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Arsenic in PDB 7mdp: Kras G12C in Complex with G-2897

Enzymatic activity of Kras G12C in Complex with G-2897

All present enzymatic activity of Kras G12C in Complex with G-2897:
3.6.5.2;

Protein crystallography data

The structure of Kras G12C in Complex with G-2897, PDB code: 7mdp was solved by A.Oh, Y.Frank, W.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.90 / 1.96
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 149.365, 68.919, 100.543, 90, 114.29, 90
R / Rfree (%) 19.5 / 22.9

Other elements in 7mdp:

The structure of Kras G12C in Complex with G-2897 also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Magnesium (Mg) 1 atom

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Kras G12C in Complex with G-2897 (pdb code 7mdp). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 4 binding sites of Arsenic where determined in the Kras G12C in Complex with G-2897, PDB code: 7mdp:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 7mdp

Go back to Arsenic Binding Sites List in 7mdp
Arsenic binding site 1 out of 4 in the Kras G12C in Complex with G-2897


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Kras G12C in Complex with G-2897 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:As301

b:146.1
occ:1.00
AS H:CAD301 0.0 146.1 1.0
O2 H:CAD301 1.7 143.5 1.0
O1 H:CAD301 1.9 146.3 1.0
C1 H:CAD301 2.0 148.3 1.0
C2 H:CAD301 2.0 146.1 1.0
O H:SER65 3.6 35.5 1.0
O H:HOH418 3.6 45.6 1.0
OG1 H:THR68 4.3 40.4 1.0
OG H:SER82A 4.3 45.8 1.0
C H:SER65 4.4 34.7 1.0
C H:ARG66 4.5 34.1 1.0
CA H:ARG66 4.5 30.9 1.0
O H:ARG66 4.6 35.7 1.0
O H:HOH441 4.6 58.0 1.0
N H:ARG66 4.8 37.9 1.0
O H:VAL67 4.9 37.3 1.0
N H:VAL67 4.9 34.9 1.0

Arsenic binding site 2 out of 4 in 7mdp

Go back to Arsenic Binding Sites List in 7mdp
Arsenic binding site 2 out of 4 in the Kras G12C in Complex with G-2897


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Kras G12C in Complex with G-2897 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:As302

b:163.8
occ:1.00
AS H:CAD302 0.0 163.8 1.0
O2 H:CAD302 1.7 164.6 1.0
O1 H:CAD302 1.9 163.6 1.0
C2 H:CAD302 2.0 163.4 1.0
C1 H:CAD302 2.0 161.9 1.0
OE2 H:GLU50 3.9 48.8 1.0
NE1 H:TRP34 4.6 46.1 1.0
CZ3 I:TRP91 4.7 37.1 1.0
CE2 H:TRP34 4.7 42.8 1.0
CD H:GLU50 4.8 46.2 1.0
OE1 H:GLU50 4.8 49.3 1.0
OG H:SER96 4.8 46.1 1.0
ND2 H:ASN58 4.8 53.2 1.0
CH2 I:TRP91 4.9 34.5 1.0
CD1 H:TRP34 4.9 45.0 1.0
CE3 I:TRP91 4.9 36.6 1.0
NE1 I:TRP96 4.9 44.4 1.0
CZ2 I:TRP96 5.0 37.5 1.0

Arsenic binding site 3 out of 4 in 7mdp

Go back to Arsenic Binding Sites List in 7mdp
Arsenic binding site 3 out of 4 in the Kras G12C in Complex with G-2897


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Kras G12C in Complex with G-2897 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:As303

b:158.8
occ:1.00
AS H:CAD303 0.0 158.8 1.0
O2 H:CAD303 1.7 159.1 1.0
O1 H:CAD303 1.9 160.6 1.0
C2 H:CAD303 2.0 160.4 1.0
C1 H:CAD303 2.0 158.2 1.0
O H:ASP101 3.9 47.1 1.0
OH H:TYR102 4.5 55.6 1.0
CZ H:TYR102 4.5 48.4 1.0
CD1 H:LEU100B 4.5 49.6 1.0
CE1 H:TYR102 4.7 48.4 1.0
C H:ASP101 4.8 46.6 1.0
CB H:ASP101 4.9 49.4 1.0
CE2 H:TYR102 4.9 45.3 1.0
CA H:ASP101 5.0 45.1 1.0

Arsenic binding site 4 out of 4 in 7mdp

Go back to Arsenic Binding Sites List in 7mdp
Arsenic binding site 4 out of 4 in the Kras G12C in Complex with G-2897


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Kras G12C in Complex with G-2897 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:As303

b:122.4
occ:1.00
AS I:CAD303 0.0 122.4 1.0
O2 I:CAD303 1.7 125.6 1.0
O1 I:CAD303 1.9 126.4 1.0
C1 I:CAD303 2.0 124.5 1.0
C2 I:CAD303 2.0 120.5 1.0
OD2 I:ASP85 4.0 51.7 1.0
CG I:ASP85 4.2 46.0 1.0
OD1 I:ASP85 4.3 53.3 1.0
O I:GLY100 4.5 37.0 1.0
OH I:TYR87 4.5 43.0 1.0
NZ I:LYS103 4.5 49.8 1.0
O I:GLY101 4.6 37.4 1.0
CE I:LYS103 4.6 43.3 1.0
O H:GLY42 4.6 49.3 1.0
O I:HOH406 4.7 42.4 1.0
C I:GLY101 4.7 35.0 1.0
CB I:LYS103 4.7 33.9 1.0
N I:LYS103 4.7 35.8 1.0
O I:PRO8 4.8 41.2 1.0
O H:HOH416 4.8 39.1 1.0
CB I:ASP85 4.9 36.5 1.0

Reference:

C.W.Davies, A.J.Oh, R.Mroue, M.Steffek, J.M.Bruning, Y.Xiao, S.Feng, S.Jayakar, E.Chan, V.Arumugam, S.C.Uribe, J.Drummond, A.Frommlet, C.Lu, Y.Franke, M.Merchant, H.Koeppen, J.G.Quinn, S.Malhotra, S.Do, L.Gazzard, H.E.Purkey, J.Rudolph, M.M.Mulvihill, J.T.Koerber, W.Wang, M.Evangelista. Conformation-Locking Antibodies For the Discovery and Characterization of Kras Inhibitors. Nat.Biotechnol. V. 40 769 2022.
ISSN: ISSN 1087-0156
PubMed: 34992247
DOI: 10.1038/S41587-021-01126-9
Page generated: Mon Jul 7 01:02:10 2025

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