Magnesium in PDB 6f76: Antibody Derived (Abd-8) Small Molecule Binding to Kras.

Protein crystallography data

The structure of Antibody Derived (Abd-8) Small Molecule Binding to Kras., PDB code: 6f76 was solved by N.Bery, A.Cruz-Migoni, C.E.Quevedo, S.V.E.Phillips, S.Carr, T.H.Rabbitts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.49 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.190, 118.424, 156.751, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 24.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Antibody Derived (Abd-8) Small Molecule Binding to Kras. (pdb code 6f76). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Antibody Derived (Abd-8) Small Molecule Binding to Kras., PDB code: 6f76:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6f76

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Magnesium binding site 1 out of 6 in the Antibody Derived (Abd-8) Small Molecule Binding to Kras.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Antibody Derived (Abd-8) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:24.1
occ:1.00
 O2B B:GNP202 1.9 21.2 1.0
O2G B:GNP202 2.0 24.2 1.0
O B:HOH308 2.1 19.6 1.0
OG1 B:THR35 2.1 25.9 1.0
OG B:SER17 2.2 22.2 1.0
O B:HOH301 2.3 21.8 1.0
CB B:THR35 3.1 29.5 1.0
PB B:GNP202 3.2 21.7 1.0
CB B:SER17 3.2 23.9 1.0
PG B:GNP202 3.2 27.6 1.0
N3B B:GNP202 3.4 24.6 1.0
N B:SER17 3.9 23.1 1.0
O1A B:GNP202 4.0 22.8 1.0
O3G B:GNP202 4.0 26.6 1.0
N B:THR35 4.0 30.2 1.0
OD2 B:ASP57 4.0 44.4 1.0
CA B:SER17 4.1 23.6 1.0
CG2 B:THR35 4.2 29.9 1.0
CA B:THR35 4.2 29.8 1.0
O3A B:GNP202 4.2 23.8 1.0
O1B B:GNP202 4.3 17.4 1.0
OD1 B:ASP57 4.3 48.0 1.0
O1G B:GNP202 4.4 26.4 1.0
PA B:GNP202 4.4 22.8 1.0
O B:ASP33 4.5 30.1 1.0
O B:THR58 4.5 27.8 1.0
O2A B:GNP202 4.5 22.4 1.0
CG B:ASP57 4.5 44.5 1.0
C B:PRO34 4.9 28.6 1.0
CB B:LYS16 4.9 21.0 1.0
C B:LYS16 5.0 23.0 1.0

Magnesium binding site 2 out of 6 in 6f76

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Magnesium binding site 2 out of 6 in the Antibody Derived (Abd-8) Small Molecule Binding to Kras.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Antibody Derived (Abd-8) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:23.1
occ:1.00
 O A:HOH301 1.9 26.6 1.0
OG1 A:THR35 2.0 27.3 1.0
O2G A:GNP202 2.1 22.8 1.0
OG A:SER17 2.1 19.0 1.0
O A:HOH305 2.1 13.5 1.0
O2B A:GNP202 2.2 23.5 1.0
CB A:THR35 3.1 24.7 1.0
CB A:SER17 3.1 20.9 1.0
PB A:GNP202 3.3 22.6 1.0
PG A:GNP202 3.3 23.4 1.0
N3B A:GNP202 3.4 24.1 1.0
N A:THR35 3.9 25.8 1.0
O1A A:GNP202 3.9 23.7 1.0
N A:SER17 4.0 21.1 1.0
OD2 A:ASP57 4.0 29.3 0.5
OD2 A:ASP57 4.0 29.2 0.5
CA A:THR35 4.1 25.1 1.0
CA A:SER17 4.1 22.8 1.0
O3G A:GNP202 4.1 22.7 1.0
CG2 A:THR35 4.2 24.1 1.0
O A:ASP33 4.2 35.8 1.0
O3A A:GNP202 4.3 25.3 1.0
PA A:GNP202 4.3 23.5 1.0
OD1 A:ASP57 4.4 35.3 0.5
OD1 A:ASP57 4.4 35.4 0.5
O1B A:GNP202 4.4 19.5 1.0
O1G A:GNP202 4.4 26.4 1.0
O2A A:GNP202 4.5 24.3 1.0
CG A:ASP57 4.6 29.6 0.5
CG A:ASP57 4.6 29.7 0.5
O A:THR58 4.7 31.4 1.0
C A:PRO34 4.7 31.4 1.0
CA A:PRO34 4.9 33.3 1.0

Magnesium binding site 3 out of 6 in 6f76

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Magnesium binding site 3 out of 6 in the Antibody Derived (Abd-8) Small Molecule Binding to Kras.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Antibody Derived (Abd-8) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:35.0
occ:1.00
 O1G C:GNP202 1.9 45.4 1.0
O C:HOH301 2.0 33.7 1.0
O1B C:GNP202 2.0 36.0 1.0
O C:HOH303 2.0 26.3 1.0
OG1 C:THR35 2.1 52.5 1.0
OG C:SER17 2.2 35.3 1.0
PG C:GNP202 3.1 43.6 1.0
CB C:THR35 3.2 54.9 1.0
PB C:GNP202 3.2 37.5 1.0
CB C:SER17 3.2 34.1 1.0
N3B C:GNP202 3.3 45.4 1.0
N C:SER17 3.9 30.8 1.0
N C:THR35 4.0 52.8 1.0
O2G C:GNP202 4.0 42.1 1.0
OD2 C:ASP57 4.0 59.5 0.5
OD2 C:ASP57 4.0 59.7 0.5
O3G C:GNP202 4.1 51.7 1.0
CA C:SER17 4.1 33.8 1.0
O2A C:GNP202 4.2 35.8 1.0
CG2 C:THR35 4.2 54.7 1.0
CA C:THR35 4.2 55.0 1.0
OD1 C:ASP57 4.2 61.6 0.5
OD1 C:ASP57 4.2 62.0 0.5
O2B C:GNP202 4.3 33.7 1.0
O3A C:GNP202 4.3 39.2 1.0
PA C:GNP202 4.4 38.4 1.0
O1A C:GNP202 4.5 41.6 1.0
O C:THR58 4.5 53.0 1.0
O C:ASP33 4.5 62.7 1.0
CG C:ASP57 4.5 58.9 0.5
CG C:ASP57 4.5 59.1 0.5
C C:PRO34 4.8 58.9 1.0
CB C:LYS16 4.9 33.3 1.0
NZ C:LYS16 4.9 47.1 1.0
C C:LYS16 5.0 32.2 1.0

Magnesium binding site 4 out of 6 in 6f76

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Magnesium binding site 4 out of 6 in the Antibody Derived (Abd-8) Small Molecule Binding to Kras.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Antibody Derived (Abd-8) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:56.2
occ:1.00
 OG D:SER17 2.0 34.0 1.0
OG1 D:THR35 2.1 83.1 1.0
O2G D:GNP201 2.1 49.3 1.0
O2B D:GNP201 2.2 37.2 1.0
O D:HOH302 2.2 53.0 1.0
O D:HOH301 2.4 43.8 1.0
CB D:SER17 3.1 31.2 1.0
CB D:THR35 3.1 95.2 1.0
PB D:GNP201 3.4 37.3 1.0
PG D:GNP201 3.4 45.6 1.0
N3B D:GNP201 3.5 44.5 1.0
OD2 D:ASP57 3.9 64.9 0.5
N D:SER17 3.9 28.4 1.0
OD2 D:ASP57 3.9 65.1 0.5
N D:THR35 4.0 0.8 1.0
CA D:SER17 4.0 28.7 1.0
O1A D:GNP201 4.0 36.5 1.0
CG2 D:THR35 4.1 90.6 1.0
OD1 D:ASP57 4.2 63.5 0.5
OD1 D:ASP57 4.2 63.4 0.5
CA D:THR35 4.2 98.7 1.0
O3G D:GNP201 4.2 43.9 1.0
O1B D:GNP201 4.4 30.9 1.0
O D:THR58 4.4 46.6 1.0
CG D:ASP57 4.4 61.2 0.5
CG D:ASP57 4.4 61.3 0.5
O3A D:GNP201 4.4 36.0 1.0
O1G D:GNP201 4.4 54.4 1.0
O2A D:GNP201 4.5 41.7 1.0
PA D:GNP201 4.5 36.6 1.0
O D:ASP33 4.5 86.5 1.0
CB D:LYS16 4.9 29.4 1.0
C D:LYS16 4.9 31.2 1.0
C D:PRO34 4.9 0.8 1.0

