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Magnesium in PDB 4isk: Crystal Structure of E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor

Enzymatic activity of Crystal Structure of E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor

All present enzymatic activity of Crystal Structure of E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor:
2.1.1.45;

Protein crystallography data

The structure of Crystal Structure of E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor, PDB code: 4isk was solved by A.Tochowicz, J.Finer-Moore, R.M.Stroud, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.81 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 95.900, 85.500, 134.300, 90.00, 109.40, 90.00
R / Rfree (%) 18.4 / 23.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor (pdb code 4isk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor, PDB code: 4isk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4isk

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Magnesium binding site 1 out of 7 in the Crystal Structure of E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor


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 E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:24.1
occ:1.00
 O A:HOH579 2.0 27.7 1.0
O A:HOH584 2.0 26.5 1.0
O A:HOH582 2.1 17.6 1.0
O A:HOH580 2.2 23.4 1.0
O A:HOH581 2.2 24.5 1.0
O A:HOH583 2.2 22.3 1.0
H1 A:HOH428 3.4 29.2 1.0
HA A:ILE79 3.7 22.9 1.0
H1 A:HOH473 3.9 36.0 1.0
O A:HOH428 3.9 24.4 1.0
OE2 A:GLU82 4.1 29.4 1.0
HG1 A:THR78 4.2 27.1 1.0
O A:THR78 4.2 20.8 1.0
OG1 A:THR78 4.2 22.6 1.0
OAG A:1JY303 4.3 27.2 1.0
H2 A:HOH428 4.3 29.2 1.0
OE1 A:1JY303 4.4 60.0 1.0
OE2 A:1JY303 4.4 42.8 1.0
OE1 A:GLU82 4.4 28.5 1.0
O A:HOH473 4.4 30.0 1.0
HB A:THR78 4.4 27.0 1.0
O A:HOH480 4.5 28.2 1.0
OAE A:1JY303 4.6 24.9 1.0
CD A:1JY303 4.6 49.4 1.0
H1 A:HOH480 4.6 33.8 1.0
C A:THR78 4.6 19.3 1.0
HG21 A:ILE79 4.7 27.2 1.0
CA A:ILE79 4.7 19.1 1.0
H2 A:HOH480 4.7 33.8 1.0
CD A:GLU82 4.7 30.9 1.0
CB A:THR78 4.9 22.5 1.0
H2 A:HOH473 4.9 36.0 1.0
CAZ A:1JY303 4.9 21.8 1.0
N A:ILE79 5.0 22.8 1.0
HG11 A:VAL262 5.0 51.2 1.0

Magnesium binding site 2 out of 7 in 4isk

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Magnesium binding site 2 out of 7 in the Crystal Structure of E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor


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 E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:26.2
occ:1.00
 O B:HOH564 1.7 30.0 1.0
O B:HOH566 2.0 29.3 1.0
O B:HOH568 2.0 33.7 1.0
O B:HOH567 2.0 33.9 1.0
O B:HOH565 2.1 23.4 1.0
O B:HOH569 2.2 26.4 1.0
H2 B:HOH421 3.4 29.9 1.0
OE2 B:GLU82 3.9 41.0 1.0
O B:HOH421 3.9 24.9 1.0
HA B:ILE79 4.0 24.9 1.0
H2 B:HOH437 4.1 36.1 1.0
O B:THR78 4.1 25.5 1.0
OE1 B:GLU82 4.1 30.5 1.0
HG1 B:THR78 4.2 36.7 1.0
OG1 B:THR78 4.3 30.6 1.0
O B:HOH539 4.4 34.4 1.0
OAG B:1JY303 4.4 24.9 1.0
H1 B:HOH539 4.4 41.3 1.0
CD B:GLU82 4.5 30.5 1.0
HG13 B:VAL262 4.5 61.1 1.0
H1 B:HOH421 4.5 29.9 1.0
OE1 B:1JY303 4.6 52.9 1.0
O B:HOH437 4.6 30.1 1.0
HG11 B:VAL262 4.6 61.1 1.0
OAE B:1JY303 4.6 28.0 1.0
HB B:THR78 4.6 33.8 1.0
O B:HOH523 4.7 35.3 1.0
C B:THR78 4.7 20.1 1.0
H1 B:HOH437 4.8 36.1 1.0
H2 B:HOH539 4.8 41.3 1.0
HG21 B:ILE79 4.9 31.3 1.0
CA B:ILE79 4.9 20.8 1.0
CAZ B:1JY303 4.9 20.2 1.0

Magnesium binding site 3 out of 7 in 4isk

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Magnesium binding site 3 out of 7 in the Crystal Structure of E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor


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 E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:24.4
occ:1.00
 O C:HOH563 2.0 26.6 1.0
O C:HOH567 2.0 22.6 1.0
O C:HOH568 2.1 20.4 1.0
O C:HOH564 2.1 26.2 1.0
O C:HOH566 2.1 25.1 1.0
O C:HOH565 2.3 23.7 1.0
HA C:ILE79 3.9 21.9 1.0
O C:HOH427 4.0 24.7 1.0
H1 C:HOH427 4.0 29.6 1.0
OE2 C:GLU82 4.0 31.9 1.0
H1 C:HOH502 4.2 47.8 1.0
O C:THR78 4.2 21.6 1.0
HG1 C:THR78 4.2 28.3 1.0
OE1 C:1JY303 4.3 38.8 1.0
O C:HOH502 4.3 39.8 1.0
OG1 C:THR78 4.3 23.6 1.0
O C:HOH410 4.3 19.8 1.0
OAG C:1JY303 4.3 24.3 1.0
OE1 C:GLU82 4.4 25.9 1.0
H2 C:HOH427 4.4 29.6 1.0
H1 C:HOH464 4.4 47.7 1.0
OE2 C:1JY303 4.4 42.6 1.0
OAE C:1JY303 4.5 24.9 1.0
CD C:1JY303 4.6 43.8 1.0
CD C:GLU82 4.6 33.0 1.0
H2 C:HOH410 4.8 23.7 1.0
H1 C:HOH410 4.8 23.7 1.0
C C:THR78 4.8 19.8 1.0
HG11 C:VAL262 4.8 39.1 1.0
HB C:THR78 4.8 29.2 1.0
H2 C:HOH502 4.9 47.8 1.0
HG13 C:VAL262 4.9 39.1 1.0
CA C:ILE79 4.9 18.2 1.0
HG21 C:ILE79 4.9 28.0 1.0
CAZ C:1JY303 4.9 20.1 1.0

Magnesium binding site 4 out of 7 in 4isk

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Magnesium binding site 4 out of 7 in the Crystal Structure of E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor


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 E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:28.1
occ:1.00
 O D:HOH531 1.8 29.4 1.0
O D:HOH530 2.1 25.9 1.0
O D:HOH526 2.1 26.2 1.0
O D:HOH527 2.1 23.0 1.0
O D:HOH528 2.2 20.2 1.0
O D:HOH529 2.2 24.9 1.0
H1 D:HOH453 3.3 34.5 1.0
H2 D:HOH429 3.8 39.2 1.0
H2 D:HOH486 3.8 43.3 1.0
HA D:ILE79 4.0 30.2 1.0
OE2 D:GLU82 4.0 40.0 1.0
H2 D:HOH453 4.0 34.5 1.0
O D:HOH486 4.1 36.1 1.0
H1 D:HOH473 4.1 48.6 1.0
O D:HOH453 4.1 28.7 1.0
O D:HOH473 4.1 40.5 1.0
O D:THR78 4.2 21.0 1.0
HG1 D:THR78 4.2 32.1 1.0
OE1 D:GLU82 4.3 31.8 1.0
OE1 D:1JY303 4.3 61.8 1.0
OG1 D:THR78 4.3 26.7 1.0
HB D:THR78 4.4 33.8 1.0
OAG D:1JY303 4.4 26.4 1.0
OAE D:1JY303 4.5 26.5 1.0
CD D:GLU82 4.6 38.9 1.0
O D:HOH429 4.6 32.7 1.0
H2 D:HOH473 4.7 48.6 1.0
HG11 D:VAL262 4.7 53.3 1.0
C D:THR78 4.7 20.5 1.0
HG13 D:VAL262 4.8 53.3 1.0
HG21 D:ILE79 4.9 30.9 1.0
CD D:1JY303 4.9 53.5 1.0
CA D:ILE79 4.9 25.1 1.0
CB D:THR78 4.9 28.2 1.0
H1 D:HOH486 4.9 43.3 1.0
H1 D:HOH429 5.0 39.2 1.0
CAZ D:1JY303 5.0 22.9 1.0

Magnesium binding site 5 out of 7 in 4isk

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Magnesium binding site 5 out of 7 in the Crystal Structure of E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor


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 E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:39.1
occ:1.00
 O E:HOH529 2.1 41.3 1.0
O E:HOH526 2.1 33.2 1.0
O E:HOH525 2.1 45.6 1.0
O E:HOH528 2.2 58.5 1.0
O E:HOH527 2.2 38.9 1.0
HG1 E:THR78 3.6 52.5 1.0
OG1 E:THR78 3.7 43.8 1.0
H1 E:HOH483 3.8 49.5 1.0
HA E:ILE79 3.8 56.0 1.0
OAG E:1JY303 4.0 33.1 1.0
O E:THR78 4.0 34.6 1.0
H2 E:HOH483 4.0 49.5 1.0
OE2 E:1JY303 4.1 72.3 1.0
HB E:THR78 4.2 50.8 1.0
H2 E:HOH509 4.3 52.4 1.0
OE2 E:GLU82 4.3 50.4 1.0
O E:HOH483 4.3 41.3 1.0
C E:THR78 4.4 37.5 1.0
O E:HOH509 4.5 43.6 1.0
CB E:THR78 4.5 42.4 1.0
CAZ E:1JY303 4.6 48.5 1.0
HG21 E:ILE79 4.6 63.3 1.0
CA E:ILE79 4.6 46.7 1.0
CBJ E:1JY303 4.7 30.4 1.0
N E:ILE79 4.8 41.8 1.0
CD E:1JY303 4.8 74.8 1.0
OE1 E:1JY303 5.0 69.3 1.0
OE1 E:GLU82 5.0 52.7 1.0

