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Magnesium in PDB 4x1y: Discovery of Cytotoxic Dolastatin 10 Analogs with N-Terminal Modifications

Protein crystallography data

The structure of Discovery of Cytotoxic Dolastatin 10 Analogs with N-Terminal Modifications, PDB code: 4x1y was solved by K.D.Parris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.59 / 3.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.610, 127.860, 255.040, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 27.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Discovery of Cytotoxic Dolastatin 10 Analogs with N-Terminal Modifications (pdb code 4x1y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Discovery of Cytotoxic Dolastatin 10 Analogs with N-Terminal Modifications, PDB code: 4x1y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4x1y

Go back to Magnesium Binding Sites List in 4x1y
Magnesium binding site 1 out of 2 in the Discovery of Cytotoxic Dolastatin 10 Analogs with N-Terminal Modifications


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Discovery of Cytotoxic Dolastatin 10 Analogs with N-Terminal Modifications within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:82.0
occ:1.00
O2B A:GTP600 1.9 0.7 1.0
O2G A:GTP600 2.5 0.2 1.0
OG1 A:THR145 2.6 0.8 1.0
NZ B:LYS254 3.2 0.9 1.0
N A:GLY144 3.2 0.5 1.0
N A:THR145 3.2 0.7 1.0
PB A:GTP600 3.2 0.7 1.0
N A:ASN101 3.4 0.1 1.0
PG A:GTP600 3.5 0.8 1.0
O3B A:GTP600 3.5 0.3 1.0
OD2 A:ASP98 3.6 0.3 1.0
CA A:GLY144 3.6 0.3 1.0
CB A:THR145 3.7 0.8 1.0
N A:ALA100 3.7 1.0 1.0
C A:GLY144 3.9 0.1 1.0
O3G A:GTP600 3.9 0.0 1.0
CA A:THR145 4.1 0.7 1.0
O3A A:GTP600 4.1 0.5 1.0
N A:ALA99 4.2 0.2 1.0
CA A:ASN101 4.2 0.1 1.0
CA A:ALA100 4.2 0.7 1.0
CB A:ASP98 4.3 0.0 1.0
CB A:ALA99 4.3 0.9 1.0
OD1 A:ASN101 4.3 0.3 1.0
O1B A:GTP600 4.3 0.0 1.0
C A:GLY143 4.3 0.6 1.0
C A:ALA99 4.3 1.0 1.0
C A:ALA100 4.3 0.5 1.0
CG A:ASP98 4.4 0.9 1.0
CE B:LYS254 4.4 0.7 1.0
CA A:ALA99 4.5 0.5 1.0
CA A:GLY143 4.7 0.2 1.0
O1G A:GTP600 4.8 0.6 1.0
C A:ASP98 4.9 0.8 1.0
O A:GLY144 5.0 0.6 1.0

Magnesium binding site 2 out of 2 in 4x1y

Go back to Magnesium Binding Sites List in 4x1y
Magnesium binding site 2 out of 2 in the Discovery of Cytotoxic Dolastatin 10 Analogs with N-Terminal Modifications


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Discovery of Cytotoxic Dolastatin 10 Analogs with N-Terminal Modifications within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:60.3
occ:1.00
O2B C:GTP600 1.9 0.7 1.0
O2G C:GTP600 2.5 0.6 1.0
O3G C:GTP600 3.1 0.1 1.0
PB C:GTP600 3.2 0.6 1.0
PG C:GTP600 3.2 0.6 1.0
OG1 C:THR145 3.4 0.6 1.0
N C:GLY144 3.4 90.0 1.0
O3B C:GTP600 3.5 0.4 1.0
OD1 C:ASP98 3.7 0.0 1.0
N C:ASN101 3.8 95.8 1.0
NZ D:LYS254 3.9 0.6 1.0
O3A C:GTP600 3.9 0.6 1.0
N C:THR145 3.9 94.9 1.0
N C:ALA99 4.0 0.2 1.0
CA C:GLY144 4.0 90.2 1.0
OD1 C:ASN101 4.1 0.8 1.0
CB C:ALA99 4.2 99.7 1.0
N C:ALA100 4.2 98.0 1.0
CG C:ASP98 4.2 0.5 1.0
CA C:ALA99 4.3 99.1 1.0
C C:ALA99 4.3 0.2 1.0
O1B C:GTP600 4.4 0.5 1.0
CA C:ASN101 4.4 95.1 1.0
C C:GLY143 4.4 95.6 1.0
CB C:THR145 4.4 0.0 1.0
C C:GLY144 4.5 96.0 1.0
CB C:ASP98 4.5 0.5 1.0
CA C:GLY143 4.6 91.4 1.0
O1G C:GTP600 4.7 0.8 1.0
CA C:THR145 4.9 95.1 1.0
CA C:ALA100 4.9 97.2 1.0
C C:ALA100 4.9 0.1 1.0
CE D:LYS254 5.0 0.9 1.0
OD2 C:ASP98 5.0 0.2 1.0
CG C:ASN101 5.0 0.5 1.0

Reference:

A.Maderna, M.Doroski, C.Subramanyam, A.Porte, C.A.Leverett, B.C.Vetelino, Z.Chen, H.Risley, K.Parris, J.Pandit, A.H.Varghese, S.Shanker, C.Song, S.C.Sukuru, K.A.Farley, M.M.Wagenaar, M.J.Shapiro, S.Musto, M.H.Lam, F.Loganzo, C.J.O'donnell. Discovery of Cytotoxic Dolastatin 10 Analogues with N-Terminal Modifications. J.Med.Chem. V. 57 10527 2014.
ISSN: ISSN 0022-2623
PubMed: 25431858
DOI: 10.1021/JM501649K
Page generated: Tue Aug 20 14:02:40 2024

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