Manganese in PDB 7jrq: Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein

The structure of Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein, PDB code: 7jrq was solved by S.I.Mann, W.F.Degrado, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.68 / 1.75
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.322, 45.322, 164.22, 90, 90, 90
R / Rfree (%)	19.5 / 23

The structure of Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein (pdb code 7jrq). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein, PDB code: 7jrq:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:19.4 occ:1.00 MN1 A:SMU202 0.0 19.4 1.0 N3 A:SMU202 2.0 19.1 1.0 N2 A:SMU202 2.0 20.9 1.0 N1 A:SMU202 2.1 18.9 1.0 N4 A:SMU202 2.1 13.9 1.0 NE2 A:HIS64 2.4 17.0 1.0 O A:HOH322 2.6 22.7 1.0 C11 A:SMU202 3.0 15.8 1.0 C9 A:SMU202 3.0 19.4 1.0 C6 A:SMU202 3.1 18.9 1.0 C14 A:SMU202 3.1 18.3 1.0 C19 A:SMU202 3.1 17.5 1.0 C4 A:SMU202 3.1 20.5 1.0 C16 A:SMU202 3.1 17.8 1.0 C1 A:SMU202 3.1 19.8 1.0 CD2 A:HIS64 3.3 15.8 1.0 C10 A:SMU202 3.4 19.4 1.0 CE1 A:HIS64 3.4 18.6 1.0 C5 A:SMU202 3.5 17.5 1.0 C20 A:SMU202 3.5 20.8 1.0 C15 A:SMU202 3.5 18.5 1.0 C8 A:SMU202 4.3 23.5 1.0 C7 A:SMU202 4.3 21.3 1.0 C12 A:SMU202 4.3 20.0 1.0 C13 A:SMU202 4.3 19.8 1.0 C18 A:SMU202 4.3 18.6 1.0 C17 A:SMU202 4.4 19.8 1.0 C3 A:SMU202 4.4 18.8 1.0 C2 A:SMU202 4.4 20.5 1.0 O A:HOH326 4.5 23.6 1.0 CG A:HIS64 4.5 16.6 1.0 ND1 A:HIS64 4.5 15.6 1.0 O A:ALA121 4.8 22.5 1.0 C21 A:SMU202 5.0 18.8 1.0 C27 A:SMU202 5.0 24.2 1.0 CA A:GLY125 5.0 23.0 1.0

Manganese binding site 2 out of 2 in the Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystallographically Characterized De Novo Designed Mn- Diphenylporphyrin Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:24.5 occ:0.52 MN1 A:SMU203 0.0 24.5 0.5 N2 A:SMU203 1.9 20.4 0.5 N1 A:SMU203 2.0 20.2 0.5 N3 A:SMU203 2.1 21.0 0.5 N4 A:SMU203 2.2 19.7 0.5 OE1 A:GLU58 2.6 24.6 1.0 C6 A:SMU203 3.0 21.3 0.5 C4 A:SMU203 3.0 20.1 0.5 C9 A:SMU203 3.0 20.3 0.5 C1 A:SMU203 3.1 21.5 0.5 C11 A:SMU203 3.1 19.9 0.5 C19 A:SMU203 3.2 21.0 0.5 C14 A:SMU203 3.2 19.1 0.5 C16 A:SMU203 3.2 21.3 0.5 CD A:GLU58 3.3 21.4 0.6 C5 A:SMU203 3.3 21.6 0.5 C10 A:SMU203 3.4 18.6 0.5 C20 A:SMU203 3.5 21.7 0.5 OE2 A:GLU58 3.5 27.1 1.0 C15 A:SMU203 3.6 19.1 0.5 NH2 A:ARG96 4.2 20.9 1.0 C7 A:SMU203 4.2 18.9 0.5 C8 A:SMU203 4.2 21.1 0.5 C3 A:SMU203 4.2 23.5 0.5 C2 A:SMU203 4.3 18.2 0.5 NE A:ARG96 4.3 18.9 1.0 C12 A:SMU203 4.4 20.2 0.5 C13 A:SMU203 4.4 18.5 0.5 C18 A:SMU203 4.4 22.7 0.5 C17 A:SMU203 4.5 21.5 0.5 CG A:GLU58 4.5 25.9 1.0 CB A:GLU58 4.6 22.4 1.0 CZ A:ARG96 4.6 24.8 1.0 C21 A:SMU203 4.8 20.9 0.5

S.I.Mann, A.Nayak, G.T.Gassner, M.J.Therien, W.F.Degrado. De Novo Design, Solution Characterization, and Crystallographic Structure of An Abiological Mn-Porphyrin-Binding Protein Capable of Stabilizing A Mn(V) Species. J.Am.Chem.Soc. 2020.
ISSN: ESSN 1520-5126
PubMed: 33373215
DOI: 10.1021/JACS.0C10136