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Magnesium in PDB 5jcb: Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1

Protein crystallography data

The structure of Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1, PDB code: 5jcb was solved by Z.Guan, W.Zhao, P.Yin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.64 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.357, 157.252, 179.631, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 20

Other elements in 5jcb:

The structure of Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1 also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1 (pdb code 5jcb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1, PDB code: 5jcb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5jcb

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Magnesium binding site 1 out of 7 in the Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:40.8
occ:1.00
 O A:HOH619 2.0 29.7 1.0
O A:HOH652 2.1 34.5 1.0
O A:HOH607 2.2 35.0 1.0
O1B A:GTP501 2.2 36.6 1.0
O1G A:GTP501 2.3 32.6 1.0
PG A:GTP501 3.3 37.7 1.0
PB A:GTP501 3.3 31.9 1.0
OE1 A:GLU71 3.6 75.3 1.0
O2G A:GTP501 3.7 39.1 1.0
O3B A:GTP501 3.7 46.4 1.0
O3A A:GTP501 3.9 45.5 1.0
OD2 A:ASP69 3.9 37.9 1.0
OD1 A:ASP69 3.9 45.5 1.0
CB A:GLN11 4.0 32.1 1.0
NZ B:LYS254 4.2 53.0 1.0
OE1 A:GLN11 4.3 45.3 1.0
N A:GLN11 4.3 29.6 1.0
CG A:ASP69 4.4 41.5 1.0
OD2 A:ASP98 4.5 58.2 1.0
CD A:GLU71 4.5 73.6 1.0
CB A:ASP98 4.6 36.7 1.0
O2B A:GTP501 4.6 38.8 1.0
O3G A:GTP501 4.7 35.5 1.0
O1A A:GTP501 4.7 45.9 1.0
CA A:GLN11 4.7 36.5 1.0
CG A:ASP98 4.8 51.5 1.0
PA A:GTP501 4.9 46.6 1.0

Magnesium binding site 2 out of 7 in 5jcb

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Magnesium binding site 2 out of 7 in the Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:74.7
occ:1.00
 OG1 A:THR130 2.0 69.7 1.0
O A:MET1 2.5 55.6 1.0
OE2 A:GLU3 2.9 56.5 1.0
CD A:GLU3 3.3 52.5 1.0
OE1 A:GLU3 3.3 50.1 1.0
CB A:THR130 3.4 54.4 1.0
CE A:MET1 3.5 52.3 1.0
C A:MET1 3.5 52.8 1.0
N A:GLY131 3.5 49.3 1.0
C A:THR130 3.9 52.2 1.0
SD A:MET1 4.0 53.2 1.0
CA A:THR130 4.0 56.4 1.0
CA A:ARG2 4.1 42.4 1.0
N A:THR130 4.1 55.4 1.0
CA A:GLY131 4.2 50.0 1.0
N A:ARG2 4.2 48.8 1.0
CG2 A:THR130 4.3 47.2 1.0
O A:HOH651 4.3 59.5 1.0
CG A:GLU3 4.5 50.2 1.0
CA A:MET1 4.6 55.2 1.0
CB A:MET1 4.6 54.8 1.0
N A:GLU3 4.7 41.7 1.0
O A:HOH623 4.8 62.8 1.0
O A:THR130 4.8 59.6 1.0
C A:ARG2 4.8 45.2 1.0
O A:GLY131 4.8 49.8 1.0
C A:GLY131 4.8 55.0 1.0
N A:MET1 4.9 54.3 1.0
CG A:MET1 5.0 58.6 1.0

Magnesium binding site 3 out of 7 in 5jcb

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Magnesium binding site 3 out of 7 in the Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:20.0
occ:1.00
 OE1 B:GLN11 2.2 33.0 1.0
O1A B:GDP501 2.3 25.5 1.0
O B:HOH619 2.6 30.2 1.0
O B:HOH669 2.9 42.2 1.0
CD B:GLN11 3.4 41.5 1.0
PA B:GDP501 3.5 28.1 1.0
OD2 B:ASP179 3.7 54.0 1.0
O3A B:GDP501 3.9 25.6 1.0
CB B:GLN11 4.1 27.6 1.0
CG B:GLN11 4.2 35.1 1.0
OD1 B:ASN101 4.3 36.8 1.0
O5' B:GDP501 4.4 28.6 1.0
C5' B:GDP501 4.4 24.9 1.0
NE2 B:GLN11 4.4 52.3 1.0
OE1 C:GLU254 4.4 51.6 1.0
O2A B:GDP501 4.6 26.8 1.0
CG B:ASP179 4.7 39.8 1.0
O2B B:GDP501 4.7 17.9 1.0
C8 B:GDP501 4.8 29.6 1.0
PB B:GDP501 4.9 28.4 1.0

Magnesium binding site 4 out of 7 in 5jcb

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Magnesium binding site 4 out of 7 in the Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:27.8
occ:1.00
 O C:HOH684 1.9 26.2 1.0
O1G C:GTP502 2.0 27.0 1.0
O C:HOH633 2.1 24.7 1.0
O C:HOH615 2.1 24.5 1.0
O1B C:GTP502 2.2 24.9 1.0
PG C:GTP502 3.1 32.2 1.0
PB C:GTP502 3.3 25.5 1.0
OE1 C:GLU71 3.4 85.3 1.0
O2G C:GTP502 3.5 31.8 1.0
O3B C:GTP502 3.6 36.5 1.0
NZ D:LYS254 3.8 35.5 1.0
O3A C:GTP502 3.8 27.4 1.0
OD1 C:ASP69 4.2 28.1 1.0
CB C:GLN11 4.2 21.6 1.0
OD2 C:ASP98 4.2 50.0 1.0
OD2 C:ASP69 4.3 22.8 1.0
O3G C:GTP502 4.4 26.9 1.0
CB C:ASP98 4.4 25.2 1.0
N C:GLN11 4.5 21.3 1.0
O2B C:GTP502 4.5 28.2 1.0
CD C:GLU71 4.6 71.5 1.0
O1A C:GTP502 4.7 27.0 1.0
CG C:ASP98 4.7 44.9 1.0
CG C:ASP69 4.7 31.1 1.0
OE1 C:GLN11 4.8 39.3 1.0
PA C:GTP502 4.9 31.3 1.0
CA C:GLN11 5.0 21.4 1.0
CE D:LYS254 5.0 33.3 1.0

Magnesium binding site 5 out of 7 in 5jcb

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Magnesium binding site 5 out of 7 in the Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:52.7
occ:1.00
 O1A D:GDP501 2.5 50.5 1.0
OE1 D:GLN11 2.6 60.0 1.0
OD2 D:ASP179 3.0 87.8 1.0
PA D:GDP501 3.6 48.9 1.0
O3A D:GDP501 3.7 50.1 1.0
CD D:GLN11 3.8 64.0 1.0
OD1 D:ASN101 3.8 68.4 1.0
C5' D:GDP501 4.0 51.0 1.0
CG D:ASP179 4.2 97.8 1.0
O5' D:GDP501 4.3 51.8 1.0
CB D:GLN11 4.6 50.7 1.0
NE2 D:GLN11 4.7 71.1 1.0
CG D:ASN101 4.7 64.7 1.0
ND2 D:ASN101 4.7 63.9 1.0
CG D:GLN11 4.7 54.6 1.0
O2B D:GDP501 4.8 43.1 1.0
O2A D:GDP501 4.8 43.5 1.0
PB D:GDP501 4.9 47.5 1.0
CB D:ASP179 4.9 99.0 1.0

Magnesium binding site 6 out of 7 in 5jcb

Go back to Magnesium Binding Sites List in 5jcb
Magnesium binding site 6 out of 7 in the Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:60.0
occ:1.00
 C28 D:NV4507 2.3 89.9 1.0
N D:CYS241 2.6 39.9 1.0
O D:VAL238 3.1 34.0 1.0
N D:THR240 3.1 37.6 1.0
O D:GLY237 3.2 36.2 1.0
CB D:CYS241 3.3 38.3 1.0
C D:VAL238 3.4 41.0 1.0
CA D:CYS241 3.5 31.4 1.0
C D:THR240 3.5 36.7 1.0
CG1 D:ILE318 3.5 62.0 1.0
O25 D:NV4507 3.5 77.0 1.0
CA D:THR240 3.6 36.3 1.0
SG D:CYS241 3.6 56.7 1.0
CB D:THR240 3.6 39.4 1.0
O24 D:NV4507 3.6 68.4 1.0
C D:THR239 3.7 35.8 1.0
CD1 D:ILE318 3.8 62.2 0.3
N D:THR239 3.9 38.7 1.0
CA D:VAL238 4.0 41.6 1.0
C10 D:NV4507 4.0 65.0 1.0
C27 D:NV4507 4.1 70.1 1.0
CA D:THR239 4.2 35.7 1.0
C D:GLY237 4.3 37.2 1.0
C9 D:NV4507 4.3 69.9 1.0
O D:THR239 4.4 33.3 1.0
C D:CYS241 4.5 28.8 1.0
N D:LEU242 4.5 35.5 1.0
CG2 D:ILE318 4.5 30.8 1.0
CB D:ILE318 4.5 41.3 1.0
CG2 D:THR240 4.5 31.8 1.0
OG1 D:THR240 4.6 43.0 1.0
N D:VAL238 4.7 33.6 1.0
O D:THR240 4.7 38.2 1.0

Magnesium binding site 7 out of 7 in 5jcb

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Magnesium binding site 7 out of 7 in the Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Microtubule Depolymerizing Agent Podophyllotoxin Derivative YJTSF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:75.5
occ:1.00
 O3G F:ACP402 2.1 0.6 1.0
O2B F:ACP402 2.6 91.3 1.0
OE2 F:GLU331 2.9 90.6 1.0
OD2 F:ASP318 3.0 80.0 1.0
NH1 F:ARG222 3.2 79.7 1.0
OD1 F:ASN333 3.4 0.4 1.0
PG F:ACP402 3.6 0.6 1.0
NH2 F:ARG202 3.7 50.8 1.0
PB F:ACP402 3.9 90.0 1.0
CG F:ASP318 4.0 64.5 1.0
CD F:GLU331 4.1 78.1 1.0
O2A F:ACP402 4.3 94.8 1.0
O2G F:ACP402 4.4 0.2 1.0
O1B F:ACP402 4.4 85.7 1.0
CZ F:ARG222 4.4 77.3 1.0
C3B F:ACP402 4.4 0.1 1.0
OD1 F:ASP318 4.5 65.2 1.0
O1G F:ACP402 4.5 0.7 1.0
CG F:ASN333 4.5 98.7 1.0
NH2 F:ARG222 4.9 72.5 1.0
CZ F:ARG202 4.9 51.3 1.0
CG F:GLU331 4.9 60.8 1.0

Reference:

W.Zhao, C.Zhou, Z.Y.Guan, P.Yin, F.Chen, Y.J.Tang. Structural Insights Into the Inhibition of Tubulin By the Antitumor Agent 4 Beta-(1,2,4-Triazol-3-Ylthio)-4-Deoxypodophyllotoxin. Acs Chem. Biol. V. 12 746 2017.
ISSN: ESSN 1554-8937
PubMed: 28035796
DOI: 10.1021/ACSCHEMBIO.6B00842
Page generated: Sun Sep 29 17:43:24 2024

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