Magnesium in PDB 7c41: Kras G12V and H-REV107 Peptide Complex

Enzymatic activity of Kras G12V and H-REV107 Peptide Complex

All present enzymatic activity of Kras G12V and H-REV107 Peptide Complex:
3.1.1.32; 3.1.1.4;

Protein crystallography data

The structure of Kras G12V and H-REV107 Peptide Complex, PDB code: 7c41 was solved by C.W.Han, M.S.Jeong, S.B.Jang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.52 / 2.28
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 41.907, 84.339, 84.335, 59.98, 89.96, 89.97
R / Rfree (%) 26 / 28.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Kras G12V and H-REV107 Peptide Complex (pdb code 7c41). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Kras G12V and H-REV107 Peptide Complex, PDB code: 7c41:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7c41

Go back to Magnesium Binding Sites List in 7c41
Magnesium binding site 1 out of 4 in the Kras G12V and H-REV107 Peptide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kras G12V and H-REV107 Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:16.3
occ:1.00
 OD2 A:ASP57 2.5 36.2 1.0
OG A:SER17 2.7 13.9 1.0
O3B A:GDP201 3.0 20.1 1.0
O A:THR58 3.0 28.9 1.0
CE2 D:TYR66 3.2 26.6 1.0
CZ D:TYR66 3.2 29.7 1.0
CG A:ASP57 3.3 31.5 1.0
CE A:LYS16 3.3 21.9 1.0
OD1 A:ASP57 3.4 29.4 1.0
CD2 D:TYR66 3.5 36.8 1.0
CE1 D:TYR66 3.6 30.7 1.0
CB A:LYS16 3.6 21.7 1.0
OH D:TYR66 3.8 23.5 1.0
N A:SER17 3.8 20.4 1.0
CG D:TYR66 3.9 38.0 1.0
CD1 D:TYR66 3.9 33.1 1.0
CB A:SER17 3.9 20.3 1.0
NZ A:LYS16 4.0 14.5 1.0
C A:THR58 4.1 28.7 1.0
PB A:GDP201 4.2 23.6 1.0
CD A:LYS16 4.2 21.4 1.0
CA A:SER17 4.2 20.7 1.0
O1B A:GDP201 4.4 19.0 1.0
CG A:LYS16 4.4 23.3 1.0
C A:LYS16 4.4 23.7 1.0
O A:ILE36 4.5 37.0 1.0
C A:ASP57 4.5 37.6 1.0
O A:ASP57 4.5 40.7 1.0
CA A:LYS16 4.6 23.5 1.0
N A:THR58 4.6 34.0 1.0
O3A A:GDP201 4.7 27.6 1.0
CB A:ASP57 4.7 34.3 1.0
CB D:TYR66 4.9 36.8 1.0
N A:ALA59 4.9 29.7 1.0
CA A:ALA59 4.9 31.2 1.0

Magnesium binding site 2 out of 4 in 7c41

Go back to Magnesium Binding Sites List in 7c41
Magnesium binding site 2 out of 4 in the Kras G12V and H-REV107 Peptide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kras G12V and H-REV107 Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg202

b:58.6
occ:1.00
 O2B J:GDP201 2.0 11.5 1.0
O1B J:GDP201 2.8 6.2 1.0
PB J:GDP201 2.8 3.8 1.0
O J:PRO34 3.3 15.8 1.0
CA J:PRO34 3.5 18.3 1.0
O3B J:GDP201 3.6 4.8 1.0
NZ J:LYS16 3.8 10.7 1.0
C J:PRO34 3.9 19.3 1.0
CB J:PRO34 3.9 17.4 1.0
O2A J:GDP201 3.9 14.2 1.0
CG2 J:VAL12 4.1 29.1 1.0
O3A J:GDP201 4.2 8.9 1.0
N J:GLY13 4.5 15.6 1.0
OG J:SER17 4.6 10.4 1.0
CE J:LYS16 4.6 9.3 1.0
PA J:GDP201 4.7 11.0 1.0
CB J:ALA59 4.7 30.3 1.0
N J:PRO34 4.7 20.3 1.0
O J:THR58 4.8 24.3 1.0
CA J:ALA59 4.9 23.4 1.0
O J:ASP33 4.9 21.5 1.0
CA J:VAL12 4.9 15.2 1.0
CG J:PRO34 4.9 17.5 1.0

