Atomistry » Magnesium » PDB 6f6u-6fch » 6f76
Atomistry »
  Magnesium »
    PDB 6f6u-6fch »
      6f76 »

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

Go back to Magnesium Binding Sites List in 6f76
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

Go back to Magnesium Binding Sites List in 6f76
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

Go back to Magnesium Binding Sites List in 6f76
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

Go back to Magnesium Binding Sites List in 6f76
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

Go back to Magnesium Binding Sites List in 6f76
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

Go back to Magnesium Binding Sites List in 6f76
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: Tue Oct 1 00:10:53 2024

Last articles

Mg in 4JI1
Mg in 4JI0
Mg in 4JI2
Mg in 4JI3
Mg in 4JHD
Mg in 4JH6
Mg in 4JH8
Mg in 4JH7
Mg in 4JH3
Mg in 4JH5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy