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Magnesium in PDB 7acf: Crystal Structure of Crystal Form 2 of An Active Kras G12D (Gppcp) Dimer in Complex with Bi-5747

Enzymatic activity of Crystal Structure of Crystal Form 2 of An Active Kras G12D (Gppcp) Dimer in Complex with Bi-5747

All present enzymatic activity of Crystal Structure of Crystal Form 2 of An Active Kras G12D (Gppcp) Dimer in Complex with Bi-5747:
3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Crystal Form 2 of An Active Kras G12D (Gppcp) Dimer in Complex with Bi-5747, PDB code: 7acf was solved by D.Kessler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.91
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 67.664, 67.664, 312.136, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 19.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Crystal Form 2 of An Active Kras G12D (Gppcp) Dimer in Complex with Bi-5747 (pdb code 7acf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Crystal Form 2 of An Active Kras G12D (Gppcp) Dimer in Complex with Bi-5747, PDB code: 7acf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7acf

Go back to Magnesium Binding Sites List in 7acf
Magnesium binding site 1 out of 4 in the Crystal Structure of Crystal Form 2 of An Active Kras G12D (Gppcp) Dimer in Complex with Bi-5747


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Crystal Form 2 of An Active Kras G12D (Gppcp) Dimer in Complex with Bi-5747 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:24.1
occ:1.00
 O A:HOH311 2.0 23.6 1.0
O3G A:GCP202 2.0 31.1 1.0
O2B A:GCP202 2.0 23.8 1.0
O A:HOH327 2.0 26.2 1.0
OG A:SER17 2.0 27.7 1.0
OG1 A:THR35 2.1 25.3 1.0
CB A:THR35 3.1 30.8 1.0
CB A:SER17 3.2 26.2 1.0
PB A:GCP202 3.3 27.1 1.0
PG A:GCP202 3.3 31.2 1.0
C3B A:GCP202 3.5 28.3 1.0
N A:SER17 3.8 23.5 1.0
N A:THR35 3.9 32.1 1.0
OD2 A:ASP57 4.0 32.2 1.0
CA A:SER17 4.1 23.7 1.0
CA A:THR35 4.1 30.4 1.0
O2A A:GCP202 4.1 29.1 1.0
OD1 A:ASP57 4.2 30.0 1.0
O1G A:GCP202 4.2 29.2 1.0
CG2 A:THR35 4.2 26.6 1.0
O1B A:GCP202 4.3 26.0 1.0
O3A A:GCP202 4.3 27.3 1.0
O A:THR58 4.4 26.9 1.0
O2G A:GCP202 4.4 28.4 1.0
O A:ASP33 4.4 39.5 1.0
CG A:ASP57 4.5 30.1 1.0
O A:HOH384 4.5 53.3 1.0
PA A:GCP202 4.5 27.4 1.0
CB A:LYS16 4.8 23.5 1.0
O1A A:GCP202 4.8 25.2 1.0
C A:PRO34 4.8 38.1 1.0
CE A:LYS16 4.9 27.4 1.0
C A:LYS16 4.9 25.8 1.0

Magnesium binding site 2 out of 4 in 7acf

Go back to Magnesium Binding Sites List in 7acf
Magnesium binding site 2 out of 4 in the Crystal Structure of Crystal Form 2 of An Active Kras G12D (Gppcp) Dimer in Complex with Bi-5747


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Crystal Form 2 of An Active Kras G12D (Gppcp) Dimer in Complex with Bi-5747 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:24.0
occ:1.00
 O2G B:GCP202 1.9 31.1 1.0
O B:HOH330 2.0 22.3 1.0
O2B B:GCP202 2.0 27.0 1.0
O B:HOH350 2.0 27.4 1.0
OG1 B:THR35 2.1 26.7 1.0
OG B:SER17 2.1 27.2 1.0
CB B:THR35 3.1 30.1 1.0
PG B:GCP202 3.2 29.6 1.0
CB B:SER17 3.2 25.5 1.0
PB B:GCP202 3.2 26.9 1.0
C3B B:GCP202 3.5 26.7 1.0
N B:THR35 3.8 30.6 1.0
N B:SER17 3.9 24.8 1.0
OD2 B:ASP57 4.0 34.5 1.0
CA B:THR35 4.1 29.2 1.0
CA B:SER17 4.1 24.4 1.0
O1A B:GCP202 4.1 31.5 1.0
O1G B:GCP202 4.1 27.6 1.0
CG2 B:THR35 4.2 29.2 1.0
OD1 B:ASP57 4.2 33.0 1.0
O B:HOH372 4.2 43.4 1.0
O1B B:GCP202 4.2 25.4 1.0
O3G B:GCP202 4.3 30.3 1.0
O3A B:GCP202 4.3 26.2 1.0
O B:THR58 4.4 30.0 1.0
O B:ASP33 4.4 37.3 1.0
CG B:ASP57 4.5 33.2 1.0
PA B:GCP202 4.5 29.4 1.0
CB B:LYS16 4.8 25.4 1.0
O2A B:GCP202 4.8 29.2 1.0
C B:PRO34 4.8 36.0 1.0
CE B:LYS16 4.9 24.4 1.0
C B:LYS16 4.9 27.4 1.0

