Atomistry » Magnesium » PDB 6f5p-6fcd » 6f76
Atomistry »
  Magnesium »
    PDB 6f5p-6fcd »
      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

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy