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Magnesium in PDB 6d3q: Crystal Structure of Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312.

Enzymatic activity of Crystal Structure of Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312.

All present enzymatic activity of Crystal Structure of Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312.:
4.2.1.11;

Protein crystallography data

The structure of Crystal Structure of Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312., PDB code: 6d3q was solved by H.Erlandsen, J.Krucinska, A.Hazeen, D.Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 207.28 / 2.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.751, 142.071, 207.280, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 21.6

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 Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312. (pdb code 6d3q). 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 Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312., PDB code: 6d3q:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 6d3q

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Magnesium binding site 1 out of 12 in the Crystal Structure of Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312.


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 Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:26.1
occ:1.00
 OE2 A:GLU289 1.9 27.0 1.0
OAF A:4NG501 2.1 26.0 1.0
OD2 A:ASP245 2.2 31.7 1.0
OD2 A:ASP316 2.2 25.8 1.0
O A:HOH627 2.2 20.4 1.0
OAG A:4NG501 2.4 29.8 1.0
NAB A:4NG501 2.9 29.3 1.0
CAA A:4NG501 3.0 26.3 1.0
CD A:GLU289 3.1 27.3 1.0
CG A:ASP245 3.1 30.4 1.0
CG A:ASP316 3.2 27.9 1.0
OD1 A:ASP245 3.5 25.9 1.0
CB A:ASP316 3.7 28.5 1.0
NZ A:LYS392 3.7 25.3 1.0
OE1 A:GLU289 3.8 27.2 1.0
NZ A:LYS341 3.8 22.3 1.0
O A:HOH638 3.9 27.9 1.0
O A:HOH645 3.9 24.7 1.0
CD2 A:LEU339 4.0 23.1 1.0
CG A:GLU289 4.2 24.9 1.0
OD2 A:ASP290 4.2 24.9 1.0
OD1 A:ASP316 4.3 27.8 1.0
MG A:MG503 4.3 29.4 1.0
CAC A:4NG501 4.3 28.6 1.0
NE2 A:GLN166 4.3 37.9 1.0
CB A:ASP245 4.5 30.2 1.0
CAE A:4NG501 4.5 27.1 1.0
OAH A:4NG501 4.6 27.6 1.0
CE A:LYS392 4.9 25.6 1.0

Magnesium binding site 2 out of 12 in 6d3q

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Magnesium binding site 2 out of 12 in the Crystal Structure of Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312.


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 Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:29.4
occ:1.00
 OAK A:4NG501 2.0 28.0 1.0
O A:HOH645 2.1 24.7 1.0
OG A:SER41 2.1 35.2 1.0
O A:SER41 2.1 32.4 1.0
O A:HOH638 2.2 27.9 1.0
OAG A:4NG501 2.3 29.8 1.0
CAA A:4NG501 3.0 26.3 1.0
C A:SER41 3.0 33.1 1.0
CB A:SER41 3.1 34.8 1.0
PAI A:4NG501 3.2 25.9 1.0
CAE A:4NG501 3.4 27.1 1.0
CA A:SER41 3.5 34.3 1.0
N A:SER41 3.8 34.7 1.0
OAJ A:4NG501 4.0 27.5 1.0
OD1 A:ASP317 4.1 34.8 1.0
OD2 A:ASP316 4.1 25.8 1.0
O A:HOH627 4.1 20.4 1.0
N A:THR42 4.2 31.0 1.0
OD2 A:ASP317 4.2 44.9 1.0
NAB A:4NG501 4.2 29.3 1.0
MG A:MG502 4.3 26.1 1.0
OAL A:4NG501 4.4 24.9 1.0
NE2 A:GLN166 4.4 37.9 1.0
OE1 A:GLN166 4.5 39.6 1.0
CG A:ASP317 4.5 40.0 1.0
NH2 A:ARG370 4.6 25.9 1.0
CA A:THR42 4.7 35.1 1.0
NZ A:LYS341 4.7 22.3 1.0
CAD A:4NG501 4.9 28.4 1.0
OAF A:4NG501 4.9 26.0 1.0
CD A:GLN166 5.0 40.3 1.0

Magnesium binding site 3 out of 12 in 6d3q

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Magnesium binding site 3 out of 12 in the Crystal Structure of Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312.


