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Magnesium in PDB 9gtk: Kras in Complex with Darpin 784_F5

Enzymatic activity of Kras in Complex with Darpin 784_F5

All present enzymatic activity of Kras in Complex with Darpin 784_F5:
3.6.5.2;

Protein crystallography data

The structure of Kras in Complex with Darpin 784_F5, PDB code: 9gtk was solved by J.N.Kapp, W.Verdurmen, J.V.Schaefer, K.Kopra, G.Nagy-Davidescu, E.Richard, M.J.Nokin, P.Ernst, R.Tamaskovic, M.Schwill, R.Degen, C.Scholl, D.Santamaria, A.Plueckthun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.28 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.32, 152.83, 149.15, 90, 90, 90
R / Rfree (%) 17.1 / 20.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Kras in Complex with Darpin 784_F5 (pdb code 9gtk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Kras in Complex with Darpin 784_F5, PDB code: 9gtk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 9gtk

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Magnesium binding site 1 out of 6 in the Kras in Complex with Darpin 784_F5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kras in Complex with Darpin 784_F5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg212

b:34.6
occ:1.00
 O2G A:GNP214 2.0 39.2 1.0
O2B A:GNP214 2.1 30.7 1.0
O A:HOH328 2.1 30.6 1.0
OG A:SER17 2.1 31.6 1.0
O A:HOH319 2.2 34.8 1.0
O A:HOH372 2.2 35.3 1.0
CB A:SER17 3.1 32.2 1.0
PG A:GNP214 3.3 48.8 1.0
PB A:GNP214 3.3 33.6 1.0
N3B A:GNP214 3.4 39.0 1.0
N A:SER17 3.8 29.5 1.0
OD2 A:ASP57 4.0 30.2 1.0
CA A:SER17 4.0 30.6 1.0
O3G A:GNP214 4.2 44.1 1.0
O A:HOH420 4.2 52.1 1.0
OD1 A:ASP57 4.2 31.9 1.0
OG1 A:THR35 4.2 41.6 1.0
O2A A:GNP214 4.2 32.6 1.0
O3A A:GNP214 4.3 32.9 1.0
O1G A:GNP214 4.3 54.2 1.0
O1B A:GNP214 4.3 32.5 1.0
CG A:ASP57 4.5 31.1 1.0
O A:THR58 4.5 34.0 1.0
O A:HOH423 4.6 59.3 1.0
PA A:GNP214 4.6 35.6 1.0
O A:HOH310 4.7 43.8 1.0
CB A:LYS16 4.7 31.3 1.0
O1A A:GNP214 4.8 34.2 1.0
C A:LYS16 4.9 28.0 1.0
CE A:LYS16 4.9 34.0 1.0
O A:ILE36 5.0 32.0 1.0

Magnesium binding site 2 out of 6 in 9gtk

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Magnesium binding site 2 out of 6 in the Kras in Complex with Darpin 784_F5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kras in Complex with Darpin 784_F5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg213

b:51.3
occ:1.00
 O B:HOH326 2.6 43.6 1.0
O A:TYR40 3.0 28.1 1.0
OD1 A:ASP54 3.3 48.3 1.0
C A:TYR40 3.5 29.1 1.0
O B:HOH347 3.6 58.8 1.0
CB A:ASP54 3.7 32.8 1.0
CG A:ASP54 3.7 39.7 1.0
CD1 B:TRP46 3.8 33.6 1.0
N A:TYR40 3.8 27.5 1.0
CB A:SER39 3.8 29.3 1.0
CA A:ASP54 3.9 31.3 1.0
O B:HOH313 4.0 49.1 1.0
OG A:SER39 4.0 29.5 1.0
OD2 B:ASP44 4.1 36.5 1.0
N A:ARG41 4.2 31.2 1.0
CA A:TYR40 4.2 28.9 1.0
N A:ILE55 4.3 31.2 1.0
CB A:ARG41 4.3 32.9 1.0
C A:SER39 4.4 29.9 1.0
C A:ASP54 4.4 30.4 1.0
NH2 B:ARG23 4.4 46.5 1.0
CA A:ARG41 4.5 29.6 1.0
O A:HOH336 4.5 33.9 1.0
O B:HOH314 4.5 51.9 1.0
O A:ILE55 4.6 30.0 1.0
CG B:TRP46 4.6 33.1 1.0
CG B:ASP44 4.7 35.7 1.0
CA A:SER39 4.7 29.1 1.0
OD2 A:ASP54 4.7 40.0 1.0
CB B:TRP46 4.7 32.4 1.0
NE1 B:TRP46 4.7 35.4 1.0
OD1 B:ASP44 5.0 34.0 1.0
O A:SER39 5.0 27.8 1.0

