Manganese in PDB 5avp: Crystal Structure of Geodermatophilus Obscurus L-Ribose Isomerase

The structure of Crystal Structure of Geodermatophilus Obscurus L-Ribose Isomerase, PDB code: 5avp was solved by Y.Terami, S.Kamitori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.06 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.533, 123.226, 109.446, 90.00, 97.38, 90.00
R / Rfree (%)	24.6 / 29.4

The binding sites of Manganese atom in the Crystal Structure of Geodermatophilus Obscurus L-Ribose Isomerase (pdb code 5avp). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Geodermatophilus Obscurus L-Ribose Isomerase, PDB code: 5avp:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Geodermatophilus Obscurus L-Ribose Isomerase


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 Geodermatophilus Obscurus L-Ribose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:20.9 occ:1.00 OE2 A:GLU117 2.1 18.2 1.0 NE2 A:HIS110 2.2 12.3 1.0 NE2 A:HIS112 2.4 33.4 1.0 NE2 A:HIS192 2.4 22.0 1.0 CD A:GLU117 2.9 20.4 1.0 CE1 A:HIS110 2.9 12.4 1.0 CE1 A:HIS192 3.0 21.8 1.0 OE1 A:GLU117 3.0 19.1 1.0 CE1 A:HIS112 3.1 33.1 1.0 CD2 A:HIS110 3.4 13.4 1.0 CD2 A:HIS112 3.5 31.4 1.0 CD2 A:HIS192 3.6 22.1 1.0 NZ A:LYS115 3.9 6.2 1.0 ND1 A:HIS110 4.1 13.0 1.0 CE A:LYS115 4.2 9.1 1.0 ND1 A:HIS192 4.2 23.1 1.0 CG A:GLU117 4.3 21.8 1.0 ND1 A:HIS112 4.3 31.4 1.0 CG A:HIS110 4.4 15.9 1.0 CG A:HIS112 4.5 29.1 1.0 CG A:HIS192 4.5 23.5 1.0 NH2 A:ARG247 4.6 30.0 1.0 OE1 A:GLU208 4.9 37.9 1.0 OH A:TYR119 4.9 32.6 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Geodermatophilus Obscurus L-Ribose Isomerase


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 Geodermatophilus Obscurus L-Ribose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:23.2 occ:1.00 NE2 B:HIS112 2.0 29.9 1.0 NE2 B:HIS192 2.2 29.5 1.0 NE2 B:HIS110 2.4 39.9 1.0 OE2 B:GLU117 2.4 26.4 1.0 CE1 B:HIS112 2.7 29.6 1.0 OE1 B:GLU117 2.8 25.0 1.0 CD B:GLU117 2.9 28.0 1.0 CE1 B:HIS192 3.1 29.8 1.0 CD2 B:HIS192 3.2 29.9 1.0 CD2 B:HIS110 3.2 38.0 1.0 CD2 B:HIS112 3.3 29.4 1.0 CE1 B:HIS110 3.3 39.5 1.0 NZ B:LYS115 3.9 13.0 1.0 ND1 B:HIS112 3.9 29.1 1.0 CG B:HIS112 4.2 28.4 1.0 ND1 B:HIS192 4.2 30.7 1.0 CE B:LYS115 4.3 14.4 1.0 CG B:HIS192 4.3 29.2 1.0 CG B:HIS110 4.4 37.0 1.0 ND1 B:HIS110 4.4 39.0 1.0 CG B:GLU117 4.4 27.5 1.0 OH B:TYR119 4.4 25.7 1.0 NH2 B:ARG247 4.9 47.8 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Geodermatophilus Obscurus L-Ribose Isomerase


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 Geodermatophilus Obscurus L-Ribose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:18.9 occ:1.00 NE2 C:HIS112 2.0 31.3 1.0 OE2 C:GLU117 2.2 27.1 1.0 NE2 C:HIS110 2.2 11.8 1.0 NE2 C:HIS192 2.3 25.5 1.0 CD2 C:HIS112 2.9 30.4 1.0 CE1 C:HIS192 3.0 25.8 1.0 CE1 C:HIS112 3.1 30.8 1.0 CD C:GLU117 3.1 28.0 1.0 CD2 C:HIS110 3.2 14.4 1.0 CE1 C:HIS110 3.2 11.4 1.0 OE1 C:GLU117 3.3 29.7 1.0 CD2 C:HIS192 3.5 26.5 1.0 NZ C:LYS115 3.8 20.8 1.0 CG C:HIS112 4.1 30.8 1.0 ND1 C:HIS112 4.1 31.3 1.0 CE C:LYS115 4.2 24.6 1.0 ND1 C:HIS192 4.3 25.2 1.0 ND1 C:HIS110 4.3 12.1 1.0 CG C:HIS110 4.3 15.1 1.0 CG C:HIS192 4.5 25.1 1.0 CG C:GLU117 4.6 26.0 1.0 OH C:TYR119 4.9 41.6 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Geodermatophilus Obscurus L-Ribose Isomerase


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 Geodermatophilus Obscurus L-Ribose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:33.9 occ:1.00 NE2 D:HIS112 2.0 30.8 1.0 OE2 D:GLU117 2.0 44.4 1.0 NE2 D:HIS110 2.4 28.6 1.0 NE2 D:HIS192 2.5 25.4 1.0 CE1 D:HIS112 2.8 30.8 1.0 CD D:GLU117 2.9 43.6 1.0 CD2 D:HIS112 3.1 31.1 1.0 OE1 D:GLU117 3.1 45.5 1.0 CD2 D:HIS110 3.3 29.0 1.0 CE1 D:HIS192 3.5 26.9 1.0 CE1 D:HIS110 3.5 28.6 1.0 NZ D:LYS115 3.5 17.5 1.0 CD2 D:HIS192 3.5 25.7 1.0 ND1 D:HIS112 3.9 31.4 1.0 CE D:LYS115 4.1 17.7 1.0 CG D:HIS112 4.1 30.0 1.0 CG D:GLU117 4.3 40.3 1.0 CG D:HIS110 4.5 28.3 1.0 ND1 D:HIS110 4.6 28.5 1.0 OE1 D:GLU208 4.6 25.6 1.0 ND1 D:HIS192 4.6 26.2 1.0 CG D:HIS192 4.7 26.0 1.0

Y.Terami, S.Kamitori. Crystal Structure of Geodermatophilus Obscurus L-Ribose Isomerase To Be Published.