Magnesium binding site 3 out of 4 in 7acf

Go back to Magnesium Binding Sites List in 7acf
Magnesium binding site 3 out of 4 in the Crystal Structure of Crystal Form 2 of An Active Kras G12D (Gppcp) Dimer in Complex with Bi-5747


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Crystal Form 2 of An Active Kras G12D (Gppcp) Dimer in Complex with Bi-5747 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:23.4
occ:1.00
 O2B C:GCP202 1.9 24.2 1.0
O C:HOH507 2.0 20.6 1.0
O C:HOH517 2.1 21.1 1.0
O1G C:GCP202 2.1 24.4 1.0
OG1 C:THR35 2.1 22.9 1.0
OG C:SER17 2.1 24.7 1.0
CB C:THR35 3.2 23.5 1.0
PB C:GCP202 3.2 25.3 1.0
CB C:SER17 3.2 25.6 1.0
PG C:GCP202 3.3 24.8 1.0
C3B C:GCP202 3.4 23.3 1.0
N C:THR35 3.8 22.1 1.0
N C:SER17 3.9 26.4 1.0
OD2 C:ASP57 4.1 31.4 1.0
OD1 C:ASP57 4.1 30.2 1.0
O2A C:GCP202 4.1 27.3 1.0
CA C:THR35 4.1 21.2 1.0
CA C:SER17 4.1 25.2 1.0
O1B C:GCP202 4.2 22.4 1.0
CG2 C:THR35 4.2 20.3 1.0
O2G C:GCP202 4.3 27.3 1.0
O C:HOH513 4.3 35.1 1.0
O3A C:GCP202 4.3 25.2 1.0
O3G C:GCP202 4.4 22.4 1.0
O C:THR58 4.4 27.8 1.0
O C:ASP33 4.5 30.5 1.0
CG C:ASP57 4.5 30.2 1.0
PA C:GCP202 4.5 27.1 1.0
O1A C:GCP202 4.7 26.5 1.0
C C:PRO34 4.8 26.4 1.0
CB C:LYS16 4.8 28.6 1.0
CE C:LYS16 4.9 28.6 1.0
C C:LYS16 5.0 30.4 1.0

Magnesium binding site 4 out of 4 in 7acf

Go back to Magnesium Binding Sites List in 7acf
Magnesium binding site 4 out of 4 in the Crystal Structure of Crystal Form 2 of An Active Kras G12D (Gppcp) Dimer in Complex with Bi-5747


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Crystal Form 2 of An Active Kras G12D (Gppcp) Dimer in Complex with Bi-5747 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:23.4
occ:1.00
 O2G D:GCP202 1.9 25.2 1.0
O2B D:GCP202 2.0 24.7 1.0
OG1 D:THR35 2.1 22.2 1.0
O D:HOH302 2.1 22.3 1.0
O D:HOH313 2.1 24.4 1.0
OG D:SER17 2.1 26.3 1.0
CB D:THR35 3.1 23.5 1.0
PB D:GCP202 3.2 25.6 1.0
PG D:GCP202 3.2 28.2 1.0
CB D:SER17 3.3 24.9 1.0
C3B D:GCP202 3.5 25.8 1.0
N D:THR35 3.8 25.5 1.0
N D:SER17 3.9 23.8 1.0
OD2 D:ASP57 4.0 36.3 1.0
O2A D:GCP202 4.1 33.7 1.0
CA D:THR35 4.1 23.9 1.0
CA D:SER17 4.1 23.8 1.0
O1B D:GCP202 4.2 23.3 1.0
OD1 D:ASP57 4.2 32.0 1.0
CG2 D:THR35 4.2 22.7 1.0
O1G D:GCP202 4.2 28.3 1.0
O3G D:GCP202 4.3 29.4 1.0
O D:HOH307 4.3 39.7 1.0
O3A D:GCP202 4.4 25.9 1.0
O D:THR58 4.4 26.3 1.0
O D:ASP33 4.5 31.9 1.0
CG D:ASP57 4.5 32.5 1.0
PA D:GCP202 4.6 29.3 1.0
CB D:LYS16 4.7 24.0 1.0
C D:PRO34 4.8 30.1 1.0
CE D:LYS16 4.9 29.4 1.0
O1A D:GCP202 4.9 28.8 1.0
C D:LYS16 4.9 26.3 1.0

Reference:

D.Kessler, A.Gollner, M.Gmachl, A.Mantoulidis, L.J.Martin, A.Zoephel, M.Mayer, D.Covini, S.Fischer, T.Gerstberger, T.Gmaschitz, C.Goodwin, P.Greb, D.Haering, W.Hela, J.Hoffmann, J.Karolyi-Oezguer, P.Knesl, S.Kornigg, M.Koegl, R.Kousek, L.Lamarre, F.Moser, S.Munico-Martinez, C.Peinsipp, J.Phan, J.Rinnenthal, J.Sai, C.Salamon, Y.Scherbantin, K.Schipany, R.Schnitzer, A.Schrenk, B.Sharps, G.Siszler, Q.Sun, A.Waterson, B.Wolkerstorfer, M.Zeeb, M.Pearson, S.W.Fesik, D.B.Mcconnell. Reply to Tran Et Al.: Dimeric Kras Protein-Protein Interaction Stabilizers. Proc. Natl. Acad. Sci. V. 117 3365 2020U.S.A..
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1921236117
Page generated: Wed Oct 2 09:11:23 2024

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