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Magnesium in PDB 6fa1: Antibody Derived (Abd-4) Small Molecule Binding to Kras.

Protein crystallography data

The structure of Antibody Derived (Abd-4) Small Molecule Binding to Kras., PDB code: 6fa1 was solved by C.E.Quevedo, A.Cruz-Migoni, M.T.Ehebauer, S.B.Carr, S.V.E.Phillips, T.H.Rabbitts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.35 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.610, 118.600, 156.610, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 20.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Antibody Derived (Abd-4) Small Molecule Binding to Kras. (pdb code 6fa1). 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-4) Small Molecule Binding to Kras., PDB code: 6fa1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6fa1

Go back to Magnesium Binding Sites List in 6fa1
Magnesium binding site 1 out of 6 in the Antibody Derived (Abd-4) 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-4) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:19.1
occ:1.00
 O2B B:GNP202 2.0 15.3 1.0
O2G B:GNP202 2.0 22.9 1.0
O B:HOH317 2.1 19.2 1.0
O B:HOH337 2.1 17.4 1.0
OG1 B:THR35 2.1 20.5 1.0
OG B:SER17 2.2 20.3 1.0
PB B:GNP202 3.1 18.5 1.0
PG B:GNP202 3.2 22.0 1.0
CB B:THR35 3.2 25.8 1.0
CB B:SER17 3.2 18.4 1.0
N3B B:GNP202 3.3 19.4 1.0
N B:SER17 3.8 16.6 1.0
N B:THR35 3.9 26.6 1.0
O3G B:GNP202 4.0 22.3 1.0
O1A B:GNP202 4.0 17.3 1.0
CA B:SER17 4.1 16.9 1.0
OD2 B:ASP57 4.1 29.1 1.0
CA B:THR35 4.2 26.9 1.0
O1G B:GNP202 4.2 22.6 1.0
O3A B:GNP202 4.2 17.1 1.0
O1B B:GNP202 4.2 17.1 1.0
OD1 B:ASP57 4.2 29.2 1.0
CG2 B:THR35 4.3 26.7 1.0
O B:HOH331 4.3 47.3 1.0
O B:THR58 4.4 25.0 1.0
PA B:GNP202 4.4 17.8 1.0
O2A B:GNP202 4.4 16.1 1.0
O B:ASP33 4.5 23.2 1.0
CG B:ASP57 4.6 28.0 1.0
CB B:LYS16 4.7 15.5 1.0
C B:PRO34 4.8 24.3 1.0
C B:LYS16 4.9 15.8 1.0
CE B:LYS16 4.9 19.0 1.0
NZ B:LYS16 4.9 19.3 1.0

Magnesium binding site 2 out of 6 in 6fa1

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Magnesium binding site 2 out of 6 in the Antibody Derived (Abd-4) 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-4) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:17.3
occ:1.00
 O2G A:GNP202 2.0 18.9 1.0
O2B A:GNP202 2.0 18.3 1.0
O A:HOH309 2.1 16.6 1.0
OG1 A:THR35 2.1 17.5 1.0
O A:HOH327 2.1 17.8 1.0
OG A:SER17 2.1 15.6 1.0
CB A:THR35 3.1 17.3 1.0
CB A:SER17 3.1 15.1 1.0
PB A:GNP202 3.2 17.6 1.0
PG A:GNP202 3.2 18.3 1.0
N3B A:GNP202 3.5 18.2 1.0
N A:SER17 3.8 14.3 1.0
N A:THR35 3.9 20.8 1.0
OD2 A:ASP57 4.0 25.4 0.5
OD2 A:ASP57 4.0 25.6 0.5
CA A:SER17 4.0 14.7 1.0
O3G A:GNP202 4.1 19.0 1.0
OD1 A:ASP57 4.1 25.9 0.5
OD1 A:ASP57 4.1 26.2 0.5
CA A:THR35 4.1 20.6 1.0
O1A A:GNP202 4.1 18.1 1.0
CG2 A:THR35 4.2 19.5 1.0
O1B A:GNP202 4.2 16.0 1.0
O A:HOH346 4.3 34.1 1.0
O3A A:GNP202 4.3 16.7 1.0
O1G A:GNP202 4.4 18.2 1.0
CG A:ASP57 4.4 23.4 0.5
CG A:ASP57 4.4 23.6 0.5
O A:THR58 4.4 22.6 1.0
PA A:GNP202 4.5 18.2 1.0
O A:ASP33 4.5 25.4 1.0
O2A A:GNP202 4.7 17.9 1.0
CB A:LYS16 4.7 15.3 1.0
C A:LYS16 4.8 14.9 1.0
C A:PRO34 4.8 23.9 1.0
CE A:LYS16 4.9 16.0 1.0
NZ A:LYS16 5.0 16.9 1.0

Magnesium binding site 3 out of 6 in 6fa1

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Magnesium binding site 3 out of 6 in the Antibody Derived (Abd-4) 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-4) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:39.0
occ:1.00
 O C:HOH316 2.0 29.6 1.0
O1B C:GNP202 2.1 26.4 1.0
O1G C:GNP202 2.1 37.0 1.0
OG1 C:THR35 2.1 43.8 1.0
OG C:SER17 2.2 30.1 1.0
O C:HOH318 2.3 34.6 1.0
CB C:THR35 3.1 51.0 1.0
CB C:SER17 3.2 28.8 1.0
PG C:GNP202 3.3 35.6 1.0
PB C:GNP202 3.3 30.0 1.0
N3B C:GNP202 3.5 30.6 1.0
N C:SER17 3.8 25.5 1.0
N C:THR35 3.8 46.7 1.0
O2G C:GNP202 4.0 31.7 1.0
OD2 C:ASP57 4.0 44.9 0.5
OD2 C:ASP57 4.0 42.5 0.5
CA C:SER17 4.1 28.8 1.0
CA C:THR35 4.1 48.2 1.0
OD1 C:ASP57 4.1 39.0 0.5
OD1 C:ASP57 4.1 41.8 0.5
CG2 C:THR35 4.1 52.8 1.0
O2A C:GNP202 4.2 28.2 1.0
O3A C:GNP202 4.3 29.4 1.0
O2B C:GNP202 4.3 25.8 1.0
O C:THR58 4.3 37.1 1.0
O3G C:GNP202 4.4 37.9 1.0
CG C:ASP57 4.4 40.7 0.5
CG C:ASP57 4.4 42.6 0.5
PA C:GNP202 4.5 29.8 1.0
O C:ASP33 4.5 57.8 1.0
O1A C:GNP202 4.6 28.9 1.0
CB C:LYS16 4.7 26.9 1.0
C C:PRO34 4.8 51.2 1.0
C C:LYS16 4.8 26.5 1.0
CE C:LYS16 4.9 32.5 1.0
NZ C:LYS16 5.0 34.7 1.0

Magnesium binding site 4 out of 6 in 6fa1

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

b:49.4
occ:1.00
 O2B D:GNP201 1.9 29.1 1.0
OG D:SER17 2.1 28.4 1.0
O2G D:GNP201 2.1 40.6 1.0
O D:HOH308 2.2 42.6 1.0
O D:HOH306 2.3 41.2 1.0
OG1 D:THR35 2.3 60.7 1.0
CB D:SER17 3.1 31.4 1.0
PB D:GNP201 3.1 29.9 1.0
CB D:THR35 3.3 73.7 1.0
PG D:GNP201 3.3 41.2 1.0
N3B D:GNP201 3.4 37.4 1.0
N D:SER17 3.7 30.3 1.0
N D:THR35 3.9 80.7 1.0
O1A D:GNP201 3.9 34.7 1.0
CA D:SER17 4.0 26.2 1.0
OD2 D:ASP57 4.1 45.1 0.5
O3A D:GNP201 4.2 30.3 1.0
OD2 D:ASP57 4.2 46.3 0.5
O3G D:GNP201 4.2 38.6 1.0
CA D:THR35 4.3 77.7 1.0
PA D:GNP201 4.3 32.2 1.0
OD1 D:ASP57 4.3 49.5 0.5
OD1 D:ASP57 4.3 50.4 0.5
O1B D:GNP201 4.3 28.4 1.0
O2A D:GNP201 4.4 35.8 1.0
CG2 D:THR35 4.4 62.2 1.0
O D:ASP33 4.4 80.7 1.0
O1G D:GNP201 4.5 38.9 1.0
O D:THR58 4.6 45.5 1.0
CG D:ASP57 4.6 44.8 0.5
CG D:ASP57 4.6 45.6 0.5
CB D:LYS16 4.8 27.6 1.0
C D:PRO34 4.8 85.3 1.0
C D:LYS16 4.8 29.2 1.0
CA D:PRO34 5.0 89.9 1.0

Magnesium binding site 5 out of 6 in 6fa1

Go back to Magnesium Binding Sites List in 6fa1
Magnesium binding site 5 out of 6 in the Antibody Derived (Abd-4) 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-4) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:35.1
occ:1.00
 OG1 E:THR35 2.0 45.3 1.0
O1G E:GNP202 2.1 34.1 1.0
OG E:SER17 2.1 35.2 1.0
O E:HOH306 2.1 28.0 1.0
O E:HOH318 2.1 32.8 1.0
O1B E:GNP202 2.2 27.4 1.0
CB E:THR35 3.0 49.3 1.0
CB E:SER17 3.1 28.4 1.0
PG E:GNP202 3.4 36.4 1.0
PB E:GNP202 3.4 28.7 1.0
N3B E:GNP202 3.6 32.5 1.0
N E:THR35 3.8 55.5 1.0
OD2 E:ASP57 3.9 40.2 0.5
N E:SER17 3.9 25.6 1.0
OD2 E:ASP57 4.0 42.9 0.5
CA E:THR35 4.0 53.5 1.0
CG2 E:THR35 4.1 49.9 1.0
CA E:SER17 4.1 26.1 1.0
O2A E:GNP202 4.1 30.2 1.0
O2G E:GNP202 4.1 34.9 1.0
OD1 E:ASP57 4.3 44.0 0.5
OD1 E:ASP57 4.3 41.9 0.5
O E:ASP33 4.4 50.5 1.0
O E:THR58 4.4 37.4 1.0
O3A E:GNP202 4.4 29.3 1.0
O2B E:GNP202 4.4 26.8 1.0
CG E:ASP57 4.5 41.5 0.5
O3G E:GNP202 4.5 45.6 1.0
CG E:ASP57 4.5 43.2 0.5
PA E:GNP202 4.5 29.0 1.0
C E:PRO34 4.7 51.9 1.0
O1A E:GNP202 4.7 30.4 1.0
CB E:LYS16 4.9 26.6 1.0
CA E:PRO34 5.0 51.6 1.0

Magnesium binding site 6 out of 6 in 6fa1

Go back to Magnesium Binding Sites List in 6fa1
Magnesium binding site 6 out of 6 in the Antibody Derived (Abd-4) 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-4) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:47.2
occ:1.00
 O F:HOH305 1.9 41.5 1.0
O1B F:GNP202 1.9 24.5 1.0
OG F:SER17 2.1 25.5 1.0
O F:HOH333 2.2 39.7 1.0
OG1 F:THR35 2.3 73.8 1.0
O1G F:GNP202 2.3 43.1 1.0
CB F:SER17 3.1 27.8 1.0
PB F:GNP202 3.2 27.4 1.0
CB F:THR35 3.2 86.3 1.0
PG F:GNP202 3.5 34.6 1.0
N F:SER17 3.5 25.9 1.0
N3B F:GNP202 3.6 28.1 1.0
CA F:SER17 3.9 25.2 1.0
OD2 F:ASP57 3.9 26.4 0.5
OD1 F:ASP57 3.9 32.6 0.5
N F:THR35 4.1 82.9 1.0
O2G F:GNP202 4.1 42.2 1.0
O2B F:GNP202 4.1 26.9 1.0
O2A F:GNP202 4.1 27.3 1.0
CG2 F:THR35 4.2 84.3 1.0
O F:THR58 4.3 51.8 1.0
CG F:ASP57 4.3 31.5 0.5
O3A F:GNP202 4.3 24.2 1.0
CA F:THR35 4.3 84.3 1.0
O F:HOH319 4.3 44.7 1.0
CB F:LYS16 4.4 24.5 1.0
O1A F:GNP202 4.5 28.3 1.0
PA F:GNP202 4.5 26.7 1.0
C F:LYS16 4.6 22.7 1.0
O3G F:GNP202 4.6 41.2 1.0
O F:ASP33 4.8 61.4 1.0
CE F:LYS16 4.8 24.5 1.0
CA F:LYS16 4.9 23.2 1.0
NZ F:LYS16 4.9 24.4 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 00:14:33 2024

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