Magnesium in PDB 6zrn: Crystal Structure of the RLIP76 Ral Binding Domain Mutant (E427S/L429M/Q433L/K440R) in Complex with Ralb-Gmppnp

Protein crystallography data

The structure of Crystal Structure of the RLIP76 Ral Binding Domain Mutant (E427S/L429M/Q433L/K440R) in Complex with Ralb-Gmppnp, PDB code: 6zrn was solved by C.Hurd, P.Brear, J.Revell, S.Ross, H.Mott, D.Owen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.15 / 1.48
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.196, 77.517, 65.767, 90.00, 90.07, 90.00
R / Rfree (%) 20.9 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the RLIP76 Ral Binding Domain Mutant (E427S/L429M/Q433L/K440R) in Complex with Ralb-Gmppnp (pdb code 6zrn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the RLIP76 Ral Binding Domain Mutant (E427S/L429M/Q433L/K440R) in Complex with Ralb-Gmppnp, PDB code: 6zrn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6zrn

Go back to Magnesium Binding Sites List in 6zrn
Magnesium binding site 1 out of 2 in the Crystal Structure of the RLIP76 Ral Binding Domain Mutant (E427S/L429M/Q433L/K440R) in Complex with Ralb-Gmppnp


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 the RLIP76 Ral Binding Domain Mutant (E427S/L429M/Q433L/K440R) in Complex with Ralb-Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:16.8
occ:1.00
O A:HOH331 2.0 17.5 1.0
O1G A:GNP201 2.0 17.3 1.0
OG A:SER28 2.1 19.4 1.0
O A:HOH328 2.1 18.0 1.0
O1B A:GNP201 2.1 15.6 1.0
OG1 A:THR46 2.1 20.2 1.0
CB A:THR46 3.1 22.4 1.0
CB A:SER28 3.1 15.3 1.0
PG A:GNP201 3.2 18.1 1.0
PB A:GNP201 3.3 17.1 1.0
N3B A:GNP201 3.5 17.2 1.0
N A:THR46 3.8 21.1 1.0
N A:SER28 3.9 15.1 1.0
O3G A:GNP201 3.9 19.5 1.0
OD2 A:ASP68 4.0 23.1 1.0
CA A:THR46 4.1 20.6 1.0
CA A:SER28 4.1 15.6 1.0
CG2 A:THR46 4.1 24.4 1.0
OD1 A:ASP68 4.1 28.2 1.0
O2A A:GNP201 4.1 19.8 1.0
O3 A:GOL203 4.2 26.8 1.0
O2B A:GNP201 4.3 18.5 1.0
O3A A:GNP201 4.3 16.5 1.0
O2G A:GNP201 4.4 19.4 1.0
CG A:ASP68 4.4 22.6 1.0
O A:THR69 4.5 23.7 1.0
O A:GLU44 4.5 23.3 1.0
C1 A:GOL203 4.5 37.0 1.0
PA A:GNP201 4.6 17.9 1.0
O1A A:GNP201 4.6 18.1 1.0
CB A:LYS27 4.8 14.4 1.0
C A:PRO45 4.8 26.9 1.0
C3 A:GOL203 4.8 35.8 1.0
CE A:LYS27 4.9 17.3 1.0
C A:LYS27 4.9 18.3 1.0
NZ A:LYS27 4.9 19.2 1.0

Magnesium binding site 2 out of 2 in 6zrn

Go back to Magnesium Binding Sites List in 6zrn
Magnesium binding site 2 out of 2 in the Crystal Structure of the RLIP76 Ral Binding Domain Mutant (E427S/L429M/Q433L/K440R) in Complex with Ralb-Gmppnp


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 the RLIP76 Ral Binding Domain Mutant (E427S/L429M/Q433L/K440R) in Complex with Ralb-Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:16.2
occ:1.00
O3G B:GNP201 2.0 15.9 1.0
O1B B:GNP201 2.0 12.9 1.0
O B:HOH316 2.1 16.9 1.0
OG1 B:THR46 2.1 15.2 1.0
OG B:SER28 2.1 15.0 1.0
O B:HOH320 2.1 16.5 1.0
CB B:THR46 3.1 14.2 1.0
CB B:SER28 3.2 15.4 1.0
PG B:GNP201 3.2 16.4 1.0
PB B:GNP201 3.2 15.0 1.0
N3B B:GNP201 3.5 16.6 1.0
N B:THR46 3.8 14.1 1.0
N B:SER28 3.9 14.4 1.0
OD2 B:ASP68 3.9 23.9 1.0
O2G B:GNP201 4.0 16.6 1.0
CA B:THR46 4.0 13.2 1.0
O B:HOH302 4.1 25.7 1.0
CA B:SER28 4.1 15.3 1.0
O2A B:GNP201 4.1 15.2 1.0
CG2 B:THR46 4.2 15.0 1.0
OD1 B:ASP68 4.2 24.6 1.0
O3A B:GNP201 4.3 15.3 1.0
O2B B:GNP201 4.3 15.2 1.0
O1G B:GNP201 4.4 16.9 1.0
CG B:ASP68 4.4 22.7 1.0
O B:THR69 4.5 19.9 1.0
PA B:GNP201 4.5 15.9 1.0
O B:GLU44 4.6 17.8 1.0
O1A B:GNP201 4.7 16.8 1.0
C B:PRO45 4.8 18.2 1.0
CB B:LYS27 4.8 18.1 1.0
CE B:LYS27 4.8 18.1 1.0
O B:HOH323 4.9 40.5 1.0
C B:LYS27 4.9 14.2 1.0
NZ B:LYS27 5.0 17.0 1.0

Reference:

C.A.Hurd, P.Brear, J.Revell, S.Ross, H.R.Mott, D.Owen. Affinity Maturation of the RLIP76 Ral Binding Domain to Inform the Design of Stapled Peptides Targeting the Ral Gtpases. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 33214225
DOI: 10.1074/JBC.RA120.015735
Page generated: Tue Dec 15 03:13:24 2020

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