Magnesium binding site 6 out of 7 in 4isk

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Magnesium binding site 6 out of 7 in the Crystal Structure of E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor


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 E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg302

b:33.9
occ:1.00
 O G:HOH471 1.9 31.4 1.0
O G:HOH473 2.1 32.3 1.0
O G:HOH470 2.1 28.8 1.0
O G:HOH474 2.1 30.7 1.0
O G:HOH469 2.1 33.4 1.0
O G:HOH472 2.3 34.2 1.0
H1 G:HOH411 3.6 34.9 1.0
OE2 G:GLU82 3.8 53.6 1.0
HA G:ILE79 4.0 34.6 1.0
O G:HOH411 4.0 29.0 1.0
HG1 G:THR78 4.1 37.9 1.0
OG1 G:THR78 4.2 31.5 1.0
OE1 G:GLU82 4.3 37.3 1.0
OAG G:1JY303 4.4 33.7 1.0
H1 G:HOH430 4.4 30.5 1.0
O G:THR78 4.4 36.6 1.0
H2 G:HOH411 4.4 34.9 1.0
O G:HOH430 4.5 25.4 1.0
O G:HOH466 4.5 30.1 1.0
CD G:GLU82 4.5 52.2 1.0
H2 G:HOH466 4.5 36.2 1.0
OAE G:1JY303 4.5 31.5 1.0
CD G:1JY303 4.6 61.0 1.0
OE1 G:1JY303 4.6 61.1 1.0
OE2 G:1JY303 4.7 62.3 1.0
HG13 G:VAL262 4.7 41.5 1.0
HG11 G:VAL262 4.7 41.5 1.0
HB G:THR78 4.7 42.5 1.0
HG21 G:ILE79 4.8 35.3 1.0
C G:THR78 4.9 37.4 1.0
CA G:ILE79 4.9 28.9 1.0
H2 G:HOH430 4.9 30.5 1.0

Magnesium binding site 7 out of 7 in 4isk

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Magnesium binding site 7 out of 7 in the Crystal Structure of E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor


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 E.Coli Thymidylate Synthase with Dump and the Bgc 945 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:36.9
occ:1.00
 O H:HOH453 2.1 43.7 1.0
O H:HOH449 2.1 38.7 1.0
O H:HOH451 2.2 38.5 1.0
O H:HOH452 2.2 45.7 1.0
O H:HOH450 2.2 32.5 1.0
O H:HOH448 2.3 44.6 1.0
H1 H:HOH409 3.3 42.4 1.0
H1 H:HOH428 3.6 45.5 1.0
H1 H:HOH420 3.9 46.9 1.0
HA H:ILE79 3.9 38.2 1.0
O H:HOH409 4.0 35.3 1.0
HG1 H:THR78 4.0 42.3 1.0
OG1 H:THR78 4.1 35.2 1.0
O H:THR78 4.1 39.1 1.0
OE2 H:GLU82 4.1 50.7 1.0
OE1 H:1JY303 4.1 1.0 1.0
OAG H:1JY303 4.4 34.5 1.0
OE1 H:GLU82 4.4 54.9 1.0
HB H:THR78 4.5 44.2 1.0
O H:HOH428 4.5 38.0 1.0
OAE H:1JY303 4.5 49.3 1.0
H2 H:HOH409 4.6 42.4 1.0
C H:THR78 4.6 34.8 1.0
CD H:1JY303 4.7 0.3 1.0
CD H:GLU82 4.7 53.8 1.0
HG11 H:VAL262 4.8 47.0 1.0
CB H:1JY303 4.8 94.5 1.0
CB H:THR78 4.8 36.8 1.0
O H:HOH420 4.8 39.1 1.0
CA H:ILE79 4.8 31.9 1.0
HG13 H:VAL262 4.9 47.0 1.0
H2 H:HOH428 5.0 45.5 1.0
H2 H:HOH420 5.0 46.9 1.0

Reference:

A.Tochowicz, S.Dalziel, O.Eidam, J.D.O'connell, S.Griner, J.S.Finer-Moore, R.M.Stroud. Development and Binding Mode Assessment of N-[4-[2-Propyn-1-Yl[(6S)-4,6,7,8-Tetrahydro-2- (Hydroxymethyl)-4-Oxo-3H-Cyclopenta[G]Quinazolin-6- Yl]Amino]Benzoyl]-L-Gamma-Glutamyl-D-Glutamic Acid (Bgc 945), A Novel Thymidylate Synthase Inhibitor That Targets Tumor Cells. J.Med.Chem. V. 56 5446 2013.
ISSN: ISSN 0022-2623
PubMed: 23710599
DOI: 10.1021/JM400490E
Page generated: Fri Aug 16 17:01:27 2024

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