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Magnesium in PDB 9bai: Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds.

Enzymatic activity of Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds.

All present enzymatic activity of Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds.:
3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds., PDB code: 9bai was solved by A.D.Landgraf, R.J.Brenner, M.K.Ghozayel, K.Bum-Erdene, G.Gonzalez-Gutierrez, S.Meroueh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.46 / 1.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.022, 83.944, 104.553, 90, 90, 90
R / Rfree (%) 18.6 / 22.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds. (pdb code 9bai). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds., PDB code: 9bai:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 9bai

Go back to Magnesium Binding Sites List in 9bai
Magnesium binding site 1 out of 4 in the Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:10.6
occ:1.00
O2B A:GDP203 2.0 10.5 1.0
O A:HOH317 2.0 10.1 1.0
O A:HOH353 2.1 8.9 1.0
OG A:SER17 2.1 9.8 1.0
O A:HOH351 2.1 9.1 1.0
O A:HOH377 2.1 11.7 1.0
HB2 A:SER17 3.0 11.0 1.0
CB A:SER17 3.1 9.2 1.0
PB A:GDP203 3.2 9.4 1.0
H A:SER17 3.2 10.2 1.0
HA A:PRO34 3.3 11.3 1.0
HD2 A:TYR32 3.5 20.2 1.0
O3B A:GDP203 3.5 10.4 1.0
HB3 A:SER17 3.8 11.0 1.0
N A:SER17 3.9 8.5 1.0
OD2 A:ASP57 4.0 12.8 1.0
CA A:SER17 4.0 6.8 1.0
O2A A:GDP203 4.1 13.5 1.0
HB2 A:LYS16 4.1 7.2 1.0
OD1 A:ASP57 4.1 14.0 1.0
CA A:PRO34 4.2 9.5 1.0
HE2 A:TYR32 4.3 22.8 1.0
O1B A:GDP203 4.3 9.4 1.0
O3A A:GDP203 4.3 9.3 1.0
O A:ASP33 4.3 11.5 1.0
CD2 A:TYR32 4.3 16.9 1.0
HA A:SER17 4.3 8.1 1.0
O A:THR58 4.3 11.3 1.0
O A:PRO34 4.3 13.4 1.0
HE2 A:LYS16 4.4 12.0 1.0
CG A:ASP57 4.5 14.1 1.0
O A:ILE36 4.5 11.0 1.0
PA A:GDP203 4.5 10.5 1.0
O1A A:GDP203 4.6 10.4 1.0
C A:PRO34 4.6 12.4 1.0
CE2 A:TYR32 4.7 19.1 1.0
HZ3 A:LYS16 4.8 8.7 1.0
HZ1 A:LYS16 4.8 8.7 1.0
HB3 A:TYR32 4.8 21.3 1.0
HB3 A:PRO34 4.9 19.8 1.0
O A:TYR32 4.9 17.6 1.0
O A:HOH389 4.9 11.7 1.0
HA A:ALA59 5.0 12.6 1.0

Magnesium binding site 2 out of 4 in 9bai

Go back to Magnesium Binding Sites List in 9bai
Magnesium binding site 2 out of 4 in the Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:9.4
occ:1.00
O B:HOH330 2.0 12.0 1.0
O2B B:GDP203 2.0 9.1 1.0
O B:HOH362 2.0 10.1 1.0
O B:HOH356 2.1 10.7 1.0
OG B:SER17 2.1 10.6 1.0
O B:HOH319 2.2 9.0 1.0
HB2 B:SER17 3.0 10.3 1.0
CB B:SER17 3.1 8.6 1.0
PB B:GDP203 3.3 9.3 1.0
H B:SER17 3.3 8.4 1.0
HA B:PRO34 3.3 15.9 1.0
HD2 B:TYR32 3.5 25.4 1.0
O3B B:GDP203 3.6 10.5 1.0
HB3 B:SER17 3.8 10.3 1.0
N B:SER17 3.9 7.0 1.0
OD2 B:ASP57 4.0 12.5 1.0
HB2 B:LYS16 4.0 9.6 1.0
O2A B:GDP203 4.1 11.8 1.0
CA B:SER17 4.1 7.6 1.0
OD1 B:ASP57 4.1 10.8 1.0
O B:ASP33 4.2 15.0 1.0
CA B:PRO34 4.3 13.3 1.0
O B:PRO34 4.3 11.4 1.0
O B:THR58 4.3 12.4 1.0
O3A B:GDP203 4.3 8.7 1.0
HE2 B:TYR32 4.3 29.5 1.0
O1B B:GDP203 4.3 10.1 1.0
HA B:SER17 4.3 9.1 1.0
CD2 B:TYR32 4.4 21.2 1.0
CG B:ASP57 4.4 10.6 1.0
O B:ILE36 4.5 10.6 1.0
HZ3 B:LYS16 4.6 11.1 1.0
PA B:GDP203 4.6 9.5 1.0
O1A B:GDP203 4.6 10.7 1.0
HE2 B:LYS16 4.6 10.1 1.0
C B:PRO34 4.6 12.3 1.0
CE2 B:TYR32 4.8 24.6 1.0
HB3 B:PRO34 4.8 17.5 1.0
HB3 B:TYR32 4.9 28.3 1.0
O B:TYR32 4.9 16.6 1.0
HZ1 B:LYS16 4.9 11.1 1.0
O B:HOH373 4.9 11.3 1.0
CB B:LYS16 5.0 8.0 1.0
HA B:ALA59 5.0 13.6 1.0
C B:ASP33 5.0 15.7 1.0

