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

Go back to Magnesium Binding Sites List in 8t75
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

Go back to Magnesium Binding Sites List in 8t75
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

Go back to Magnesium Binding Sites List in 8t75
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

Go back to Magnesium Binding Sites List in 8t75
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy