Magnesium in PDB 8ek7: Crystal Structure of Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes

Enzymatic activity of Crystal Structure of Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes

All present enzymatic activity of Crystal Structure of Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes:
4.1.1.23;

Protein crystallography data

The structure of Crystal Structure of Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes, PDB code: 8ek7 was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural 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) 41.69 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.517, 70.141, 115.985, 90, 93.34, 90
R / Rfree (%) 18.4 / 23

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (pdb code 8ek7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes, PDB code: 8ek7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 8ek7

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Magnesium binding site 1 out of 10 in the Crystal Structure of Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes


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 Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:25.4
occ:1.00
 O A:HOH491 2.0 26.1 1.0
O A:HOH511 2.1 30.4 1.0
O A:HOH429 2.1 29.7 1.0
O A:HOH423 2.1 30.6 1.0
O A:HOH428 2.1 21.7 1.0
O A:HOH434 2.2 27.1 1.0
O2S A:EPE301 4.0 35.4 1.0
O A:ALA129 4.1 21.8 1.0
O A:GLU128 4.1 23.9 1.0
O1S A:EPE301 4.2 33.5 1.0
O A:HOH439 4.3 23.7 1.0
CA A:TRP102 4.4 16.7 1.0
CD1 A:TRP102 4.4 16.8 1.0
O A:LYS127 4.5 27.6 1.0
OE2 A:GLU75 4.5 27.7 1.0
O A:TRP102 4.6 17.6 1.0
C A:GLU128 4.6 24.2 1.0
O A:VAL101 4.6 18.8 1.0
S A:EPE301 4.7 35.0 1.0
C A:ALA129 4.8 20.2 1.0
CA A:GLU128 4.8 27.6 1.0
CB A:TRP102 4.9 17.5 1.0
C A:TRP102 5.0 15.9 1.0
CA A:PRO130 5.0 17.4 1.0

Magnesium binding site 2 out of 10 in 8ek7

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Magnesium binding site 2 out of 10 in the Crystal Structure of Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes


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 Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:32.6
occ:1.00
 O A:HOH477 2.2 30.5 1.0
O A:HOH497 2.3 49.0 1.0
O A:GLU42 2.4 35.0 1.0
O A:HOH510 2.4 42.1 1.0
MG A:MG304 2.5 54.5 1.0
O A:HOH503 2.6 29.2 1.0
C A:GLU42 3.6 32.3 1.0
CA A:GLU42 4.3 34.0 1.0
O A:ILE44 4.4 30.6 1.0
O A:ARG43 4.4 28.3 1.0
N A:ARG43 4.6 28.2 1.0
OE1 A:GLU42 4.6 48.0 1.0
CA A:ARG43 4.6 28.7 1.0
C A:ARG43 4.6 27.3 1.0
CB A:GLU42 4.7 38.5 1.0
O A:HOH442 5.0 41.1 1.0

Magnesium binding site 3 out of 10 in 8ek7

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Magnesium binding site 3 out of 10 in the Crystal Structure of Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes


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 Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:54.5
occ:1.00
 O A:HOH510 2.0 42.1 1.0
MG A:MG303 2.5 32.6 1.0
O A:HOH477 2.7 30.5 1.0
O A:ILE44 2.7 30.6 1.0
O A:GLU42 3.1 35.0 1.0
O A:HOH442 3.4 41.1 1.0
C A:ILE44 3.8 27.8 1.0
C A:GLU42 4.0 32.3 1.0
O A:HOH420 4.2 35.7 1.0
OD2 A:ASP45 4.2 32.8 1.0
O A:HOH497 4.2 49.0 1.0
CA A:ASP45 4.2 25.1 1.0
O A:ARG43 4.5 28.3 1.0
O A:VAL41 4.5 28.2 1.0
N A:ASP45 4.5 26.3 1.0
CA A:GLU42 4.5 34.0 1.0
CB A:ASP45 4.5 27.5 1.0
C A:ARG43 4.6 27.3 1.0
N A:ILE44 4.8 26.0 1.0
CG A:ASP45 4.8 28.6 1.0
CA A:ILE44 4.9 27.6 1.0
O A:HOH503 5.0 29.2 1.0
N A:ARG43 5.0 28.2 1.0

Magnesium binding site 4 out of 10 in 8ek7

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Magnesium binding site 4 out of 10 in the Crystal Structure of Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes


