Magnesium in PDB 8t75: Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)

Enzymatic activity of Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)

All present enzymatic activity of Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd):
2.7.11.1; 3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd), PDB code: 8t75 was solved by M.J.Whitley, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.45 / 2.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.409, 199.509, 113.428, 90, 112.28, 90
R / Rfree (%) 17.8 / 21.9

Other elements in 8t75:

The structure of Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) also contains other interesting chemical elements:

Zinc (Zn) 8 atoms
Arsenic (As) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) (pdb code 8t75). 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 KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd), PDB code: 8t75:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8t75

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Magnesium binding site 1 out of 4 in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)


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 KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:61.3
occ:1.00
 OG1 A:THR35 1.9 63.8 1.0
O2B A:GNP201 1.9 61.2 1.0
O A:HOH303 2.0 58.1 1.0
O1G A:GNP201 2.0 68.7 1.0
O A:HOH302 2.1 54.6 1.0
OG A:SER17 2.1 64.5 1.0
PG A:GNP201 3.0 60.6 1.0
CB A:THR35 3.1 58.5 1.0
PB A:GNP201 3.2 49.1 1.0
CB A:SER17 3.3 60.4 1.0
N3B A:GNP201 3.3 52.9 1.0
OD2 A:ASP57 3.7 99.7 1.0
O3G A:GNP201 3.7 48.0 1.0
N A:THR35 3.7 60.4 1.0
N A:SER17 3.9 68.5 1.0
CA A:THR35 4.0 53.8 1.0
O2A A:GNP201 4.1 59.8 1.0
O1B A:GNP201 4.1 60.2 1.0
CA A:SER17 4.1 57.6 1.0
CG2 A:THR35 4.2 60.5 1.0
O3A A:GNP201 4.2 68.0 1.0
OD1 A:ASP57 4.2 103.4 1.0
O A:ASP33 4.2 75.4 1.0
CG A:ASP57 4.3 93.9 1.0
O A:THR58 4.4 70.2 1.0
O2G A:GNP201 4.4 61.1 1.0
PA A:GNP201 4.5 57.5 1.0
O1A A:GNP201 4.7 66.1 1.0
NZ A:LYS16 4.7 53.8 1.0
C A:PRO34 4.7 64.5 1.0
CB A:LYS16 4.8 56.5 1.0
CE A:LYS16 4.8 58.5 1.0
C A:LYS16 4.9 67.3 1.0

Magnesium binding site 2 out of 4 in 8t75

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Magnesium binding site 2 out of 4 in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)


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 KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:44.1
occ:1.00
 OG C:SER17 2.0 46.9 1.0
O C:HOH306 2.0 39.3 1.0
O3G C:GNP201 2.0 49.2 1.0
O C:HOH302 2.0 33.0 1.0
OG1 C:THR35 2.3 58.8 1.0
CG2 C:THR35 2.4 68.2 1.0
O2B C:GNP201 2.6 49.7 1.0
CB C:THR35 2.9 62.4 1.0
CB C:SER17 3.3 44.5 1.0
OD2 C:ASP57 3.4 93.0 1.0
N C:THR35 3.4 58.6 1.0
PG C:GNP201 3.5 56.3 1.0
CA C:THR35 3.7 66.7 1.0
N3B C:GNP201 3.8 50.1 1.0
PB C:GNP201 3.8 50.6 1.0
O C:ASP33 4.0 63.3 1.0
CG C:ASP57 4.1 88.0 1.0
OD1 C:ASP57 4.2 94.7 1.0
N C:SER17 4.2 40.9 1.0
O1G C:GNP201 4.3 51.6 1.0
CA C:SER17 4.3 45.7 1.0
O2A C:GNP201 4.4 47.4 1.0
O C:THR58 4.4 62.4 1.0
O2G C:GNP201 4.4 63.6 1.0
C C:PRO34 4.5 58.8 1.0
C C:THR35 4.8 60.1 1.0
O3A C:GNP201 4.8 45.5 1.0
O1B C:GNP201 4.8 50.7 1.0
CA C:PRO34 4.8 63.5 1.0
O C:THR35 4.9 60.0 1.0
PA C:GNP201 5.0 43.7 1.0

