Atomistry » Magnesium » PDB 6bcr-6bqz » 6bfy
Atomistry »
  Magnesium »
    PDB 6bcr-6bqz »
      6bfy »

Magnesium in PDB 6bfy: Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate

Enzymatic activity of Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate

All present enzymatic activity of Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate:
4.2.1.11;

Protein crystallography data

The structure of Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate, PDB code: 6bfy was solved by H.Erlandsen, D.Wright, J.Krucinska, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.61 / 1.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.940, 142.400, 206.640, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 23.2

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate (pdb code 6bfy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate, PDB code: 6bfy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 6bfy

Go back to Magnesium Binding Sites List in 6bfy
Magnesium binding site 1 out of 12 in the Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate


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 Escherichia Coli with Bound 2- Phosphoglycerate Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:29.9
occ:1.00
 O1 A:2PG501 2.1 18.8 1.0
O4P A:2PG501 2.1 17.5 1.0
OG A:SER41 2.1 21.1 1.0
O A:HOH719 2.1 29.1 1.0
O A:SER41 2.1 23.0 1.0
O A:HOH603 2.3 28.5 1.0
CB A:SER41 3.0 24.4 1.0
C A:SER41 3.1 25.1 1.0
C1 A:2PG501 3.1 22.9 1.0
P A:2PG501 3.2 20.2 1.0
CA A:SER41 3.5 23.1 1.0
O1P A:2PG501 3.6 18.0 1.0
C2 A:2PG501 3.7 19.9 1.0
O2P A:2PG501 3.8 21.2 1.0
OD2 A:ASP316 4.0 26.3 1.0
N A:SER41 4.1 26.4 1.0
OD1 A:ASP317 4.1 36.5 1.0
MG A:MG503 4.1 33.6 1.0
O2 A:2PG501 4.1 23.3 1.0
NZ A:LYS341 4.2 32.3 1.0
OD2 A:ASP317 4.2 28.0 1.0
OE1 A:GLN166 4.3 21.0 1.0
N A:THR42 4.3 25.4 1.0
NE2 A:GLN166 4.3 23.5 1.0
NH2 A:ARG370 4.3 17.9 1.0
O3P A:2PG501 4.5 16.9 1.0
CG A:ASP317 4.5 27.7 1.0
CD A:GLN166 4.8 21.3 1.0
CA A:THR42 4.8 30.4 1.0

Magnesium binding site 2 out of 12 in 6bfy

Go back to Magnesium Binding Sites List in 6bfy
Magnesium binding site 2 out of 12 in the Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate


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 Escherichia Coli with Bound 2- Phosphoglycerate Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:33.6
occ:1.00
 O A:HOH719 2.6 29.1 1.0
OD1 A:ASP245 2.7 22.8 1.0
OD2 A:ASP316 2.9 26.3 1.0
OD2 A:ASP245 3.0 24.4 1.0
OD2 A:ASP290 3.0 20.9 1.0
OE2 A:GLU289 3.2 23.7 1.0
CG A:ASP245 3.3 27.1 1.0
O1 A:2PG501 3.3 18.8 1.0
CB A:ALA247 3.5 24.7 1.0
CA A:ALA247 3.6 21.0 1.0
CG A:ASP290 3.7 21.6 1.0
CB A:ASP290 3.8 18.7 1.0
CG A:ASP316 3.9 24.9 1.0
O2 A:2PG501 4.0 23.3 1.0
N A:ALA247 4.0 20.4 1.0
C1 A:2PG501 4.1 22.9 1.0
MG A:MG502 4.1 29.9 1.0
CB A:ASP316 4.1 22.0 1.0
CD A:GLU289 4.2 22.8 1.0
OD2 A:ASP317 4.2 28.0 1.0
O A:HOH603 4.3 28.5 1.0
NE2 A:GLN166 4.4 23.5 1.0
CG A:GLU289 4.5 19.5 1.0
CG A:ASP317 4.7 27.7 1.0
CB A:ASP245 4.8 20.9 1.0
OD1 A:ASP290 4.9 26.6 1.0
C A:ALA247 4.9 22.2 1.0
OD1 A:ASP317 5.0 36.5 1.0
OG A:SER41 5.0 21.1 1.0

Magnesium binding site 3 out of 12 in 6bfy

Go back to Magnesium Binding Sites List in 6bfy
Magnesium binding site 3 out of 12 in the Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate


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 Escherichia Coli with Bound 2- Phosphoglycerate Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:27.5
occ:1.00
 O2P B:2PG501 2.0 17.4 1.0
O B:SER41 2.0 16.9 1.0
O2 B:2PG501 2.1 18.2 1.0
O B:HOH657 2.1 21.8 1.0
OG B:SER41 2.2 18.8 1.0
O B:HOH624 2.2 24.9 1.0
C B:SER41 3.0 22.8 1.0
CB B:SER41 3.0 25.3 1.0
P B:2PG501 3.1 16.9 1.0
C1 B:2PG501 3.2 19.6 1.0
CA B:SER41 3.5 21.8 1.0
O1P B:2PG501 3.5 16.4 1.0
C2 B:2PG501 3.7 19.9 1.0
O3P B:2PG501 3.8 19.8 1.0
N B:SER41 4.0 21.1 1.0
NZ B:LYS341 4.1 28.5 1.0
OD2 B:ASP316 4.1 19.7 1.0
OD2 B:ASP317 4.1 31.6 1.0
MG B:MG503 4.1 28.2 1.0
O1 B:2PG501 4.2 19.8 1.0
NH2 B:ARG370 4.2 14.1 1.0
OD1 B:ASP317 4.2 28.3 1.0
N B:THR42 4.2 22.9 1.0
NE2 B:GLN166 4.2 19.6 1.0
O4P B:2PG501 4.3 16.9 1.0
OE1 B:GLN166 4.4 18.3 1.0
CG B:ASP317 4.6 25.7 1.0
CA B:THR42 4.7 21.9 1.0
CD B:GLN166 4.7 18.6 1.0

Magnesium binding site 4 out of 12 in 6bfy

Go back to Magnesium Binding Sites List in 6bfy
Magnesium binding site 4 out of 12 in the Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate


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 Escherichia Coli with Bound 2- Phosphoglycerate Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:28.2
occ:1.00
 OD1 B:ASP245 2.7 21.6 1.0
O B:HOH624 2.8 24.9 1.0
OD2 B:ASP316 2.9 19.7 1.0
OD2 B:ASP290 2.9 21.8 1.0
OD2 B:ASP245 3.0 24.9 1.0
OE2 B:GLU289 3.1 19.1 1.0
O2 B:2PG501 3.3 18.2 1.0
CG B:ASP245 3.3 24.6 1.0
CA B:ALA247 3.6 19.7 1.0
CB B:ALA247 3.7 20.8 1.0
CG B:ASP290 3.7 21.9 1.0
CB B:ASP290 3.7 21.0 1.0
CG B:ASP316 3.8 21.9 1.0
O1 B:2PG501 3.9 19.8 1.0
C1 B:2PG501 4.0 19.6 1.0
CB B:ASP316 4.0 23.9 1.0
N B:ALA247 4.0 19.2 1.0
CD B:GLU289 4.1 17.4 1.0
MG B:MG502 4.1 27.5 1.0
OD2 B:ASP317 4.2 31.6 1.0
O B:HOH657 4.2 21.8 1.0
NE2 B:GLN166 4.3 19.6 1.0
O B:HOH612 4.4 25.7 1.0
CG B:GLU289 4.4 19.0 1.0
CG B:ASP317 4.6 25.7 1.0
OD1 B:ASP290 4.8 21.7 1.0
CB B:ASP245 4.9 20.2 1.0
N B:ASP317 4.9 16.8 1.0
OD1 B:ASP317 4.9 28.3 1.0
C B:ALA247 5.0 19.8 1.0

Magnesium binding site 5 out of 12 in 6bfy

Go back to Magnesium Binding Sites List in 6bfy
Magnesium binding site 5 out of 12 in the Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:20.0
occ:1.00
 O C:HOH643 2.0 25.4 1.0
O C:HOH732 2.0 24.0 1.0
O C:SER41 2.1 12.6 1.0
O4P C:2PG501 2.1 16.5 1.0
O2 C:2PG501 2.2 16.5 1.0
OG C:SER41 2.2 22.6 1.0
C C:SER41 3.1 20.4 1.0
CB C:SER41 3.1 22.7 1.0
C1 C:2PG501 3.2 21.5 1.0
P C:2PG501 3.2 15.3 1.0
CA C:SER41 3.5 23.5 1.0
O1P C:2PG501 3.6 15.0 1.0
C2 C:2PG501 3.8 17.7 1.0
O3P C:2PG501 3.8 17.9 1.0
OD2 C:ASP316 3.9 22.9 1.0
OD1 C:ASP317 4.0 24.1 1.0
N C:SER41 4.1 21.1 1.0
NZ C:LYS341 4.1 26.8 1.0
OD2 C:ASP317 4.1 29.6 1.0
O1 C:2PG501 4.1 21.0 1.0
NH2 C:ARG370 4.2 17.0 1.0
MG C:MG503 4.2 27.1 1.0
N C:THR42 4.2 21.1 1.0
NE2 C:GLN166 4.3 21.0 1.0
OE1 C:GLN166 4.4 21.2 1.0
O2P C:2PG501 4.5 14.4 1.0
CG C:ASP317 4.5 22.0 1.0
CA C:THR42 4.7 24.7 1.0
CD C:GLN166 4.8 20.4 1.0
O C:HOH654 4.9 37.0 1.0
CG C:ASP316 4.9 19.5 1.0

