Manganese in PDB 9ppm: Mn-Bound Structure of the H77C Variant of TRICYT2

The structure of Mn-Bound Structure of the H77C Variant of TRICYT2, PDB code: 9ppm was solved by V.H.Eng, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.31 / 2.53
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.19, 47.36, 166.23, 90, 97.27, 90
R / Rfree (%)	23.4 / 29.2

The structure of Mn-Bound Structure of the H77C Variant of TRICYT2 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the Mn-Bound Structure of the H77C Variant of TRICYT2 (pdb code 9ppm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Mn-Bound Structure of the H77C Variant of TRICYT2, PDB code: 9ppm:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Mn-Bound Structure of the H77C Variant of TRICYT2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Mn-Bound Structure of the H77C Variant of TRICYT2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn201 b:66.4 occ:0.94 NE2 C:HIS73 2.2 48.6 1.0 O A:HOH301 2.4 65.8 1.0 NE2 H:HIS73 2.4 40.0 1.0 NE2 A:HIS73 2.5 44.3 1.0 CD2 C:HIS73 3.1 46.4 1.0 O C:HOH306 3.1 62.7 1.0 CD2 A:HIS73 3.3 41.9 1.0 CE1 C:HIS73 3.3 44.1 1.0 CE1 H:HIS73 3.4 35.9 1.0 CD2 H:HIS73 3.4 43.0 1.0 CE1 A:HIS73 3.5 39.1 1.0 SG C:CYS77 4.3 60.7 0.6 CG C:HIS73 4.3 45.8 1.0 ND1 C:HIS73 4.4 40.6 1.0 ND1 H:HIS73 4.5 42.7 1.0 CG A:HIS73 4.5 48.7 1.0 CG H:HIS73 4.5 44.2 1.0 ND1 A:HIS73 4.6 42.2 1.0 SG H:CYS77 4.6 66.7 1.0 SG A:CYS77 4.8 63.0 1.0 O C:HOH304 4.9 45.8 1.0

Manganese binding site 2 out of 4 in the Mn-Bound Structure of the H77C Variant of TRICYT2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Mn-Bound Structure of the H77C Variant of TRICYT2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn201 b:68.9 occ:0.94 NE2 E:HIS73 2.3 44.1 1.0 NE2 G:HIS73 2.4 57.2 1.0 O B:HOH202 2.5 54.5 1.0 NE2 B:HIS73 2.5 45.2 1.0 O E:HOH304 2.8 63.9 1.0 CD2 E:HIS73 3.2 47.0 1.0 CD2 B:HIS73 3.3 46.5 1.0 CE1 G:HIS73 3.3 52.5 1.0 CE1 E:HIS73 3.4 41.5 1.0 CD2 G:HIS73 3.4 51.7 1.0 CE1 B:HIS73 3.6 42.4 1.0 SG B:CYS77 3.6 49.3 0.3 SG E:CYS77 4.2 60.6 1.0 O B:HOH201 4.3 54.8 1.0 CG E:HIS73 4.4 47.1 1.0 ND1 E:HIS73 4.5 40.8 1.0 ND1 G:HIS73 4.5 51.8 1.0 CG G:HIS73 4.5 51.1 1.0 CG B:HIS73 4.5 51.1 1.0 ND1 B:HIS73 4.6 38.0 1.0

Manganese binding site 3 out of 4 in the Mn-Bound Structure of the H77C Variant of TRICYT2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Mn-Bound Structure of the H77C Variant of TRICYT2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn201 b:72.4 occ:0.90 NE2 F:HIS73 2.3 52.2 1.0 NE2 K:HIS73 2.4 54.0 1.0 CD2 F:HIS73 3.3 41.0 1.0 CE1 F:HIS73 3.3 45.7 1.0 CE1 K:HIS73 3.4 54.2 1.0 CD2 K:HIS73 3.4 55.4 1.0 ND1 F:HIS73 4.4 39.8 1.0 CG F:HIS73 4.4 44.7 1.0 ND1 K:HIS73 4.5 53.5 1.0 SG K:CYS77 4.5 60.1 1.0 CG K:HIS73 4.6 54.5 1.0 SG F:CYS77 4.8 65.5 1.0

Manganese binding site 4 out of 4 in the Mn-Bound Structure of the H77C Variant of TRICYT2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Mn-Bound Structure of the H77C Variant of TRICYT2 within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn201 b:76.0 occ:0.89 NE2 J:HIS73 2.5 56.3 1.0 O L:HOH202 2.6 49.9 1.0 NE2 L:HIS73 2.8 60.4 1.0 CE1 J:HIS73 3.3 52.1 1.0 CD2 L:HIS73 3.4 49.4 1.0 CD2 J:HIS73 3.5 53.5 1.0 CE1 L:HIS73 4.0 61.4 1.0 ND1 J:HIS73 4.4 53.1 1.0 SG L:CYS77 4.6 74.2 1.0 CG J:HIS73 4.6 55.8 1.0 CG L:HIS73 4.7 57.4 1.0 CB J:CYS77 4.7 60.4 1.0 SG J:CYS77 4.8 59.3 1.0 ND1 L:HIS73 4.9 59.7 1.0 CB L:CYS77 5.0 75.8 1.0

V.H.Eng, M.Gascon, A.Kakkis, F.A.Tezcan. Design of A Protein Scaffold with A Selective, Bi-Containing Heterodinuclear Metal Coordination Motif. J.Inorg.Biochem. V. 274 13104 2025.
ISSN: ISSN 0162-0134
PubMed: 41072111
DOI: 10.1016/J.JINORGBIO.2025.113104