Manganese in PDB 5a61: Crystal Structure of Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Manganese Ions.

All present enzymatic activity of Crystal Structure of Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Manganese Ions.:
3.6.1.25;

The structure of Crystal Structure of Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Manganese Ions., PDB code: 5a61 was solved by J.Martinez, V.Truffault, M.Hothorn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.77 / 1.50
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	89.676, 89.676, 125.329, 90.00, 90.00, 120.00
R / Rfree (%)	15.145 / 17.087

The binding sites of Manganese atom in the Crystal Structure of Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Manganese Ions. (pdb code 5a61). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Manganese Ions., PDB code: 5a61:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Manganese Ions.


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 Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Manganese Ions. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:42.1 occ:1.00 O1G A:3PO500 2.1 42.4 1.0 OE2 A:GLU6 2.1 46.7 1.0 O5' A:3PO500 2.1 41.7 1.0 O1B A:3PO500 2.2 42.2 1.0 OE1 A:GLU160 2.2 42.5 1.0 OE2 A:GLU160 2.3 46.0 1.0 CD A:GLU160 2.6 45.1 1.0 CD A:GLU6 3.1 46.9 1.0 PB A:3PO500 3.2 42.2 1.0 PA A:3PO500 3.3 43.0 1.0 O3A A:3PO500 3.3 43.5 1.0 PG A:3PO500 3.3 43.0 1.0 OE1 A:GLU6 3.4 50.7 1.0 O3B A:3PO500 3.6 42.1 1.0 MN A:MN502 3.6 42.9 0.5 O A:HOH2008 3.8 54.7 1.0 O2G A:3PO500 3.9 42.0 1.0 O A:HOH2009 4.0 49.9 1.0 CG A:GLU160 4.1 43.6 1.0 O1A A:3PO500 4.1 44.6 1.0 NZ A:LYS8 4.1 42.1 1.0 NH2 A:ARG81 4.2 46.5 1.0 NH2 A:ARG126 4.3 45.4 1.0 O2A A:3PO500 4.4 44.1 1.0 CG A:GLU6 4.5 45.2 1.0 NZ A:LYS191 4.5 41.5 1.0 O3G A:3PO500 4.5 45.0 1.0 O2B A:3PO500 4.6 41.0 1.0 NZ A:LYS69 4.6 58.6 1.0 OE2 A:GLU4 4.8 53.5 1.0 CB A:GLU160 4.8 41.6 1.0 OE1 A:GLU4 5.0 54.5 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Manganese Ions.


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 Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Manganese Ions. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:42.9 occ:0.50 OE1 A:GLU6 2.1 50.7 1.0 O A:HOH2003 2.2 61.7 1.0 OE2 A:GLU4 2.2 53.5 1.0 O5' A:3PO500 2.3 41.7 1.0 OE1 A:GLU162 2.3 57.5 1.0 O A:HOH2008 2.3 54.7 1.0 CD A:GLU6 3.1 46.9 1.0 CD A:GLU4 3.2 53.7 1.0 CD A:GLU162 3.3 52.2 1.0 PA A:3PO500 3.3 43.0 1.0 OE2 A:GLU6 3.5 46.7 1.0 O A:HOH2004 3.6 52.9 1.0 MN A:MN501 3.6 42.1 1.0 O2A A:3PO500 3.7 44.1 1.0 OE1 A:GLU160 3.9 42.5 1.0 OE1 A:GLU4 3.9 54.5 1.0 O1A A:3PO500 3.9 44.6 1.0 OE2 A:GLU162 4.0 58.9 1.0 CG A:GLU4 4.1 52.1 1.0 O A:HOH2005 4.3 73.5 1.0 CG A:GLU162 4.3 49.1 1.0 CG A:GLU6 4.4 45.2 1.0 CB A:GLU162 4.4 48.0 1.0 NZ A:LYS69 4.6 58.6 1.0 O3A A:3PO500 4.7 43.5 1.0 CB A:GLU6 4.8 45.9 1.0 O A:HOH2079 4.8 59.8 1.0 CD A:GLU160 5.0 45.1 1.0 O1G A:3PO500 5.0 42.4 1.0

J.Martinez, V.Truffault, M.Hothorn. Structural Determinants For Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes. J.Biol.Chem. V. 290 23348 2015.
ISSN: ISSN 0021-9258
PubMed: 26221030
DOI: 10.1074/JBC.M115.674473