Magnesium binding site 6 out of 12 in 6bfy

Go back to Magnesium Binding Sites List in 6bfy
Magnesium binding site 6 out of 12 in the Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:27.1
occ:1.00
 OD1 C:ASP245 2.6 18.8 1.0
OD2 C:ASP290 2.7 17.4 1.0
O C:HOH732 2.8 24.0 1.0
OD2 C:ASP245 2.9 29.8 1.0
OD2 C:ASP316 3.0 22.9 1.0
CG C:ASP245 3.1 23.4 1.0
OE2 C:GLU289 3.1 21.8 1.0
O2 C:2PG501 3.4 16.5 1.0
CG C:ASP290 3.5 21.2 1.0
CB C:ALA247 3.5 21.8 1.0
CB C:ASP290 3.6 20.0 1.0
CA C:ALA247 3.7 20.6 1.0
O1 C:2PG501 3.9 21.0 1.0
CG C:ASP316 3.9 19.5 1.0
N C:ALA247 4.0 20.8 1.0
CB C:ASP316 4.0 16.8 1.0
C1 C:2PG501 4.1 21.5 1.0
CD C:GLU289 4.1 20.6 1.0
OD2 C:ASP317 4.1 29.6 1.0
O C:HOH643 4.2 25.4 1.0
CG C:GLU289 4.2 18.3 1.0
MG C:MG502 4.2 20.0 1.0
NE2 C:GLN166 4.3 21.0 1.0
O C:HOH633 4.5 22.1 1.0
OD1 C:ASP290 4.7 19.3 1.0
CG C:ASP317 4.7 22.0 1.0
CB C:ASP245 4.7 20.0 1.0
CA C:ASP290 5.0 17.6 1.0
N C:ASP317 5.0 16.8 1.0

Magnesium binding site 7 out of 12 in 6bfy

Go back to Magnesium Binding Sites List in 6bfy
Magnesium binding site 7 out of 12 in the Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:31.1
occ:1.00
 O4P F:2PG501 2.0 25.3 1.0
O F:HOH642 2.0 32.9 1.0
O1 F:2PG501 2.1 31.1 1.0
O F:SER41 2.2 27.4 1.0
OG F:SER41 2.3 36.4 1.0
P F:2PG501 3.1 28.5 1.0
C F:SER41 3.1 35.5 1.0
CB F:SER41 3.1 35.2 1.0
C1 F:2PG501 3.2 37.7 1.0
O1P F:2PG501 3.3 25.4 1.0
CA F:SER41 3.5 34.2 1.0
O2P F:2PG501 3.7 29.6 1.0
C2 F:2PG501 3.7 32.1 1.0
N F:SER41 4.0 33.2 1.0
NZ F:LYS341 4.1 40.3 1.0
OD2 F:ASP317 4.1 44.0 1.0
OD2 F:ASP316 4.1 37.3 1.0
NE2 F:GLN166 4.1 36.0 1.0
NH2 F:ARG370 4.1 30.0 1.0
OD1 F:ASP317 4.1 33.6 1.0
O2 F:2PG501 4.1 36.0 1.0
OE1 F:GLN166 4.2 40.9 1.0
MG F:MG503 4.3 48.9 1.0
N F:THR42 4.3 41.3 1.0
O3P F:2PG501 4.4 27.5 1.0
CG F:ASP317 4.5 50.9 1.0
CD F:GLN166 4.6 37.3 1.0
CA F:THR42 4.8 42.5 1.0

Magnesium binding site 8 out of 12 in 6bfy

Go back to Magnesium Binding Sites List in 6bfy
Magnesium binding site 8 out of 12 in the Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg503

b:48.9
occ:1.00
 OD1 F:ASP245 2.7 37.5 1.0
O F:HOH642 2.8 32.9 1.0
OD2 F:ASP316 2.9 37.3 1.0
OD2 F:ASP290 2.9 34.9 1.0
OD2 F:ASP245 3.1 38.8 1.0
CG F:ASP245 3.3 34.8 1.0
O1 F:2PG501 3.4 31.1 1.0
OE2 F:GLU289 3.4 27.8 1.0
CA F:ALA247 3.5 40.1 1.0
CB F:ALA247 3.6 34.6 1.0
CG F:ASP290 3.6 34.7 1.0
CB F:ASP290 3.6 30.0 1.0
CG F:ASP316 3.9 36.2 1.0
N F:ALA247 3.9 35.0 1.0
O2 F:2PG501 3.9 36.0 1.0
C1 F:2PG501 4.1 37.7 1.0
OD2 F:ASP317 4.1 44.0 1.0
CB F:ASP316 4.1 36.2 1.0
NE2 F:GLN166 4.2 36.0 1.0
CD F:GLU289 4.2 27.8 1.0
MG F:MG502 4.3 31.1 1.0
CG F:GLU289 4.4 26.1 1.0
CG F:ASP317 4.6 50.9 1.0
OD1 F:ASP290 4.8 33.9 1.0
C F:ALA247 4.8 44.5 1.0
CB F:ASP245 4.9 31.7 1.0
N F:ASP317 5.0 29.4 1.0
CD F:GLN166 5.0 37.3 1.0

