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Magnesium in PDB 6nbm: Crystal Structure of Enolase From Legionella Pneumophila Bound to Phosphate and Magnesium

Enzymatic activity of Crystal Structure of Enolase From Legionella Pneumophila Bound to Phosphate and Magnesium

All present enzymatic activity of Crystal Structure of Enolase From Legionella Pneumophila Bound to Phosphate and Magnesium:
4.2.1.11;

Protein crystallography data

The structure of Crystal Structure of Enolase From Legionella Pneumophila Bound to Phosphate and Magnesium, PDB code: 6nbm was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.19 / 1.90
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 116.770, 116.770, 142.770, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 19.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Enolase From Legionella Pneumophila Bound to Phosphate and Magnesium (pdb code 6nbm). 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 Enolase From Legionella Pneumophila Bound to Phosphate and Magnesium, PDB code: 6nbm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6nbm

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Magnesium binding site 1 out of 4 in the Crystal Structure of Enolase From Legionella Pneumophila Bound to Phosphate and Magnesium


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 Enolase From Legionella Pneumophila Bound to Phosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:18.9
occ:1.00
 O A:HOH962 2.0 18.9 1.0
O A:HOH809 2.1 23.2 1.0
OE2 A:GLU292 2.1 24.7 1.0
O A:HOH828 2.1 22.2 1.0
OD2 A:ASP319 2.1 25.8 1.0
OD2 A:ASP249 2.2 24.1 1.0
CG A:ASP249 3.1 24.0 1.0
CG A:ASP319 3.2 28.3 1.0
CD A:GLU292 3.2 27.4 1.0
OD1 A:ASP249 3.3 25.1 1.0
MG A:MG702 3.6 22.0 1.0
NZ A:LYS395 3.6 24.3 1.0
NZ A:LYS344 3.7 29.8 1.0
O A:HOH821 3.8 19.2 1.0
O A:HOH860 3.8 20.4 1.0
CB A:ASP319 3.8 28.0 1.0
NE2 A:GLN170 3.8 21.1 1.0
OE1 A:GLU292 4.0 26.0 1.0
CD2 A:LEU342 4.1 27.5 1.0
CG A:GLU292 4.2 24.1 1.0
OD1 A:ASP319 4.2 23.6 1.0
O3 A:PO4703 4.3 23.4 1.0
OD2 A:ASP293 4.3 29.4 1.0
CB A:ASP249 4.4 23.7 1.0
OE2 A:GLU171 4.5 26.0 1.0
O1 A:PO4703 4.7 24.0 1.0
CE A:LYS344 4.8 23.1 1.0
CD A:GLN170 4.9 21.0 1.0
OG A:SER49 5.0 29.6 1.0

Magnesium binding site 2 out of 4 in 6nbm

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Magnesium binding site 2 out of 4 in the Crystal Structure of Enolase From Legionella Pneumophila Bound to Phosphate and Magnesium


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 Enolase From Legionella Pneumophila Bound to Phosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:22.0
occ:1.00
 O A:HOH962 1.9 18.9 1.0
O1 A:PO4703 2.0 24.0 1.0
O A:HOH860 2.1 20.4 1.0
OG A:SER49 2.1 29.6 1.0
O A:HOH821 2.1 19.2 1.0
O A:SER49 2.2 27.4 1.0
CB A:SER49 3.1 30.7 1.0
C A:SER49 3.1 28.6 1.0
P A:PO4703 3.2 24.9 1.0
O3 A:PO4703 3.4 23.4 1.0
CA A:SER49 3.6 30.9 1.0
MG A:MG701 3.6 18.9 1.0
OD2 A:ASP319 3.7 25.8 1.0
O4 A:PO4703 3.8 24.1 1.0
NZ A:LYS344 3.9 29.8 1.0
O A:HOH828 3.9 22.2 1.0
N A:SER49 4.0 26.4 1.0
NE2 A:GLN170 4.1 21.1 1.0
O A:HOH809 4.1 23.2 1.0
OE1 A:GLN170 4.1 21.9 1.0
OD1 A:ASP320 4.2 29.4 1.0
OD2 A:ASP320 4.3 28.5 1.0
N A:THR50 4.3 25.4 1.0
NH2 A:ARG373 4.3 24.8 1.0
O2 A:PO4703 4.4 24.0 1.0
CD A:GLN170 4.6 21.0 1.0
CG A:ASP320 4.6 31.0 1.0
CG A:ASP319 4.8 28.3 1.0
CA A:THR50 4.8 28.2 1.0