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 Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:41.4
occ:1.00
 OE2 C:GLU289 1.9 32.1 1.0
OAF C:4NG501 1.9 50.8 1.0
O C:HOH609 2.0 40.7 1.0
OD2 C:ASP316 2.1 46.3 1.0
OD2 C:ASP245 2.3 45.7 1.0
OAG C:4NG501 2.7 46.2 1.0
NAB C:4NG501 2.9 44.3 1.0
CD C:GLU289 3.1 42.7 1.0
CG C:ASP245 3.1 48.1 1.0
CAA C:4NG501 3.1 43.0 1.0
CG C:ASP316 3.2 47.3 1.0
OD1 C:ASP245 3.3 40.7 1.0
O C:HOH603 3.3 44.7 1.0
CB C:ASP316 3.6 47.7 1.0
NZ C:LYS392 3.8 46.6 1.0
CG C:GLU289 3.9 40.0 1.0
OD2 C:ASP290 3.9 51.6 1.0
OE1 C:GLU289 4.0 38.7 1.0
O C:HOH616 4.0 43.1 1.0
NZ C:LYS341 4.0 45.5 1.0
MG C:MG503 4.2 35.9 1.0
OD1 C:ASP316 4.3 39.6 1.0
CAC C:4NG501 4.3 44.0 1.0
CD2 C:LEU339 4.3 42.9 1.0
CB C:ASP245 4.4 43.2 1.0
NE2 C:GLN166 4.6 53.7 1.0
CAE C:4NG501 4.6 40.9 1.0
CG C:ASP290 4.7 54.7 1.0
OAH C:4NG501 4.7 43.1 1.0
OE2 C:GLU167 5.0 58.8 1.0
CB C:ASP290 5.0 52.1 1.0

Magnesium binding site 4 out of 12 in 6d3q

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Magnesium binding site 4 out of 12 in the Crystal Structure of Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312.


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 Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:35.9
occ:1.00
 OAG C:4NG501 2.0 46.2 1.0
O C:SER41 2.2 46.5 1.0
OAJ C:4NG501 2.2 45.0 1.0
OG C:SER41 2.3 51.6 1.0
O C:HOH603 2.3 44.7 1.0
O C:HOH616 2.4 43.1 1.0
CAA C:4NG501 2.9 43.0 1.0
CB C:SER41 3.0 55.2 1.0
C C:SER41 3.1 51.5 1.0
PAI C:4NG501 3.3 47.5 1.0
CAE C:4NG501 3.3 40.9 1.0
CA C:SER41 3.4 58.4 1.0
N C:SER41 4.0 58.7 1.0
OD2 C:ASP317 4.0 59.2 1.0
OD1 C:ASP317 4.0 52.7 1.0
NAB C:4NG501 4.1 44.3 1.0
OAK C:4NG501 4.1 49.6 1.0
OD2 C:ASP316 4.1 46.3 1.0
N C:THR42 4.2 52.8 1.0
MG C:MG502 4.2 41.4 1.0
O C:HOH609 4.4 40.7 1.0
OE1 C:GLN166 4.4 70.0 1.0
CG C:ASP317 4.4 60.1 1.0
OAL C:4NG501 4.5 41.8 1.0
NZ C:LYS341 4.6 45.5 1.0
NH2 C:ARG370 4.6 49.0 1.0
OAF C:4NG501 4.7 50.8 1.0
CA C:THR42 4.7 60.0 1.0
CAD C:4NG501 4.8 39.6 1.0
NE2 C:GLN166 4.9 53.7 1.0

Magnesium binding site 5 out of 12 in 6d3q

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Magnesium binding site 5 out of 12 in the Crystal Structure of Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312.