Magnesium binding site 3 out of 4 in 9bai

Go back to Magnesium Binding Sites List in 9bai
Magnesium binding site 3 out of 4 in the Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:10.6
occ:1.00
O2B C:GDP203 2.0 10.5 1.0
O C:HOH382 2.0 9.4 1.0
O C:HOH313 2.0 11.9 1.0
O C:HOH342 2.1 10.6 1.0
OG C:SER17 2.1 9.7 1.0
O C:HOH362 2.2 12.2 1.0
HB2 C:SER17 3.1 9.4 1.0
CB C:SER17 3.2 7.9 1.0
PB C:GDP203 3.3 9.1 1.0
H C:SER17 3.3 9.7 1.0
HA C:PRO34 3.3 14.5 1.0
HD2 C:TYR32 3.4 21.1 1.0
O3B C:GDP203 3.5 12.7 1.0
HB3 C:SER17 3.8 9.4 1.0
N C:SER17 3.9 8.1 1.0
OD2 C:ASP57 4.1 15.2 1.0
O2A C:GDP203 4.1 12.7 1.0
CA C:SER17 4.1 8.0 1.0
OD1 C:ASP57 4.1 15.7 1.0
HB2 C:LYS16 4.1 7.8 1.0
HE2 C:TYR32 4.2 21.8 1.0
CA C:PRO34 4.2 12.1 1.0
O3A C:GDP203 4.3 8.6 1.0
CD2 C:TYR32 4.3 17.6 1.0
O1B C:GDP203 4.3 9.5 1.0
O C:ASP33 4.3 11.5 1.0
O C:THR58 4.3 11.6 1.0
HA C:SER17 4.4 9.5 1.0
O C:PRO34 4.4 12.7 1.0
HE2 C:LYS16 4.4 13.0 1.0
PA C:GDP203 4.5 9.9 1.0
CG C:ASP57 4.5 14.2 1.0
O C:ILE36 4.5 10.1 1.0
O1A C:GDP203 4.6 10.5 1.0
C C:PRO34 4.6 12.2 1.0
CE2 C:TYR32 4.6 18.2 1.0
HB3 C:PRO34 4.8 18.2 1.0
HB3 C:TYR32 4.8 22.6 1.0
HZ3 C:LYS16 4.8 8.7 1.0
O C:TYR32 4.8 18.4 1.0
HZ1 C:LYS16 4.9 8.7 1.0
O C:HOH412 4.9 12.2 1.0
HA C:ALA59 5.0 12.8 1.0
C C:ASP33 5.0 11.1 1.0

Magnesium binding site 4 out of 4 in 9bai

Go back to Magnesium Binding Sites List in 9bai
Magnesium binding site 4 out of 4 in the Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Gdp-Bound Human K-Ras in A Covalent Complex with Aryl Sulfonyl Fluoride Compounds. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:10.1
occ:1.00
O D:HOH391 2.0 10.2 1.0
O D:HOH364 2.0 9.4 1.0
OG D:SER17 2.0 10.2 1.0
O2B D:GDP203 2.0 8.1 1.0
O D:HOH335 2.1 14.0 1.0
O D:HOH338 2.1 9.9 1.0
HB2 D:SER17 3.0 12.0 1.0
CB D:SER17 3.1 10.0 1.0
PB D:GDP203 3.3 9.1 1.0
H D:SER17 3.3 9.7 1.0
HA D:PRO34 3.3 16.5 1.0
HD1 D:TYR32 3.5 30.4 1.0
O3B D:GDP203 3.6 10.0 1.0
HB3 D:SER17 3.8 12.0 1.0
N D:SER17 3.9 8.1 1.0
OD2 D:ASP57 4.0 11.2 1.0
CA D:SER17 4.0 7.7 1.0
O2A D:GDP203 4.1 11.3 1.0
OD1 D:ASP57 4.1 10.7 1.0
HB2 D:LYS16 4.1 10.0 1.0
O D:ASP33 4.2 17.3 1.0
CA D:PRO34 4.2 13.8 1.0
O D:PRO34 4.3 13.6 1.0
HA D:SER17 4.3 9.3 1.0
O D:THR58 4.3 12.2 1.0
O1B D:GDP203 4.3 10.2 1.0
O3A D:GDP203 4.3 8.8 1.0
CD1 D:TYR32 4.4 25.3 1.0
CG D:ASP57 4.4 12.7 1.0
O D:ILE36 4.5 11.3 1.0
PA D:GDP203 4.6 9.9 1.0
C D:PRO34 4.6 12.0 1.0
HB3 D:TYR32 4.6 25.2 1.0
HE2 D:LYS16 4.7 10.7 1.0
HE1 D:TYR32 4.7 28.1 1.0
O1A D:GDP203 4.7 10.0 1.0
HZ3 D:LYS16 4.7 11.3 1.0
HB3 D:PRO34 4.8 20.1 1.0
O D:TYR32 4.9 13.7 1.0
HZ1 D:LYS16 5.0 11.3 1.0
O D:HOH385 5.0 11.0 1.0
HA D:ALA59 5.0 15.6 1.0
C D:ASP33 5.0 15.0 1.0

Reference:

A.Landgraf, R.Brenner, M.Ghozayel, K.Bum-Erdene, G.Gonzalez-Gutierrez, S.Meroueh. Small-Molecule Kras Inhibitors By Tyrosine Covalent Bond Formation. Chemmedchem 00624 2025.
ISSN: ESSN 1860-7187
PubMed: 40099978
DOI: 10.1002/CMDC.202400624
Page generated: Fri Aug 15 23:15:29 2025

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