Cobalt in PDB 6wf6: Streptomyces Coelicolor Methylmalonyl-Coa Epimerase

Protein crystallography data

The structure of Streptomyces Coelicolor Methylmalonyl-Coa Epimerase, PDB code: 6wf6 was solved by L.M.Stunkard, A.B.Benjamin, J.B.Bower, T.J.Huth, J.R.Lohman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.59 / 1.39
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.224, 75.849, 80.650, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 18.2

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Streptomyces Coelicolor Methylmalonyl-Coa Epimerase (pdb code 6wf6). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Streptomyces Coelicolor Methylmalonyl-Coa Epimerase, PDB code: 6wf6:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 6wf6

Go back to Cobalt Binding Sites List in 6wf6
Cobalt binding site 1 out of 2 in the Streptomyces Coelicolor Methylmalonyl-Coa Epimerase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Streptomyces Coelicolor Methylmalonyl-Coa Epimerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co201

b:14.1
occ:1.00
OE1 A:GLU134 2.0 9.8 0.5
OE2 A:GLU134 2.1 13.7 0.5
NE2 A:HIS84 2.1 10.9 1.0
O A:HOH401 2.2 16.0 1.0
OE1 A:GLN60 2.2 14.5 0.5
NE2 A:HIS7 2.2 10.3 1.0
OE1 A:GLN60 2.2 10.7 0.5
O A:HOH308 2.6 16.8 1.0
CE1 A:HIS84 3.0 11.3 1.0
CD A:GLU134 3.0 13.1 0.5
CD A:GLU134 3.1 9.6 0.5
CE1 A:HIS7 3.1 11.3 1.0
CD A:GLN60 3.1 8.8 0.5
CD A:GLN60 3.2 12.2 0.5
CD2 A:HIS84 3.2 10.9 1.0
CD2 A:HIS7 3.2 10.4 1.0
OE1 A:GLU134 3.4 15.8 0.5
NE2 A:GLN60 3.4 9.1 0.5
OE2 A:GLU134 3.4 11.1 0.5
NE2 A:GLN60 3.6 13.7 0.5
ND1 A:HIS84 4.2 11.7 1.0
O A:HOH383 4.2 29.7 1.0
ND1 A:HIS7 4.3 10.7 1.0
CG A:HIS84 4.3 10.7 1.0
CG A:HIS7 4.3 9.8 1.0
CG A:GLU134 4.4 11.3 0.5
CG A:GLU134 4.4 9.1 0.5
CG A:GLN60 4.5 11.6 0.5
CG A:GLN60 4.5 8.9 0.5
O A:HOH325 4.6 19.0 1.0
CZ A:PHE122 4.7 16.5 1.0
CB A:GLU134 4.7 9.8 0.5
CB A:GLU134 4.7 8.4 0.5
CB A:ALA86 4.8 9.9 1.0
CB A:GLN60 4.8 10.5 0.5
CB A:GLN60 4.9 8.9 0.5

Cobalt binding site 2 out of 2 in 6wf6

Go back to Cobalt Binding Sites List in 6wf6
Cobalt binding site 2 out of 2 in the Streptomyces Coelicolor Methylmalonyl-Coa Epimerase


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Streptomyces Coelicolor Methylmalonyl-Coa Epimerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co201

b:14.5
occ:1.00
OE1 B:GLN60 2.0 10.9 0.5
OE1 B:GLU134 2.1 14.8 1.0
NE2 B:HIS84 2.2 11.7 1.0
NE2 B:HIS7 2.2 11.1 1.0
O B:HOH388 2.2 16.0 1.0
OE1 B:GLN60 2.3 14.6 0.5
O B:HOH338 2.6 17.6 1.0
CD B:GLN60 3.1 9.0 0.5
CE1 B:HIS84 3.1 12.3 1.0
CD B:GLU134 3.1 14.1 1.0
CE1 B:HIS7 3.2 10.5 1.0
CD B:GLN60 3.2 11.5 0.5
CD2 B:HIS7 3.2 10.0 1.0
CD2 B:HIS84 3.2 11.0 1.0
NE2 B:GLN60 3.4 8.9 0.5
NE2 B:GLN60 3.4 14.5 0.5
OE2 B:GLU134 3.4 18.1 1.0
ND1 B:HIS84 4.2 11.6 1.0
O B:HOH389 4.3 24.3 1.0
ND1 B:HIS7 4.3 10.2 1.0
CG B:HIS84 4.3 11.3 1.0
CG B:HIS7 4.3 9.5 1.0
CG B:GLN60 4.4 10.1 0.5
CG B:GLU134 4.5 11.2 1.0
CG B:GLN60 4.5 12.4 0.5
O B:HOH329 4.6 38.9 1.0
CZ B:PHE122 4.6 16.9 1.0
O B:HOH356 4.7 20.0 1.0
CB B:GLU134 4.7 10.4 1.0
CB B:ALA86 4.8 10.1 1.0
CB B:GLN60 4.8 9.3 0.5
CB B:GLN60 4.9 10.6 0.5

Reference:

L.M.Stunkard, A.B.Benjamin, J.B.Bower, T.J.Huth, J.R.Lohman. Structures of Methylmalonyl-Coa Epimerase Contradict General Acid-Base Catalytic Mechanism To Be Published.
Page generated: Sun Dec 13 10:53:41 2020

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