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 Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:26.3
occ:1.00
 OE2 B:GLU289 1.9 20.3 1.0
OD2 B:ASP245 2.0 35.2 1.0
OAF B:4NG501 2.1 28.5 1.0
OD2 B:ASP316 2.1 25.4 1.0
O B:HOH632 2.2 25.5 1.0
OAG B:4NG501 2.4 26.7 1.0
NAB B:4NG501 2.9 29.1 1.0
CAA B:4NG501 3.0 26.3 1.0
CG B:ASP245 3.0 34.6 1.0
CD B:GLU289 3.1 28.3 1.0
CG B:ASP316 3.2 25.8 1.0
OD1 B:ASP245 3.3 27.9 1.0
NZ B:LYS392 3.7 29.8 1.0
CB B:ASP316 3.7 25.8 1.0
O B:HOH652 3.8 32.3 1.0
OE1 B:GLU289 4.0 24.6 1.0
O B:HOH645 4.0 25.5 1.0
NZ B:LYS341 4.0 22.4 1.0
OD2 B:ASP290 4.1 37.4 1.0
CD2 B:LEU339 4.1 22.7 1.0
CG B:GLU289 4.1 27.3 1.0
NE2 B:GLN166 4.2 36.3 1.0
MG B:MG503 4.2 34.4 1.0
OD1 B:ASP316 4.2 25.1 1.0
CB B:ASP245 4.3 28.8 1.0
CAC B:4NG501 4.3 28.1 1.0
CAE B:4NG501 4.5 27.5 1.0
OAH B:4NG501 4.8 29.1 1.0
OE2 B:GLU167 4.9 37.9 1.0
CE B:LYS392 4.9 27.8 1.0

Magnesium binding site 6 out of 12 in 6d3q

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Magnesium binding site 6 out of 12 in the Crystal Structure of Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312.


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 Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:34.4
occ:1.00
 OAJ B:4NG501 2.0 34.2 1.0
O B:HOH645 2.0 25.5 1.0
O B:SER41 2.1 32.4 1.0
O B:HOH652 2.1 32.3 1.0
OAG B:4NG501 2.1 26.7 1.0
OG B:SER41 2.4 34.5 1.0
CAA B:4NG501 2.9 26.3 1.0
C B:SER41 3.0 33.1 1.0
PAI B:4NG501 3.1 29.9 1.0
CB B:SER41 3.2 34.1 1.0
CAE B:4NG501 3.2 27.5 1.0
CA B:SER41 3.4 33.7 1.0
OAL B:4NG501 3.7 29.3 1.0
N B:SER41 3.8 37.5 1.0
OD2 B:ASP316 4.0 25.4 1.0
OD1 B:ASP317 4.0 39.7 1.0
O B:HOH632 4.1 25.5 1.0
NAB B:4NG501 4.1 29.1 1.0
N B:THR42 4.2 33.6 1.0
MG B:MG502 4.2 26.3 1.0
OAK B:4NG501 4.3 29.1 1.0
NH2 B:ARG370 4.3 25.0 1.0
OD2 B:ASP317 4.3 40.5 1.0
NZ B:LYS341 4.4 22.4 1.0
CG B:ASP317 4.6 36.5 1.0
OE1 B:GLN166 4.6 34.9 1.0
NE2 B:GLN166 4.7 36.3 1.0
CA B:THR42 4.7 35.9 1.0
CAD B:4NG501 4.7 30.5 1.0
OAF B:4NG501 4.8 28.5 1.0
CG B:ASP316 5.0 25.8 1.0

Magnesium binding site 7 out of 12 in 6d3q

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Magnesium binding site 7 out of 12 in the Crystal Structure of Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312.


