Manganese in PDB 7b0h: TGOT_6G12 Ternary Complex

All present enzymatic activity of TGOT_6G12 Ternary Complex:
2.7.7.7;

The structure of TGOT_6G12 Ternary Complex, PDB code: 7b0h was solved by C.Samson, P.Legrand, M.Tekpinar, J.Rozenski, M.Abramov, P.Holliger, V.Pinheiro, P.Herdewijn, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.92 / 3.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	111.823, 112.331, 186.518, 90, 90, 90
R / Rfree (%)	23.2 / 24.7

The structure of TGOT_6G12 Ternary Complex also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese atom in the TGOT_6G12 Ternary Complex (pdb code 7b0h). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the TGOT_6G12 Ternary Complex, PDB code: 7b0h:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the TGOT_6G12 Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of TGOT_6G12 Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn801 b:165.6 occ:1.00 O2G E:TTP804 2.2 96.6 1.0 OE2 E:GLU580 2.3 129.6 1.0 OD2 E:ASP404 2.4 102.8 1.0 PG E:TTP804 3.2 96.5 1.0 CD E:GLU580 3.3 127.2 1.0 CG E:ASP404 3.3 100.2 1.0 O3G E:TTP804 3.4 96.5 1.0 OE1 E:GLU580 3.6 128.7 1.0 MN E:MN802 3.6 100.6 1.0 CB E:ASP404 3.8 94.3 1.0 O1G E:TTP804 3.8 96.6 1.0 O E:PHE405 4.0 86.9 1.0 OD1 E:ASP404 4.3 101.2 1.0 O1A E:TTP804 4.3 95.6 1.0 OE2 E:GLU578 4.5 124.6 1.0 O E:ASP404 4.6 90.6 1.0 O3B E:TTP804 4.6 96.3 1.0 CG E:GLU580 4.6 119.9 1.0 C E:ASP404 4.7 90.5 1.0 C E:PHE405 4.8 86.7 1.0 CA E:ASP404 4.9 92.0 1.0 MG E:MG803 5.0 80.1 1.0

Manganese binding site 2 out of 4 in the TGOT_6G12 Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of TGOT_6G12 Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn802 b:100.6 occ:1.00 OD2 E:ASP542 2.0 86.7 1.0 O1B E:TTP804 2.2 95.9 1.0 O E:PHE405 2.3 86.9 1.0 OD2 E:ASP404 2.3 102.8 1.0 O2G E:TTP804 2.3 96.6 1.0 O1A E:TTP804 2.4 95.6 1.0 CG E:ASP542 3.0 84.6 1.0 CG E:ASP404 3.2 100.2 1.0 PB E:TTP804 3.3 96.0 1.0 OD1 E:ASP542 3.4 84.7 1.0 PA E:TTP804 3.5 95.5 1.0 C E:PHE405 3.5 86.7 1.0 MG E:MG803 3.5 80.1 1.0 PG E:TTP804 3.6 96.5 1.0 OD1 E:ASP404 3.6 101.2 1.0 O3A E:TTP804 3.6 95.7 1.0 MN E:MN801 3.6 165.6 1.0 O3B E:TTP804 3.7 96.3 1.0 N E:PHE405 4.0 88.9 1.0 C5' E:TTP804 4.1 95.0 1.0 CA E:PHE405 4.2 87.9 1.0 O5' E:TTP804 4.3 95.3 1.0 CB E:ASP542 4.3 81.2 1.0 O1G E:TTP804 4.3 96.6 1.0 CB E:ASP404 4.5 94.3 1.0 N E:SER407 4.5 79.7 1.0 N E:ARG406 4.5 85.3 1.0 C E:ASP404 4.5 90.5 1.0 N E:LEU408 4.6 73.3 1.0 CB E:PHE405 4.6 87.7 1.0 O2B E:TTP804 4.6 95.9 1.0 O3G E:TTP804 4.7 96.5 1.0 O2A E:TTP804 4.7 95.3 1.0 CA E:ARG406 4.8 84.4 1.0 C E:ARG406 4.8 82.1 1.0 O E:ASP542 4.8 81.2 1.0 CB E:LEU408 4.9 71.9 1.0

