Cobalt in PDB 3rmu: Crystal Structure of Human Methylmalonyl-Coa Epimerase, Mcee

All present enzymatic activity of Crystal Structure of Human Methylmalonyl-Coa Epimerase, Mcee:
5.1.99.1;

The structure of Crystal Structure of Human Methylmalonyl-Coa Epimerase, Mcee, PDB code: 3rmu was solved by A.Chaikuad, E.Krysztofinska, D.S.Froese, W.W.Yue, M.Vollmar, J.R.C.Muniz, F.Von Delft, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, C.Bountra, U.Oppermann, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.59 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.120, 66.690, 76.980, 90.00, 90.10, 90.00
R / Rfree (%)	18.7 / 23.7

The binding sites of Cobalt atom in the Crystal Structure of Human Methylmalonyl-Coa Epimerase, Mcee (pdb code 3rmu). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of Human Methylmalonyl-Coa Epimerase, Mcee, PDB code: 3rmu:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of Human Methylmalonyl-Coa Epimerase, Mcee


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Human Methylmalonyl-Coa Epimerase, Mcee within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1 b:20.8 occ:1.00 OE1 A:GLU172 1.9 22.0 1.0 NE2 A:HIS122 2.0 20.9 1.0 NE2 A:HIS50 2.0 15.2 1.0 O A:HOH180 2.3 28.8 1.0 O A:HOH178 2.3 29.2 1.0 O A:HOH179 2.4 34.0 1.0 CE1 A:HIS122 2.9 16.6 1.0 CE1 A:HIS50 2.9 22.6 1.0 CD A:GLU172 3.0 19.0 1.0 CD2 A:HIS122 3.0 21.2 1.0 CD2 A:HIS50 3.1 17.1 1.0 OE2 A:GLU172 3.4 28.7 1.0 O A:HOH259 3.4 36.8 1.0 ND1 A:HIS122 4.0 22.1 1.0 ND1 A:HIS50 4.0 18.1 1.0 OE1 A:GLU97 4.1 24.6 1.0 CG A:HIS122 4.1 16.4 1.0 O A:HOH214 4.1 33.8 1.0 O A:HOH210 4.2 39.7 1.0 CG A:HIS50 4.2 18.3 1.0 O A:HOH187 4.3 41.0 1.0 CG A:GLU172 4.4 24.1 1.0 CB A:CYS124 4.4 16.6 1.0 O1 A:EDO8 4.6 54.2 1.0 CB A:ALA52 4.7 16.6 1.0 CB A:GLU172 4.7 18.3 1.0 O A:HOH199 4.7 48.0 1.0 CD A:GLU97 4.8 14.5 1.0 C1 A:EDO8 4.8 41.9 1.0 CZ A:PHE160 4.9 39.0 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of Human Methylmalonyl-Coa Epimerase, Mcee


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Human Methylmalonyl-Coa Epimerase, Mcee within 5.0Å range: probe atom residue distance (Å) B Occ B:Co2 b:20.9 occ:1.00 OE1 B:GLU172 1.8 19.6 1.0 NE2 B:HIS122 2.0 17.2 1.0 NE2 B:HIS50 2.0 17.9 1.0 O B:HOH6 2.2 25.4 1.0 O B:HOH4 2.2 23.1 1.0 O B:HOH5 2.3 36.3 1.0 CE1 B:HIS50 3.0 24.9 1.0 CD B:GLU172 3.0 19.9 1.0 CE1 B:HIS122 3.0 18.0 1.0 CD2 B:HIS122 3.0 18.8 1.0 CD2 B:HIS50 3.1 18.8 1.0 OE2 B:GLU172 3.4 27.3 1.0 O B:HOH270 3.4 45.3 1.0 OE1 B:GLU97 4.1 19.5 1.0 ND1 B:HIS50 4.1 16.8 1.0 ND1 B:HIS122 4.1 22.0 1.0 CG B:HIS122 4.2 22.4 1.0 O B:HOH192 4.2 32.7 1.0 CG B:HIS50 4.2 16.4 1.0 CG B:GLU172 4.3 26.2 1.0 CB B:CYS124 4.4 19.7 1.0 O B:HOH181 4.6 32.1 1.0 CB B:GLU172 4.6 20.6 1.0 CB B:ALA52 4.6 17.5 1.0 CD B:GLU97 4.8 28.4 1.0 CZ B:PHE160 4.9 32.8 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of Human Methylmalonyl-Coa Epimerase, Mcee


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Human Methylmalonyl-Coa Epimerase, Mcee within 5.0Å range: probe atom residue distance (Å) B Occ C:Co3 b:19.3 occ:1.00 OE1 C:GLU172 1.9 21.5 1.0 NE2 C:HIS122 2.0 20.3 1.0 NE2 C:HIS50 2.0 14.8 1.0 O C:HOH8 2.2 34.6 1.0 O C:HOH7 2.3 21.3 1.0 O C:HOH9 2.4 39.8 1.0 CE1 C:HIS122 2.8 20.8 1.0 CE1 C:HIS50 2.9 20.7 1.0 CD C:GLU172 3.0 17.2 1.0 CD2 C:HIS122 3.1 18.0 1.0 CD2 C:HIS50 3.1 14.7 1.0 O C:HOH199 3.2 35.8 1.0 OE2 C:GLU172 3.4 21.6 1.0 O C:HOH188 4.0 34.0 1.0 ND1 C:HIS122 4.0 24.4 1.0 ND1 C:HIS50 4.1 17.1 1.0 OE1 C:GLU97 4.1 23.2 1.0 CG C:HIS122 4.1 14.6 1.0 CG C:HIS50 4.2 14.0 1.0 CG C:GLU172 4.4 22.0 1.0 CB C:CYS124 4.4 11.6 1.0 CB C:ALA52 4.7 17.4 1.0 O C:HOH184 4.7 46.5 1.0 CB C:GLU172 4.7 15.7 1.0 CD C:GLU97 4.8 23.4 1.0 C2 C:EDO6 5.0 52.2 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of Human Methylmalonyl-Coa Epimerase, Mcee


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Human Methylmalonyl-Coa Epimerase, Mcee within 5.0Å range: probe atom residue distance (Å) B Occ D:Co4 b:19.2 occ:1.00 OE1 D:GLU172 1.9 20.2 1.0 NE2 D:HIS122 1.9 24.4 1.0 NE2 D:HIS50 2.0 15.5 1.0 O D:HOH11 2.2 27.7 1.0 O D:HOH12 2.3 25.1 1.0 O D:HOH10 2.4 33.5 1.0 CE1 D:HIS122 2.8 14.6 1.0 CE1 D:HIS50 3.0 25.8 1.0 CD D:GLU172 3.0 16.6 1.0 CD2 D:HIS122 3.1 20.1 1.0 CD2 D:HIS50 3.1 16.2 1.0 OE2 D:GLU172 3.4 22.4 1.0 O D:HOH241 3.7 34.0 1.0 ND1 D:HIS122 4.0 22.1 1.0 CG D:HIS122 4.1 21.4 1.0 ND1 D:HIS50 4.1 17.3 1.0 O D:HOH316 4.2 32.5 1.0 OE1 D:GLU97 4.2 19.8 1.0 CG D:HIS50 4.2 17.8 1.0 CG D:GLU172 4.4 15.8 1.0 CB D:CYS124 4.5 14.2 1.0 CB D:ALA52 4.6 17.6 1.0 CB D:GLU172 4.6 16.6 1.0 O D:HOH304 4.7 40.6 1.0 O D:HOH305 4.7 52.8 1.0 O2 D:EDO177 4.9 53.9 1.0 CD D:GLU97 4.9 23.5 1.0 CZ D:PHE160 4.9 32.9 1.0

A.Chaikuad, E.Krysztofinska, D.S.Froese, W.W.Yue, M.Vollmar, J.R.C.Muniz, F.Von Delft, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, C.Bountra, U.Oppermann, Structural Genomics Consortium (Sgc). Crystal Structure of Human Methylmalonyl-Coa Epimerase, Mcee To Be Published.