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 Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:24.1
occ:1.00
 OE2 E:GLU289 1.9 25.9 1.0
O E:HOH637 2.0 24.3 1.0
OD2 E:ASP245 2.0 26.5 1.0
OD2 E:ASP316 2.1 28.3 1.0
OAF E:4NG501 2.2 29.1 1.0
OAG E:4NG501 2.4 26.7 1.0
NAB E:4NG501 2.9 26.3 1.0
CG E:ASP245 2.9 28.2 1.0
CAA E:4NG501 2.9 26.6 1.0
CD E:GLU289 3.1 26.0 1.0
OD1 E:ASP245 3.1 28.4 1.0
CG E:ASP316 3.2 27.5 1.0
CB E:ASP316 3.8 26.4 1.0
O E:HOH607 3.8 24.0 1.0
OE1 E:GLU289 3.9 26.0 1.0
NZ E:LYS392 3.9 27.5 1.0
NZ E:LYS341 3.9 24.8 1.0
O E:HOH641 4.0 28.6 1.0
CG E:GLU289 4.1 26.0 1.0
NE2 E:GLN166 4.1 33.0 1.0
OD2 E:ASP290 4.2 29.1 1.0
MG E:MG503 4.2 26.9 1.0
OD1 E:ASP316 4.2 30.8 1.0
CD2 E:LEU339 4.3 22.2 1.0
CB E:ASP245 4.3 27.1 1.0
CAC E:4NG501 4.3 30.4 1.0
CAE E:4NG501 4.5 29.1 1.0
OAH E:4NG501 4.7 28.6 1.0
OE2 E:GLU167 4.9 33.2 1.0
CG E:ASP290 5.0 30.7 1.0

Magnesium binding site 8 out of 12 in 6d3q

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Magnesium binding site 8 out of 12 in the Crystal Structure of Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312.


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 Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg503

b:26.9
occ:1.00
 OAJ E:4NG501 2.0 27.4 1.0
O E:HOH641 2.1 28.6 1.0
O E:SER41 2.1 32.6 1.0
OAG E:4NG501 2.2 26.7 1.0
OG E:SER41 2.2 35.8 1.0
O E:HOH607 2.3 24.0 1.0
CAA E:4NG501 2.9 26.6 1.0
C E:SER41 3.0 35.6 1.0
PAI E:4NG501 3.1 28.0 1.0
CB E:SER41 3.1 37.6 1.0
CAE E:4NG501 3.3 29.1 1.0
CA E:SER41 3.5 37.1 1.0
OAL E:4NG501 3.7 30.8 1.0
N E:SER41 4.0 38.9 1.0
OD2 E:ASP316 4.0 28.3 1.0
OD1 E:ASP317 4.0 34.6 1.0
NAB E:4NG501 4.1 26.3 1.0
O E:HOH637 4.1 24.3 1.0
OD2 E:ASP317 4.1 37.8 1.0
N E:THR42 4.2 33.7 1.0
MG E:MG502 4.2 24.1 1.0
OAK E:4NG501 4.3 25.0 1.0
NH2 E:ARG370 4.4 22.9 1.0
NZ E:LYS341 4.4 24.8 1.0
CG E:ASP317 4.5 34.8 1.0
OE1 E:GLN166 4.5 37.8 1.0
CA E:THR42 4.6 34.1 1.0
CAD E:4NG501 4.7 30.0 1.0
OAF E:4NG501 4.8 29.1 1.0
NE2 E:GLN166 4.8 33.0 1.0
CG E:ASP316 5.0 27.5 1.0

Magnesium binding site 9 out of 12 in 6d3q

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Magnesium binding site 9 out of 12 in the Crystal Structure of Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312.


