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Cobalt in PDB 3ka9: Frog M-Ferritin, Eeh Mutant, with Cobalt

Enzymatic activity of Frog M-Ferritin, Eeh Mutant, with Cobalt

All present enzymatic activity of Frog M-Ferritin, Eeh Mutant, with Cobalt:
1.16.3.1;

Protein crystallography data

The structure of Frog M-Ferritin, Eeh Mutant, with Cobalt, PDB code: 3ka9 was solved by T.Tosha, H.L.Ng, E.Theil, T.Alber, O.Bhattasali, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.45
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.452, 183.452, 183.452, 90.00, 90.00, 90.00
R / Rfree (%) 12.9 / 16.5

Other elements in 3ka9:

The structure of Frog M-Ferritin, Eeh Mutant, with Cobalt also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Chlorine (Cl) 5 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Frog M-Ferritin, Eeh Mutant, with Cobalt (pdb code 3ka9). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the Frog M-Ferritin, Eeh Mutant, with Cobalt, PDB code: 3ka9:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in 3ka9

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Cobalt binding site 1 out of 7 in the Frog M-Ferritin, Eeh Mutant, with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Frog M-Ferritin, Eeh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co176

b:12.7
occ:0.25
 NE2 A:HIS169 2.2 11.8 1.0
CL A:CL185 2.3 12.6 0.2
CL A:CL187 2.3 16.7 0.1
CE1 A:HIS169 3.1 12.9 1.0
CD2 A:HIS169 3.3 12.3 1.0
ND1 A:HIS169 4.3 13.4 1.0
CG A:HIS169 4.4 11.4 1.0
O A:HOH243 4.6 43.3 1.0

Cobalt binding site 2 out of 7 in 3ka9

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Cobalt binding site 2 out of 7 in the Frog M-Ferritin, Eeh Mutant, with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Frog M-Ferritin, Eeh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co177

b:14.7
occ:1.00
 OE1 A:GLU58 1.9 16.2 1.0
OE1 A:GLU23 2.0 13.0 1.0
O A:HOH376 2.0 12.2 1.0
ND1 A:HIS61 2.0 13.7 1.0
O A:HOH381 2.2 22.7 1.0
CE1 A:HIS61 3.0 17.4 1.0
CD A:GLU58 3.0 17.8 1.0
CD A:GLU23 3.0 10.9 1.0
CG A:HIS61 3.1 11.9 1.0
OE2 A:GLU23 3.2 13.8 1.0
OE2 A:GLU58 3.3 28.9 1.0
CB A:HIS61 3.5 10.7 1.0
O A:HOH426 3.9 20.8 1.0
OE2 A:GLU137 4.0 24.6 1.0
CG1 A:VAL106 4.1 13.1 1.0
NE2 A:HIS61 4.1 17.7 1.0
CD2 A:HIS61 4.2 15.6 1.0
CG A:GLU58 4.3 14.2 1.0
CG A:GLU23 4.3 10.8 1.0
CA A:GLU58 4.4 10.4 1.0
CB A:GLU58 4.6 10.7 1.0
CB A:GLU23 4.7 9.6 1.0
CD2 A:TYR133 5.0 12.9 1.0

Cobalt binding site 3 out of 7 in 3ka9

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Cobalt binding site 3 out of 7 in the Frog M-Ferritin, Eeh Mutant, with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Frog M-Ferritin, Eeh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co178

b:15.7
occ:1.00
 OE2 A:GLU136 1.9 20.5 1.0
O A:HOH355 2.1 18.9 1.0
NE2 A:HIS140 2.1 12.4 1.0
O A:HOH390 2.1 19.3 1.0
OE2 A:GLU57 2.2 18.5 1.0
OE1 A:GLU57 2.3 15.6 1.0
CD A:GLU57 2.5 17.1 1.0
CD A:GLU136 3.0 18.0 1.0
CE1 A:HIS140 3.1 12.2 1.0
CD2 A:HIS140 3.1 12.6 1.0
CG A:GLU136 3.3 15.4 1.0
CG A:GLU57 4.0 14.0 1.0
OE1 A:GLU136 4.1 21.1 1.0
ND1 A:HIS140 4.2 12.0 1.0
CG A:HIS140 4.2 10.7 1.0
O A:HOH427 4.3 26.4 1.0
O A:HOH201 4.4 34.8 1.0
CE1 A:HIS54 4.5 16.3 1.0
O A:HOH398 4.6 22.2 1.0
O A:HOH428 4.7 29.9 1.0
CB A:GLU136 4.9 14.8 1.0
O A:HOH348 4.9 18.0 1.0
CB A:GLU57 4.9 11.1 1.0