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 Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:34.8
occ:1.00
 O B:HOH441 2.0 33.0 1.0
O B:HOH423 2.1 29.4 1.0
O B:HOH455 2.2 26.3 1.0
O B:HOH403 2.2 35.8 1.0
O B:HOH442 2.3 31.5 1.0
O B:ALA129 3.9 24.4 1.0
O B:LYS127 4.1 26.9 1.0
O B:HOH443 4.2 29.7 1.0
O B:GLU128 4.3 26.5 1.0
CA B:TRP102 4.4 20.4 1.0
OE2 B:GLU75 4.4 28.4 1.0
CD1 B:TRP102 4.4 24.1 1.0
O B:VAL101 4.5 19.6 1.0
C B:GLU128 4.5 24.1 1.0
O B:TRP102 4.5 19.0 1.0
O B:HOH478 4.5 44.0 1.0
C B:ALA129 4.6 23.3 1.0
CA B:GLU128 4.7 27.4 1.0
CA B:PRO130 4.8 18.8 1.0
OE1 B:GLU128 4.8 39.5 1.0
CB B:TRP102 4.9 21.2 1.0
N B:PRO130 4.9 23.5 1.0
C B:TRP102 4.9 19.4 1.0

Magnesium binding site 5 out of 10 in 8ek7

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Magnesium binding site 5 out of 10 in the Crystal Structure of Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes


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 Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:19.7
occ:1.00
 O C:HOH539 1.9 25.2 1.0
O C:HOH481 2.0 18.5 1.0
O C:HOH434 2.1 25.0 1.0
O C:HOH417 2.2 22.9 1.0
O C:HOH457 2.2 20.4 1.0
O C:HOH415 2.2 16.9 1.0
O C:HOH547 3.9 57.7 1.0
O C:GLU128 4.0 19.3 1.0
O C:ALA129 4.0 17.5 1.0
O1S C:EPE301 4.1 30.9 1.0
O2S C:EPE301 4.2 27.1 1.0
O C:HOH469 4.2 21.6 1.0
O C:HOH407 4.4 31.4 1.0
CA C:TRP102 4.4 12.0 1.0
C C:GLU128 4.5 18.5 1.0
OE2 C:GLU75 4.5 23.2 1.0
O C:LYS127 4.5 22.3 1.0
CD1 C:TRP102 4.5 12.6 1.0
O C:VAL101 4.6 14.3 1.0
O C:TRP102 4.6 13.0 1.0
CA C:GLU128 4.7 20.6 1.0
C C:ALA129 4.7 17.1 1.0
S C:EPE301 4.8 29.2 1.0
CB C:TRP102 5.0 12.3 1.0
CA C:PRO130 5.0 13.2 1.0
OE1 C:GLU128 5.0 46.6 1.0

Magnesium binding site 6 out of 10 in 8ek7

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Magnesium binding site 6 out of 10 in the Crystal Structure of Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes


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 Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:44.0
occ:1.00
 O C:HOH522 2.1 34.9 1.0
O C:HOH526 2.3 32.6 1.0
MG C:MG304 2.5 35.6 1.0
O C:ILE44 2.5 25.1 1.0
O C:HOH488 2.6 37.6 1.0
O C:GLU42 2.6 24.1 1.0
O C:HOH445 2.9 31.7 1.0
O C:HOH451 3.5 24.2 1.0
C C:GLU42 3.6 23.5 1.0
C C:ILE44 3.7 20.0 1.0
O C:HOH432 4.2 26.5 1.0
O C:VAL41 4.2 20.1 1.0
C C:ARG43 4.2 21.1 1.0
CA C:GLU42 4.3 24.4 1.0
O C:ARG43 4.3 21.2 1.0
CA C:ASP45 4.4 20.1 1.0
N C:ILE44 4.4 19.8 1.0
OD2 C:ASP45 4.5 23.4 1.0
N C:ASP45 4.5 18.9 1.0
N C:ARG43 4.5 21.8 1.0
O C:HOH493 4.6 48.9 1.0
CB C:ASP45 4.7 20.4 1.0
OE2 C:GLU42 4.7 41.8 1.0
CA C:ILE44 4.7 18.6 1.0
O C:HOH542 4.7 33.1 1.0
CA C:ARG43 4.8 21.8 1.0

Magnesium binding site 7 out of 10 in 8ek7

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Magnesium binding site 7 out of 10 in the Crystal Structure of Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes


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 Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg304

b:35.6
occ:1.00
 O C:HOH526 2.2 32.6 1.0
O C:HOH522 2.3 34.9 1.0
MG C:MG303 2.5 44.0 1.0
O C:GLU42 2.5 24.1 1.0
O C:HOH542 2.6 33.1 1.0
O C:HOH493 2.6 48.9 1.0
C C:GLU42 3.7 23.5 1.0
OE2 C:GLU42 4.1 41.8 1.0
O C:HOH451 4.2 24.2 1.0
CG C:GLU42 4.3 35.2 1.0
O C:HOH488 4.5 37.6 1.0
O C:ILE44 4.5 25.1 1.0
O C:ARG43 4.6 21.2 1.0
CD C:GLU42 4.6 39.8 1.0
CA C:GLU42 4.6 24.4 1.0
CA C:ARG43 4.6 21.8 1.0
N C:ARG43 4.6 21.8 1.0
C C:ARG43 4.7 21.1 1.0
O C:HOH445 4.9 31.7 1.0
CB C:GLU42 5.0 28.9 1.0

