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Magnesium in PDB 6fa4: Antibody Derived (Abd-7) Small Molecule Binding to Kras.

Protein crystallography data

The structure of Antibody Derived (Abd-7) Small Molecule Binding to Kras., PDB code: 6fa4 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) 65.06 / 2.02
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.704, 118.619, 157.329, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 23.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Antibody Derived (Abd-7) Small Molecule Binding to Kras. (pdb code 6fa4). 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-7) Small Molecule Binding to Kras., PDB code: 6fa4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6fa4

Go back to Magnesium Binding Sites List in 6fa4
Magnesium binding site 1 out of 6 in the Antibody Derived (Abd-7) 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-7) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:21.8
occ:1.00
 O2B B:GNP202 2.0 15.4 1.0
O2G B:GNP202 2.0 21.9 1.0
O B:HOH310 2.1 21.2 1.0
OG1 B:THR35 2.1 18.9 1.0
O B:HOH317 2.1 22.1 1.0
OG B:SER17 2.2 20.6 1.0
CB B:THR35 3.1 22.1 1.0
PB B:GNP202 3.2 18.1 1.0
CB B:SER17 3.2 22.3 1.0
PG B:GNP202 3.3 21.4 1.0
N3B B:GNP202 3.5 20.4 1.0
N B:THR35 3.8 22.7 1.0
N B:SER17 3.9 18.4 1.0
OD2 B:ASP57 4.1 26.9 1.0
CA B:THR35 4.1 25.7 1.0
O3G B:GNP202 4.1 19.8 1.0
CA B:SER17 4.1 21.5 1.0
O1A B:GNP202 4.2 18.1 1.0
CG2 B:THR35 4.2 26.2 1.0
O3A B:GNP202 4.2 19.5 1.0
OD1 B:ASP57 4.3 28.1 1.0
O1B B:GNP202 4.3 16.6 1.0
O1G B:GNP202 4.4 22.6 1.0
O B:ASP33 4.4 21.8 1.0
O B:THR58 4.5 23.4 1.0
PA B:GNP202 4.5 17.7 1.0
O2A B:GNP202 4.5 18.2 1.0
CG B:ASP57 4.5 27.3 1.0
C B:PRO34 4.7 25.1 1.0
CB B:LYS16 4.8 17.5 1.0
C B:LYS16 5.0 18.4 1.0

Magnesium binding site 2 out of 6 in 6fa4

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Magnesium binding site 2 out of 6 in the Antibody Derived (Abd-7) 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-7) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:21.2
occ:1.00
 OG1 A:THR35 2.0 21.5 1.0
O2G A:GNP202 2.0 18.9 1.0
O A:HOH317 2.1 16.5 1.0
O2B A:GNP202 2.1 20.1 1.0
OG A:SER17 2.1 18.8 1.0
O A:HOH309 2.2 19.5 1.0
CB A:THR35 3.1 22.6 1.0
CB A:SER17 3.2 17.0 1.0
PG A:GNP202 3.2 20.7 1.0
PB A:GNP202 3.3 19.9 1.0
N3B A:GNP202 3.5 22.2 1.0
N A:THR35 3.8 25.1 1.0
N A:SER17 3.9 17.9 1.0
OD2 A:ASP57 4.0 28.6 0.5
OD2 A:ASP57 4.0 28.6 0.5
CA A:THR35 4.0 24.3 1.0
O3G A:GNP202 4.1 23.0 1.0
CA A:SER17 4.1 19.4 1.0
O1A A:GNP202 4.1 18.5 1.0
CG2 A:THR35 4.2 23.5 1.0
OD1 A:ASP57 4.3 28.8 0.5
OD1 A:ASP57 4.3 28.8 0.5
O1B A:GNP202 4.3 17.0 1.0
O3A A:GNP202 4.4 22.9 1.0
O1G A:GNP202 4.5 20.5 1.0
O A:THR58 4.5 19.3 1.0
O A:ASP33 4.5 25.3 1.0
CG A:ASP57 4.5 26.6 0.5
CG A:ASP57 4.5 26.6 0.5
PA A:GNP202 4.6 20.6 1.0
C A:PRO34 4.7 27.5 1.0
O2A A:GNP202 4.8 18.2 1.0
CB A:LYS16 4.9 19.7 1.0
O A:HOH304 4.9 32.5 1.0
CE A:LYS16 5.0 19.6 1.0
C A:LYS16 5.0 17.9 1.0
CA A:PRO34 5.0 27.0 1.0

