Atomistry » Magnesium » PDB 2g9z-2gqp » 2gm1
Atomistry »
  Magnesium »
    PDB 2g9z-2gqp »
      2gm1 »

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

Go back to Magnesium Binding Sites List in 2gm1
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

Go back to Magnesium Binding Sites List in 2gm1
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

Go back to Magnesium Binding Sites List in 2gm1
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: Mon Dec 14 07:24:41 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy