Manganese in PDB 3c5m: Crystal Structure of Oligogalacturonate Lyase (VPA0088) From Vibrio Parahaemolyticus. Northeast Structural Genomics Consortium Target VPR199

The structure of Crystal Structure of Oligogalacturonate Lyase (VPA0088) From Vibrio Parahaemolyticus. Northeast Structural Genomics Consortium Target VPR199, PDB code: 3c5m was solved by F.Forouhar, M.Abashidze, J.Seetharaman, H.Janjua, L.Mao, R.Xiao, L.A.Owens, D.Wang, M.C.Baran, T.B.Acton, G.T.Montelione, J.F.Hunt, L.Tong, Northeast Structural Genomics Consortium(Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.60
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.233, 115.233, 209.950, 90.00, 90.00, 120.00
R / Rfree (%)	23.4 / 27.7

The binding sites of Manganese atom in the Crystal Structure of Oligogalacturonate Lyase (VPA0088) From Vibrio Parahaemolyticus. Northeast Structural Genomics Consortium Target VPR199 (pdb code 3c5m). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Oligogalacturonate Lyase (VPA0088) From Vibrio Parahaemolyticus. Northeast Structural Genomics Consortium Target VPR199, PDB code: 3c5m:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of Oligogalacturonate Lyase (VPA0088) From Vibrio Parahaemolyticus. Northeast Structural Genomics Consortium Target VPR199


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 Oligogalacturonate Lyase (VPA0088) From Vibrio Parahaemolyticus. Northeast Structural Genomics Consortium Target VPR199 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:31.0 occ:1.00 NE2 A:HIS287 2.0 34.6 1.0 NE2 A:HIS355 2.2 26.9 1.0 ND1 A:HIS353 2.2 38.3 1.0 O A:HOH477 2.3 6.8 1.0 OE1 A:GLN350 2.3 47.0 1.0 CD2 A:HIS287 2.8 38.6 1.0 CD2 A:HIS355 3.0 23.9 1.0 CE1 A:HIS287 3.1 50.0 1.0 CE1 A:HIS353 3.1 32.6 1.0 O A:HOH473 3.1 26.2 1.0 CE1 A:HIS355 3.2 31.6 1.0 CD A:GLN350 3.3 53.6 1.0 CG A:HIS353 3.3 34.3 1.0 NE2 A:GLN350 3.6 58.8 1.0 CB A:HIS353 3.7 38.6 1.0 CG A:HIS287 4.0 33.6 1.0 ND1 A:HIS287 4.1 42.8 1.0 CG A:HIS355 4.2 15.9 1.0 NE2 A:HIS353 4.3 38.9 1.0 ND1 A:HIS355 4.3 27.0 1.0 CD2 A:HIS353 4.4 27.6 1.0 CG A:GLN350 4.7 41.4 1.0 CE2 A:PHE38 4.8 42.2 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Oligogalacturonate Lyase (VPA0088) From Vibrio Parahaemolyticus. Northeast Structural Genomics Consortium Target VPR199


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 Oligogalacturonate Lyase (VPA0088) From Vibrio Parahaemolyticus. Northeast Structural Genomics Consortium Target VPR199 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:20.5 occ:1.00 NE2 B:HIS287 2.0 29.7 1.0 OE1 B:GLN350 2.2 36.4 1.0 ND1 B:HIS353 2.2 36.9 1.0 NE2 B:HIS355 2.3 29.2 1.0 O B:HOH402 2.6 18.2 1.0 CD2 B:HIS287 2.8 37.4 1.0 CE1 B:HIS353 3.1 46.6 1.0 CD B:GLN350 3.1 50.3 1.0 CE1 B:HIS287 3.1 41.5 1.0 CD2 B:HIS355 3.1 25.0 1.0 CE1 B:HIS355 3.3 25.6 1.0 CG B:HIS353 3.3 41.3 1.0 NE2 B:GLN350 3.4 63.0 1.0 CB B:HIS353 3.7 35.3 1.0 CG B:HIS287 4.0 28.9 1.0 ND1 B:HIS287 4.1 37.4 1.0 NE2 B:HIS353 4.3 52.7 1.0 CG B:HIS355 4.3 25.2 1.0 ND1 B:HIS355 4.4 33.6 1.0 CD2 B:HIS353 4.4 40.8 1.0 CG B:GLN350 4.6 41.1 1.0 CE2 B:PHE38 4.9 50.0 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Oligogalacturonate Lyase (VPA0088) From Vibrio Parahaemolyticus. Northeast Structural Genomics Consortium Target VPR199


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 Oligogalacturonate Lyase (VPA0088) From Vibrio Parahaemolyticus. Northeast Structural Genomics Consortium Target VPR199 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:30.2 occ:1.00 NE2 C:HIS287 2.1 44.4 1.0 ND1 C:HIS353 2.3 43.8 1.0 OE1 C:GLN350 2.3 54.7 1.0 NE2 C:HIS355 2.5 26.5 1.0 O C:HOH452 2.6 28.6 1.0 CD2 C:HIS287 2.8 43.3 1.0 CE1 C:HIS353 3.0 44.9 1.0 O C:HOH417 3.1 28.5 1.0 CD C:GLN350 3.2 52.1 1.0 CE1 C:HIS287 3.2 50.3 1.0 NE2 C:GLN350 3.3 52.5 1.0 CD2 C:HIS355 3.3 39.2 1.0 CG C:HIS353 3.4 44.3 1.0 CE1 C:HIS355 3.5 39.3 1.0 CB C:HIS353 3.9 47.7 1.0 CG C:HIS287 4.1 34.5 1.0 ND1 C:HIS287 4.2 42.3 1.0 NE2 C:HIS353 4.2 43.1 1.0 CD2 C:HIS353 4.5 43.5 1.0 CG C:HIS355 4.6 32.3 1.0 CG C:GLN350 4.6 49.1 1.0 ND1 C:HIS355 4.6 39.8 1.0 CE2 C:PHE38 5.0 39.5 1.0

F.Forouhar, M.Abashidze, J.Seetharaman, H.Janjua, L.Mao, R.Xiao, L.A.Owens, D.Wang, M.C.Baran, T.B.Acton, G.T.Montelione, J.F.Hunt, L.Tong. Crystal Structure of Oligogalacturonate Lyase (VPA0088) From Vibrio Parahaemolyticus. To Be Published.