Magnesium binding site 8 out of 10 in 8ek7

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Magnesium binding site 8 out of 10 in the Crystal Structure of Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes


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 Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:22.9
occ:1.00
 O E:HOH472 2.0 24.0 1.0
O E:HOH525 2.1 24.6 1.0
O E:HOH450 2.1 25.1 1.0
O E:HOH413 2.2 18.9 1.0
O E:HOH437 2.2 22.2 1.0
O E:HOH417 2.2 23.2 1.0
O2S E:EPE301 4.0 30.5 1.0
O E:ALA129 4.1 17.8 1.0
O E:GLU128 4.1 20.3 1.0
O1S E:EPE301 4.2 29.6 1.0
O E:HOH434 4.3 21.9 1.0
CA E:TRP102 4.4 12.9 1.0
CD1 E:TRP102 4.4 15.1 1.0
OE2 E:GLU75 4.5 21.8 1.0
O E:LYS127 4.5 22.4 1.0
O E:VAL101 4.5 14.3 1.0
C E:GLU128 4.6 19.9 1.0
O E:TRP102 4.6 13.7 1.0
C E:ALA129 4.8 16.0 1.0
S E:EPE301 4.8 30.2 1.0
CA E:GLU128 4.8 23.6 1.0
CB E:TRP102 4.9 12.2 1.0
C E:TRP102 5.0 12.0 1.0

Magnesium binding site 9 out of 10 in 8ek7

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Magnesium binding site 9 out of 10 in the Crystal Structure of Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes


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 Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg303

b:36.9
occ:1.00
 O E:HOH518 2.3 35.0 1.0
O E:HOH521 2.4 33.0 1.0
O E:GLU42 2.5 27.5 1.0
O E:HOH510 2.5 38.5 1.0
O E:HOH475 2.6 45.8 1.0
MG E:MG304 2.7 30.5 1.0
C E:GLU42 3.7 25.9 1.0
OE2 E:GLU42 4.2 46.7 1.0
CG E:GLU42 4.4 39.6 1.0
CA E:ARG43 4.5 21.6 1.0
O E:ARG43 4.6 20.5 1.0
N E:ARG43 4.6 22.5 1.0
O E:HOH490 4.6 37.9 1.0
CD E:GLU42 4.6 45.1 1.0
CA E:GLU42 4.6 27.7 1.0
O E:ILE44 4.7 23.2 1.0
C E:ARG43 4.7 19.8 1.0
O E:HOH488 4.8 31.4 1.0
O E:HOH421 4.9 29.1 1.0

Magnesium binding site 10 out of 10 in 8ek7

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Magnesium binding site 10 out of 10 in the Crystal Structure of Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes


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 Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl- 1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg304

b:30.5
occ:1.00
 O E:HOH510 2.1 38.5 1.0
O E:HOH518 2.4 35.0 1.0
O E:GLU42 2.4 27.5 1.0
O E:HOH421 2.5 29.1 1.0
O E:ILE44 2.6 23.2 1.0
O E:HOH490 2.6 37.9 1.0
MG E:MG303 2.7 36.9 1.0
C E:GLU42 3.3 25.9 1.0
C E:ILE44 3.8 20.8 1.0
O E:VAL41 3.9 22.2 1.0
CA E:GLU42 4.0 27.7 1.0
O E:HOH429 4.1 31.2 1.0
C E:ARG43 4.2 19.8 1.0
N E:ARG43 4.3 22.5 1.0
O E:ARG43 4.3 20.5 1.0
N E:ILE44 4.4 19.5 1.0
O E:HOH475 4.5 45.8 1.0
CA E:ASP45 4.5 19.6 1.0
CA E:ARG43 4.6 21.6 1.0
OE2 E:GLU42 4.6 46.7 1.0
N E:ASP45 4.6 20.9 1.0
CD E:GLU42 4.7 45.1 1.0
CA E:ILE44 4.8 19.0 1.0
O E:HOH521 4.8 33.0 1.0
OD2 E:ASP45 4.8 24.0 1.0
C E:VAL41 4.9 23.3 1.0
CG E:GLU42 4.9 39.6 1.0
N E:GLU42 5.0 24.4 1.0
CB E:ASP45 5.0 20.2 1.0

Reference:

S.Lovell, L.Liu, S.Seibold, K.P.Battaile. Crystal Structure of Hepes and Mg Bound 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes To Be Published.
Page generated: Fri Apr 7 09:27:14 2023

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