Magnesium in PDB 7lz7: Tubulin-RB3_SLD-Ttl in Complex with Compound 5K

Protein crystallography data

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5K, PDB code: 7lz7 was solved by S.W.White, M.Yun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.88 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.211, 157.998, 182.056, 90, 90, 90
R / Rfree (%) 17.1 / 21.1

Other elements in 7lz7:

The structure of Tubulin-RB3_SLD-Ttl in Complex with Compound 5K also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5K (pdb code 7lz7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5K, PDB code: 7lz7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7lz7

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Magnesium binding site 1 out of 5 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-RB3_SLD-Ttl in Complex with Compound 5K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:32.7
occ:1.00
O2G A:GTP501 2.0 23.5 1.0
O A:HOH609 2.1 32.5 1.0
O A:HOH604 2.1 30.9 1.0
O A:HOH601 2.1 37.1 1.0
O A:HOH620 2.2 35.3 1.0
O2B A:GTP501 2.2 15.8 1.0
PG A:GTP501 3.1 34.1 1.0
PB A:GTP501 3.2 27.7 1.0
O3B A:GTP501 3.5 40.8 1.0
O3A A:GTP501 3.5 36.4 1.0
O3G A:GTP501 3.6 30.2 1.0
OE2 A:GLU71 3.8 59.7 1.0
NZ B:LYS252 4.0 55.8 1.0
CB A:GLN11 4.1 30.9 1.0
OD1 A:ASP69 4.3 42.2 1.0
O2A A:GTP501 4.3 36.6 1.0
N A:GLN11 4.4 31.7 1.0
O1G A:GTP501 4.4 23.5 1.0
PA A:GTP501 4.5 34.0 1.0
OD2 A:ASP69 4.5 46.0 1.0
O1B A:GTP501 4.5 39.6 1.0
CB A:ASP98 4.6 35.7 1.0
OE1 A:GLN11 4.7 39.0 1.0
O A:HOH619 4.8 37.6 1.0
CA A:GLN11 4.8 35.3 1.0
CG A:ASP69 4.9 44.5 1.0
O1A A:GTP501 4.9 19.3 1.0

Magnesium binding site 2 out of 5 in 7lz7

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Magnesium binding site 2 out of 5 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-RB3_SLD-Ttl in Complex with Compound 5K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg505

b:22.4
occ:1.00
OE1 B:GLN11 2.1 53.1 1.0
O B:HOH603 2.2 29.0 1.0
O2A B:GDP502 2.2 25.6 1.0
O B:HOH601 2.2 57.1 1.0
O C:HOH638 2.2 49.0 1.0
O B:HOH628 2.3 32.2 1.0
CD B:GLN11 3.3 54.3 1.0
PA B:GDP502 3.4 25.9 1.0
O3A B:GDP502 3.6 36.3 1.0
OD2 B:ASP177 3.6 56.9 1.0
CB B:GLN11 4.1 34.5 1.0
ND2 B:ASN99 4.1 25.6 1.0
C5' B:GDP502 4.2 18.6 1.0
O5' B:GDP502 4.2 8.3 1.0
CG B:GLN11 4.2 46.0 1.0
NE2 B:GLN11 4.2 55.1 1.0
O1A B:GDP502 4.6 14.3 1.0
O2B B:GDP502 4.7 18.9 1.0
OE1 C:GLU254 4.7 54.6 1.0
CG B:ASP177 4.7 54.1 1.0
PB B:GDP502 4.8 25.1 1.0
C8 B:GDP502 5.0 31.6 1.0

