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Magnesium in PDB 6nb2: Crystal Structure of Enolase From Legionella Pneumophila Bound to 2- Phosphoglyceric Acid and Magnesium

Enzymatic activity of Crystal Structure of Enolase From Legionella Pneumophila Bound to 2- Phosphoglyceric Acid and Magnesium

All present enzymatic activity of Crystal Structure of Enolase From Legionella Pneumophila Bound to 2- Phosphoglyceric Acid and Magnesium:
4.2.1.11;

Protein crystallography data

The structure of Crystal Structure of Enolase From Legionella Pneumophila Bound to 2- Phosphoglyceric Acid and Magnesium, PDB code: 6nb2 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) 45.12 / 1.85
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 116.450, 116.450, 142.780, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 17.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Enolase From Legionella Pneumophila Bound to 2- Phosphoglyceric Acid and Magnesium (pdb code 6nb2). 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 2- Phosphoglyceric Acid and Magnesium, PDB code: 6nb2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6nb2

Go back to Magnesium Binding Sites List in 6nb2
Magnesium binding site 1 out of 4 in the Crystal Structure of Enolase From Legionella Pneumophila Bound to 2- Phosphoglyceric Acid 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 2- Phosphoglyceric Acid and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:18.5
occ:1.00
 OD2 A:ASP311 2.1 20.1 1.0
OE2 A:GLU284 2.1 24.9 1.0
O A:HOH636 2.2 19.6 1.0
OD2 A:ASP241 2.2 22.4 1.0
O1 A:2PG501 2.2 20.2 1.0
O2 A:2PG501 2.3 20.9 1.0
C1 A:2PG501 2.6 20.0 1.0
CG A:ASP241 3.1 25.5 1.0
CG A:ASP311 3.1 23.8 1.0
CD A:GLU284 3.2 22.5 1.0
OD1 A:ASP241 3.3 19.4 1.0
CB A:ASP311 3.6 17.5 1.0
NZ A:LYS387 3.7 19.8 1.0
O A:HOH840 3.7 23.4 1.0
OE1 A:GLU284 4.0 25.3 1.0
CG A:GLU284 4.0 20.4 1.0
MG A:MG503 4.0 25.5 1.0
CD2 A:LEU334 4.0 25.6 1.0
NZ A:LYS336 4.1 28.6 1.0
C2 A:2PG501 4.1 21.6 1.0
OE1 A:GLN162 4.2 24.3 1.0
OD1 A:ASP311 4.2 23.3 1.0
OD2 A:ASP285 4.3 23.9 1.0
CB A:ASP241 4.5 19.1 1.0
OE2 A:GLU163 4.6 22.4 1.0
O A:HOH601 4.6 27.8 1.0
CE A:LYS336 4.8 25.9 1.0
O1P A:2PG501 4.9 21.1 1.0
C3 A:2PG501 4.9 23.4 1.0
CG A:ASP285 5.0 25.1 1.0

Magnesium binding site 2 out of 4 in 6nb2

Go back to Magnesium Binding Sites List in 6nb2
Magnesium binding site 2 out of 4 in the Crystal Structure of Enolase From Legionella Pneumophila Bound to 2- Phosphoglyceric Acid 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 2- Phosphoglyceric Acid and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:25.5
occ:1.00
 O A:SER41 2.1 28.4 1.0
O A:HOH840 2.1 23.4 1.0
O2P A:2PG501 2.2 22.1 1.0
OG A:SER41 2.3 21.5 1.0
O2 A:2PG501 2.4 20.9 1.0
O A:HOH601 2.5 27.8 1.0
CB A:SER41 3.1 20.7 1.0
C A:SER41 3.1 24.9 1.0
P A:2PG501 3.3 20.2 1.0
C1 A:2PG501 3.4 20.0 1.0
CA A:SER41 3.6 19.0 1.0
O1P A:2PG501 3.6 21.1 1.0
NZ A:LYS336 3.6 28.6 1.0
O4P A:2PG501 3.8 20.6 1.0
C2 A:2PG501 3.9 21.6 1.0
OD2 A:ASP311 3.9 20.1 1.0
N A:SER41 4.0 23.5 1.0
MG A:MG502 4.0 18.5 1.0
OD2 A:ASP312 4.0 32.1 1.0
OE1 A:GLN162 4.1 24.3 1.0
O A:HOH636 4.2 19.6 1.0
NE2 A:GLN162 4.3 16.0 1.0
N A:THR42 4.3 25.5 1.0
O1 A:2PG501 4.4 20.2 1.0
NH2 A:ARG365 4.4 23.8 1.0
OD1 A:ASP312 4.4 37.1 1.0
O A:HOH604 4.4 42.0 1.0
O3P A:2PG501 4.5 19.6 1.0
CD A:GLN162 4.7 18.4 1.0
CG A:ASP312 4.7 30.2 1.0
CA A:THR42 4.8 23.6 1.0
CG A:ASP311 4.9 23.8 1.0

Magnesium binding site 3 out of 4 in 6nb2

Go back to Magnesium Binding Sites List in 6nb2
Magnesium binding site 3 out of 4 in the Crystal Structure of Enolase From Legionella Pneumophila Bound to 2- Phosphoglyceric Acid 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 2- Phosphoglyceric Acid and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:17.6
occ:1.00
 OE2 B:GLU284 2.0 21.2 1.0
OD2 B:ASP311 2.1 18.2 1.0
O2 B:2PG502 2.1 18.9 1.0
OD1 B:ASP241 2.1 22.2 1.0
O B:HOH676 2.3 20.1 1.0
O1 B:2PG502 2.3 20.7 1.0
C1 B:2PG502 2.5 20.4 1.0
CG B:ASP241 3.1 22.7 1.0
CD B:GLU284 3.1 22.5 1.0
CG B:ASP311 3.1 25.0 1.0
OD2 B:ASP241 3.3 18.3 1.0
CB B:ASP311 3.6 18.2 1.0
NZ B:LYS387 3.6 19.1 1.0
O B:HOH863 3.7 22.3 1.0
OE1 B:GLU284 3.9 21.2 1.0
CG B:GLU284 4.0 20.5 1.0
MG B:MG504 4.0 22.5 1.0
NZ B:LYS336 4.0 27.5 1.0
CD2 B:LEU334 4.1 19.8 1.0
C2 B:2PG502 4.1 20.5 1.0
NE2 B:GLN162 4.1 18.3 1.0
OD1 B:ASP311 4.2 22.7 1.0
OD2 B:ASP285 4.3 23.7 1.0
CB B:ASP241 4.4 19.4 1.0
OE2 B:GLU163 4.5 24.6 1.0
O B:HOH603 4.7 26.6 1.0
O1P B:2PG502 4.8 17.8 1.0
CE B:LYS336 4.8 22.2 1.0
C3 B:2PG502 4.9 22.7 1.0
CE B:LYS387 5.0 17.4 1.0
CG B:ASP285 5.0 22.8 1.0

Magnesium binding site 4 out of 4 in 6nb2

Go back to Magnesium Binding Sites List in 6nb2
Magnesium binding site 4 out of 4 in the Crystal Structure of Enolase From Legionella Pneumophila Bound to 2- Phosphoglyceric Acid 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 2- Phosphoglyceric Acid and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:22.5
occ:1.00
 O B:SER41 2.1 25.4 1.0
O B:HOH863 2.2 22.3 1.0
O3P B:2PG502 2.2 19.4 1.0
O1 B:2PG502 2.3 20.7 1.0
OG B:SER41 2.3 18.4 1.0
O B:HOH603 2.5 26.6 1.0
C B:SER41 3.1 29.1 1.0
CB B:SER41 3.1 16.9 1.0
P B:2PG502 3.3 18.1 1.0
C1 B:2PG502 3.3 20.4 1.0
O1P B:2PG502 3.6 17.8 1.0
CA B:SER41 3.6 24.7 1.0
NZ B:LYS336 3.7 27.5 1.0
OD2 B:ASP311 3.8 18.2 1.0
C2 B:2PG502 3.8 20.5 1.0
O2P B:2PG502 3.9 21.5 1.0
MG B:MG503 4.0 17.6 1.0
N B:SER41 4.0 20.4 1.0
OD1 B:ASP312 4.1 33.0 1.0
NE2 B:GLN162 4.1 18.3 1.0
O B:HOH676 4.2 20.1 1.0
OE1 B:GLN162 4.3 20.1 1.0
N B:THR42 4.3 29.9 1.0
O2 B:2PG502 4.3 18.9 1.0
NH2 B:ARG365 4.4 19.6 1.0
O B:HOH601 4.5 42.2 1.0
O4P B:2PG502 4.6 17.9 1.0
OD2 B:ASP312 4.6 37.2 1.0
CD B:GLN162 4.7 20.8 1.0
CG B:ASP312 4.7 26.3 1.0
CA B:THR42 4.8 24.4 1.0
CG B:ASP311 4.8 25.0 1.0

Reference:

D.R.Davies, J.Abendroth, D.D.Lorimer, T.E.Edwards. Crystal Structure of Enolase From Legionella Pneumophila Bound to 2-Phosphoglyceric Acid and Magnesium To Be Published.
Page generated: Tue Oct 1 12:37:27 2024

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