Magnesium in PDB 5wfn: Revised Model of Leiomodin 2-Mediated Actin Regulation (Alternate Refinement of Pdb 4RWT)

The structure of Revised Model of Leiomodin 2-Mediated Actin Regulation (Alternate Refinement of Pdb 4RWT), PDB code: 5wfn was solved by Z.Yurtsever, M.J.Eck, R.Dominguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.25 / 3.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	65.350, 65.650, 81.920, 101.29, 90.94, 107.97
R / Rfree (%)	20.8 / 24.6

The binding sites of Magnesium atom in the Revised Model of Leiomodin 2-Mediated Actin Regulation (Alternate Refinement of Pdb 4RWT) (pdb code 5wfn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Revised Model of Leiomodin 2-Mediated Actin Regulation (Alternate Refinement of Pdb 4RWT), PDB code: 5wfn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Revised Model of Leiomodin 2-Mediated Actin Regulation (Alternate Refinement of Pdb 4RWT)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Revised Model of Leiomodin 2-Mediated Actin Regulation (Alternate Refinement of Pdb 4RWT) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:50.5 occ:1.00 O2G A:ANP401 2.3 69.0 1.0 OE1 A:GLN137 2.5 63.4 1.0 O2B A:ANP401 3.2 52.6 1.0 OD1 A:ASP154 3.5 67.5 1.0 PG A:ANP401 3.6 93.8 1.0 CD A:GLN137 3.7 49.9 1.0 OD2 A:ASP154 3.8 55.6 1.0 O1G A:ANP401 3.8 63.0 1.0 HG21 A:VAL339 3.8 64.3 1.0 CG A:ASP154 4.0 53.0 1.0 O3A A:ANP401 4.0 0.4 1.0 HA3 A:GLY156 4.1 73.0 1.0 PB A:ANP401 4.2 91.3 1.0 HB3 A:GLN137 4.2 61.9 1.0 HE22 A:GLN137 4.3 64.6 1.0 NE2 A:GLN137 4.5 53.8 1.0 N3B A:ANP401 4.5 60.8 1.0 HB2 A:GLN137 4.5 61.9 1.0 HA2 A:GLY13 4.7 73.8 1.0 CG2 A:VAL339 4.7 53.0 1.0 CB A:GLN137 4.7 51.2 1.0 CG A:GLN137 4.8 31.8 1.0 O3G A:ANP401 4.8 63.1 1.0 HZ3 A:LYS18 4.9 49.4 1.0 O2A A:ANP401 4.9 54.9 1.0 CA A:GLY156 4.9 60.4 1.0 HG23 A:VAL339 5.0 64.3 1.0 HA2 A:GLY301 5.0 52.0 1.0

Magnesium binding site 2 out of 2 in the Revised Model of Leiomodin 2-Mediated Actin Regulation (Alternate Refinement of Pdb 4RWT)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Revised Model of Leiomodin 2-Mediated Actin Regulation (Alternate Refinement of Pdb 4RWT) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:59.0 occ:1.00 OE1 B:GLN137 2.4 63.3 1.0 O2G B:ANP401 2.4 52.9 1.0 O1B B:ANP401 3.0 42.1 1.0 HG21 B:VAL339 3.4 64.3 1.0 CD B:GLN137 3.5 49.8 1.0 PG B:ANP401 3.6 80.9 1.0 O3G B:ANP401 3.7 46.6 1.0 OD1 B:ASP154 3.9 67.8 1.0 OD2 B:ASP154 3.9 56.1 1.0 HB3 B:GLN137 4.0 61.9 1.0 HE22 B:GLN137 4.1 64.6 1.0 PB B:ANP401 4.2 81.3 1.0 NE2 B:GLN137 4.2 53.5 1.0 CG B:ASP154 4.3 53.4 1.0 CG2 B:VAL339 4.3 53.6 1.0 HZ3 B:LYS18 4.4 49.4 1.0 O3A B:ANP401 4.4 94.9 1.0 HB2 B:GLN137 4.4 61.9 1.0 HA2 B:GLY13 4.5 73.8 1.0 CB B:GLN137 4.5 51.4 1.0 CG B:GLN137 4.5 31.8 1.0 HA3 B:GLY156 4.6 73.0 1.0 N3B B:ANP401 4.6 52.5 1.0 HG11 B:VAL339 4.6 51.0 1.0 HG23 B:VAL339 4.6 64.3 1.0 OD2 B:ASP11 4.7 48.2 1.0 OD1 B:ASP11 4.8 61.3 1.0 HG2 B:GLN137 4.8 38.5 1.0 HG22 B:VAL339 4.8 64.3 1.0 O1G B:ANP401 4.8 55.7 1.0 HZ1 B:LYS18 4.8 49.4 1.0 O1A B:ANP401 5.0 60.3 1.0 NZ B:LYS18 5.0 41.0 1.0

M.Boczkowska, Z.Yurtsever, G.Rebowski, M.J.Eck, R.Dominguez. Crystal Structure of Leiomodin 2 in Complex with Actin: A Structural and Functional Reexamination Biophys.J. V. 113 889 2017.
ISSN: ISSN 0006-3495
DOI: 10.1016/J.BPJ.2017.07.007