Magnesium binding site 3 out of 4 in 8t75

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Magnesium binding site 3 out of 4 in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)


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 KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:53.4
occ:1.00
 O E:HOH302 2.0 63.2 1.0
OG E:SER17 2.0 51.0 1.0
O2B E:GNP201 2.0 49.6 1.0
O2G E:GNP201 2.0 58.2 1.0
O E:HOH305 2.2 47.8 1.0
OG1 E:THR35 2.6 63.2 1.0
CB E:THR35 3.0 55.4 1.0
CB E:SER17 3.2 45.5 1.0
PG E:GNP201 3.2 60.5 1.0
OD2 E:ASP57 3.3 98.5 1.0
PB E:GNP201 3.4 55.7 1.0
N3B E:GNP201 3.6 61.2 1.0
O3G E:GNP201 3.7 43.0 1.0
N E:SER17 3.8 50.0 1.0
N E:THR35 3.8 57.7 1.0
OD1 E:ASP57 3.9 90.8 1.0
CG E:ASP57 4.0 98.8 1.0
CA E:THR35 4.0 53.4 1.0
CG2 E:THR35 4.1 50.0 1.0
CA E:SER17 4.1 52.0 1.0
O1B E:GNP201 4.2 59.9 1.0
O E:THR58 4.3 74.4 1.0
O2A E:GNP201 4.3 64.6 1.0
O E:ASP33 4.4 75.9 1.0
O3A E:GNP201 4.4 53.8 1.0
O1G E:GNP201 4.5 75.6 1.0
O1A E:GNP201 4.7 56.9 1.0
PA E:GNP201 4.7 57.3 1.0
CB E:LYS16 4.7 35.8 1.0
C E:LYS16 4.8 51.6 1.0
CE E:LYS16 4.8 43.2 1.0
C E:PRO34 5.0 56.8 1.0

Magnesium binding site 4 out of 4 in 8t75

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Magnesium binding site 4 out of 4 in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)


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 KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg202

b:57.4
occ:1.00
 OG G:SER17 2.0 77.4 1.0
O3G G:GNP201 2.0 95.6 1.0
OG1 G:THR35 2.2 90.3 1.0
O2B G:GNP201 2.3 85.4 1.0
O G:HOH301 2.3 56.3 1.0
CB G:SER17 3.1 60.4 1.0
CB G:THR35 3.2 72.8 1.0
PG G:GNP201 3.2 77.6 1.0
O G:ASP33 3.3 92.4 1.0
N3B G:GNP201 3.3 71.8 1.0
PB G:GNP201 3.4 82.6 1.0
N G:THR35 3.4 79.4 1.0
O2A G:GNP201 3.5 91.0 1.0
CA G:THR35 3.9 73.8 1.0
N G:SER17 4.1 86.3 1.0
O3A G:GNP201 4.1 73.8 1.0
OD2 G:ASP57 4.2 103.2 1.0
CA G:SER17 4.2 72.7 1.0
O2G G:GNP201 4.2 82.2 1.0
PA G:GNP201 4.2 83.2 1.0
O1G G:GNP201 4.3 68.5 1.0
C G:PRO34 4.4 87.7 1.0
CG2 G:THR35 4.4 90.0 1.0
C G:ASP33 4.4 100.7 1.0
O1A G:GNP201 4.5 91.5 1.0
O1B G:GNP201 4.5 77.2 1.0
CA G:PRO34 4.6 93.5 1.0
OD1 G:ASP57 4.9 103.2 1.0
CG G:ASP57 4.9 96.5 1.0

Reference:

M.J.Whitley, T.H.Tran, M.Yi, S.Dharmaiah, G.Cornilescu, D.K.Simanshu. Comparative Analysis of KRAS4A and KRAS4B Splice Variants Reveals Distinctive Structural and Functional Properties Sci Adv 2024.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ADJ4137
Page generated: Fri Oct 4 20:31:29 2024

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