Cobalt binding site 4 out of 7 in 3ka9

Go back to Cobalt Binding Sites List in 3ka9
Cobalt binding site 4 out of 7 in the Frog M-Ferritin, Eeh Mutant, with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Frog M-Ferritin, Eeh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co179

b:23.9
occ:1.00
 OE2 A:GLU60 1.9 31.5 1.0
O A:HOH450 2.2 27.6 1.0
O A:HOH449 2.2 23.8 1.0
OE1 A:GLU63 2.3 23.3 1.0
OE1 A:GLU60 2.4 29.1 1.0
CD A:GLU60 2.5 23.1 1.0
CD A:GLU63 3.1 21.7 1.0
OE2 A:GLU63 3.2 30.8 1.0
CG A:GLU60 4.0 20.0 1.0
O A:HOH441 4.2 32.9 1.0
O A:HOH280 4.5 41.6 1.0
CG A:GLU63 4.5 18.8 1.0
CA A:GLU60 5.0 12.7 1.0
CB A:GLU60 5.0 14.0 1.0
CB A:GLU63 5.0 13.3 1.0

Cobalt binding site 5 out of 7 in 3ka9

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Cobalt binding site 5 out of 7 in the Frog M-Ferritin, Eeh Mutant, with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Frog M-Ferritin, Eeh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co180

b:12.0
occ:0.16
 O A:HOH323 2.1 13.8 1.0
O A:HOH378 2.1 13.7 1.0
O A:HOH292 3.5 71.5 1.0
OE2 A:GLU130 3.8 13.1 1.0
O A:HOH337 4.3 20.5 1.0
OE1 A:GLU130 4.3 17.6 1.0
O A:HOH343 4.3 16.1 1.0
CD A:GLU130 4.5 12.7 1.0

Cobalt binding site 6 out of 7 in 3ka9

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Cobalt binding site 6 out of 7 in the Frog M-Ferritin, Eeh Mutant, with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Frog M-Ferritin, Eeh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co181

b:20.0
occ:0.16
 O A:HOH405 1.7 27.9 1.0
O A:HOH302 1.9 11.4 0.3
OD1 A:ASP127 3.7 18.0 1.0
OG A:SER131 4.2 21.4 1.0
OE1 A:GLU130 4.3 17.6 1.0
O A:HOH255 4.4 33.0 1.0
CG A:ASP127 4.8 13.5 1.0
O A:HOH448 4.8 20.3 1.0

Cobalt binding site 7 out of 7 in 3ka9

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Cobalt binding site 7 out of 7 in the Frog M-Ferritin, Eeh Mutant, with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Frog M-Ferritin, Eeh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co182

b:30.9
occ:0.50
 NE2 A:HIS45 1.9 22.4 0.5
OE2 A:GLU49 2.0 25.1 0.5
O A:HOH305 2.1 48.0 1.0
O A:HOH253 2.1 41.6 1.0
O A:HOH304 2.2 39.5 1.0
CE1 A:HIS45 2.8 22.7 0.5
CD2 A:HIS45 3.0 22.5 0.5
CD A:GLU49 3.0 22.1 0.5
OE2 A:GLU49 3.4 27.7 0.5
CD A:GLU49 3.5 22.2 0.5
CG A:GLU49 3.5 17.3 0.5
CG A:GLU49 3.5 15.8 0.5
O A:HOH293 3.7 45.2 1.0
ND1 A:HIS45 3.9 22.3 0.5
CG A:HIS45 4.0 17.9 0.5
OE1 A:GLU49 4.1 23.5 0.5
OE1 A:GLU49 4.2 27.1 0.5
O A:HOH268 4.6 34.5 1.0
O A:HOH406 4.8 27.8 1.0
CB A:GLU49 4.8 10.5 0.5
O A:HOH212 4.9 41.5 1.0

Reference:

T.Tosha, H.L.Ng, E.Theil, T.Alber, O.Bhattasali. Frog M-Ferritin, Eeh Mutant, with Cobalt To Be Published.
Page generated: Tue Jul 30 16:12:56 2024

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