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Magnesium in PDB 4yix: Structure of MRB1590 Bound to Adp

Protein crystallography data

The structure of Structure of MRB1590 Bound to Adp, PDB code: 4yix was solved by P.L.R.Shaw, M.A.Schumacher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.60 / 2.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 105.584, 184.709, 73.639, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 26.2

Other elements in 4yix:

The structure of Structure of MRB1590 Bound to Adp also contains other interesting chemical elements:

Mercury (Hg) 11 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of MRB1590 Bound to Adp (pdb code 4yix). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of MRB1590 Bound to Adp, PDB code: 4yix:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4yix

Go back to Magnesium Binding Sites List in 4yix
Magnesium binding site 1 out of 3 in the Structure of MRB1590 Bound to Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of MRB1590 Bound to Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:22.9
occ:1.00
O A:HOH843 3.1 20.5 1.0
O A:HOH844 3.1 15.6 1.0
OD2 A:ASP411 3.4 20.2 1.0
OG A:SER320 3.4 19.0 1.0
CG1 A:VAL456 3.6 18.8 1.0
OD1 A:ASP409 3.6 19.4 1.0
O3B A:ADP715 3.8 14.8 1.0
NZ A:LYS319 3.9 17.6 1.0
CG A:ASP411 4.0 21.4 1.0
CE A:LYS319 4.0 18.2 1.0
O1B A:ADP715 4.3 16.2 1.0
PB A:ADP715 4.4 14.5 1.0
OD1 A:ASP411 4.4 22.4 1.0
CG A:ASP409 4.5 19.0 1.0
OD2 A:ASP409 4.6 20.1 1.0
CB A:LYS319 4.7 15.8 1.0
CB A:SER320 4.7 15.0 1.0
CB A:VAL456 4.8 18.8 1.0
CB A:ASP411 4.9 21.4 1.0
N A:SER320 4.9 14.1 1.0
O2B A:ADP715 4.9 15.4 1.0

Magnesium binding site 2 out of 3 in 4yix

Go back to Magnesium Binding Sites List in 4yix
Magnesium binding site 2 out of 3 in the Structure of MRB1590 Bound to Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of MRB1590 Bound to Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:11.6
occ:1.00
SG A:CYS570 1.2 5.9 1.0
O A:CYS620 2.2 29.2 1.0
CB A:CYS570 2.2 16.8 1.0
C A:CYS620 3.0 26.6 1.0
CA A:CYS620 3.4 24.0 1.0
CA A:CYS570 3.4 19.4 1.0
OE1 A:GLN624 3.8 24.5 1.0
CB A:CYS620 3.9 21.9 1.0
CD1 A:LEU631 4.0 21.8 1.0
CB A:GLN624 4.1 28.7 1.0
N A:CYS621 4.2 26.9 1.0
N A:CYS570 4.4 18.8 1.0
SG A:CYS620 4.4 6.4 1.0
C A:CYS570 4.5 19.1 1.0
CA A:CYS621 4.5 29.6 1.0
CD A:GLN624 4.6 25.3 1.0
O A:CYS570 4.6 19.6 1.0
N A:GLN624 4.7 28.7 1.0
MG A:MG703 4.8 2.7 1.0
N A:CYS620 4.8 26.9 1.0
O A:GLY619 4.8 25.4 1.0
CA A:GLN624 4.9 28.8 1.0
CD2 A:HIS623 4.9 28.2 1.0
CG A:GLN624 4.9 27.2 1.0

Magnesium binding site 3 out of 3 in 4yix

Go back to Magnesium Binding Sites List in 4yix
Magnesium binding site 3 out of 3 in the Structure of MRB1590 Bound to Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of MRB1590 Bound to Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:2.7
occ:1.00
SG A:CYS620 1.6 6.4 1.0
CB A:CYS620 3.2 21.9 1.0
CB A:CYS570 3.7 16.8 1.0
CG2 A:ILE651 3.8 14.6 1.0
CD2 A:LEU574 3.9 19.7 1.0
SG A:CYS570 3.9 5.9 1.0
CD1 A:LEU574 4.0 23.0 1.0
CG A:LEU574 4.3 22.3 1.0
O A:CYS570 4.3 19.6 1.0
C A:CYS570 4.3 19.1 1.0
CA A:CYS620 4.4 24.0 1.0
CB A:LEU574 4.5 21.5 1.0
CD1 A:ILE617 4.5 17.1 1.0
CA A:CYS570 4.6 19.4 1.0
N A:LEU571 4.7 19.8 1.0
MG A:MG702 4.8 11.6 1.0
CE A:MET616 4.9 19.5 1.0

Reference:

P.L.Shaw, N.M.Mcadams, M.A.Hast, M.L.Ammerman, L.K.Read, M.A.Schumacher. Structures of the T. Brucei Krna Editing Factor MRB1590 Reveal Unique Rna-Binding Pore Motif Contained Within An Abc-Atpase Fold. Nucleic Acids Res. V. 43 7096 2015.
ISSN: ESSN 1362-4962
PubMed: 26117548
DOI: 10.1093/NAR/GKV647
Page generated: Mon Dec 14 19:54:13 2020

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