Magnesium binding site 9 out of 12 in 6bfy

Go back to Magnesium Binding Sites List in 6bfy
Magnesium binding site 9 out of 12 in the Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg803

b:28.1
occ:1.00
 O4P D:2PG802 2.0 18.6 1.0
O D:HOH938 2.0 24.7 1.0
O2 D:2PG802 2.1 24.5 1.0
O D:SER41 2.2 19.7 1.0
O D:HOH903 2.3 31.6 1.0
OG D:SER41 2.3 31.3 1.0
P D:2PG802 3.1 20.0 1.0
C D:SER41 3.1 27.2 1.0
CB D:SER41 3.1 29.2 1.0
C1 D:2PG802 3.1 28.2 1.0
O1P D:2PG802 3.4 23.7 1.0
CA D:SER41 3.5 24.5 1.0
C2 D:2PG802 3.7 26.5 1.0
O3P D:2PG802 3.7 22.8 1.0
N D:SER41 3.9 21.1 1.0
OD2 D:ASP316 4.0 23.3 1.0
NZ D:LYS341 4.0 22.2 1.0
O1 D:2PG802 4.1 29.1 1.0
OD1 D:ASP317 4.1 34.3 1.0
NE2 D:GLN166 4.1 33.5 1.0
OD2 D:ASP317 4.1 36.3 1.0
OE1 D:GLN166 4.2 31.2 1.0
MG D:MG804 4.2 37.0 1.0
NH2 D:ARG370 4.3 18.4 1.0
N D:THR42 4.3 29.1 1.0
O2P D:2PG802 4.3 18.2 1.0
CG D:ASP317 4.6 35.2 1.0
CD D:GLN166 4.6 32.8 1.0
CA D:THR42 4.8 29.4 1.0

Magnesium binding site 10 out of 12 in 6bfy

Go back to Magnesium Binding Sites List in 6bfy
Magnesium binding site 10 out of 12 in the Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Enolase From Escherichia Coli with Bound 2- Phosphoglycerate Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg804

b:37.0
occ:1.00
 OD1 D:ASP245 2.6 22.6 1.0
O D:HOH938 2.7 24.7 1.0
OD2 D:ASP290 2.8 28.0 1.0
OD2 D:ASP316 3.0 23.3 1.0
OD2 D:ASP245 3.0 37.0 1.0
CG D:ASP245 3.2 29.5 1.0
OE2 D:GLU289 3.3 24.9 1.0
O2 D:2PG802 3.5 24.5 1.0
CB D:ALA247 3.5 25.9 1.0
CA D:ALA247 3.5 26.7 1.0
CG D:ASP290 3.6 24.6 1.0
CB D:ASP290 3.7 24.9 1.0
N D:ALA247 3.9 29.5 1.0
OD2 D:ASP317 3.9 36.3 1.0
O1 D:2PG802 3.9 29.1 1.0
CG D:ASP316 4.0 24.1 1.0
C1 D:2PG802 4.1 28.2 1.0
O D:HOH903 4.2 31.6 1.0
CB D:ASP316 4.2 20.1 1.0
MG D:MG803 4.2 28.1 1.0
CD D:GLU289 4.2 23.2 1.0
O D:HOH909 4.2 27.4 1.0
NE2 D:GLN166 4.2 33.5 1.0
CG D:GLU289 4.5 18.8 1.0
CG D:ASP317 4.5 35.2 1.0
CB D:ASP245 4.8 24.2 1.0
OD1 D:ASP290 4.8 22.7 1.0
C D:ALA247 4.9 24.1 1.0
CD D:GLN166 5.0 32.8 1.0
OD1 D:ASP317 5.0 34.3 1.0

Reference:

J.Krucinska, E.Falcone, H.Erlandsen, A.Hazeen, M.N.Lombardo, A.Estrada, V.L.Robinson, A.C.Anderson, D.L.Wright. Structural and Functional Studies of Bacterial Enolase, A Potential Target Against Gram-Negative Pathogens. Biochemistry V. 58 1188 2019.
ISSN: ISSN 1520-4995
PubMed: 30714720
DOI: 10.1021/ACS.BIOCHEM.8B01298
Page generated: Mon Sep 30 19:44:32 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy