Manganese in PDB 3ww1: X-Ray Structure of Cellulomonas Parahominis L-Ribose Isomerase with L- Ribose

The structure of X-Ray Structure of Cellulomonas Parahominis L-Ribose Isomerase with L- Ribose, PDB code: 3ww1 was solved by Y.Terami, H.Yoshida, G.Takata, S.Kamitori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.33 / 1.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	76.730, 88.550, 152.020, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.2

The binding sites of Manganese atom in the X-Ray Structure of Cellulomonas Parahominis L-Ribose Isomerase with L- Ribose (pdb code 3ww1). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the X-Ray Structure of Cellulomonas Parahominis L-Ribose Isomerase with L- Ribose, PDB code: 3ww1:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the X-Ray Structure of Cellulomonas Parahominis L-Ribose Isomerase with L- Ribose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Structure of Cellulomonas Parahominis L-Ribose Isomerase with L- Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:40.1 occ:1.00 NE2 A:HIS108 2.2 28.0 1.0 NE2 A:HIS106 2.3 27.3 1.0 NE2 A:HIS188 2.4 29.8 1.0 OE1 A:GLU113 2.6 41.9 1.0 O5 A:0MK402 2.8 79.0 1.0 C1 A:0MK402 3.0 79.0 1.0 O1 A:0MK402 3.0 78.9 1.0 OE2 A:GLU113 3.0 43.2 1.0 CE1 A:HIS108 3.1 29.1 1.0 CD2 A:HIS108 3.2 29.3 1.0 CD A:GLU113 3.2 40.5 1.0 CE1 A:HIS106 3.2 26.8 1.0 CE1 A:HIS188 3.3 29.9 1.0 CD2 A:HIS106 3.4 27.4 1.0 CD2 A:HIS188 3.5 27.6 1.0 C5 A:0MK402 3.6 79.2 1.0 ND1 A:HIS108 4.2 28.2 1.0 CG A:HIS108 4.3 28.5 1.0 ND1 A:HIS106 4.4 26.9 1.0 ND1 A:HIS188 4.4 29.5 1.0 CE A:LYS111 4.5 27.7 1.0 NZ A:LYS111 4.5 30.7 1.0 C2 A:0MK402 4.5 79.2 1.0 CG A:HIS106 4.5 27.5 1.0 CG A:HIS188 4.6 28.5 1.0 CG A:GLU113 4.7 36.5 1.0 OH A:TYR115 4.8 37.2 1.0 OE1 A:GLU204 5.0 46.4 1.0 C4 A:0MK402 5.0 79.4 1.0

Manganese binding site 2 out of 2 in the X-Ray Structure of Cellulomonas Parahominis L-Ribose Isomerase with L- Ribose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Structure of Cellulomonas Parahominis L-Ribose Isomerase with L- Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:38.0 occ:1.00 NE2 B:HIS108 2.1 25.6 1.0 OE2 B:GLU113 2.2 37.8 1.0 O4 B:ROR402 2.3 67.1 1.0 NE2 B:HIS106 2.3 33.1 1.0 NE2 B:HIS188 2.4 31.5 1.0 C5 B:ROR402 2.7 67.4 1.0 O5 B:ROR402 2.8 66.4 1.0 C4 B:ROR402 3.0 67.8 1.0 CD B:GLU113 3.1 40.7 1.0 CD2 B:HIS108 3.1 26.6 1.0 CE1 B:HIS108 3.1 25.5 1.0 CE1 B:HIS106 3.1 32.0 1.0 CE1 B:HIS188 3.2 31.0 1.0 OE1 B:GLU113 3.2 42.5 1.0 CD2 B:HIS106 3.4 32.7 1.0 CD2 B:HIS188 3.6 29.8 1.0 O2 B:ROR402 3.6 68.9 1.0 ND1 B:HIS108 4.2 26.4 1.0 CG B:HIS108 4.2 28.5 1.0 C3 B:ROR402 4.3 68.4 1.0 ND1 B:HIS106 4.3 32.4 1.0 C2 B:ROR402 4.4 69.2 1.0 ND1 B:HIS188 4.4 29.8 1.0 CE B:LYS111 4.4 35.1 1.0 NZ B:LYS111 4.4 35.0 1.0 CG B:GLU113 4.4 37.5 1.0 CG B:HIS106 4.5 31.6 1.0 CG B:HIS188 4.6 30.3 1.0 OH B:TYR115 4.8 37.0 1.0

Y.Terami, H.Yoshida, K.Uechi, K.Morimoto, G.Takata, S.Kamitori. Essentiality of Tetramer Formation of Cellulomonas Parahominis L-Ribose Isomerase Involved in Novel L-Ribose Metabolic Pathway. Appl.Microbiol.Biotechnol. 2015.
ISSN: ESSN 1432-0614
PubMed: 25661811
DOI: 10.1007/S00253-015-6417-4