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Magnesium in PDB 7w5r: Kras G12V and Peptide Complex

Enzymatic activity of Kras G12V and Peptide Complex

All present enzymatic activity of Kras G12V and Peptide Complex:
3.6.5.2;

Protein crystallography data

The structure of Kras G12V and Peptide Complex, PDB code: 7w5r was solved by H.J.Kim, C.W.Han, S.B.Jang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.76 / 3.87
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 40.556, 82.513, 82.573, 119.99, 90.06, 90.02
R / Rfree (%) 22.3 / 31

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Kras G12V and Peptide Complex (pdb code 7w5r). 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 G12V and Peptide Complex, PDB code: 7w5r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7w5r

Go back to Magnesium Binding Sites List in 7w5r
Magnesium binding site 1 out of 6 in the Kras G12V and 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 Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:25.6
occ:1.00
 O1B A:GDP1002 2.1 56.0 1.0
PB A:GDP1002 2.4 54.9 1.0
O3A A:GDP1002 2.6 67.7 1.0
O2B A:GDP1002 2.7 55.2 1.0
CE A:LYS16 3.3 71.2 1.0
OG A:SER17 3.3 82.3 1.0
CA A:PRO34 3.4 120.7 1.0
CB A:PRO34 3.7 122.0 1.0
NZ A:LYS16 3.8 72.8 1.0
O3B A:GDP1002 3.9 48.3 1.0
PA A:GDP1002 4.1 80.7 1.0
CB A:SER17 4.2 77.4 1.0
C A:PRO34 4.2 122.2 1.0
O A:PRO34 4.2 117.3 1.0
N A:PRO34 4.3 117.9 1.0
N A:SER17 4.4 79.4 1.0
O A:ASP33 4.4 116.8 1.0
OD2 A:ASP57 4.4 109.7 1.0
CD A:LYS16 4.6 77.6 1.0
O2A A:GDP1002 4.7 89.3 1.0
O A:TYR32 4.7 33.4 1.0
C A:ASP33 4.7 112.8 1.0
CB A:LYS16 4.7 84.5 1.0
O5' A:GDP1002 4.8 79.6 1.0
CA A:SER17 4.9 67.9 1.0
CG A:LYS16 5.0 79.6 1.0

Magnesium binding site 2 out of 6 in 7w5r

Go back to Magnesium Binding Sites List in 7w5r
Magnesium binding site 2 out of 6 in the Kras G12V and 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 Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1001

b:31.8
occ:1.00
 OG E:SER17 2.0 27.3 1.0
O2B E:GDP1002 2.2 47.8 1.0
O3B E:GDP1002 2.2 57.7 1.0
PB E:GDP1002 2.5 56.7 1.0
N E:SER17 2.5 42.8 1.0
CB E:SER17 2.9 12.4 1.0
O3A E:GDP1002 3.0 59.0 1.0
O1A E:GDP1002 3.1 65.3 1.0
CB E:LYS16 3.2 40.4 1.0
CA E:SER17 3.2 38.0 1.0
C E:LYS16 3.4 38.4 1.0
OD2 E:ASP57 3.4 27.9 1.0
CE E:LYS16 3.5 32.6 1.0
OD1 E:ASP57 3.5 31.5 1.0
CA E:LYS16 3.6 32.6 1.0
PA E:GDP1002 3.7 64.4 1.0
N E:LYS16 3.7 24.7 1.0
CG E:ASP57 3.9 26.8 1.0
O1B E:GDP1002 3.9 57.9 1.0
CG E:LYS16 4.0 45.6 1.0
CD E:LYS16 4.3 46.9 1.0
O2A E:GDP1002 4.4 66.9 1.0
O E:LYS16 4.5 38.8 1.0
C E:SER17 4.5 36.0 1.0
C E:GLY15 4.6 28.5 1.0
NZ E:LYS16 4.6 23.6 1.0
N E:ALA18 4.7 34.0 1.0
CD2 E:TYR32 4.8 47.5 1.0
CA E:PRO34 4.9 36.1 1.0

Magnesium binding site 3 out of 6 in 7w5r

Go back to Magnesium Binding Sites List in 7w5r
Magnesium binding site 3 out of 6 in the Kras G12V and 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 Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1001

b:44.4
occ:1.00
 O2B I:GDP1002 2.1 63.7 1.0
OG I:SER17 2.2 155.9 1.0
PB I:GDP1002 3.4 83.5 1.0
CA I:PRO34 3.4 73.2 1.0
CB I:SER17 3.6 150.6 1.0
O1B I:GDP1002 3.7 114.5 1.0
O I:PRO34 3.7 73.8 1.0
O I:ILE36 3.9 51.0 1.0
O3A I:GDP1002 4.0 70.1 1.0
CB I:PRO34 4.0 75.0 1.0
C I:PRO34 4.0 73.3 1.0
OD2 I:ASP57 4.1 192.4 1.0
CD2 I:TYR32 4.1 58.4 1.0
CE I:LYS16 4.2 97.2 1.0
N I:SER17 4.2 139.0 1.0
CA I:SER17 4.4 145.1 1.0
O I:ASP33 4.4 68.0 1.0
N I:PRO34 4.4 72.1 1.0
O I:ASP57 4.5 173.5 1.0
O3B I:GDP1002 4.6 74.1 1.0
NZ I:LYS16 4.6 91.8 1.0
CG I:ASP57 4.7 189.2 1.0
CB I:LYS16 4.7 123.4 1.0
CE2 I:TYR32 4.7 62.2 1.0
C I:ASP33 4.7 65.6 1.0
CB I:ALA59 4.8 162.8 1.0
CB I:ASP57 4.8 179.7 1.0

