Cobalt in PDB 6e2w: Mddef in Complex with Mvapp, Adp, Sulfate and Cobalt

All present enzymatic activity of Mddef in Complex with Mvapp, Adp, Sulfate and Cobalt:
4.1.1.33;

The structure of Mddef in Complex with Mvapp, Adp, Sulfate and Cobalt, PDB code: 6e2w was solved by C.V.Stauffacher, C.-L.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.51 / 1.95
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.997, 98.071, 45.908, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 21.9

The binding sites of Cobalt atom in the Mddef in Complex with Mvapp, Adp, Sulfate and Cobalt (pdb code 6e2w). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Mddef in Complex with Mvapp, Adp, Sulfate and Cobalt, PDB code: 6e2w:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Mddef in Complex with Mvapp, Adp, Sulfate and Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Mddef in Complex with Mvapp, Adp, Sulfate and Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co404 b:21.8 occ:1.00 O2A A:ADP402 2.0 17.4 1.0 O3B A:ADP402 2.2 19.8 1.0 O1 A:SO4401 2.2 11.8 0.8 O1A A:DP6403 2.2 21.1 1.0 O A:HOH521 2.2 18.3 1.0 OG A:SER106 2.4 23.4 1.0 HG A:SER106 2.9 28.0 1.0 HG A:SER191 3.1 31.5 1.0 PA A:ADP402 3.2 26.6 1.0 HB3 A:SER106 3.2 33.0 1.0 S A:SO4401 3.3 17.7 0.8 PB A:ADP402 3.3 26.6 1.0 CB A:SER106 3.4 27.6 1.0 H A:SER106 3.5 26.4 1.0 O3A A:ADP402 3.5 18.9 1.0 PA A:DP6403 3.5 17.5 1.0 HA A:ALA104 3.5 32.7 1.0 O4 A:SO4401 3.6 16.7 0.8 H51 A:DP6403 3.7 16.7 1.0 OG A:SER191 3.8 26.3 1.0 O A:HOH522 3.9 19.9 1.0 HB2 A:SER191 3.9 19.0 1.0 O5' A:ADP402 3.9 20.2 1.0 HG A:SER140 3.9 13.6 1.0 O2 A:SO4401 4.0 16.1 0.8 O2B A:ADP402 4.0 31.9 1.0 HB2 A:SER106 4.1 33.0 1.0 OG A:SER140 4.1 11.4 1.0 O5 A:DP6403 4.1 14.9 1.0 H A:ALA107 4.1 20.2 1.0 O2A A:DP6403 4.2 15.1 1.0 N A:SER106 4.2 22.1 1.0 CB A:SER191 4.3 15.9 1.0 CA A:SER106 4.3 16.9 1.0 HZ2 A:LYS187 4.3 32.6 1.0 C5 A:DP6403 4.4 14.0 1.0 HG A:SER138 4.4 28.3 1.0 O3 A:SO4401 4.4 13.5 0.8 O1A A:ADP402 4.5 23.1 1.0 OG A:SER138 4.5 23.7 1.0 HB3 A:SER191 4.5 19.0 1.0 CA A:ALA104 4.5 27.3 1.0 O1B A:ADP402 4.5 21.9 1.0 O6 A:DP6403 4.6 15.5 1.0 N A:ALA107 4.6 16.9 1.0 HZ1 A:LYS187 4.7 32.6 1.0 H A:ALA104 4.7 28.1 1.0 C A:SER106 4.8 15.3 1.0 H52 A:DP6403 4.9 16.7 1.0 C A:ALA104 4.9 26.1 1.0 NZ A:LYS187 5.0 27.3 1.0

Cobalt binding site 2 out of 2 in the Mddef in Complex with Mvapp, Adp, Sulfate and Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Mddef in Complex with Mvapp, Adp, Sulfate and Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co405 b:18.6 occ:0.66 HO3A A:DP6403 1.6 26.8 1.0 OD2 A:ASP282 2.0 35.8 1.0 O1 A:DP6403 2.1 12.5 1.0 O4 A:SO4401 2.2 16.7 0.8 O A:HOH548 2.3 18.0 1.0 O3A A:DP6403 2.4 22.4 1.0 CG A:ASP282 2.9 25.5 1.0 C1 A:DP6403 3.0 10.6 1.0 H51 A:DP6403 3.1 16.7 1.0 HB3 A:ASP282 3.3 18.8 1.0 C3 A:DP6403 3.3 19.2 1.0 S A:SO4401 3.4 17.7 0.8 C2 A:DP6403 3.4 7.7 1.0 H22 A:DP6403 3.5 9.1 1.0 H A:ALA13 3.5 19.8 1.0 O3 A:SO4401 3.6 13.5 0.8 HH22 A:ARG143 3.6 16.9 1.0 OD1 A:ASP282 3.6 23.4 1.0 H52 A:DP6403 3.6 16.7 1.0 CB A:ASP282 3.6 15.7 1.0 C5 A:DP6403 3.7 14.0 1.0 HB2 A:ALA104 3.8 26.8 1.0 HB2 A:ALA13 3.8 16.5 1.0 HB3 A:ALA13 4.0 16.5 1.0 C4 A:DP6403 4.1 22.9 1.0 O A:HOH521 4.1 18.3 1.0 HB3 A:SER140 4.1 11.7 1.0 HH21 A:ARG143 4.1 16.9 1.0 HA A:ILE12 4.1 20.6 1.0 O2 A:DP6403 4.1 21.6 1.0 HB2 A:ASP282 4.2 18.8 1.0 NH2 A:ARG143 4.2 14.2 1.0 O2 A:SO4401 4.2 16.1 0.8 HB2 A:SER140 4.3 11.7 1.0 N A:ALA13 4.3 16.6 1.0 H21 A:DP6403 4.3 9.1 1.0 CB A:ALA13 4.3 13.8 1.0 O1 A:SO4401 4.5 11.8 0.8 HB1 A:ALA104 4.5 26.8 1.0 O A:ASN11 4.5 16.6 1.0 C3A A:DP6403 4.5 18.1 1.0 CB A:ALA104 4.5 22.4 1.0 H42 A:DP6403 4.6 27.3 1.0 CB A:SER140 4.6 9.8 1.0 H3A2 A:DP6403 4.6 21.7 1.0 H A:ALA283 4.7 25.9 1.0 HD13 A:ILE12 4.7 31.1 1.0 HA A:ALA104 4.7 32.7 1.0 HA A:ASP282 4.8 33.4 1.0 H3A1 A:DP6403 4.8 21.7 1.0 H41 A:DP6403 4.8 27.3 1.0 CA A:ASP282 4.9 27.9 1.0 OG A:SER140 5.0 11.4 1.0 CA A:ALA13 5.0 12.1 1.0 CA A:ILE12 5.0 17.3 1.0

C.V.Stauffacher, C.-L.Chen. Visualizing the Enzyme Mechanism of the Mevalonate Diphosphate Decarboxylase To Be Published.