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Magnesium in PDB 6bky: Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2

Enzymatic activity of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2

All present enzymatic activity of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2:
1.1.1.42;

Protein crystallography data

The structure of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2, PDB code: 6bky was solved by C.G.Jakob, W.Qiu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 137.44 / 2.17
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 98.665, 274.889, 116.798, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.1

Other elements in 6bky:

The structure of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 also contains other interesting chemical elements:

Bromine (Br) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 (pdb code 6bky). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2, PDB code: 6bky:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6bky

Go back to Magnesium Binding Sites List in 6bky
Magnesium binding site 1 out of 4 in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:54.1
occ:1.00
 OD2 C:ASP252 2.4 61.1 1.0
OD1 D:ASP275 2.5 51.1 1.0
OD2 D:ASP279 2.8 62.5 1.0
OD1 D:ASP279 2.9 50.1 1.0
CG D:ASP279 3.0 51.0 1.0
O1B D:LMR501 3.1 82.2 1.0
O D:ASP275 3.1 29.4 1.0
CG C:ASP252 3.3 50.5 1.0
CB C:ASP252 3.6 35.2 1.0
CG D:ASP275 3.6 47.7 1.0
C D:ASP275 3.9 29.2 1.0
C1 D:LMR501 3.9 81.1 1.0
CB D:ASP279 4.1 33.3 1.0
O1A D:LMR501 4.2 79.0 1.0
OD2 D:ASP275 4.3 55.3 1.0
CA D:ASP275 4.3 27.4 1.0
NH1 D:ARG109 4.4 35.0 1.0
OD1 C:ASP252 4.5 48.6 1.0
CB D:ASP275 4.6 31.0 1.0
OG D:SER278 4.7 33.6 1.0
N D:VAL276 4.9 27.0 1.0
O C:HOH803 5.0 58.4 1.0

Magnesium binding site 2 out of 4 in 6bky

Go back to Magnesium Binding Sites List in 6bky
Magnesium binding site 2 out of 4 in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg504

b:52.1
occ:1.00
 OD2 D:ASP252 2.3 63.3 1.0
OD1 C:ASP275 2.3 45.9 1.0
OD2 C:ASP279 2.4 57.1 1.0
O C:HOH789 3.0 51.1 1.0
O C:ASP275 3.2 29.6 1.0
CG C:ASP279 3.3 49.1 1.0
CG D:ASP252 3.3 50.1 1.0
CG C:ASP275 3.4 42.9 1.0
CB D:ASP252 3.6 33.9 1.0
OD1 C:ASP279 3.7 48.0 1.0
C C:ASP275 4.0 29.2 1.0
OD2 C:ASP275 4.1 54.0 1.0
CA C:ASP275 4.3 26.2 1.0
NH1 C:ARG109 4.3 30.7 1.0
CB C:ASP279 4.4 33.8 1.0
OD1 D:ASP252 4.5 49.1 1.0
CB C:ASP275 4.5 28.6 1.0
OG C:SER278 4.8 33.9 1.0
NZ D:LYS212 4.8 30.4 1.0
O C:HOH748 4.9 47.4 1.0
O D:HOH786 5.0 51.5 1.0
N C:VAL276 5.0 26.6 1.0

Magnesium binding site 3 out of 4 in 6bky

Go back to Magnesium Binding Sites List in 6bky
Magnesium binding site 3 out of 4 in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:46.5
occ:1.00
 OD2 F:ASP252 2.0 53.9 1.0
O E:HOH604 2.1 40.3 1.0
OD1 E:ASP275 2.2 43.4 1.0
O F:HOH703 2.3 38.7 1.0
O1B F:LMR501 2.4 63.9 1.0
CG F:ASP252 3.1 49.9 1.0
C1 F:LMR501 3.2 65.5 1.0
CG E:ASP275 3.4 44.4 1.0
OD1 E:ASP279 3.5 46.3 1.0
O1A F:LMR501 3.6 65.7 1.0
CB F:ASP252 3.7 41.7 1.0
O E:ASP275 3.8 37.1 1.0
CG E:ASP279 3.9 47.4 1.0
OD2 E:ASP279 3.9 55.7 1.0
OD2 E:ASP275 4.0 51.2 1.0
OD1 F:ASP252 4.1 50.9 1.0
O F:HOH623 4.2 52.0 1.0
NZ F:LYS212 4.3 35.6 1.0
NH1 E:ARG109 4.4 38.4 1.0
C E:ASP275 4.4 36.7 1.0
C2 F:LMR501 4.5 63.0 1.0
CB E:ASP275 4.5 33.0 1.0
CA E:ASP275 4.6 32.4 1.0
O2 F:LMR501 4.7 56.1 1.0

Magnesium binding site 4 out of 4 in 6bky

Go back to Magnesium Binding Sites List in 6bky
Magnesium binding site 4 out of 4 in the Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with CMPD2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:49.4
occ:1.00
 O B:HOH610 2.1 45.3 1.0
OD2 A:ASP252 2.1 50.4 1.0
OD1 B:ASP275 2.2 41.5 1.0
O1A A:LMR503 2.2 61.9 1.0
O A:HOH681 2.4 39.2 1.0
C1 A:LMR503 3.0 62.8 1.0
CG A:ASP252 3.2 47.8 1.0
CG B:ASP275 3.3 42.0 1.0
O1B A:LMR503 3.4 63.3 1.0
OD2 B:ASP279 3.7 55.2 1.0
OD1 B:ASP279 3.8 50.0 1.0
CB A:ASP252 3.8 38.2 1.0
OD2 B:ASP275 3.9 49.7 1.0
O B:ASP275 3.9 35.7 1.0
CG B:ASP279 4.0 49.6 1.0
OD1 A:ASP252 4.3 49.6 1.0
NZ A:LYS212 4.3 40.2 1.0
NH1 B:ARG109 4.3 40.2 1.0
C2 A:LMR503 4.4 59.6 1.0
C B:ASP275 4.5 35.5 1.0
CB B:ASP275 4.5 31.3 1.0
CA B:ASP275 4.5 30.7 1.0
O2 A:LMR503 4.6 51.6 1.0
C3 A:LMR503 4.9 60.3 1.0
O B:ALA308 5.0 64.8 1.0

Reference:

C.G.Jakob, A.K.Upadhyay, P.L.Donner, E.Nicholl, S.N.Addo, W.Qiu, C.Ling, S.M.Gopalakrishnan, M.Torrent, S.P.Cepa, J.Shanley, A.R.Shoemaker, C.C.Sun, A.Vasudevan, K.R.Woller, J.B.Shotwell, B.Shaw, Z.Bian, J.E.Hutti. Novel Modes of Inhibition of Wild-Type Isocitrate Dehydrogenase 1 (IDH1): Direct Covalent Modification of HIS315. J. Med. Chem. V. 61 6647 2018.
ISSN: ISSN 1520-4804
PubMed: 30004704
DOI: 10.1021/ACS.JMEDCHEM.8B00305
Page generated: Mon Sep 30 19:46:55 2024

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