Magnesium binding site 4 out of 6 in 7w5r

Go back to Magnesium Binding Sites List in 7w5r
Magnesium binding site 4 out of 6 in the Kras G12V and 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 Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1001

b:33.7
occ:1.00
 OG M:SER17 2.0 53.2 1.0
OD2 M:ASP57 2.4 69.3 1.0
OD1 M:ASP57 2.4 69.6 1.0
CG M:ASP57 2.7 72.6 1.0
O3B M:GDP1002 2.8 90.4 1.0
N M:SER17 3.2 45.4 1.0
CB M:SER17 3.2 56.4 1.0
O2B M:GDP1002 3.2 95.0 1.0
CE M:LYS16 3.3 20.7 1.0
CB M:LYS16 3.5 30.1 1.0
PB M:GDP1002 3.6 90.2 1.0
CA M:SER17 3.7 50.8 1.0
C M:LYS16 4.0 34.4 1.0
CB M:ASP57 4.1 82.9 1.0
NZ M:LYS16 4.2 17.8 1.0
CA M:LYS16 4.2 31.3 1.0
CD M:LYS16 4.3 25.1 1.0
O1B M:GDP1002 4.4 86.3 1.0
CG M:LYS16 4.4 26.3 1.0
O2A M:GDP1002 4.5 82.6 1.0
N M:LYS16 4.6 33.5 1.0
CB M:ALA59 4.7 65.1 1.0
CD2 M:TYR32 4.8 222.9 1.0
O M:THR58 4.8 78.1 1.0
O3A M:GDP1002 4.9 86.1 1.0
O M:LYS16 4.9 29.0 1.0

Magnesium binding site 5 out of 6 in 7w5r

Go back to Magnesium Binding Sites List in 7w5r
Magnesium binding site 5 out of 6 in the Kras G12V and Peptide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Kras G12V and Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg1001

b:10.6
occ:1.00
 OG Q:SER17 2.3 81.3 1.0
O2B Q:GDP1002 2.3 70.8 1.0
CA Q:PRO34 3.4 94.7 1.0
CD2 Q:TYR32 3.4 90.9 1.0
CB Q:SER17 3.6 83.5 1.0
CE2 Q:TYR32 3.7 89.8 1.0
PB Q:GDP1002 3.7 76.2 1.0
CE Q:LYS16 4.0 97.9 1.0
O Q:ASP33 4.0 112.5 1.0
O Q:ILE36 4.1 78.8 1.0
CB Q:PRO34 4.1 101.2 1.0
C Q:PRO34 4.1 76.1 1.0
O3B Q:GDP1002 4.2 74.5 1.0
N Q:PRO34 4.3 102.8 1.0
N Q:SER17 4.3 74.1 1.0
O Q:PRO34 4.3 59.5 1.0
NZ Q:LYS16 4.3 96.7 1.0
O3A Q:GDP1002 4.4 76.7 1.0
C Q:ASP33 4.4 113.6 1.0
CA Q:SER17 4.5 84.4 1.0
O Q:TYR32 4.5 102.2 1.0
CG Q:TYR32 4.6 92.2 1.0
OD2 Q:ASP57 4.8 141.8 1.0
O1B Q:GDP1002 4.8 77.8 1.0
CB Q:LYS16 4.9 78.7 1.0
CB Q:ALA59 4.9 72.8 1.0

Magnesium binding site 6 out of 6 in 7w5r

Go back to Magnesium Binding Sites List in 7w5r
Magnesium binding site 6 out of 6 in the Kras G12V and Peptide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Kras G12V and Peptide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg1001

b:9.8
occ:1.00
 O2B U:GDP1002 2.0 17.4 1.0
OG U:SER17 2.2 20.8 1.0
PB U:GDP1002 3.3 26.6 1.0
CA U:PRO34 3.3 54.4 1.0
CB U:SER17 3.4 22.5 1.0
O1B U:GDP1002 3.6 23.8 1.0
O U:ASP33 3.7 71.7 1.0
CD2 U:TYR32 4.0 142.7 1.0
N U:SER17 4.0 31.9 1.0
N U:PRO34 4.0 59.5 1.0
CB U:PRO34 4.0 53.3 1.0
O3A U:GDP1002 4.0 26.6 1.0
C U:PRO34 4.2 46.1 1.0
C U:ASP33 4.2 67.6 1.0
CE U:LYS16 4.2 46.6 1.0
O U:TYR32 4.3 93.0 1.0
CA U:SER17 4.3 25.9 1.0
O U:ILE36 4.4 55.6 1.0
O3B U:GDP1002 4.5 28.7 1.0
O U:PRO34 4.5 34.1 1.0
CE2 U:TYR32 4.5 147.7 1.0
OD2 U:ASP57 4.5 207.5 1.0
CB U:LYS16 4.5 40.3 1.0
NZ U:LYS16 4.8 45.2 1.0
O1A U:GDP1002 4.9 28.0 1.0
C U:TYR32 5.0 96.7 1.0

Reference:

H.J.Kim, C.W.Han, S.B.Jang. Structure of Kras G12V and Peptide Complex To Be Published.
Page generated: Thu Oct 3 11:10:56 2024

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