6lla

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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+ and Nad


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+ and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:21.8
occ:1.00
 OE2 B:GLU184 2.1 24.6 1.0
O B:HOH548 2.1 21.8 1.0
O B:HOH586 2.2 18.1 1.0
O B:HOH674 2.2 19.1 1.0
NE2 B:HIS265 2.3 19.6 1.0
NE2 B:HIS248 2.3 22.5 1.0
CD2 B:HIS265 3.1 18.5 1.0
CD B:GLU184 3.1 22.3 1.0
CD2 B:HIS248 3.2 20.9 1.0
CE1 B:HIS265 3.3 23.6 1.0
CE1 B:HIS248 3.4 18.6 1.0
OD2 B:ASP136 3.6 27.1 1.0
OE1 B:GLU184 3.6 24.8 1.0
O B:HOH763 4.2 29.8 1.0
CG B:GLU184 4.2 24.7 1.0
O B:HOH773 4.2 51.8 1.0
O B:HOH714 4.2 29.5 1.0
CG B:HIS265 4.3 21.9 1.0
ND1 B:HIS265 4.4 20.8 1.0
CG B:HIS248 4.4 18.0 1.0
ND1 B:HIS248 4.5 24.4 1.0
CG2 B:VAL269 4.5 25.1 1.0
NZ B:LYS187 4.6 19.7 1.0
CG B:ASP136 4.9 28.4 1.0

Magnesium binding site 3 out of 4 in 6lla

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


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+ and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:41.2
occ:1.00
 O C:HOH522 2.0 38.0 1.0
O C:HOH576 2.1 34.9 1.0
OE1 C:GLU184 2.1 44.6 1.0
NE2 C:HIS248 2.1 41.1 1.0
O C:HOH601 2.2 34.6 1.0
NE2 C:HIS265 2.4 38.6 1.0
CD C:GLU184 3.1 49.4 1.0
CD2 C:HIS248 3.1 40.9 1.0
CE1 C:HIS248 3.1 44.2 1.0
CD2 C:HIS265 3.3 41.6 1.0
CE1 C:HIS265 3.3 47.0 1.0
OE2 C:GLU184 3.5 49.1 1.0
OD2 C:ASP136 3.7 36.2 1.0
CG C:GLU184 4.2 34.7 1.0
ND1 C:HIS248 4.3 42.7 1.0
CG C:HIS248 4.3 42.4 1.0
O C:HOH638 4.4 30.8 1.0
CG C:HIS265 4.5 44.1 1.0
ND1 C:HIS265 4.5 42.0 1.0
NZ C:LYS187 4.5 38.4 1.0
CG2 C:VAL269 4.5 40.2 1.0
CG C:ASP136 5.0 34.4 1.0

Magnesium binding site 4 out of 4 in 6lla

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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+ and Nad


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+ and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:28.5
occ:1.00
 O D:HOH524 2.0 32.2 1.0
OE2 D:GLU184 2.0 29.8 1.0
O D:HOH606 2.1 31.6 1.0
CE1 D:HIS248 2.1 31.4 1.0
O D:HOH541 2.2 33.6 1.0
NE2 D:HIS265 2.3 26.9 1.0
CD D:GLU184 3.0 39.0 1.0
ND1 D:HIS248 3.0 40.5 1.0
NE2 D:HIS248 3.1 33.1 1.0
CD2 D:HIS265 3.2 27.3 1.0
CE1 D:HIS265 3.3 33.0 1.0
OE1 D:GLU184 3.5 33.1 1.0
O D:HOH617 3.6 53.0 1.0
OD2 D:ASP136 3.7 39.3 1.0
O D:HOH663 4.1 47.6 1.0
CG D:GLU184 4.2 36.2 1.0
CG D:HIS248 4.3 37.1 1.0
CD2 D:HIS248 4.3 31.3 1.0
CG2 D:VAL269 4.3 29.9 1.0
CG D:HIS265 4.4 29.6 1.0
ND1 D:HIS265 4.4 29.0 1.0
O D:HOH669 4.4 32.1 1.0
NZ D:LYS187 4.5 31.4 1.0
CG D:ASP136 5.0 36.0 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: Mon Dec 14 23:13:33 2020

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