Magnesium binding site 3 out of 5 in 7lz7

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Magnesium binding site 3 out of 5 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-RB3_SLD-Ttl in Complex with Compound 5K within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:29.0
occ:1.00
O C:HOH606 1.9 36.5 1.0
O2B C:GTP501 2.0 23.0 1.0
O3G C:GTP501 2.1 18.9 1.0
O C:HOH609 2.1 16.7 1.0
O C:HOH603 2.1 26.6 1.0
O C:HOH649 2.2 43.3 1.0
PB C:GTP501 3.1 27.0 1.0
PG C:GTP501 3.3 23.7 1.0
OE1 C:GLU71 3.4 68.2 1.0
O3B C:GTP501 3.6 25.1 1.0
O3A C:GTP501 3.6 38.8 1.0
O2G C:GTP501 3.9 24.7 1.0
CB C:GLN11 4.1 22.6 1.0
OD1 C:ASP69 4.2 32.0 1.0
OD2 C:ASP69 4.3 31.9 1.0
NZ D:LYS252 4.4 64.1 1.0
N C:GLN11 4.4 22.0 1.0
O1B C:GTP501 4.4 25.4 1.0
O1G C:GTP501 4.5 18.7 1.0
O2A C:GTP501 4.5 31.1 1.0
PA C:GTP501 4.6 28.5 1.0
OD2 C:ASP98 4.6 53.6 1.0
CD C:GLU71 4.6 63.3 1.0
CB C:ASP98 4.7 29.0 1.0
CG C:ASP69 4.7 33.9 1.0
OE1 C:GLN11 4.8 36.0 1.0
CA C:GLN11 4.8 28.8 1.0
O1A C:GTP501 5.0 25.0 1.0

Magnesium binding site 4 out of 5 in 7lz7

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Magnesium binding site 4 out of 5 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-RB3_SLD-Ttl in Complex with Compound 5K within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:62.4
occ:1.00
OE1 D:GLN11 2.2 110.0 1.0
O2A D:GTP501 2.2 68.2 1.0
O D:HOH601 3.2 45.9 1.0
CD D:GLN11 3.3 99.1 1.0
PA D:GTP501 3.5 51.9 1.0
O2G D:GTP501 3.5 107.8 1.0
O3A D:GTP501 3.7 62.6 1.0
NE2 D:GLN11 4.1 92.3 1.0
CB D:GLN11 4.2 83.6 1.0
OD1 D:ASN99 4.3 63.6 1.0
CG D:GLN11 4.4 94.8 1.0
O1A D:GTP501 4.5 43.4 1.0
C5' D:GTP501 4.5 42.4 1.0
O5' D:GTP501 4.5 50.1 1.0
O1B D:GTP501 4.6 51.6 1.0
PB D:GTP501 4.8 65.2 1.0
PG D:GTP501 4.9 106.4 1.0

Magnesium binding site 5 out of 5 in 7lz7

Go back to Magnesium Binding Sites List in 7lz7
Magnesium binding site 5 out of 5 in the Tubulin-RB3_SLD-Ttl in Complex with Compound 5K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-RB3_SLD-Ttl in Complex with Compound 5K within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:95.2
occ:1.00
O3G F:ACP402 2.0 110.1 1.0
OE1 F:GLU331 2.1 132.9 1.0
O2B F:ACP402 2.3 138.5 1.0
CD F:GLU331 3.1 119.8 1.0
PG F:ACP402 3.4 119.0 1.0
ND2 F:ASN333 3.4 92.1 1.0
OE2 F:GLU331 3.6 134.8 1.0
PB F:ACP402 3.7 131.3 1.0
NZ F:LYS74 3.8 77.4 1.0
O1G F:ACP402 3.8 119.0 1.0
CG F:ASN333 4.1 76.8 1.0
C3B F:ACP402 4.2 126.5 1.0
O1B F:ACP402 4.2 132.9 1.0
CG F:GLU331 4.4 91.6 1.0
O2G F:ACP402 4.5 114.1 1.0
CB F:ASN333 4.6 55.5 1.0
OD1 F:ASN333 4.8 75.6 1.0
O3A F:ACP402 5.0 120.0 1.0

Reference:

S.Banerjee, F.Mahmud, S.Deng, L.Ma, M.K.Yun, S.O.Fakayode, K.E.Arnst, L.Yang, H.Chen, Z.Wu, P.B.Lukka, K.Parmar, B.Meibohm, S.W.White, Y.Wang, W.Li, D.D.Miller. X-Ray Crystallography-Guided Design, Antitumor Efficacy, and Qsar Analysis of Metabolically Stable Cyclopenta-Pyrimidinyl Dihydroquinoxalinone As A Potent Tubulin Polymerization Inhibitor. J.Med.Chem. V. 64 13072 2021.
ISSN: ISSN 0022-2623
PubMed: 34406768
DOI: 10.1021/ACS.JMEDCHEM.1C01202
Page generated: Fri Sep 24 15:24:56 2021

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