Manganese in PDB 6vbz: Crystal Structure of the Rat Mlkl Pseudokinase Domain

The structure of Crystal Structure of the Rat Mlkl Pseudokinase Domain, PDB code: 6vbz was solved by K.A.Davies, P.E.Czabotar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.58 / 2.19
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	190.057, 190.057, 77.759, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 21.5

The binding sites of Manganese atom in the Crystal Structure of the Rat Mlkl Pseudokinase Domain (pdb code 6vbz). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of the Rat Mlkl Pseudokinase Domain, PDB code: 6vbz:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Crystal Structure of the Rat Mlkl Pseudokinase Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Rat Mlkl Pseudokinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:90.2 occ:1.00 OD2 A:ASP377 2.3 64.6 1.0 CG A:ASP377 3.2 59.8 1.0 OD1 A:ASP377 3.5 49.9 1.0 CB A:PRO440 4.4 56.8 1.0 CG A:PRO440 4.5 61.4 1.0 CB A:ASP377 4.5 44.9 1.0 OE1 A:GLU367 4.6 48.8 1.0 O A:LYS375 4.7 73.0 1.0 CG A:GLU367 4.7 56.7 1.0 CB A:LYS379 4.7 43.1 1.0 SG A:CYS374 4.7 83.2 1.0

Manganese binding site 2 out of 6 in the Crystal Structure of the Rat Mlkl Pseudokinase Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Rat Mlkl Pseudokinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:0.5 occ:1.00 OD1 A:ASP371 2.5 89.6 1.0 O A:HOH698 2.7 78.6 1.0 CG A:ASP371 3.8 86.6 1.0 OD2 A:ASP371 4.5 88.0 1.0 CB A:ASP371 4.8 83.1 1.0 SG A:CYS374 4.9 83.2 1.0

Manganese binding site 3 out of 6 in the Crystal Structure of the Rat Mlkl Pseudokinase Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Rat Mlkl Pseudokinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:58.5 occ:1.00 O A:HOH651 2.1 52.2 1.0 OE2 A:GLU426 2.1 50.0 1.0 OE2 A:GLU430 2.2 87.0 1.0 O A:HOH686 2.5 49.6 1.0 O A:HOH601 2.6 50.0 1.0 CD A:GLU426 2.9 47.6 1.0 CD A:GLU430 3.0 78.0 1.0 OE1 A:GLU426 3.0 42.2 1.0 CG A:GLU430 3.6 68.2 1.0 OE1 A:GLU430 3.7 82.0 1.0 CG A:GLU426 4.3 47.8 1.0

Manganese binding site 4 out of 6 in the Crystal Structure of the Rat Mlkl Pseudokinase Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Rat Mlkl Pseudokinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:0.7 occ:1.00 NE2 B:HIS311 2.5 68.4 1.0 CD2 B:HIS311 3.4 67.0 1.0 CE1 B:HIS311 3.5 67.1 1.0 OD1 A:ASP190 3.5 54.5 1.0 O A:GLU189 4.3 51.4 1.0 ND1 B:HIS311 4.6 71.8 1.0 CG B:HIS311 4.6 67.0 1.0 C A:GLU189 4.7 44.7 1.0 CG A:ASP190 4.7 51.8 1.0 CB A:GLU189 4.8 57.2 1.0 CA A:ASP190 4.9 40.2 1.0

Manganese binding site 5 out of 6 in the Crystal Structure of the Rat Mlkl Pseudokinase Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the Rat Mlkl Pseudokinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:0.2 occ:1.00 OE2 B:GLU409 2.2 84.6 1.0 OE2 B:GLU405 2.2 94.1 1.0 CD B:GLU409 3.2 76.0 1.0 CD B:GLU405 3.2 81.0 1.0 OE1 B:GLU409 3.6 73.7 1.0 CG B:GLU405 3.8 74.2 1.0 OE1 B:GLU405 4.1 79.9 1.0 CG B:GLU409 4.5 67.4 1.0

Manganese binding site 6 out of 6 in the Crystal Structure of the Rat Mlkl Pseudokinase Domain


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of the Rat Mlkl Pseudokinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn503 b:89.8 occ:1.00 O B:HOH669 2.3 66.5 1.0 OD2 B:ASP371 2.3 75.0 1.0 O B:HOH679 2.4 62.7 1.0 O B:HOH639 2.7 60.1 1.0 CG B:ASP371 3.2 56.4 1.0 OD1 B:ASP371 3.6 50.1 1.0 CB B:ASP371 4.5 50.9 1.0

K.A.Davies, C.Fitzgibbon, S.N.Young, S.E.Garnish, W.Yeung, D.Coursier, R.W.Birkinshaw, J.J.Sandow, W.I.L.Lehmann, L.Y.Liang, I.S.Lucet, J.D.Chalmers, W.M.Patrick, N.Kannan, E.J.Petrie, P.E.Czabotar, J.M.Murphy. Distinct Pseudokinase Domain Conformations Underlie Divergent Activation Mechanisms Among Vertebrate Mlkl Orthologues. Nat Commun V. 11 3060 2020.
ISSN: ESSN 2041-1723
PubMed: 32561735
DOI: 10.1038/S41467-020-16823-3