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Magnesium in PDB 2gm1: Crystal Structure of the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide

Protein crystallography data

The structure of Crystal Structure of the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide, PDB code: 2gm1 was solved by S.Sheriff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.86 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.700, 112.600, 108.100, 90.00, 90.20, 90.00
R / Rfree (%) 23 / 26.9

Other elements in 2gm1:

The structure of Crystal Structure of the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide (pdb code 2gm1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide, PDB code: 2gm1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2gm1

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Magnesium binding site 1 out of 8 in the Crystal Structure of the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide


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 the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg369

b:19.1
occ:1.00
 OG1 A:THR112 2.2 18.7 1.0
O A:HOH375 2.2 12.7 1.0
O A:HOH376 2.3 11.3 1.0
O A:HOH373 2.3 14.4 1.0
O A:HOH374 2.3 19.1 1.0
O3B A:ADP372 2.4 13.9 1.0
CB A:THR112 3.1 17.6 1.0
PB A:ADP372 3.5 13.9 1.0
O1B A:ADP372 3.5 16.5 1.0
O2A A:ADP372 4.0 15.2 1.0
CG2 A:THR112 4.1 15.3 1.0
N A:THR112 4.1 16.6 1.0
OD2 A:ASP265 4.2 26.6 1.0
CA A:THR112 4.2 16.2 1.0
O A:SER232 4.3 31.2 1.0
O A:HOH379 4.3 23.1 1.0
O3A A:ADP372 4.4 15.5 1.0
O2B A:ADP372 4.5 13.4 1.0
O A:HOH381 4.6 14.9 1.0
PA A:ADP372 4.6 16.4 1.0
OD1 A:ASP265 4.7 24.8 1.0
O1A A:ADP372 4.8 18.2 1.0
O A:HOH391 4.8 20.1 1.0
CG A:ASP265 4.9 23.7 1.0

Magnesium binding site 2 out of 8 in 2gm1

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Magnesium binding site 2 out of 8 in the Crystal Structure of the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide


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 the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg370

b:41.2
occ:1.00
 O A:SER232 2.3 31.2 1.0
O A:SER235 2.5 22.9 1.0
O A:HOH379 2.6 23.1 1.0
OG A:SER235 2.7 24.8 1.0
C A:SER235 3.3 22.9 1.0
C A:SER232 3.3 29.3 1.0
O A:HOH374 3.6 19.1 1.0
N A:SER235 3.6 22.7 1.0
CA A:SER235 3.7 22.9 1.0
CB A:SER235 3.8 22.9 1.0
CA A:SER232 4.0 30.0 1.0
O A:HOH373 4.1 14.4 1.0
O A:TYR231 4.1 26.4 1.0
O A:HOH396 4.1 21.9 1.0
N A:SER233 4.2 26.5 1.0
C A:SER233 4.3 24.8 1.0
O A:LEU266 4.3 20.1 1.0
N A:HIS236 4.4 22.5 1.0
CA A:SER233 4.4 26.5 1.0
N A:ARG234 4.5 25.5 1.0
CA A:ALA267 4.5 17.1 1.0
O A:SER233 4.5 24.9 1.0
C A:ARG234 4.6 24.2 1.0
O A:ASP265 4.7 15.4 1.0
CA A:HIS236 4.8 21.9 1.0
C A:LEU266 4.8 18.0 1.0
O A:HOH376 4.8 11.3 1.0
N A:ALA267 4.8 18.6 1.0
C A:TYR231 5.0 28.2 1.0

Magnesium binding site 3 out of 8 in 2gm1

Go back to Magnesium Binding Sites List in 2gm1
Magnesium binding site 3 out of 8 in the Crystal Structure of the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide


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 the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg369

b:23.8
occ:1.00
 OG1 B:THR112 2.3 17.6 1.0
O B:HOH375 2.3 11.8 1.0
O3B B:ADP372 2.3 15.6 1.0
O B:HOH376 2.3 21.1 1.0
O B:HOH373 2.4 19.7 1.0
O B:HOH374 2.4 22.4 1.0
CB B:THR112 3.2 18.1 1.0
PB B:ADP372 3.4 16.9 1.0
O1B B:ADP372 3.4 17.3 1.0
OD2 B:ASP265 4.1 27.8 1.0
O2A B:ADP372 4.1 15.8 1.0
N B:THR112 4.2 16.9 1.0
O B:SER232 4.2 34.6 1.0
O B:HOH390 4.2 29.5 1.0
CG2 B:THR112 4.2 15.2 1.0
O B:HOH385 4.2 20.0 1.0
CA B:THR112 4.3 16.3 1.0
O2B B:ADP372 4.4 14.1 1.0
O B:HOH384 4.4 19.7 1.0
O3A B:ADP372 4.4 15.8 1.0
OD1 B:ASP265 4.6 27.4 1.0
PA B:ADP372 4.7 18.3 1.0
CG B:ASP265 4.8 24.9 1.0
O1A B:ADP372 4.8 20.0 1.0
O B:HOH407 4.9 39.5 1.0
CB B:LYS111 5.0 15.5 1.0
MG B:MG370 5.0 51.8 1.0

