Manganese in PDB 4xjk: Crystal Structure of Mn(II) Ca(II) Na(I) Bound Calprotectin

The structure of Crystal Structure of Mn(II) Ca(II) Na(I) Bound Calprotectin, PDB code: 4xjk was solved by C.L.Drennan, S.E.J.Bowman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.24 / 1.76
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	55.279, 49.239, 218.067, 90.00, 94.07, 90.00
R / Rfree (%)	18.5 / 22

The structure of Crystal Structure of Mn(II) Ca(II) Na(I) Bound Calprotectin also contains other interesting chemical elements:

Calcium	(Ca)	10 atoms
Sodium	(Na)	10 atoms

The binding sites of Manganese atom in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound Calprotectin (pdb code 4xjk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound Calprotectin, PDB code: 4xjk:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound Calprotectin


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 Mn(II) Ca(II) Na(I) Bound Calprotectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn103 b:28.4 occ:1.00 NE2 B:HIS95 2.3 31.4 1.0 NE2 B:HIS105 2.3 24.6 1.0 NE2 A:HIS17 2.3 29.4 1.0 NE2 A:HIS27 2.3 27.3 1.0 NE2 B:HIS103 2.3 31.3 1.0 NE2 B:HIS91 2.3 24.9 1.0 CE1 A:HIS17 3.1 24.5 1.0 CD2 B:HIS105 3.2 25.1 1.0 CE1 B:HIS95 3.2 33.9 1.0 CE1 B:HIS91 3.2 27.2 1.0 CE1 B:HIS103 3.2 34.0 1.0 CE1 A:HIS27 3.2 35.7 1.0 CD2 A:HIS27 3.3 30.6 1.0 CD2 A:HIS17 3.3 25.7 1.0 CD2 B:HIS95 3.3 27.6 1.0 CE1 B:HIS105 3.3 26.7 1.0 CD2 B:HIS103 3.3 33.8 1.0 CD2 B:HIS91 3.3 27.7 1.0 ND1 A:HIS17 4.2 26.8 1.0 ND1 B:HIS95 4.3 33.8 1.0 CG A:HIS17 4.3 27.7 1.0 CG B:HIS105 4.3 31.2 1.0 ND1 B:HIS91 4.4 29.1 1.0 ND1 A:HIS27 4.4 36.7 1.0 ND1 B:HIS105 4.4 30.9 1.0 ND1 B:HIS103 4.4 30.6 1.0 CG B:HIS95 4.4 34.0 1.0 CG A:HIS27 4.4 27.4 1.0 CG B:HIS91 4.4 26.5 1.0 CG B:HIS103 4.4 34.3 1.0

Manganese binding site 2 out of 5 in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound Calprotectin


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 Mn(II) Ca(II) Na(I) Bound Calprotectin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn103 b:23.9 occ:1.00 NE2 D:HIS95 2.3 27.2 1.0 NE2 C:HIS17 2.3 28.1 1.0 NE2 C:HIS27 2.3 25.7 1.0 NE2 D:HIS105 2.3 27.6 1.0 NE2 D:HIS91 2.3 22.5 1.0 NE2 D:HIS103 2.4 23.7 1.0 CE1 C:HIS17 3.1 25.5 1.0 CD2 D:HIS105 3.2 26.2 1.0 CD2 D:HIS95 3.2 25.5 1.0 CE1 C:HIS27 3.3 29.2 1.0 CE1 D:HIS95 3.3 21.9 1.0 CE1 D:HIS91 3.3 30.9 1.0 CD2 C:HIS27 3.3 25.1 1.0 CD2 C:HIS17 3.3 28.4 1.0 CD2 D:HIS103 3.3 27.0 1.0 CD2 D:HIS91 3.3 25.7 1.0 CE1 D:HIS105 3.4 30.3 1.0 CE1 D:HIS103 3.4 27.4 1.0 ND1 C:HIS17 4.2 26.4 1.0 CG C:HIS17 4.3 32.6 1.0 CG D:HIS105 4.4 25.1 1.0 ND1 D:HIS95 4.4 30.9 1.0 ND1 C:HIS27 4.4 24.4 1.0 CG D:HIS95 4.4 26.8 1.0 ND1 D:HIS91 4.4 23.5 1.0 ND1 D:HIS105 4.4 25.7 1.0 CG C:HIS27 4.4 26.0 1.0 CG D:HIS91 4.5 25.9 1.0 ND1 D:HIS103 4.5 22.5 1.0 CG D:HIS103 4.5 26.5 1.0

Manganese binding site 3 out of 5 in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound Calprotectin