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 Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:33.6
occ:1.00
 OE2 F:GLU289 1.9 26.3 1.0
OD2 F:ASP316 2.0 27.9 1.0
OAF F:4NG501 2.1 33.1 1.0
O F:HOH637 2.1 30.9 1.0
OD2 F:ASP245 2.2 28.8 1.0
OAG F:4NG501 2.4 34.4 1.0
NAB F:4NG501 2.8 33.9 1.0
CAA F:4NG501 2.9 31.5 1.0
CG F:ASP245 3.1 32.4 1.0
CD F:GLU289 3.2 28.0 1.0
CG F:ASP316 3.2 27.3 1.0
OD1 F:ASP245 3.5 31.3 1.0
NZ F:LYS392 3.6 27.6 1.0
CB F:ASP316 3.7 29.5 1.0
NZ F:LYS341 3.8 27.9 1.0
O F:HOH614 3.9 36.1 1.0
OE1 F:GLU289 3.9 32.9 1.0
O F:HOH640 4.0 32.9 1.0
CD2 F:LEU339 4.1 29.7 1.0
MG F:MG503 4.1 31.9 1.0
CG F:GLU289 4.1 25.9 1.0
OD1 F:ASP316 4.2 29.8 1.0
CAC F:4NG501 4.3 32.2 1.0
NE2 F:GLN166 4.3 48.3 1.0
OD2 F:ASP290 4.3 35.8 1.0
CB F:ASP245 4.4 31.5 1.0
CAE F:4NG501 4.4 30.9 1.0
OAH F:4NG501 4.7 31.3 1.0
CE F:LYS392 4.8 27.8 1.0
OE2 F:GLU167 4.9 34.3 1.0

Magnesium binding site 10 out of 12 in 6d3q

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Magnesium binding site 10 out of 12 in the Crystal Structure of Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312.


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 Escherichia Coli Enolase Complexed with A Natural Inhibitor SF2312. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg503

b:31.9
occ:1.00
 OAK F:4NG501 2.0 31.1 1.0
O F:HOH640 2.1 32.9 1.0
O F:SER41 2.1 37.2 1.0
O F:HOH614 2.1 36.1 1.0
OAG F:4NG501 2.2 34.4 1.0
OG F:SER41 2.3 40.7 1.0
CAA F:4NG501 3.0 31.5 1.0
C F:SER41 3.0 35.5 1.0
CB F:SER41 3.1 41.1 1.0
PAI F:4NG501 3.1 28.9 1.0
CAE F:4NG501 3.4 30.9 1.0
CA F:SER41 3.4 38.9 1.0
OAL F:4NG501 3.8 31.5 1.0
N F:SER41 3.9 41.9 1.0
OD2 F:ASP316 4.0 27.9 1.0
OD1 F:ASP317 4.1 45.0 1.0
OD2 F:ASP317 4.1 46.5 1.0
O F:HOH637 4.1 30.9 1.0
MG F:MG502 4.1 33.6 1.0
N F:THR42 4.1 35.5 1.0
NAB F:4NG501 4.2 33.9 1.0
OAJ F:4NG501 4.3 29.2 1.0
NH2 F:ARG370 4.4 29.5 1.0
CG F:ASP317 4.5 45.6 1.0
NZ F:LYS341 4.5 27.9 1.0
OE1 F:GLN166 4.6 45.6 1.0
CA F:THR42 4.6 37.7 1.0
NE2 F:GLN166 4.7 48.3 1.0
OAF F:4NG501 4.8 33.1 1.0
CAD F:4NG501 4.9 31.5 1.0
O F:HOH610 5.0 38.1 1.0
CG F:ASP316 5.0 27.3 1.0

Reference:

J.Krucinska, M.N.Lombardo, H.Erlandsen, A.Hazeen, S.S.Duay, J.G.Pattis, V.L.Robinson, E.R.May, D.L.Wright. Functional and Structural Basis of E. Coli Enolase Inhibition By SF2312: A Mimic of the Carbanion Intermediate. Sci Rep V. 9 17106 2019.
ISSN: ESSN 2045-2322
PubMed: 31745118
DOI: 10.1038/S41598-019-53301-3
Page generated: Mon Sep 30 22:53:12 2024

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