Magnesium binding site 3 out of 6 in 9gtk

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Magnesium binding site 3 out of 6 in the Kras in Complex with Darpin 784_F5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Kras in Complex with Darpin 784_F5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg210

b:47.4
occ:1.00
 O2G C:GNP211 1.9 30.9 0.5
O C:HOH320 2.0 52.4 1.0
O C:HOH332 2.0 44.2 1.0
O2B C:GNP211 2.1 36.0 1.0
OG C:SER17 2.1 42.2 1.0
O C:HOH316 2.1 44.3 1.0
PG C:GNP211 3.1 48.9 0.5
CB C:SER17 3.2 41.2 1.0
PB C:GNP211 3.4 43.5 1.0
N3B C:GNP211 3.5 48.5 1.0
N C:SER17 3.9 38.9 1.0
OD2 C:ASP57 3.9 46.7 1.0
O3G C:GNP211 4.0 40.6 0.5
O1G C:GNP211 4.1 57.4 0.5
OG1 C:THR35 4.1 70.1 1.0
CA C:SER17 4.1 41.7 1.0
O2A C:GNP211 4.1 45.5 1.0
O C:HOH388 4.2 52.9 1.0
OD1 C:ASP57 4.2 45.0 1.0
O1B C:GNP211 4.4 41.4 1.0
O C:HOH304 4.4 66.8 1.0
O3A C:GNP211 4.4 43.8 1.0
CG C:ASP57 4.5 47.0 1.0
PA C:GNP211 4.6 47.4 1.0
O C:THR58 4.6 50.0 1.0
O1A C:GNP211 4.7 45.7 1.0
CB C:LYS16 4.8 39.3 1.0
CB C:THR35 4.9 68.0 1.0
CE C:LYS16 4.9 47.9 1.0
CB C:ALA59 5.0 73.2 1.0
C C:LYS16 5.0 38.5 1.0

Magnesium binding site 4 out of 6 in 9gtk

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Magnesium binding site 4 out of 6 in the Kras in Complex with Darpin 784_F5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Kras in Complex with Darpin 784_F5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg203

b:40.6
occ:1.00
 O D:HOH312 2.0 40.8 1.0
O2B D:GNP204 2.0 37.7 1.0
O D:HOH353 2.1 41.1 1.0
O D:HOH304 2.1 40.0 1.0
O2G D:GNP204 2.1 45.9 1.0
OG D:SER17 2.2 37.8 1.0
CB D:SER17 3.2 37.7 1.0
PB D:GNP204 3.3 38.7 1.0
PG D:GNP204 3.3 48.5 1.0
N3B D:GNP204 3.4 44.3 1.0
O D:HOH396 3.8 59.5 1.0
N D:SER17 3.9 38.5 1.0
OD2 D:ASP57 3.9 38.4 1.0
O D:HOH347 4.0 52.3 1.0
OG1 D:THR35 4.0 61.9 1.0
CA D:SER17 4.1 38.4 1.0
OD1 D:ASP57 4.1 39.8 1.0
O3G D:GNP204 4.2 45.6 1.0
O1G D:GNP204 4.2 49.8 1.0
O1B D:GNP204 4.3 35.6 1.0
O2A D:GNP204 4.3 36.8 1.0
O3A D:GNP204 4.4 46.1 1.0
CG D:ASP57 4.4 40.2 1.0
O D:HOH338 4.5 56.6 1.0
O D:THR58 4.5 42.7 1.0
O1A D:GNP204 4.7 36.3 1.0
PA D:GNP204 4.7 37.9 1.0
CB D:LYS16 4.8 37.2 1.0
CE D:LYS16 4.9 43.1 1.0
C D:LYS16 4.9 36.0 1.0
CB D:THR35 4.9 57.7 1.0