Magnesium binding site 3 out of 4 in 6nbm

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Magnesium binding site 3 out of 4 in the Crystal Structure of Enolase From Legionella Pneumophila Bound to Phosphate and Magnesium


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 Enolase From Legionella Pneumophila Bound to Phosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:19.0
occ:1.00
 O B:HOH805 2.0 18.8 1.0
O B:HOH965 2.0 15.9 1.0
OE2 B:GLU292 2.0 25.7 1.0
OD2 B:ASP319 2.1 27.3 1.0
OD2 B:ASP249 2.2 22.9 1.0
O B:HOH828 2.3 21.9 1.0
CG B:ASP249 3.1 26.3 1.0
CG B:ASP319 3.2 24.9 1.0
CD B:GLU292 3.2 27.9 1.0
OD1 B:ASP249 3.4 24.3 1.0
NZ B:LYS344 3.6 22.7 1.0
NZ B:LYS395 3.6 21.1 1.0
MG B:MG702 3.6 20.1 1.0
CB B:ASP319 3.8 23.8 1.0
NE2 B:GLN170 3.8 22.0 1.0
O B:HOH809 3.8 22.1 1.0
O B:HOH847 3.9 21.5 1.0
OE1 B:GLU292 4.0 25.0 1.0
CD2 B:LEU342 4.1 21.1 1.0
OD1 B:ASP319 4.2 26.3 1.0
O3 B:PO4703 4.2 19.3 1.0
CG B:GLU292 4.3 25.8 1.0
OD2 B:ASP293 4.3 23.4 1.0
CB B:ASP249 4.4 24.9 1.0
OE2 B:GLU171 4.5 22.6 1.0
O4 B:PO4703 4.7 23.9 1.0
CE B:LYS344 4.8 21.1 1.0
O B:HOH808 4.9 21.6 1.0
CD B:GLN170 4.9 19.0 1.0
CE B:LYS395 5.0 19.9 1.0

Magnesium binding site 4 out of 4 in 6nbm

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Magnesium binding site 4 out of 4 in the Crystal Structure of Enolase From Legionella Pneumophila Bound to Phosphate and Magnesium


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 Enolase From Legionella Pneumophila Bound to Phosphate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:20.1
occ:1.00
 O B:HOH965 1.9 15.9 1.0
O B:SER49 2.1 23.6 1.0
O4 B:PO4703 2.1 23.9 1.0
O B:HOH847 2.1 21.5 1.0
OG B:SER49 2.2 20.5 1.0
O B:HOH809 2.2 22.1 1.0
C B:SER49 3.1 26.9 1.0
CB B:SER49 3.1 17.6 1.0
P B:PO4703 3.2 22.3 1.0
O3 B:PO4703 3.4 19.3 1.0
CA B:SER49 3.6 24.5 1.0
OD2 B:ASP319 3.6 27.3 1.0
MG B:MG701 3.6 19.0 1.0
O1 B:PO4703 3.9 23.9 1.0
NZ B:LYS344 3.9 22.7 1.0
O B:HOH828 4.0 21.9 1.0
N B:SER49 4.0 21.8 1.0
NE2 B:GLN170 4.1 22.0 1.0
O B:HOH805 4.1 18.8 1.0
OD1 B:ASP320 4.1 26.0 1.0
OE1 B:GLN170 4.1 22.7 1.0
OD2 B:ASP320 4.2 28.1 1.0
N B:THR50 4.3 25.9 1.0
NH2 B:ARG373 4.3 24.4 1.0
O2 B:PO4703 4.5 21.7 1.0
CG B:ASP320 4.6 29.1 1.0
CD B:GLN170 4.6 19.0 1.0
CG B:ASP319 4.7 24.9 1.0
CA B:THR50 4.8 28.2 1.0

Reference:

D.R.Davies, D.G.Conrady, D.D.Lorimer, T.E.Edwards, P.S.Horanyi. Crystal Structure of Enolase From Legionella Pneumophila Bound to Phosphate and Magnesium To Be Published.
Page generated: Tue Oct 1 12:38:22 2024

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