Magnesium binding site 5 out of 6 in 6f76

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Magnesium binding site 5 out of 6 in the Antibody Derived (Abd-8) Small Molecule Binding to Kras.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Antibody Derived (Abd-8) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:44.2
occ:1.00
 O E:HOH301 2.0 39.3 1.0
O E:HOH302 2.0 29.0 1.0
O1B E:GNP202 2.1 32.6 1.0
O1G E:GNP202 2.1 39.8 1.0
OG E:SER17 2.2 33.5 1.0
OG1 E:THR35 2.3 61.2 1.0
CB E:SER17 3.1 33.9 1.0
PB E:GNP202 3.2 35.0 1.0
PG E:GNP202 3.3 42.5 1.0
N3B E:GNP202 3.3 39.5 1.0
CB E:THR35 3.3 65.2 1.0
O2A E:GNP202 3.8 33.8 1.0
N E:THR35 3.9 68.7 1.0
N E:SER17 4.0 31.4 1.0
CA E:SER17 4.1 35.0 1.0
O2G E:GNP202 4.2 40.0 1.0
OD2 E:ASP57 4.2 56.5 0.5
OD2 E:ASP57 4.2 56.5 0.5
CA E:THR35 4.2 68.3 1.0
O3A E:GNP202 4.2 35.4 1.0
O3G E:GNP202 4.2 47.4 1.0
O E:ASP33 4.3 68.1 1.0
PA E:GNP202 4.3 34.3 1.0
CG2 E:THR35 4.4 65.3 1.0
O2B E:GNP202 4.4 31.5 1.0
O1A E:GNP202 4.4 32.0 1.0
OD1 E:ASP57 4.6 60.6 0.5
OD1 E:ASP57 4.6 60.6 0.5
O E:THR58 4.7 38.9 1.0
C E:PRO34 4.8 71.0 1.0
CG E:ASP57 4.8 55.1 0.5
CG E:ASP57 4.8 55.1 0.5
CA E:PRO34 4.9 67.9 1.0

Magnesium binding site 6 out of 6 in 6f76

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Magnesium binding site 6 out of 6 in the Antibody Derived (Abd-8) Small Molecule Binding to Kras.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Antibody Derived (Abd-8) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:53.8
occ:1.00
 O1G F:GNP202 2.1 47.3 1.0
O1B F:GNP202 2.2 35.8 1.0
OG1 F:THR35 2.2 69.8 1.0
OG F:SER17 2.4 28.9 1.0
CB F:THR35 3.0 76.2 1.0
PB F:GNP202 3.4 33.2 1.0
PG F:GNP202 3.4 41.1 1.0
CB F:SER17 3.5 29.1 1.0
OD1 F:ASP57 3.6 62.8 1.0
OD2 F:ASP57 3.7 59.7 1.0
N3B F:GNP202 3.7 36.6 1.0
O F:THR58 3.8 46.9 1.0
N F:SER17 3.8 29.7 1.0
CG2 F:THR35 3.9 74.6 1.0
O2G F:GNP202 4.0 45.6 1.0
CG F:ASP57 4.0 58.5 1.0
CA F:SER17 4.1 28.4 1.0
O2B F:GNP202 4.2 37.5 1.0
N F:THR35 4.2 74.5 1.0
CA F:THR35 4.3 75.5 1.0
CB F:LYS16 4.3 28.4 1.0
CE F:LYS16 4.5 32.0 1.0
NZ F:LYS16 4.5 34.5 1.0
O3G F:GNP202 4.6 45.2 1.0
O1A F:GNP202 4.6 34.5 1.0
O3A F:GNP202 4.6 30.6 1.0
C F:LYS16 4.7 29.8 1.0
O2A F:GNP202 4.8 30.1 1.0
PA F:GNP202 4.9 31.6 1.0
C F:THR58 4.9 47.4 1.0
CA F:LYS16 4.9 30.5 1.0

Reference:

N.Bery, A.Cruz-Migoni, C.J.Bataille, C.E.Quevedo, H.Tulmin, A.Miller, A.Russell, S.E.Phillips, S.B.Carr, T.H.Rabbitts. Bret-Based Ras Biosensors That Show A Novel Small Molecule Is An Inhibitor of Ras-Effector Protein-Protein Interactions. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 29989546
DOI: 10.7554/ELIFE.37122
Page generated: Mon Dec 14 22:40:18 2020

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