Manganese in PDB 6l9i: Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex

The structure of Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex, PDB code: 6l9i was solved by F.Wu, L.K.Cheng, C.Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 2.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	92.957, 122.842, 115.223, 90, 92.48, 90
R / Rfree (%)	19.7 / 22.9

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex (pdb code 6l9i). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex, PDB code: 6l9i:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in the Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex


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 Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:31.0 occ:1.00 OE2 A:GLU101 1.7 35.7 1.0 O1 A:FMT401 2.0 31.1 1.0 C A:FMT401 2.2 41.7 1.0 NE2 A:HIS140 2.3 15.5 1.0 NE2 A:HIS95 2.3 29.3 1.0 NE2 A:HIS97 2.6 29.5 1.0 CD A:GLU101 2.9 32.2 1.0 CE1 A:HIS140 3.2 17.4 1.0 CE1 A:HIS95 3.2 23.9 1.0 CD2 A:HIS140 3.3 16.1 1.0 CD2 A:HIS95 3.3 20.8 1.0 O2 A:FMT401 3.3 41.7 1.0 CD2 A:HIS97 3.5 17.7 1.0 OE1 A:GLU101 3.6 33.8 1.0 CE1 A:HIS97 3.6 37.9 1.0 CG A:GLU101 4.1 25.1 1.0 ND1 A:HIS140 4.3 18.1 1.0 ND1 A:HIS95 4.4 25.0 1.0 CG A:HIS140 4.4 19.6 1.0 CE2 A:PHE155 4.4 24.7 1.0 CG A:HIS95 4.4 23.9 1.0 CZ A:PHE155 4.6 27.1 1.0 CG A:HIS97 4.7 22.3 1.0 ND1 A:HIS97 4.7 39.0 1.0 CB A:GLU101 4.7 24.3 1.0 OE2 A:GLU162 4.8 34.6 1.0

Manganese binding site 2 out of 12 in the Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex


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 Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:32.8 occ:1.00 NE2 A:HIS273 2.2 37.7 1.0 NE2 A:HIS275 2.2 27.6 1.0 NE2 A:HIS319 2.4 34.1 1.0 OE1 A:GLU280 2.4 37.4 1.0 OE2 A:GLU333 2.9 53.0 1.0 CE1 A:HIS273 3.1 33.6 1.0 CE1 A:HIS275 3.2 24.8 1.0 CD2 A:HIS275 3.2 22.6 1.0 CD A:GLU280 3.2 34.6 1.0 CD2 A:HIS273 3.3 30.0 1.0 CD2 A:HIS319 3.3 28.2 1.0 CE1 A:HIS319 3.3 28.9 1.0 CD A:GLU333 3.4 44.3 1.0 OE2 A:GLU280 3.4 32.2 1.0 OE1 A:GLU333 3.5 46.9 1.0 NH2 A:ARG270 4.2 47.8 1.0 ND1 A:HIS273 4.2 28.5 1.0 ND1 A:HIS275 4.3 23.2 1.0 CG A:HIS273 4.3 27.8 1.0 CG A:HIS275 4.3 21.1 1.0 CG A:HIS319 4.4 27.6 1.0 ND1 A:HIS319 4.4 24.1 1.0 CG A:GLU333 4.5 27.5 1.0 CZ A:ARG270 4.6 54.8 1.0 CG A:GLU280 4.6 20.6 1.0 NE A:ARG270 4.8 50.8 1.0 CD1 A:ILE321 4.9 33.8 1.0

Manganese binding site 3 out of 12 in the Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex


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 Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:23.9 occ:1.00 OE2 B:GLU101 1.6 28.5 1.0 NE2 B:HIS95 2.1 26.9 1.0 NE2 B:HIS140 2.3 17.6 1.0 C B:FMT401 2.4 35.5 1.0 O1 B:FMT401 2.6 18.9 1.0 NE2 B:HIS97 2.7 22.1 1.0 CD B:GLU101 2.9 28.2 1.0 CE1 B:HIS95 2.9 24.9 1.0 CD2 B:HIS95 3.1 18.4 1.0 CE1 B:HIS140 3.2 18.1 1.0 CD2 B:HIS140 3.4 17.2 1.0 CD2 B:HIS97 3.4 13.0 1.0 O2 B:FMT401 3.6 33.7 1.0 OE1 B:GLU101 3.7 25.9 1.0 CG B:GLU101 3.8 24.3 1.0 CE1 B:HIS97 3.8 30.7 1.0 ND1 B:HIS95 4.1 20.0 1.0 CG B:HIS95 4.2 19.6 1.0 ND1 B:HIS140 4.4 17.9 1.0 CG B:HIS140 4.5 19.6 1.0 CE1 B:PHE155 4.5 19.9 1.0 CZ B:PHE155 4.6 22.2 1.0 CG B:HIS97 4.6 21.1 1.0 ND1 B:HIS97 4.8 34.7 1.0 CB B:GLU101 4.9 24.6 1.0

Manganese binding site 4 out of 12 in the Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex


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 Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:36.5 occ:1.00 NE2 B:HIS275 2.2 24.6 1.0 OE1 B:GLU280 2.2 31.3 1.0 NE2 B:HIS273 2.4 22.2 1.0 NE2 B:HIS319 2.5 20.4 1.0 OE2 B:GLU333 2.7 47.4 1.0 CD B:GLU280 3.0 30.2 1.0 CD2 B:HIS275 3.1 23.6 1.0 OE2 B:GLU280 3.1 25.7 1.0 CE1 B:HIS275 3.2 27.3 1.0 CE1 B:HIS273 3.2 26.0 1.0 CE1 B:HIS319 3.4 18.2 1.0 CD2 B:HIS273 3.4 25.2 1.0 CD B:GLU333 3.5 46.7 1.0 CD2 B:HIS319 3.5 19.8 1.0 OE1 B:GLU333 3.9 37.9 1.0 CG B:HIS275 4.2 24.4 1.0 ND1 B:HIS275 4.3 27.4 1.0 ND1 B:HIS273 4.4 26.5 1.0 CG B:GLU280 4.4 21.4 1.0 CG B:HIS273 4.5 26.1 1.0 ND1 B:HIS319 4.5 16.6 1.0 CG B:GLU333 4.5 27.9 1.0 CG B:HIS319 4.6 19.4 1.0 NH2 B:ARG270 4.7 49.5 1.0 CB B:GLU280 4.9 21.2 1.0

Manganese binding site 5 out of 12 in the Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn402 b:41.2 occ:1.00 NE2 C:HIS95 1.9 43.0 1.0 OE2 C:GLU101 2.0 43.3 1.0 NE2 C:HIS140 2.2 35.1 1.0 O1 C:FMT401 2.3 46.2 1.0 CE1 C:HIS97 2.6 35.3 1.0 CD2 C:HIS95 2.7 27.9 1.0 CE1 C:HIS140 3.0 32.5 1.0 CE1 C:HIS95 3.0 34.7 1.0 C C:FMT401 3.0 50.9 1.0 CD C:GLU101 3.3 44.1 1.0 ND1 C:HIS97 3.3 31.2 1.0 CD2 C:HIS140 3.3 38.1 1.0 NE2 C:HIS97 3.8 42.6 1.0 CG C:HIS95 3.9 30.9 1.0 ND1 C:HIS95 4.0 29.8 1.0 OE1 C:GLU101 4.1 52.2 1.0 ND1 C:HIS140 4.1 34.9 1.0 CG C:GLU101 4.2 35.6 1.0 O2 C:FMT401 4.2 50.9 1.0 CG C:HIS140 4.4 33.4 1.0 CG C:HIS97 4.6 29.8 1.0 CE2 C:PHE155 4.6 35.6 1.0 CZ C:PHE155 4.7 33.1 1.0 CD2 C:HIS97 4.8 36.6 1.0 OE1 C:GLU162 4.9 44.7 1.0 CB C:GLU101 4.9 36.3 1.0