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 Mn(II) Ca(II) Na(I) Bound Calprotectin within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn103 b:26.1 occ:1.00 NE2 F:HIS95 2.2 27.9 1.0 NE2 F:HIS103 2.3 27.6 1.0 NE2 F:HIS105 2.3 27.1 1.0 NE2 E:HIS27 2.3 26.4 1.0 NE2 E:HIS17 2.3 22.8 1.0 NE2 F:HIS91 2.4 22.7 1.0 CE1 F:HIS95 3.1 31.3 1.0 CD2 F:HIS105 3.2 31.9 1.0 CE1 E:HIS17 3.2 23.8 1.0 CE1 F:HIS103 3.2 30.1 1.0 CE1 E:HIS27 3.2 33.2 1.0 CD2 F:HIS103 3.3 28.0 1.0 CD2 F:HIS95 3.3 31.1 1.0 CE1 F:HIS105 3.3 25.9 1.0 CD2 E:HIS17 3.3 20.5 1.0 CD2 E:HIS27 3.3 24.2 1.0 CD2 F:HIS91 3.3 24.4 1.0 CE1 F:HIS91 3.4 22.7 1.0 ND1 F:HIS95 4.3 31.0 1.0 ND1 E:HIS17 4.3 24.2 1.0 ND1 F:HIS103 4.3 30.7 1.0 CG F:HIS105 4.3 35.2 1.0 ND1 F:HIS105 4.4 31.3 1.0 ND1 E:HIS27 4.4 30.4 1.0 CG F:HIS95 4.4 37.9 1.0 CG E:HIS17 4.4 23.1 1.0 CG F:HIS103 4.4 30.9 1.0 CG E:HIS27 4.4 23.9 1.0 ND1 F:HIS91 4.5 24.0 1.0 CG F:HIS91 4.5 22.0 1.0

Manganese binding site 4 out of 5 in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound Calprotectin


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 Mn(II) Ca(II) Na(I) Bound Calprotectin within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn103 b:32.6 occ:1.00 NE2 H:HIS95 2.2 37.6 1.0 NE2 G:HIS17 2.3 29.9 1.0 NE2 H:HIS105 2.3 36.1 1.0 NE2 G:HIS27 2.4 28.8 1.0 NE2 H:HIS103 2.4 28.9 1.0 NE2 H:HIS91 2.4 29.7 1.0 CE1 G:HIS17 3.1 28.3 1.0 CE1 H:HIS95 3.1 37.8 1.0 CD2 H:HIS105 3.2 32.1 1.0 CD2 H:HIS95 3.2 34.9 1.0 CD2 H:HIS103 3.3 38.5 1.0 CD2 G:HIS17 3.3 30.0 1.0 CE1 H:HIS105 3.3 37.2 1.0 CE1 H:HIS91 3.3 32.4 1.0 CE1 G:HIS27 3.3 36.3 1.0 CD2 G:HIS27 3.3 27.0 1.0 CD2 H:HIS91 3.4 32.4 1.0 CE1 H:HIS103 3.4 38.5 1.0 ND1 G:HIS17 4.2 29.2 1.0 ND1 H:HIS95 4.3 39.1 1.0 CG G:HIS17 4.3 31.6 1.0 CG H:HIS95 4.4 39.1 1.0 ND1 H:HIS105 4.4 35.9 1.0 CG H:HIS105 4.4 42.7 1.0 ND1 H:HIS91 4.4 25.7 1.0 ND1 G:HIS27 4.4 34.5 1.0 CG H:HIS103 4.4 40.5 1.0 CG G:HIS27 4.5 32.1 1.0 ND1 H:HIS103 4.5 36.7 1.0 CG H:HIS91 4.5 31.2 1.0

Manganese binding site 5 out of 5 in the Crystal Structure of Mn(II) Ca(II) Na(I) Bound Calprotectin


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 Mn(II) Ca(II) Na(I) Bound Calprotectin within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn103 b:18.2 occ:1.00 NE2 I:HIS27 2.3 18.6 1.0 NE2 J:HIS105 2.3 19.5 1.0 NE2 J:HIS95 2.3 19.5 1.0 NE2 J:HIS91 2.3 19.3 1.0 NE2 J:HIS103 2.3 19.9 1.0 NE2 I:HIS17 2.4 19.1 1.0 CD2 J:HIS105 3.2 18.8 1.0 CE1 I:HIS17 3.2 16.9 1.0 CD2 I:HIS27 3.2 18.7 1.0 CE1 J:HIS91 3.3 19.5 1.0 CE1 J:HIS95 3.3 18.3 1.0 CD2 J:HIS103 3.3 18.0 1.0 CE1 J:HIS103 3.3 20.6 1.0 CE1 I:HIS27 3.3 19.4 1.0 CD2 J:HIS95 3.3 18.6 1.0 CD2 J:HIS91 3.3 19.6 1.0 CE1 J:HIS105 3.3 21.1 1.0 CD2 I:HIS17 3.4 20.6 1.0 ND1 I:HIS17 4.3 17.3 1.0 CG J:HIS105 4.4 18.2 1.0 ND1 J:HIS91 4.4 19.0 1.0 ND1 I:HIS27 4.4 20.7 1.0 CG I:HIS27 4.4 21.4 1.0 ND1 J:HIS95 4.4 23.3 1.0 ND1 J:HIS103 4.4 17.4 1.0 ND1 J:HIS105 4.4 20.7 1.0 CG I:HIS17 4.4 17.9 1.0 CG J:HIS103 4.4 17.4 1.0 CG J:HIS95 4.4 20.8 1.0 CG J:HIS91 4.4 19.1 1.0

D.M.Gagnon, M.B.Brophy, S.E.Bowman, T.A.Stich, C.L.Drennan, R.D.Britt, E.M.Nolan. Manganese Binding Properties of Human Calprotectin Under Conditions of High and Low Calcium: X-Ray Crystallographic and Advanced Electron Paramagnetic Resonance Spectroscopic Analysis. J.Am.Chem.Soc. V. 137 3004 2015.
ISSN: ESSN 1520-5126
PubMed: 25597447
DOI: 10.1021/JA512204S