Magnesium binding site 3 out of 6 in 6fa4

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Magnesium binding site 3 out of 6 in the Antibody Derived (Abd-7) 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-7) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:32.8
occ:1.00
 O1B C:GNP202 1.9 25.8 1.0
O C:HOH305 2.0 31.4 1.0
O1G C:GNP202 2.1 33.3 1.0
O C:HOH306 2.1 32.7 1.0
OG C:SER17 2.2 27.9 1.0
OG1 C:THR35 2.2 38.5 1.0
PB C:GNP202 3.1 30.0 1.0
CB C:SER17 3.1 31.7 1.0
PG C:GNP202 3.3 33.4 1.0
CB C:THR35 3.3 39.0 1.0
N3B C:GNP202 3.3 32.2 1.0
N C:SER17 3.8 30.4 1.0
N C:THR35 3.9 39.6 1.0
O2G C:GNP202 4.0 30.7 1.0
CA C:SER17 4.0 29.7 1.0
O3A C:GNP202 4.1 27.7 1.0
OD2 C:ASP57 4.1 40.9 0.5
OD2 C:ASP57 4.1 38.6 0.5
O2A C:GNP202 4.1 29.7 1.0
OD1 C:ASP57 4.2 38.7 0.5
CA C:THR35 4.2 38.1 1.0
OD1 C:ASP57 4.2 36.0 0.5
O2B C:GNP202 4.2 29.5 1.0
CG2 C:THR35 4.4 37.7 1.0
O1A C:GNP202 4.4 32.9 1.0
O3G C:GNP202 4.4 35.7 1.0
PA C:GNP202 4.4 31.3 1.0
O C:THR58 4.5 36.7 1.0
O C:ASP33 4.5 49.5 1.0
CG C:ASP57 4.6 38.2 0.5
CG C:ASP57 4.6 36.3 0.5
CB C:LYS16 4.7 29.9 1.0
C C:LYS16 4.8 28.3 1.0
C C:PRO34 4.8 43.6 1.0
CE C:LYS16 4.9 29.5 1.0

Magnesium binding site 4 out of 6 in 6fa4

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Magnesium binding site 4 out of 6 in the Antibody Derived (Abd-7) 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-7) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:49.1
occ:1.00
 O2B D:GNP201 2.0 30.7 1.0
OG D:SER17 2.1 26.6 1.0
O2G D:GNP201 2.2 39.2 1.0
OG1 D:THR35 2.3 57.3 1.0
O D:HOH302 2.4 37.5 1.0
O D:HOH301 2.6 36.3 1.0
CB D:SER17 3.0 31.9 1.0
PB D:GNP201 3.2 30.4 1.0
CB D:THR35 3.3 68.9 1.0
PG D:GNP201 3.4 36.1 1.0
N3B D:GNP201 3.6 36.4 1.0
N D:SER17 3.8 29.7 1.0
N D:THR35 3.8 79.8 1.0
CA D:SER17 4.0 29.8 1.0
O1A D:GNP201 4.0 33.5 1.0
OD2 D:ASP57 4.1 58.0 0.5
OD2 D:ASP57 4.1 58.0 0.5
CA D:THR35 4.2 74.4 1.0
O1B D:GNP201 4.2 25.4 1.0
O3A D:GNP201 4.3 31.3 1.0
O2A D:GNP201 4.3 30.7 1.0
CG2 D:THR35 4.4 68.0 1.0
PA D:GNP201 4.4 29.8 1.0
OD1 D:ASP57 4.4 51.4 0.5
O1G D:GNP201 4.4 38.1 1.0
OD1 D:ASP57 4.4 51.4 0.5
O D:ASP33 4.4 73.5 1.0
O3G D:GNP201 4.5 45.9 1.0
O D:THR58 4.6 48.6 1.0
CG D:ASP57 4.6 49.7 0.5
CG D:ASP57 4.6 49.6 0.5
C D:PRO34 4.8 84.6 1.0
CB D:LYS16 4.9 28.0 1.0
C D:LYS16 4.9 27.7 1.0
CA D:PRO34 5.0 92.3 1.0

Magnesium binding site 5 out of 6 in 6fa4

Go back to Magnesium Binding Sites List in 6fa4
Magnesium binding site 5 out of 6 in the Antibody Derived (Abd-7) 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-7) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:54.3
occ:1.00
 O1G E:GNP202 2.0 41.2 1.0
O1B E:GNP202 2.0 30.7 1.0
O E:HOH304 2.3 37.1 1.0
OG1 E:THR35 2.3 82.5 1.0
OG E:SER17 2.3 37.6 1.0
O E:HOH303 2.4 31.9 1.0
PG E:GNP202 3.2 43.0 1.0
PB E:GNP202 3.2 33.5 1.0
CB E:THR35 3.3 81.0 1.0
CB E:SER17 3.3 32.3 1.0
N3B E:GNP202 3.4 41.8 1.0
N E:THR35 3.8 79.1 1.0
N E:SER17 3.9 32.4 1.0
O2A E:GNP202 3.9 37.5 1.0
O2G E:GNP202 4.0 44.6 1.0
CA E:SER17 4.2 34.5 1.0
CA E:THR35 4.2 79.9 1.0
O3A E:GNP202 4.2 32.4 1.0
OD2 E:ASP57 4.2 54.3 0.5
OD2 E:ASP57 4.3 54.0 0.5
O3G E:GNP202 4.3 48.5 1.0
O2B E:GNP202 4.3 32.2 1.0
OD1 E:ASP57 4.4 54.5 0.5
CG2 E:THR35 4.4 71.8 1.0
PA E:GNP202 4.4 33.4 1.0
OD1 E:ASP57 4.4 53.7 0.5
O E:THR58 4.5 45.0 1.0
O1A E:GNP202 4.5 30.6 1.0
O E:ASP33 4.6 74.2 1.0
CG E:ASP57 4.7 54.5 0.5
CG E:ASP57 4.7 54.1 0.5
C E:PRO34 4.8 76.5 1.0
CB E:LYS16 4.8 29.7 1.0
CA E:PRO34 5.0 78.4 1.0
C E:LYS16 5.0 31.0 1.0
CE E:LYS16 5.0 34.0 1.0

Magnesium binding site 6 out of 6 in 6fa4

Go back to Magnesium Binding Sites List in 6fa4
Magnesium binding site 6 out of 6 in the Antibody Derived (Abd-7) 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-7) Small Molecule Binding to Kras. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:37.2
occ:1.00
 O1B F:GNP202 1.9 23.6 1.0
O1G F:GNP202 2.1 31.1 1.0
O F:HOH301 2.2 29.0 1.0
OG1 F:THR35 2.2 42.6 1.0
O F:HOH309 2.2 38.1 1.0
OG F:SER17 2.3 22.2 1.0
PB F:GNP202 3.1 26.6 1.0
CB F:SER17 3.2 27.4 1.0
CB F:THR35 3.3 51.7 1.0
PG F:GNP202 3.3 30.8 1.0
N3B F:GNP202 3.5 27.2 1.0
OD2 F:ASP57 3.8 51.3 0.5
N F:SER17 3.8 26.9 1.0
N F:THR35 3.9 47.7 1.0
CA F:SER17 4.0 24.1 1.0
O2G F:GNP202 4.0 39.8 1.0
OD2 F:ASP57 4.1 31.7 0.5
OD1 F:ASP57 4.1 26.2 0.5
O2A F:GNP202 4.2 26.7 1.0
O2B F:GNP202 4.2 23.6 1.0
CA F:THR35 4.2 50.5 1.0
O3A F:GNP202 4.2 26.5 1.0
CG2 F:THR35 4.3 47.2 1.0
O F:THR58 4.4 34.7 1.0
O3G F:GNP202 4.4 32.9 1.0
O1A F:GNP202 4.4 28.7 1.0
CG F:ASP57 4.5 31.9 0.5
PA F:GNP202 4.6 27.1 1.0
CB F:LYS16 4.6 22.6 1.0
O F:ASP33 4.6 58.6 1.0
C F:LYS16 4.8 24.8 1.0
C F:PRO34 4.9 58.2 1.0
CE F:LYS16 4.9 26.9 1.0
NZ F:LYS16 4.9 28.2 1.0
CG F:ASP57 5.0 49.1 0.5

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 00:15:36 2024

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