Magnesium binding site 4 out of 8 in 2gm1

Go back to Magnesium Binding Sites List in 2gm1
Magnesium binding site 4 out of 8 in the Crystal Structure of the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide


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 the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg370

b:51.8
occ:1.00
 O B:SER232 2.3 34.6 1.0
O B:SER235 2.4 24.7 1.0
O B:HOH407 2.5 39.5 1.0
OG B:SER235 2.7 29.4 1.0
O B:HOH385 2.8 20.0 1.0
C B:SER235 3.2 24.4 1.0
C B:SER232 3.3 32.0 1.0
N B:SER235 3.5 25.3 1.0
CA B:SER235 3.7 25.1 1.0
O B:HOH374 3.7 22.4 1.0
CB B:SER235 3.7 27.1 1.0
CA B:SER232 4.0 31.9 1.0
O B:HOH373 4.0 19.7 1.0
O B:TYR231 4.0 31.2 1.0
N B:SER233 4.2 30.2 1.0
C B:SER233 4.2 28.8 1.0
O B:LEU266 4.3 23.6 1.0
N B:HIS236 4.3 24.0 1.0
CA B:SER233 4.3 29.8 1.0
N B:ARG234 4.4 28.6 1.0
CA B:ALA267 4.4 19.9 1.0
O B:SER233 4.5 28.9 1.0
C B:ARG234 4.5 27.5 1.0
O B:ASP265 4.7 19.8 1.0
CA B:HIS236 4.7 23.2 1.0
C B:LEU266 4.7 21.2 1.0
N B:ALA267 4.8 20.6 1.0
O B:HOH376 5.0 21.1 1.0
C B:TYR231 5.0 31.7 1.0
MG B:MG369 5.0 23.8 1.0

Magnesium binding site 5 out of 8 in 2gm1

Go back to Magnesium Binding Sites List in 2gm1
Magnesium binding site 5 out of 8 in the Crystal Structure of the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide


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 the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg369

b:24.2
occ:1.00
 O D:HOH375 2.3 17.2 1.0
OG1 D:THR112 2.3 15.5 1.0
O D:HOH374 2.3 17.5 1.0
O D:HOH373 2.3 22.0 1.0
O3B D:ADP372 2.3 15.4 1.0
O D:HOH376 2.3 13.1 1.0
CB D:THR112 3.3 16.2 1.0
PB D:ADP372 3.4 13.6 1.0
O1B D:ADP372 3.4 16.4 1.0
OD2 D:ASP265 4.1 26.4 1.0
O D:SER232 4.1 31.2 1.0
O2A D:ADP372 4.1 16.9 1.0
N D:THR112 4.2 14.8 1.0
O D:HOH380 4.2 18.1 1.0
CG2 D:THR112 4.2 13.4 1.0
CA D:THR112 4.3 14.4 1.0
O2B D:ADP372 4.4 14.8 1.0
O D:HOH377 4.4 10.4 1.0
O3A D:ADP372 4.4 16.5 1.0
OD1 D:ASP265 4.5 26.7 1.0
PA D:ADP372 4.7 16.4 1.0
CG D:ASP265 4.7 24.5 1.0
MG D:MG370 4.7 41.6 1.0
O1A D:ADP372 4.9 16.5 1.0
O D:HOH389 4.9 24.1 1.0
C D:SER232 4.9 30.3 1.0
CB D:LYS111 5.0 14.9 1.0

Magnesium binding site 6 out of 8 in 2gm1

Go back to Magnesium Binding Sites List in 2gm1
Magnesium binding site 6 out of 8 in the Crystal Structure of the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide


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 the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg370

b:41.6
occ:1.00
 O D:SER232 2.4 31.2 1.0
O D:HOH389 2.4 24.1 1.0
O D:SER235 2.6 21.6 1.0
O D:HOH380 2.7 18.1 1.0
OG D:SER235 2.8 23.1 1.0
C D:SER232 3.3 30.3 1.0
C D:SER235 3.4 21.3 1.0
O D:HOH374 3.4 17.5 1.0
O D:HOH373 3.7 22.0 1.0
N D:SER235 3.8 22.1 1.0
CB D:SER235 3.8 21.4 1.0
CA D:SER235 3.8 21.6 1.0
CA D:SER232 4.0 31.7 1.0
O D:TYR231 4.2 30.4 1.0
O D:LEU266 4.3 17.6 1.0
N D:SER233 4.3 28.3 1.0
C D:SER233 4.4 26.5 1.0
N D:HIS236 4.4 20.9 1.0
CA D:SER233 4.5 26.9 1.0
O D:ASP265 4.6 15.9 1.0
CA D:ALA267 4.6 17.6 1.0
N D:ARG234 4.6 26.0 1.0
O D:SER233 4.6 25.5 1.0
C D:ARG234 4.7 23.9 1.0
MG D:MG369 4.7 24.2 1.0
C D:LEU266 4.7 17.3 1.0
CA D:HIS236 4.8 20.7 1.0
O D:HOH376 4.8 13.1 1.0
N D:ALA267 4.9 17.4 1.0

