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Magnesium in PDB 6fa3: Antibody Derived (Abd-6) Small Molecule Binding to Kras.

Protein crystallography data

The structure of Antibody Derived (Abd-6) Small Molecule Binding to Kras., PDB code: 6fa3 was solved by C.E.Quevedo, A.Cruz-Migoni, M.T.Ehebauer, S.B.Carr, S.E.V.Phillips, T.H.Rabbitts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.23 / 1.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.390, 118.480, 156.280, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 20.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Antibody Derived (Abd-6) Small Molecule Binding to Kras. (pdb code 6fa3). 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-6) Small Molecule Binding to Kras., PDB code: 6fa3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6fa3

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Magnesium binding site 1 out of 6 in the Antibody Derived (Abd-6) 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-6) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:18.7
occ:1.00
 O2B B:GNP202 2.0 14.5 1.0
OG1 B:THR35 2.1 18.5 1.0
O2G B:GNP202 2.1 23.1 1.0
O B:HOH313 2.1 19.2 1.0
O B:HOH323 2.1 18.8 1.0
OG B:SER17 2.1 20.1 1.0
CB B:THR35 3.1 22.3 1.0
CB B:SER17 3.2 18.0 1.0
PB B:GNP202 3.2 17.6 1.0
PG B:GNP202 3.2 21.1 1.0
N3B B:GNP202 3.4 20.0 1.0
N B:SER17 3.8 16.5 1.0
N B:THR35 3.9 21.3 1.0
OD2 B:ASP57 4.0 30.4 1.0
CA B:SER17 4.0 17.5 1.0
O3G B:GNP202 4.1 24.7 1.0
O1A B:GNP202 4.1 18.6 1.0
CA B:THR35 4.1 23.3 1.0
CG2 B:THR35 4.1 25.9 1.0
OD1 B:ASP57 4.2 26.2 1.0
O B:HOH343 4.2 41.6 1.0
O3A B:GNP202 4.2 17.3 1.0
O1B B:GNP202 4.3 16.4 1.0
O1G B:GNP202 4.3 21.0 1.0
O B:THR58 4.4 23.2 1.0
O B:ASP33 4.4 21.1 1.0
CG B:ASP57 4.5 29.5 1.0
PA B:GNP202 4.5 17.4 1.0
O2A B:GNP202 4.6 17.6 1.0
CB B:LYS16 4.8 14.9 1.0
C B:PRO34 4.8 22.3 1.0
C B:LYS16 4.9 16.9 1.0

Magnesium binding site 2 out of 6 in 6fa3

Go back to Magnesium Binding Sites List in 6fa3
Magnesium binding site 2 out of 6 in the Antibody Derived (Abd-6) 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-6) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:18.0
occ:1.00
 O2G A:GNP203 2.0 18.7 1.0
O A:HOH322 2.1 15.8 1.0
O A:HOH336 2.1 17.4 1.0
O2B A:GNP203 2.1 17.6 1.0
OG1 A:THR35 2.1 18.3 1.0
OG A:SER17 2.1 17.5 1.0
CB A:THR35 3.1 19.4 1.0
CB A:SER17 3.1 15.7 1.0
PB A:GNP203 3.2 18.1 1.0
PG A:GNP203 3.3 20.6 1.0
N3B A:GNP203 3.5 19.1 1.0
N A:THR35 3.8 19.7 1.0
N A:SER17 3.8 16.1 1.0
OD2 A:ASP57 4.0 22.7 0.5
OD2 A:ASP57 4.0 21.1 0.5
CA A:SER17 4.1 16.6 1.0
CA A:THR35 4.1 21.7 1.0
O3G A:GNP203 4.1 19.8 1.0
CG2 A:THR35 4.2 19.6 1.0
O1A A:GNP203 4.2 20.2 1.0
OD1 A:ASP57 4.2 24.4 0.5
OD1 A:ASP57 4.2 25.8 0.5
O1B A:GNP203 4.3 15.8 1.0
O3A A:GNP203 4.3 19.5 1.0
O1G A:GNP203 4.3 21.8 1.0
O A:ASP33 4.4 24.8 1.0
O A:THR58 4.5 20.9 1.0
CG A:ASP57 4.5 24.7 0.5
CG A:ASP57 4.5 25.8 0.5
PA A:GNP203 4.5 19.4 1.0
O2A A:GNP203 4.7 19.1 1.0
C A:PRO34 4.7 27.0 1.0
CB A:LYS16 4.8 16.6 1.0
C A:LYS16 4.9 15.3 1.0
CE A:LYS16 5.0 17.9 1.0
CA A:PRO34 5.0 27.8 1.0