Magnesium binding site 3 out of 4 in 7c41

Go back to Magnesium Binding Sites List in 7c41
Magnesium binding site 3 out of 4 in the Kras G12V and H-REV107 Peptide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Kras G12V and H-REV107 Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg202

b:16.9
occ:1.00
 O3B M:GDP201 2.1 17.4 1.0
O M:HOH321 2.2 24.6 1.0
OG M:SER17 2.4 23.3 1.0
O2B M:GDP201 2.9 10.6 1.0
PB M:GDP201 3.0 10.4 1.0
CB M:SER17 3.2 20.7 1.0
O1A M:GDP201 3.5 14.4 1.0
CA M:PRO34 3.7 17.4 1.0
CD2 M:TYR32 3.9 24.0 1.0
O M:ASP33 4.0 19.0 1.0
O M:TYR32 4.0 29.1 1.0
O3A M:GDP201 4.0 18.0 1.0
N M:SER17 4.1 26.7 1.0
PA M:GDP201 4.1 13.5 1.0
O1B M:GDP201 4.1 15.6 1.0
O M:PRO34 4.2 14.8 1.0
CA M:SER17 4.3 27.6 1.0
C M:PRO34 4.3 18.3 1.0
N M:PRO34 4.4 14.7 1.0
C M:ASP33 4.5 21.4 1.0
CE2 M:TYR32 4.5 23.1 1.0
CB M:PRO34 4.5 16.9 1.0
O2A M:GDP201 4.5 19.9 1.0
OD2 M:ASP57 4.6 26.7 1.0
OD1 M:ASP57 4.9 25.7 1.0
C M:TYR32 4.9 25.1 1.0
CG M:TYR32 5.0 22.6 1.0

Magnesium binding site 4 out of 4 in 7c41

Go back to Magnesium Binding Sites List in 7c41
Magnesium binding site 4 out of 4 in the Kras G12V and H-REV107 Peptide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Kras G12V and H-REV107 Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg202

b:17.5
occ:1.00
 O G:ASP33 2.3 34.9 1.0
OG G:SER17 2.9 25.9 1.0
O G:ILE36 3.0 27.3 1.0
CD2 G:TYR32 3.2 37.0 1.0
C G:ASP33 3.3 32.3 1.0
CE2 G:TYR32 3.4 38.4 1.0
CA G:PRO34 3.6 24.3 1.0
C G:PRO34 3.6 25.5 1.0
O G:PRO34 3.7 21.5 1.0
N G:PRO34 3.9 30.0 1.0
N G:ILE36 4.0 24.9 1.0
C G:ILE36 4.0 28.8 1.0
CB G:SER17 4.0 27.0 1.0
OD2 G:ASP57 4.0 31.7 1.0
O G:TYR32 4.1 32.2 1.0
O1B G:GDP201 4.3 13.7 1.0
CA G:ILE36 4.3 23.3 1.0
N G:THR35 4.4 26.9 1.0
CB G:ILE36 4.4 27.7 1.0
CG G:TYR32 4.4 40.2 1.0
C G:TYR32 4.5 32.5 1.0
CA G:ASP33 4.5 26.5 1.0
N G:ASP33 4.6 29.8 1.0
CZ G:TYR32 4.7 37.6 1.0
CB G:ALA59 4.8 23.9 1.0
C G:THR35 4.9 26.1 1.0
O2A G:GDP201 4.9 16.0 1.0
CB G:TYR32 5.0 35.1 1.0

Reference:

C.W.Han, M.S.Jeong, S.C.Ha, S.B.Jang. A H-REV107 Peptide Inhibits Tumor Growth and Interacts Directly with Oncogenic Kras Mutants. Cancers (Basel) V. 12 2020.
ISSN: ESSN 2072-6694
PubMed: 32486141
DOI: 10.3390/CANCERS12061412
Page generated: Sun Jul 11 16:06:18 2021

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