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Magnesium in PDB 5usj: Crystal Structure of Human Kras G12D Mutant in Complex with Gdpnp

Protein crystallography data

The structure of Crystal Structure of Human Kras G12D Mutant in Complex with Gdpnp, PDB code: 5usj was solved by C.S.Huang, A.Kaplan, B.R.Stockwell, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.65 / 1.94
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.423, 63.491, 81.991, 91.51, 112.63, 115.44
R / Rfree (%) 17.7 / 23.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Kras G12D Mutant in Complex with Gdpnp (pdb code 5usj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Human Kras G12D Mutant in Complex with Gdpnp, PDB code: 5usj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5usj

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Magnesium binding site 1 out of 6 in the Crystal Structure of Human Kras G12D Mutant in Complex with Gdpnp


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 Human Kras G12D Mutant in Complex with Gdpnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:12.8
occ:1.00
 O1B A:GNP1002 2.0 9.8 1.0
OG A:SER17 2.1 10.6 1.0
O A:HOH1131 2.1 11.6 1.0
O A:HOH1104 2.1 10.8 1.0
OG1 A:THR35 2.1 13.7 1.0
O1G A:GNP1002 2.2 13.6 1.0
CB A:SER17 3.1 9.8 1.0
CB A:THR35 3.1 14.9 1.0
PB A:GNP1002 3.2 10.4 1.0
PG A:GNP1002 3.3 13.7 1.0
N3B A:GNP1002 3.5 11.8 1.0
N A:SER17 3.8 9.6 1.0
OD2 A:ASP57 3.9 20.9 1.0
N A:THR35 4.0 16.3 1.0
CA A:SER17 4.0 10.3 1.0
O2A A:GNP1002 4.0 11.3 1.0
OD1 A:ASP57 4.0 19.2 1.0
CG2 A:THR35 4.0 14.5 1.0
CA A:THR35 4.2 15.3 1.0
O2B A:GNP1002 4.2 9.5 1.0
O2G A:GNP1002 4.2 14.7 1.0
O A:HOH1123 4.2 26.9 1.0
O3A A:GNP1002 4.3 11.0 1.0
CG A:ASP57 4.3 18.7 1.0
O A:THR58 4.4 15.6 1.0
O3G A:GNP1002 4.4 14.9 1.0
O A:ASP33 4.5 21.3 1.0
PA A:GNP1002 4.5 12.7 1.0
O1A A:GNP1002 4.7 12.4 1.0
CB A:LYS16 4.7 10.2 1.0
NZ A:LYS16 4.8 12.3 1.0
C A:LYS16 4.9 10.1 1.0
C A:PRO34 4.9 19.4 1.0
CE A:LYS16 4.9 11.7 1.0

Magnesium binding site 2 out of 6 in 5usj

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Magnesium binding site 2 out of 6 in the Crystal Structure of Human Kras G12D Mutant in Complex with Gdpnp


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 Human Kras G12D Mutant in Complex with Gdpnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:12.8
occ:1.00
 O1B B:GNP1002 1.9 11.3 1.0
OG1 B:THR35 2.0 17.4 1.0
O1G B:GNP1002 2.0 12.5 1.0
O B:HOH1121 2.1 13.0 1.0
O B:HOH1117 2.1 10.9 1.0
OG B:SER17 2.1 11.6 1.0
CB B:THR35 3.0 19.4 1.0
CB B:SER17 3.2 11.6 1.0
PG B:GNP1002 3.2 12.6 1.0
PB B:GNP1002 3.2 11.5 1.0
N3B B:GNP1002 3.5 12.2 1.0
N B:SER17 3.9 11.2 1.0
N B:THR35 3.9 22.1 1.0
OD2 B:ASP57 3.9 23.5 1.0
O1A B:GNP1002 4.0 13.4 1.0
O B:HOH1109 4.0 28.1 1.0
CG2 B:THR35 4.0 20.0 1.0
CA B:THR35 4.1 20.2 1.0
CA B:SER17 4.1 11.3 1.0
O2G B:GNP1002 4.1 11.5 1.0
OD1 B:ASP57 4.2 20.1 1.0
O3A B:GNP1002 4.2 12.4 1.0
O2B B:GNP1002 4.3 10.8 1.0
O3G B:GNP1002 4.3 16.3 1.0
CG B:ASP57 4.5 22.3 1.0
PA B:GNP1002 4.5 14.4 1.0
O B:THR58 4.5 15.3 1.0
O B:ASP33 4.5 26.2 1.0
O2A B:GNP1002 4.6 14.6 1.0
CB B:LYS16 4.7 11.5 1.0
C B:PRO34 4.7 24.8 1.0
C B:LYS16 4.9 11.7 1.0
CE B:LYS16 4.9 13.9 1.0
CA B:PRO34 4.9 26.9 1.0

Magnesium binding site 3 out of 6 in 5usj

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Magnesium binding site 3 out of 6 in the Crystal Structure of Human Kras G12D Mutant in Complex with Gdpnp


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 Human Kras G12D Mutant in Complex with Gdpnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1001

b:16.8
occ:1.00
 O C:HOH1103 1.6 30.9 1.0
O2B C:GNP1002 1.9 16.1 1.0
O2G C:GNP1002 2.0 16.1 1.0
O C:HOH1123 2.1 13.4 1.0
OG1 C:THR35 2.1 16.8 1.0
OG C:SER17 2.2 13.1 1.0
CB C:THR35 3.0 19.2 1.0
PG C:GNP1002 3.2 17.3 1.0
CB C:SER17 3.2 12.7 1.0
PB C:GNP1002 3.2 13.6 1.0
N3B C:GNP1002 3.5 15.0 1.0
N C:THR35 3.8 18.8 1.0
N C:SER17 3.9 13.4 1.0
CA C:THR35 4.0 18.9 1.0
OD2 C:ASP57 4.1 24.2 1.0
OD1 C:ASP57 4.1 23.7 1.0
CG2 C:THR35 4.1 18.2 1.0
O1G C:GNP1002 4.1 19.2 1.0
O C:HOH1121 4.1 24.0 1.0
CA C:SER17 4.1 13.3 1.0
O2A C:GNP1002 4.2 15.3 1.0
O1B C:GNP1002 4.2 13.1 1.0
O3A C:GNP1002 4.3 15.6 1.0
O3G C:GNP1002 4.3 19.9 1.0
O C:ASP33 4.4 25.3 1.0
O C:THR58 4.4 17.4 1.0
CG C:ASP57 4.5 20.0 1.0
PA C:GNP1002 4.6 16.9 1.0
C C:PRO34 4.7 22.3 1.0
O1A C:GNP1002 4.7 15.5 1.0
CB C:LYS16 4.8 14.3 1.0
CA C:PRO34 4.9 23.7 1.0
C C:LYS16 4.9 13.3 1.0
NZ C:LYS16 5.0 17.1 1.0

Magnesium binding site 4 out of 6 in 5usj

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Magnesium binding site 4 out of 6 in the Crystal Structure of Human Kras G12D Mutant in Complex with Gdpnp


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 Human Kras G12D Mutant in Complex with Gdpnp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1001

b:10.2
occ:1.00
 O1B D:GNP1002 1.8 11.3 1.0
O D:HOH1138 1.9 14.1 1.0
O1G D:GNP1002 2.0 13.9 1.0
O D:HOH1137 2.0 13.0 1.0
OG D:SER17 2.1 9.4 1.0
OG1 D:THR35 2.1 13.8 1.0
CB D:SER17 3.1 9.9 1.0
PB D:GNP1002 3.1 12.0 1.0
CB D:THR35 3.1 15.7 1.0
PG D:GNP1002 3.2 14.5 1.0
N3B D:GNP1002 3.4 12.3 1.0
N D:SER17 3.9 10.2 1.0
N D:THR35 3.9 20.1 1.0
O3G D:GNP1002 3.9 16.5 1.0
CA D:SER17 4.0 10.0 1.0
O D:HOH1114 4.0 29.1 1.0
O2A D:GNP1002 4.1 11.6 1.0
O3A D:GNP1002 4.1 12.6 1.0
OD2 D:ASP57 4.1 22.6 1.0
CA D:THR35 4.1 17.7 1.0
CG2 D:THR35 4.2 16.3 1.0
O2B D:GNP1002 4.2 10.9 1.0
O2G D:GNP1002 4.3 16.1 1.0
OD1 D:ASP57 4.3 18.6 1.0
PA D:GNP1002 4.4 11.2 1.0
O D:ASP33 4.5 23.6 1.0
CG D:ASP57 4.6 19.2 1.0
O1A D:GNP1002 4.6 10.7 1.0
O D:THR58 4.6 18.0 1.0
C D:PRO34 4.8 23.9 1.0
CB D:LYS16 4.9 10.7 1.0
C D:LYS16 4.9 10.2 1.0
NZ D:LYS16 4.9 13.8 1.0

Magnesium binding site 5 out of 6 in 5usj

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Magnesium binding site 5 out of 6 in the Crystal Structure of Human Kras G12D Mutant in Complex with Gdpnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human Kras G12D Mutant in Complex with Gdpnp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1001

b:17.2
occ:1.00
 O E:HOH1123 1.9 18.5 1.0
O2B E:GNP1002 2.0 17.7 1.0
OG1 E:THR35 2.0 20.8 1.0
O3G E:GNP1002 2.1 23.9 1.0
O E:HOH1111 2.1 19.9 1.0
OG E:SER17 2.2 18.0 1.0
CB E:THR35 3.1 23.5 1.0
CB E:SER17 3.2 19.0 1.0
PG E:GNP1002 3.2 21.1 1.0
PB E:GNP1002 3.3 18.8 1.0
N3B E:GNP1002 3.6 17.9 1.0
N E:THR35 3.8 23.9 1.0
N E:SER17 3.8 18.2 1.0
OD2 E:ASP57 3.9 29.4 1.0
CA E:SER17 4.1 18.7 1.0
CA E:THR35 4.1 22.4 1.0
O2G E:GNP1002 4.1 22.0 1.0
O1A E:GNP1002 4.2 19.5 1.0
CG2 E:THR35 4.2 23.2 1.0
OD1 E:ASP57 4.2 28.4 1.0
O1B E:GNP1002 4.4 20.1 1.0
O3A E:GNP1002 4.4 19.6 1.0
CG E:ASP57 4.4 26.2 1.0
O1G E:GNP1002 4.4 23.6 1.0
O E:THR58 4.5 17.5 1.0
PA E:GNP1002 4.6 19.8 1.0
O E:ASP33 4.6 27.3 1.0
CB E:LYS16 4.7 19.6 1.0
O2A E:GNP1002 4.7 20.5 1.0
C E:PRO34 4.8 27.8 1.0
C E:LYS16 4.9 19.0 1.0

Magnesium binding site 6 out of 6 in 5usj

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Magnesium binding site 6 out of 6 in the Crystal Structure of Human Kras G12D Mutant in Complex with Gdpnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Human Kras G12D Mutant in Complex with Gdpnp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1001

b:18.0
occ:1.00
 O2B F:GNP1002 2.0 15.7 1.0
O3G F:GNP1002 2.0 20.4 1.0
O F:HOH1110 2.0 20.4 1.0
O F:HOH1118 2.0 16.7 1.0
OG1 F:THR35 2.1 27.8 1.0
OG F:SER17 2.3 13.7 1.0
PG F:GNP1002 3.1 21.1 1.0
CB F:THR35 3.2 31.2 1.0
CB F:SER17 3.2 14.5 1.0
PB F:GNP1002 3.3 16.2 1.0
N3B F:GNP1002 3.5 19.1 1.0
N F:SER17 3.8 15.0 1.0
N F:THR35 4.0 33.8 1.0
O1A F:GNP1002 4.0 16.9 1.0
OD2 F:ASP57 4.0 29.9 1.0
CA F:SER17 4.0 14.0 1.0
O2G F:GNP1002 4.1 21.6 1.0
CA F:THR35 4.2 30.2 1.0
CG2 F:THR35 4.2 32.4 1.0
OD1 F:ASP57 4.2 29.1 1.0
O1G F:GNP1002 4.3 23.3 1.0
O3A F:GNP1002 4.4 17.3 1.0
O1B F:GNP1002 4.4 16.9 1.0
O F:THR58 4.4 21.2 1.0
O F:ASP33 4.4 34.1 1.0
CG F:ASP57 4.5 26.2 1.0
PA F:GNP1002 4.5 18.8 1.0
O2A F:GNP1002 4.7 18.5 1.0
CB F:LYS16 4.7 16.6 1.0
C F:PRO34 4.8 38.3 1.0
C F:LYS16 4.9 15.8 1.0
CA F:PRO34 4.9 39.4 1.0
CE F:LYS16 4.9 15.3 1.0

Reference:

M.E.Welsch, A.Kaplan, J.M.Chambers, M.E.Stokes, P.H.Bos, A.Zask, Y.Zhang, M.Sanchez-Martin, M.A.Badgley, C.S.Huang, T.H.Tran, H.Akkiraju, L.M.Brown, R.Nandakumar, S.Cremers, W.S.Yang, L.Tong, K.P.Olive, A.Ferrando, B.R.Stockwell. Multivalent Small-Molecule Pan-Ras Inhibitors. Cell V. 168 878 2017.
ISSN: ISSN 1097-4172
PubMed: 28235199
DOI: 10.1016/J.CELL.2017.02.006
Page generated: Mon Sep 30 05:24:59 2024

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