Manganese binding site 6 out of 12 in the Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn403 b:39.1 occ:1.00 NE2 C:HIS319 2.1 32.2 1.0 NE2 C:HIS275 2.1 35.7 1.0 OE2 C:GLU333 2.2 40.2 1.0 OE1 C:GLU280 2.2 41.5 1.0 NE2 C:HIS273 2.3 32.8 1.0 CE1 C:HIS273 2.9 28.5 1.0 CE1 C:HIS319 2.9 27.4 1.0 CD2 C:HIS275 3.1 30.3 1.0 CE1 C:HIS275 3.1 32.2 1.0 CD C:GLU280 3.2 36.7 1.0 CD2 C:HIS319 3.2 32.1 1.0 OE2 C:GLU280 3.4 29.8 1.0 CD C:GLU333 3.4 41.8 1.0 CD2 C:HIS273 3.5 29.4 1.0 OE1 C:GLU333 4.0 41.3 1.0 ND1 C:HIS273 4.1 22.9 1.0 ND1 C:HIS319 4.1 31.0 1.0 ND1 C:HIS275 4.2 23.0 1.0 CG C:HIS275 4.3 19.6 1.0 CG C:HIS319 4.3 28.6 1.0 CG C:HIS273 4.4 28.5 1.0 CG C:GLU333 4.5 32.6 1.0 NH2 C:ARG270 4.6 41.2 1.0 CG C:GLU280 4.6 29.7 1.0 CD1 C:ILE321 4.9 31.5 1.0 CZ C:ARG270 4.9 45.2 1.0 CB C:GLU333 5.0 27.5 1.0

Manganese binding site 7 out of 12 in the Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn402 b:28.5 occ:1.00 OE2 D:GLU101 1.8 32.1 1.0 NE2 D:HIS95 2.0 26.0 1.0 O1 D:FMT401 2.3 40.2 1.0 NE2 D:HIS140 2.3 25.6 1.0 NE2 D:HIS97 2.6 35.7 1.0 CE1 D:HIS95 2.9 27.3 1.0 CD2 D:HIS95 3.0 22.3 1.0 C D:FMT401 3.0 46.7 1.0 CD D:GLU101 3.0 31.0 1.0 CE1 D:HIS140 3.2 23.2 1.0 CD2 D:HIS97 3.3 31.7 1.0 CD2 D:HIS140 3.4 29.8 1.0 OE1 D:GLU101 3.7 28.1 1.0 CE1 D:HIS97 3.8 55.5 1.0 ND1 D:HIS95 4.0 27.4 1.0 CG D:GLU101 4.1 30.2 1.0 CG D:HIS95 4.1 20.8 1.0 O2 D:FMT401 4.2 46.6 1.0 ND1 D:HIS140 4.4 26.0 1.0 CG D:HIS140 4.5 28.1 1.0 CE2 D:PHE155 4.5 25.1 1.0 CG D:HIS97 4.5 30.7 1.0 CZ D:PHE155 4.6 28.4 1.0 ND1 D:HIS97 4.8 54.9 1.0 CB D:GLU101 4.9 25.4 1.0

Manganese binding site 8 out of 12 in the Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn403 b:44.0 occ:1.00 NE2 D:HIS319 2.2 36.0 1.0 OE1 D:GLU280 2.2 41.4 1.0 NE2 D:HIS275 2.3 33.9 1.0 NE2 D:HIS273 2.4 38.7 1.0 OE2 D:GLU333 2.9 50.3 1.0 CD D:GLU280 3.0 39.9 1.0 CE1 D:HIS273 3.1 39.2 1.0 CE1 D:HIS319 3.1 35.7 1.0 CD2 D:HIS275 3.2 38.7 1.0 CD2 D:HIS319 3.2 35.0 1.0 OE2 D:GLU280 3.2 38.9 1.0 CE1 D:HIS275 3.3 31.6 1.0 CD D:GLU333 3.4 47.6 1.0 CD2 D:HIS273 3.5 42.0 1.0 OE1 D:GLU333 3.6 43.3 1.0 NH2 D:ARG270 4.1 46.6 1.0 ND1 D:HIS319 4.2 35.7 1.0 ND1 D:HIS273 4.2 40.2 1.0 CG D:GLU280 4.3 32.0 1.0 CG D:HIS319 4.3 36.2 1.0 CG D:HIS275 4.3 34.9 1.0 ND1 D:HIS275 4.4 33.7 1.0 CG D:HIS273 4.5 38.6 1.0 CG D:GLU333 4.6 36.7 1.0 CZ D:ARG270 4.7 59.8 1.0 NE D:ARG270 4.9 55.3 1.0 CB D:GLU280 4.9 29.0 1.0 CB D:GLU333 5.0 32.7 1.0

Manganese binding site 9 out of 12 in the Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn402 b:28.8 occ:1.00 OE2 E:GLU101 1.7 29.9 1.0 O1 E:FMT401 2.0 66.0 1.0 NE2 E:HIS95 2.1 27.9 1.0 NE2 E:HIS140 2.2 30.8 1.0 NE2 E:HIS97 2.3 29.9 1.0 CE1 E:HIS95 2.9 28.0 1.0 CE1 E:HIS140 2.9 27.0 1.0 C E:FMT401 2.9 74.2 1.0 CD E:GLU101 3.0 25.8 1.0 CD2 E:HIS95 3.1 24.5 1.0 CE1 E:HIS97 3.2 27.5 1.0 CD2 E:HIS97 3.3 23.3 1.0 CD2 E:HIS140 3.4 30.7 1.0 CG E:GLU101 3.8 28.3 1.0 OE1 E:GLU101 3.9 27.9 1.0 O2 E:FMT401 3.9 68.8 1.0 ND1 E:HIS95 4.1 25.3 1.0 ND1 E:HIS140 4.2 32.0 1.0 CG E:HIS95 4.2 23.9 1.0 ND1 E:HIS97 4.4 30.0 1.0 CG E:HIS140 4.4 31.1 1.0 CG E:HIS97 4.4 28.2 1.0 CE2 E:PHE155 4.5 21.3 1.0 CZ E:PHE155 4.5 27.9 1.0 CB E:GLU101 4.9 29.2 1.0

Manganese binding site 10 out of 12 in the Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn403 b:49.8 occ:1.00 NE2 E:HIS275 2.1 35.2 1.0 NE2 E:HIS273 2.4 34.5 1.0 NE2 E:HIS319 2.5 35.7 1.0 OE2 E:GLU333 2.6 55.0 1.0 OE1 E:GLU280 2.6 43.5 1.0 CD2 E:HIS275 3.0 30.7 1.0 CE1 E:HIS273 3.1 38.1 1.0 CD E:GLU280 3.1 41.3 1.0 CE1 E:HIS275 3.1 31.1 1.0 OE2 E:GLU280 3.1 38.6 1.0 CD E:GLU333 3.4 47.6 1.0 CE1 E:HIS319 3.4 35.2 1.0 CD2 E:HIS319 3.5 28.7 1.0 CD2 E:HIS273 3.5 40.0 1.0 OE1 E:GLU333 3.8 44.5 1.0 CG E:HIS275 4.2 27.7 1.0 ND1 E:HIS275 4.2 28.4 1.0 ND1 E:HIS273 4.3 38.3 1.0 CG E:GLU280 4.4 31.4 1.0 NH2 E:ARG270 4.4 59.0 1.0 CG E:GLU333 4.4 37.3 1.0 CG E:HIS273 4.5 39.7 1.0 ND1 E:HIS319 4.6 30.5 1.0 CG E:HIS319 4.7 31.5 1.0 CZ E:ARG270 4.8 62.2 1.0 CZ E:PHE335 4.9 27.2 1.0 CB E:GLU333 4.9 33.2 1.0

F.Wu, L.K.Cheng, C.Y.Wang. Crystal Structure of Lactobacillus Farciminis Oxalate Decarboxylase Formate Complex To Be Published.