Magnesium binding site 7 out of 8 in 2gm1

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Magnesium binding site 7 out of 8 in the Crystal Structure of the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide


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 the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg369

b:22.4
occ:1.00
 O E:HOH375 2.2 11.8 1.0
O3B E:ADP372 2.2 15.9 1.0
OG1 E:THR112 2.3 17.9 1.0
O E:HOH376 2.3 14.9 1.0
O E:HOH373 2.4 15.7 1.0
O E:HOH374 2.4 23.3 1.0
CB E:THR112 3.2 16.4 1.0
PB E:ADP372 3.3 15.3 1.0
O1B E:ADP372 3.4 18.8 1.0
O2A E:ADP372 4.1 18.5 1.0
N E:THR112 4.1 14.5 1.0
OD2 E:ASP265 4.1 23.8 1.0
O E:SER232 4.2 32.6 1.0
O E:HOH389 4.2 13.7 1.0
CG2 E:THR112 4.2 14.2 1.0
CA E:THR112 4.3 16.0 1.0
O E:HOH420 4.3 31.0 1.0
O2B E:ADP372 4.3 12.9 1.0
O3A E:ADP372 4.3 16.7 1.0
O E:HOH379 4.5 10.7 1.0
OD1 E:ASP265 4.5 23.5 1.0
PA E:ADP372 4.6 17.9 1.0
O1A E:ADP372 4.7 18.4 1.0
CG E:ASP265 4.7 21.5 1.0
MG E:MG370 4.9 39.4 1.0
CB E:LYS111 4.9 15.7 1.0
CE E:LYS111 5.0 14.3 1.0

Magnesium binding site 8 out of 8 in 2gm1

Go back to Magnesium Binding Sites List in 2gm1
Magnesium binding site 8 out of 8 in the Crystal Structure of the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide


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 the Mitotic Kinesin EG5 in Complex with Mg-Adp and N-(3-Aminopropyl)-N-((3-Benzyl-5-Chloro-4-Oxo-3,4- Dihydropyrrolo[2,1-F][1,2,4]Triazin-2-Yl)(Cyclopropyl)Methyl)-4- Methylbenzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg370

b:39.4
occ:1.00
 O E:SER232 2.4 32.6 1.0
O E:HOH410 2.4 24.4 1.0
O E:SER235 2.5 22.4 1.0
O E:HOH389 2.7 13.7 1.0
OG E:SER235 2.9 25.9 1.0
C E:SER235 3.3 21.7 1.0
C E:SER232 3.4 31.5 1.0
O E:HOH374 3.6 23.3 1.0
N E:SER235 3.7 23.1 1.0
O E:HOH373 3.7 15.7 1.0
CA E:SER235 3.8 22.9 1.0
CB E:SER235 3.9 22.8 1.0
O E:LEU266 4.1 16.5 1.0
CA E:SER232 4.2 32.1 1.0
O E:TYR231 4.3 30.8 1.0
C E:SER233 4.3 27.5 1.0
N E:SER233 4.3 29.0 1.0
CA E:ALA267 4.4 18.1 1.0
N E:HIS236 4.4 21.0 1.0
CA E:SER233 4.4 28.4 1.0
O E:SER233 4.5 27.8 1.0
O E:ASP265 4.5 15.3 1.0
N E:ARG234 4.5 25.9 1.0
C E:LEU266 4.6 17.7 1.0
C E:ARG234 4.6 24.8 1.0
N E:ALA267 4.7 17.6 1.0
CA E:HIS236 4.7 19.7 1.0
MG E:MG369 4.9 22.4 1.0
O E:HOH376 4.9 14.9 1.0
O E:HOH379 4.9 10.7 1.0
OD1 E:ASP265 5.0 23.5 1.0

Reference:

K.S.Kim, S.Lu, L.A.Cornelius, L.J.Lombardo, R.M.Borzilleri, G.M.Schroeder, C.Sheng, G.Rovnyak, D.Crews, R.J.Schmidt, D.K.Williams, R.S.Bhide, S.C.Traeger, P.A.Mcdonnell, L.Mueller, S.Sheriff, J.A.Newitt, A.T.Pudzianowski, Z.Yang, R.Wild, F.Y.Lee, R.Batorsky, J.S.Ryder, M.Ortega-Nanos, H.Shen, M.Gottardis, D.L.Roussell. Synthesis and Sar of Pyrrolotriazine-4-One Based EG5 Inhibitors. Bioorg.Med.Chem.Lett. V. 16 3937 2006.
ISSN: ISSN 0960-894X
PubMed: 16730979
DOI: 10.1016/J.BMCL.2006.05.037
Page generated: Tue Aug 13 23:32:07 2024

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