Manganese binding site 3 out of 4 in the TGOT_6G12 Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of TGOT_6G12 Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn801 b:118.5 occ:1.00 O2G F:TTP804 2.2 69.5 1.0 OE2 F:GLU580 2.3 106.6 1.0 OD2 F:ASP404 2.3 90.9 1.0 CG F:ASP404 3.2 88.8 1.0 PG F:TTP804 3.2 69.6 1.0 CD F:GLU580 3.3 104.5 1.0 O3G F:TTP804 3.4 69.6 1.0 MN F:MN802 3.5 71.5 1.0 OE1 F:GLU580 3.6 105.5 1.0 CB F:ASP404 3.7 84.2 1.0 O1G F:TTP804 3.8 69.7 1.0 O F:PHE405 3.9 83.3 1.0 OD1 F:ASP404 4.2 89.6 1.0 O1A F:TTP804 4.3 70.0 1.0 OE1 F:GLU578 4.3 105.0 1.0 O F:ASP404 4.5 82.6 1.0 O3B F:TTP804 4.6 69.4 1.0 CG F:GLU580 4.6 98.2 1.0 C F:ASP404 4.6 82.5 1.0 C F:PHE405 4.8 83.0 1.0 CA F:ASP404 4.8 82.5 1.0 MG F:MG803 4.9 96.9 1.0

Manganese binding site 4 out of 4 in the TGOT_6G12 Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of TGOT_6G12 Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn802 b:71.5 occ:1.00 OD2 F:ASP542 2.0 75.9 1.0 O F:PHE405 2.2 83.3 1.0 OD2 F:ASP404 2.2 90.9 1.0 O1B F:TTP804 2.2 68.7 1.0 O2G F:TTP804 2.3 69.5 1.0 O1A F:TTP804 2.5 70.0 1.0 CG F:ASP542 3.0 74.7 1.0 CG F:ASP404 3.2 88.8 1.0 PB F:TTP804 3.3 69.2 1.0 C F:PHE405 3.4 83.0 1.0 OD1 F:ASP542 3.4 75.1 1.0 OD1 F:ASP404 3.5 89.6 1.0 MN F:MN801 3.5 118.5 1.0 PA F:TTP804 3.5 69.7 1.0 PG F:TTP804 3.5 69.6 1.0 MG F:MG803 3.6 96.9 1.0 O3A F:TTP804 3.6 69.5 1.0 O3B F:TTP804 3.7 69.4 1.0 N F:PHE405 4.0 82.2 1.0 CA F:PHE405 4.1 82.6 1.0 C5' F:TTP804 4.2 69.5 1.0 O1G F:TTP804 4.3 69.7 1.0 CB F:ASP542 4.3 72.8 1.0 O5' F:TTP804 4.4 69.6 1.0 CB F:ASP404 4.4 84.2 1.0 N F:ARG406 4.4 83.0 1.0 C F:ASP404 4.4 82.5 1.0 N F:SER407 4.5 82.4 1.0 CB F:PHE405 4.5 82.6 1.0 N F:LEU408 4.6 80.8 1.0 O2B F:TTP804 4.6 69.2 1.0 O3G F:TTP804 4.7 69.6 1.0 CA F:ARG406 4.7 83.3 1.0 C F:ARG406 4.7 83.0 1.0 O2A F:TTP804 4.8 69.4 1.0 O F:ASP542 4.8 73.7 1.0 CB F:LEU408 4.9 80.8 1.0 CA F:ASP404 5.0 82.5 1.0 O F:ASP404 5.0 82.6 1.0

C.Samson, P.Legrand, M.Tekpinar, J.Rozenski, M.Abramov, P.Holliger, V.B.Pinheiro, P.Herdwijn, M.Delarue. Structural Studies of Hna Substrate Specificity in Mutants of An Archaeal Dna Polymerase Obtained By Directed Evolution. Biomolecules V. 10 2020.
ISSN: ESSN 2218-273X
PubMed: 33302546
DOI: 10.3390/BIOM10121647