Magnesium in PDB 6gim: Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18)

Protein crystallography data

The structure of Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18), PDB code: 6gim was solved by C.R.Millan, C.Dardonvile, H.P.De Koning, N.Saperas, J.L.Campos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.04 / 1.43
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 22.630, 40.470, 72.255, 90.00, 93.91, 90.00
R / Rfree (%) 14.3 / 19.3

Other elements in 6gim:

The structure of Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18) (pdb code 6gim). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18), PDB code: 6gim:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6gim

Go back to Magnesium Binding Sites List in 6gim
Magnesium binding site 1 out of 3 in the Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg102

b:31.3
occ:0.50
O C:HOH224 1.9 23.9 1.0
O C:HOH223 2.1 25.2 1.0
O C:HOH217 2.3 27.6 1.0
O C:HOH209 4.1 29.4 1.0
OP2 C:DT4 4.3 20.9 1.0
O C:HOH208 4.3 23.6 1.0
O C:HOH204 4.6 27.8 1.0
OP2 C:DA3 4.8 27.6 1.0

Magnesium binding site 2 out of 3 in 6gim

Go back to Magnesium Binding Sites List in 6gim
Magnesium binding site 2 out of 3 in the Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:14.5
occ:1.00
O A:HOH208 2.0 14.0 1.0
O A:HOH211 2.1 15.1 1.0
O A:HOH221 2.1 13.2 1.0
O A:HOH207 2.2 14.9 1.0
O A:HOH216 4.1 15.2 1.0
O A:HOH202 4.1 15.0 1.0
O A:HOH220 4.1 27.1 1.0
O B:HOH222 4.2 28.2 1.0
N7 A:DA3 4.2 9.1 1.0
O B:HOH217 4.3 30.1 1.0
O A:HOH212 4.4 14.5 1.0
C2' A:DA2 4.5 12.6 1.0
O4 A:DT4 4.5 10.3 1.0
OP2 A:DA3 4.5 15.6 1.0
C7 A:DT4 4.6 10.8 1.0
C8 A:DA3 4.8 10.3 1.0

Magnesium binding site 3 out of 3 in 6gim

Go back to Magnesium Binding Sites List in 6gim
Magnesium binding site 3 out of 3 in the Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:20.2
occ:1.00
O B:HOH210 1.9 25.8 1.0
O C:HOH226 2.0 31.5 1.0
O C:HOH220 2.0 26.6 1.0
O C:HOH221 3.8 45.8 1.0
O4' B:DA2 4.1 15.7 1.0
O B:HOH219 4.2 17.3 1.0
O A:HOH213 4.3 20.3 1.0
N3 B:DA1 4.4 14.5 1.0
C4' B:DA2 4.6 19.0 1.0
N3 C:DA1 4.7 15.7 1.0
C2' B:DA1 4.9 21.0 1.0

Reference:

C.R.Millan, F.J.Acosta-Reyes, L.Lagartera, G.U.Ebiloma, L.Lemgruber, J.J.Nue Martinez, N.Saperas, C.Dardonville, H.P.De Koning, J.L.Campos. Functional and Structural Analysis of at-Specific Minor Groove Binders That Disrupt Dna-Protein Interactions and Cause Disintegration of the Trypanosoma Brucei Kinetoplast. Nucleic Acids Res. V. 45 8378 2017.
ISSN: ESSN 1362-4962
PubMed: 28637278
DOI: 10.1093/NAR/GKX521
Page generated: Mon Dec 14 22:45:06 2020

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