Magnesium binding site 3 out of 6 in 6fa3

Go back to Magnesium Binding Sites List in 6fa3
Magnesium binding site 3 out of 6 in the Antibody Derived (Abd-6) 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-6) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:32.3
occ:1.00
 O C:HOH318 1.9 33.2 1.0
O1G C:GNP202 2.0 34.1 1.0
O1B C:GNP202 2.0 26.9 1.0
O C:HOH305 2.0 30.2 1.0
OG1 C:THR35 2.1 34.3 1.0
OG C:SER17 2.1 30.6 1.0
CB C:THR35 3.0 39.0 1.0
PG C:GNP202 3.2 32.8 1.0
CB C:SER17 3.2 31.0 1.0
PB C:GNP202 3.2 29.2 1.0
N3B C:GNP202 3.4 32.1 1.0
N C:THR35 3.8 43.3 1.0
N C:SER17 3.9 27.4 1.0
O2G C:GNP202 4.0 33.2 1.0
OD2 C:ASP57 4.0 39.2 1.0
CA C:THR35 4.0 38.2 1.0
CG2 C:THR35 4.1 41.6 1.0
CA C:SER17 4.1 29.8 1.0
O2A C:GNP202 4.2 30.8 1.0
OD1 C:ASP57 4.2 41.4 1.0
O3G C:GNP202 4.2 35.3 1.0
O3A C:GNP202 4.3 28.4 1.0
O2B C:GNP202 4.4 28.4 1.0
O C:ASP33 4.4 48.0 1.0
O C:THR58 4.4 40.5 1.0
CG C:ASP57 4.5 40.8 1.0
PA C:GNP202 4.5 31.3 1.0
O1A C:GNP202 4.7 31.3 1.0
C C:PRO34 4.7 44.2 1.0
CB C:LYS16 4.8 27.0 1.0
CA C:PRO34 4.9 45.2 1.0
C C:LYS16 5.0 26.0 1.0

Magnesium binding site 4 out of 6 in 6fa3

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Magnesium binding site 4 out of 6 in the Antibody Derived (Abd-6) 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-6) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:35.5
occ:1.00
 O2B D:GNP201 2.0 24.4 1.0
O2G D:GNP201 2.1 35.5 1.0
O D:HOH305 2.2 32.4 1.0
OG D:SER17 2.2 29.3 1.0
OG1 D:THR35 2.2 40.6 1.0
O D:HOH313 2.3 39.3 1.0
PB D:GNP201 3.1 28.2 1.0
CB D:THR35 3.2 52.4 1.0
CB D:SER17 3.2 32.0 1.0
PG D:GNP201 3.2 35.0 1.0
N3B D:GNP201 3.4 33.2 1.0
N D:SER17 3.8 29.7 1.0
N D:THR35 3.9 52.6 1.0
O3G D:GNP201 4.0 37.0 1.0
CA D:SER17 4.1 27.6 1.0
OD2 D:ASP57 4.1 38.9 0.5
OD2 D:ASP57 4.1 39.2 0.5
CA D:THR35 4.2 53.3 1.0
O1A D:GNP201 4.2 31.2 1.0
O1B D:GNP201 4.2 26.6 1.0
CG2 D:THR35 4.2 49.6 1.0
O3A D:GNP201 4.2 28.0 1.0
OD1 D:ASP57 4.3 40.0 0.5
OD1 D:ASP57 4.3 39.3 0.5
O1G D:GNP201 4.4 39.1 1.0
O D:THR58 4.4 39.7 1.0
PA D:GNP201 4.4 30.4 1.0
O D:ASP33 4.5 58.5 1.0
O2A D:GNP201 4.5 32.1 1.0
CG D:ASP57 4.6 37.9 0.5
CG D:ASP57 4.6 38.3 0.5
CB D:LYS16 4.7 24.1 1.0
C D:PRO34 4.8 63.5 1.0
C D:LYS16 4.9 25.5 1.0
CA D:PRO34 5.0 66.8 1.0
CE D:LYS16 5.0 26.7 1.0
NZ D:LYS16 5.0 29.5 1.0

Magnesium binding site 5 out of 6 in 6fa3

Go back to Magnesium Binding Sites List in 6fa3
Magnesium binding site 5 out of 6 in the Antibody Derived (Abd-6) 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-6) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:32.2
occ:1.00
 O1B E:GNP202 2.0 25.7 1.0
O1G E:GNP202 2.0 29.9 1.0
O E:HOH309 2.1 30.1 1.0
OG E:SER17 2.1 28.6 1.0
OG1 E:THR35 2.1 34.0 1.0
O E:HOH322 2.1 30.0 1.0
CB E:THR35 3.1 42.4 1.0
CB E:SER17 3.1 28.6 1.0
PB E:GNP202 3.2 29.4 1.0
PG E:GNP202 3.3 34.5 1.0
N3B E:GNP202 3.6 33.8 1.0
N E:SER17 3.8 26.8 1.0
N E:THR35 3.9 42.9 1.0
OD2 E:ASP57 3.9 35.0 0.5
OD2 E:ASP57 4.0 40.6 0.5
CA E:SER17 4.0 27.7 1.0
O2G E:GNP202 4.1 32.3 1.0
CA E:THR35 4.1 43.2 1.0
CG2 E:THR35 4.1 41.9 1.0
O2A E:GNP202 4.1 30.9 1.0
OD1 E:ASP57 4.2 44.3 0.5
OD1 E:ASP57 4.2 37.8 0.5
O3A E:GNP202 4.3 30.7 1.0
O2B E:GNP202 4.3 29.3 1.0
O3G E:GNP202 4.3 37.4 1.0
O E:THR58 4.4 36.4 1.0
CG E:ASP57 4.4 38.2 0.5
CG E:ASP57 4.5 42.7 0.5
O E:ASP33 4.5 45.7 1.0
PA E:GNP202 4.6 31.4 1.0
O1A E:GNP202 4.6 27.1 1.0
CB E:LYS16 4.7 25.6 1.0
C E:PRO34 4.8 49.4 1.0
C E:LYS16 4.9 26.4 1.0

Magnesium binding site 6 out of 6 in 6fa3

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Magnesium binding site 6 out of 6 in the Antibody Derived (Abd-6) 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-6) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:31.1
occ:1.00
 O F:HOH319 2.0 31.4 1.0
O1G F:GNP203 2.0 31.0 1.0
O1B F:GNP203 2.0 23.9 1.0
O F:HOH314 2.0 29.5 1.0
OG1 F:THR35 2.1 38.9 1.0
OG F:SER17 2.2 25.1 1.0
CB F:THR35 3.1 44.8 1.0
CB F:SER17 3.2 27.2 1.0
PG F:GNP203 3.2 31.1 1.0
PB F:GNP203 3.3 25.7 1.0
N3B F:GNP203 3.4 26.9 1.0
N F:THR35 3.8 45.7 1.0
N F:SER17 3.8 23.1 1.0
OD2 F:ASP57 4.0 39.4 1.0
CA F:THR35 4.0 48.6 1.0
O2G F:GNP203 4.1 34.3 1.0
CA F:SER17 4.1 25.1 1.0
CG2 F:THR35 4.1 48.5 1.0
O2A F:GNP203 4.2 27.5 1.0
OD1 F:ASP57 4.2 40.2 1.0
O3A F:GNP203 4.2 24.7 1.0
O3G F:GNP203 4.3 30.9 1.0
O2B F:GNP203 4.4 25.8 1.0
O F:ASP33 4.4 42.6 1.0
O F:THR58 4.4 37.2 1.0
CG F:ASP57 4.5 40.7 1.0
PA F:GNP203 4.6 27.1 1.0
O1A F:GNP203 4.6 26.8 1.0
C F:PRO34 4.7 49.8 1.0
CB F:LYS16 4.7 23.2 1.0
C F:LYS16 4.9 22.8 1.0
CA F:PRO34 5.0 52.9 1.0

Reference:

C.E.Quevedo, A.Cruz-Migoni, N.Bery, A.Miller, T.Tanaka, D.Petch, C.J.R.Bataille, L.Y.W.Lee, P.S.Fallon, H.Tulmin, M.T.Ehebauer, N.Fernandez-Fuentes, A.J.Russell, S.B.Carr, S.E.V.Phillips, T.H.Rabbitts. Small Molecule Inhibitors of Ras-Effector Protein Interactions Derived Using An Intracellular Antibody Fragment. Nat Commun V. 9 3169 2018.
ISSN: ESSN 2041-1723
PubMed: 30093669
DOI: 10.1038/S41467-018-05707-2
Page generated: Tue Oct 1 00:14:53 2024

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