Magnesium binding site 5 out of 6 in 9gtk

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Magnesium binding site 5 out of 6 in the Kras in Complex with Darpin 784_F5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Kras in Complex with Darpin 784_F5 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg201

b:83.3
occ:1.00
 OD1 H:ASP44 2.6 62.2 1.0
OG H:SER48 2.6 51.2 1.0
OG D:SER39 2.7 40.4 1.0
OD2 H:ASP44 3.0 60.4 1.0
O H:HOH303 3.1 63.7 1.0
CG H:ASP44 3.1 59.6 1.0
CB H:SER48 3.3 52.1 1.0
O H:HOH321 3.4 46.7 1.0
CB H:TRP46 3.4 49.5 1.0
N H:SER48 3.6 53.5 1.0
C H:TRP46 3.7 51.3 1.0
CB D:SER39 3.7 40.5 1.0
CA H:TRP46 3.8 50.7 1.0
O D:HOH388 3.8 59.4 1.0
O H:TRP46 3.8 49.8 1.0
N H:TRP46 3.9 51.3 1.0
O H:HOH327 4.0 50.9 1.0
CA H:SER48 4.0 52.4 1.0
N H:GLY47 4.2 53.7 1.0
O H:HOH301 4.5 45.0 1.0
CG H:TRP46 4.6 47.8 1.0
CB H:ASP44 4.6 60.4 1.0
C H:GLY47 4.7 56.2 1.0
CD2 H:LEU53 4.9 54.9 1.0
CD1 H:TRP46 4.9 45.3 1.0

Magnesium binding site 6 out of 6 in 9gtk

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Magnesium binding site 6 out of 6 in the Kras in Complex with Darpin 784_F5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Kras in Complex with Darpin 784_F5 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg202

b:75.8
occ:1.00
 O I:HOH308 2.1 67.4 1.0
O C:HOH359 3.3 76.0 1.0
OD2 I:ASP44 3.4 64.8 1.0
OD1 C:ASP54 3.6 64.3 1.0
O I:HOH301 3.7 62.0 1.0
O C:TYR40 3.8 50.0 1.0
OG C:SER39 3.8 52.8 1.0
CG C:ASP54 3.9 57.9 1.0
CD1 I:TRP46 3.9 48.8 1.0
CG I:ASP44 3.9 63.5 1.0
CB C:ASP54 4.0 52.6 1.0
CB C:SER39 4.1 46.9 1.0
OD1 I:ASP44 4.2 58.7 1.0
C C:TYR40 4.2 51.0 1.0
NH2 I:ARG23 4.3 76.3 1.0
CB I:TRP46 4.4 52.7 1.0
O C:HOH368 4.5 54.6 1.0
N C:TYR40 4.5 44.8 1.0
CA C:ASP54 4.5 48.7 1.0
N I:TRP46 4.5 59.5 1.0
OD2 C:ASP54 4.5 64.6 1.0
CB C:ARG41 4.5 58.3 1.0
CG I:TRP46 4.5 50.4 1.0
O I:HOH302 4.7 80.8 1.0
N C:ARG41 4.7 53.5 1.0
CB I:THR45 4.8 66.7 1.0
C C:SER39 4.8 47.6 1.0
CA C:TYR40 4.9 47.7 1.0
CB I:ASP44 4.9 65.0 1.0
CA C:ARG41 4.9 51.4 1.0

Reference:

J.N.Kapp, W.P.R.Verdurmen, J.V.Schaefer, K.Kopra, G.Nagy-Davidescu, E.Richard, M.J.Nokin, P.Ernst, R.Tamaskovic, M.Schwill, R.Degen, C.Scholl, D.Santamaria, A.Pluckthun. A Nucleotide-Independent, Pan-Ras-Targeted Darpin Elicits Anti-Tumor Activity in A Multimodal Manner. Mol Oncol 2025.
ISSN: ISSN 1878-0261
PubMed: 40517320
DOI: 10.1002/1878-0261.70061
Page generated: Sat Aug 16 03:06:21 2025

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