Atomistry » Magnesium » PDB 9b2d-9bm0 » 9bak
Atomistry »
  Magnesium »
    PDB 9b2d-9bm0 »
      9bak »

Magnesium in PDB 9bak: 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: 9bak 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) 52.34 / 1.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.867, 83.885, 104.689, 90, 90, 90
R / Rfree (%) 27 / 28.9

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 9bak). 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: 9bak:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 9bak

Go back to Magnesium Binding Sites List in 9bak
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:13.2
occ:1.00
O A:HOH368 2.0 11.9 1.0
OG A:SER17 2.0 11.1 1.0
O3B A:GDP202 2.1 14.1 1.0
O A:HOH310 2.1 9.2 1.0
O A:HOH357 2.2 16.2 1.0
O A:HOH324 2.2 15.2 1.0
HB2 A:SER17 3.1 13.6 1.0
CB A:SER17 3.1 11.6 1.0
PB A:GDP202 3.2 15.5 1.0
H A:SER17 3.2 12.1 1.0
HA A:PRO34 3.4 14.6 1.0
O2B A:GDP202 3.4 14.8 1.0
HD2 A:TYR32 3.6 18.3 1.0
HB3 A:SER17 3.8 13.6 1.0
N A:SER17 3.8 10.3 1.0
O1A A:GDP202 3.9 20.2 1.0
OD2 A:ASP57 4.0 17.2 1.0
CA A:SER17 4.0 11.3 1.0
OD1 A:ASP57 4.0 16.1 1.0
HB2 A:LYS16 4.0 10.1 1.0
O1B A:GDP202 4.2 16.2 1.0
O3A A:GDP202 4.3 14.7 1.0
CA A:PRO34 4.3 12.4 1.0
HA A:SER17 4.3 13.2 1.0
HE2 A:LYS16 4.3 8.9 1.0
O A:ASP33 4.4 12.3 1.0
PA A:GDP202 4.4 18.9 1.0
O A:THR58 4.4 19.4 1.0
O A:PRO34 4.4 12.9 1.0
CG A:ASP57 4.4 16.4 1.0
O2A A:GDP202 4.5 15.2 1.0
CD2 A:TYR32 4.5 15.5 1.0
HZ3 A:LYS16 4.7 8.6 1.0
O A:ILE36 4.7 11.7 1.0
HE2 A:TYR32 4.7 18.1 1.0
C A:PRO34 4.7 12.3 1.0
HZ1 A:LYS16 4.8 8.6 1.0
HB3 A:TYR32 4.8 19.6 1.0
O A:TYR32 4.9 15.2 1.0
HB3 A:PRO34 4.9 13.8 1.0
O A:HOH373 4.9 15.8 1.0
C A:LYS16 4.9 10.0 1.0
CB A:LYS16 5.0 8.6 1.0

Magnesium binding site 2 out of 4 in 9bak

Go back to Magnesium Binding Sites List in 9bak
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:15.5
occ:1.00
O B:HOH313 2.0 15.8 1.0
O B:HOH341 2.1 17.0 1.0
O B:HOH343 2.1 19.0 1.0
O1B B:GDP202 2.1 15.2 1.0
OG B:SER17 2.2 15.2 1.0
O B:HOH303 2.2 14.8 1.0
HB2 B:SER17 3.1 17.6 1.0
CB B:SER17 3.2 14.9 1.0
PB B:GDP202 3.3 15.4 1.0
H B:SER17 3.3 16.3 1.0
HA B:PRO34 3.3 20.3 1.0
HD1 B:TYR32 3.4 25.1 1.0
O3B B:GDP202 3.5 18.8 1.0
OD2 B:ASP57 3.8 17.7 1.0
HB3 B:SER17 3.9 17.6 1.0
N B:SER17 3.9 13.8 1.0
O2A B:GDP202 4.0 21.2 1.0
HE1 B:TYR32 4.0 25.4 1.0
OD1 B:ASP57 4.1 17.5 1.0
CA B:SER17 4.1 14.4 1.0
HB2 B:LYS16 4.2 18.2 1.0
CD1 B:TYR32 4.2 21.1 1.0
O B:ASP33 4.2 19.4 1.0
O B:PRO34 4.2 17.1 1.0
O2B B:GDP202 4.2 15.6 1.0
CA B:PRO34 4.3 17.2 1.0
O B:THR58 4.3 21.6 1.0
CG B:ASP57 4.4 17.5 1.0
O3A B:GDP202 4.4 15.3 1.0
HA B:SER17 4.4 17.0 1.0
CE1 B:TYR32 4.4 21.4 1.0
HZ3 B:LYS16 4.5 18.7 1.0
PA B:GDP202 4.5 17.9 1.0
HE2 B:LYS16 4.5 17.9 1.0
C B:PRO34 4.6 17.6 1.0
O B:ILE36 4.6 17.5 1.0
O1A B:GDP202 4.6 13.3 1.0
O B:TYR32 4.8 21.7 1.0
O B:HOH384 4.9 20.4 1.0
HB3 B:PRO34 4.9 20.3 1.0
C B:ASP33 5.0 19.7 1.0
HA B:ALA59 5.0 27.6 1.0
HB3 B:TYR32 5.0 24.9 1.0

Magnesium binding site 3 out of 4 in 9bak

Go back to Magnesium Binding Sites List in 9bak
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:17.6
occ:1.00
O C:HOH306 2.0 14.2 1.0
OG C:SER17 2.1 15.4 1.0
O C:HOH374 2.1 18.3 1.0
O C:HOH322 2.1 21.8 1.0
O1B C:GDP202 2.1 13.4 1.0
O C:HOH351 2.2 23.9 1.0
HB2 C:SER17 3.1 17.6 1.0
CB C:SER17 3.1 14.8 1.0
PB C:GDP202 3.3 16.2 1.0
H C:SER17 3.3 16.8 1.0
HA C:PRO34 3.3 27.7 1.0
O3B C:GDP202 3.5 16.9 1.0
HD2 C:TYR32 3.5 33.0 1.0
HB3 C:SER17 3.8 17.6 1.0
N C:SER17 3.9 14.2 1.0
OD2 C:ASP57 3.9 19.5 1.0
O2A C:GDP202 3.9 21.9 1.0
OD1 C:ASP57 4.0 18.6 1.0
HB2 C:LYS16 4.0 14.9 1.0
CA C:SER17 4.1 14.2 1.0
CA C:PRO34 4.3 23.3 1.0
O2B C:GDP202 4.3 16.2 1.0
HE2 C:TYR32 4.3 32.5 1.0
HE2 C:LYS16 4.3 16.2 1.0
O C:THR58 4.3 14.1 1.0
O C:PRO34 4.3 22.2 1.0
O C:ASP33 4.3 25.7 1.0
O3A C:GDP202 4.3 12.5 1.0
CD2 C:TYR32 4.3 27.8 1.0
HA C:SER17 4.4 16.8 1.0
CG C:ASP57 4.4 18.9 1.0
PA C:GDP202 4.4 16.2 1.0
O1A C:GDP202 4.5 17.5 1.0
O C:ILE36 4.6 21.1 1.0
C C:PRO34 4.6 23.1 1.0
HZ1 C:LYS16 4.7 16.2 1.0
CE2 C:TYR32 4.7 27.3 1.0
HZ3 C:LYS16 4.7 16.2 1.0
O C:HOH353 4.8 15.6 1.0
HB3 C:PRO34 4.8 28.1 1.0
O C:TYR32 4.9 30.9 1.0
CB C:LYS16 5.0 12.6 1.0
HB3 C:TYR32 5.0 35.1 1.0
C C:LYS16 5.0 12.2 1.0

Magnesium binding site 4 out of 4 in 9bak

Go back to Magnesium Binding Sites List in 9bak
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:12.0
occ:1.00
O D:HOH307 2.0 13.8 1.0
O D:HOH361 2.0 20.1 1.0
O D:HOH340 2.1 15.4 1.0
O1B D:GDP202 2.1 14.0 1.0
O D:HOH320 2.1 12.6 1.0
OG D:SER17 2.1 14.6 1.0
HB2 D:SER17 3.2 17.7 1.0
CB D:SER17 3.2 15.0 1.0
PB D:GDP202 3.2 13.9 1.0
HA D:PRO34 3.3 19.2 1.0
H D:SER17 3.4 17.3 1.0
HD2 D:TYR32 3.4 25.2 1.0
O3B D:GDP202 3.5 16.4 1.0
OD2 D:ASP57 3.9 16.7 1.0
HB3 D:SER17 3.9 17.7 1.0
HE2 D:TYR32 3.9 25.6 1.0
N D:SER17 4.0 14.6 1.0
O2A D:GDP202 4.0 18.8 1.0
OD1 D:ASP57 4.1 16.2 1.0
CA D:SER17 4.2 15.0 1.0
O D:PRO34 4.2 14.9 1.0
HB2 D:LYS16 4.2 12.8 1.0
CD2 D:TYR32 4.2 21.2 1.0
O2B D:GDP202 4.2 14.5 1.0
CA D:PRO34 4.2 16.2 1.0
O D:ASP33 4.3 20.1 1.0
O D:THR58 4.3 14.8 1.0
O3A D:GDP202 4.4 17.3 1.0
CG D:ASP57 4.4 16.9 1.0
CE2 D:TYR32 4.4 21.5 1.0
HZ3 D:LYS16 4.4 14.3 1.0
HA D:SER17 4.4 17.7 1.0
HE2 D:LYS16 4.5 13.3 1.0
PA D:GDP202 4.5 16.1 1.0
C D:PRO34 4.5 15.8 1.0
O D:ILE36 4.6 12.6 1.0
O1A D:GDP202 4.6 14.3 1.0
HB3 D:PRO34 4.8 20.5 1.0
O D:TYR32 4.9 23.1 1.0
O D:HOH390 4.9 6.5 1.0
HZ1 D:LYS16 4.9 14.3 1.0
HA D:ALA59 5.0 15.3 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

Last articles

Mn in 4PXE
Mn in 4PTH
Mn in 4Q0B
Mn in 4PXC
Mn in 4PXD
Mn in 4PTJ
Mn in 4PXB
Mn in 4PJ0
Mn in 4PST
Mn in 4PSY
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy