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Cobalt in PDB 3ka6: Frog M-Ferritin, Eed Mutant, with Cobalt

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

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

Protein crystallography data

The structure of Frog M-Ferritin, Eed Mutant, with Cobalt, PDB code: 3ka6 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 / 1.40
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.708, 183.708, 183.708, 90.00, 90.00, 90.00
R / Rfree (%) 13.9 / 16.6

Other elements in 3ka6:

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

Magnesium (Mg) 5 atoms
Chlorine (Cl) 4 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Frog M-Ferritin, Eed Mutant, with Cobalt (pdb code 3ka6). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 10 binding sites of Cobalt where determined in the Frog M-Ferritin, Eed Mutant, with Cobalt, PDB code: 3ka6:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 10 in 3ka6

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Cobalt binding site 1 out of 10 in the Frog M-Ferritin, Eed 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, Eed Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co176

b:13.6
occ:0.25
 NE2 A:HIS169 2.2 12.6 1.0
CL A:CL189 2.3 13.4 0.2
O A:HOH430 2.4 16.1 0.2
CE1 A:HIS169 3.1 13.8 1.0
CD2 A:HIS169 3.3 12.2 1.0
ND1 A:HIS169 4.2 13.1 1.0
CG A:HIS169 4.4 12.2 1.0
O A:HOH268 4.6 38.3 1.0

Cobalt binding site 2 out of 10 in 3ka6

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Cobalt binding site 2 out of 10 in the Frog M-Ferritin, Eed 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, Eed Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co177

b:14.6
occ:0.70
 OE1 A:GLU58 2.0 17.6 1.0
OE1 A:GLU23 2.0 15.8 1.0
ND1 A:HIS61 2.1 9.2 0.5
O A:HOH387 2.1 21.1 1.0
O A:HOH386 2.2 16.2 1.0
CD A:GLU23 2.9 13.4 1.0
CE1 A:HIS61 2.9 9.8 0.5
CD A:GLU58 3.0 14.9 1.0
CG A:HIS61 3.2 10.3 0.5
OE2 A:GLU23 3.2 16.3 1.0
ND1 A:HIS61 3.4 22.2 0.5
OE2 A:GLU58 3.4 21.4 1.0
CB A:HIS61 3.6 10.4 0.5
O A:HOH347 3.6 38.7 1.0
CO A:CO178 3.7 16.9 0.5
CB A:HIS61 3.8 13.8 0.5
CG A:HIS61 4.0 17.1 0.5
OE2 A:GLU137 4.0 26.4 1.0
CG1 A:VAL106 4.1 13.7 1.0
NE2 A:HIS61 4.1 10.7 0.5
CD2 A:HIS61 4.2 11.3 0.5
CG A:GLU23 4.3 11.4 1.0
CG A:GLU58 4.3 16.6 1.0
O A:HOH438 4.4 22.1 1.0
CA A:GLU58 4.4 12.5 1.0
CE1 A:HIS61 4.4 22.9 0.5
CB A:GLU58 4.5 14.8 1.0
CB A:GLU23 4.7 10.7 1.0
O A:HOH491 4.8 33.9 1.0
O A:HOH344 4.9 27.0 1.0
CA A:GLU23 5.0 9.6 1.0
O A:GLU58 5.0 12.3 1.0

Cobalt binding site 3 out of 10 in 3ka6

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Cobalt binding site 3 out of 10 in the Frog M-Ferritin, Eed 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, Eed Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co178

b:16.9
occ:0.50
 OE2 A:GLU58 1.8 21.4 1.0
O A:HOH491 2.0 33.9 1.0
OE2 A:GLU103 2.0 19.1 1.0
O A:HOH387 2.1 21.1 1.0
OE1 A:GLU103 2.5 21.1 1.0
NE2 A:HIS54 2.5 18.2 0.5
CD A:GLU103 2.5 17.5 1.0
O A:HOH347 2.6 38.7 1.0
CD A:GLU58 2.8 14.9 1.0
OE1 A:GLU58 3.3 17.6 1.0
CO A:CO184 3.3 19.4 0.2
CE1 A:HIS54 3.4 20.8 0.5
CD2 A:HIS54 3.6 19.1 0.5
CO A:CO177 3.7 14.6 0.7
OD2 A:ASP140 3.8 24.0 0.5
CG A:GLU103 4.0 13.5 1.0
CG A:GLU58 4.0 16.6 1.0
OE2 A:GLU137 4.1 26.4 1.0
CE2 A:TYR30 4.2 12.6 1.0
CE1 A:HIS61 4.2 9.8 0.5
OD2 A:ASP140 4.3 16.8 0.5
O A:HOH349 4.4 42.7 1.0
OH A:TYR30 4.4 22.7 1.0
O A:HOH344 4.4 27.0 1.0
OE1 A:GLU137 4.5 19.0 1.0
ND1 A:HIS61 4.5 9.2 0.5
ND1 A:HIS54 4.6 22.1 0.5
CD A:GLU137 4.6 20.8 1.0
CG A:HIS54 4.7 15.9 0.5
ND1 A:HIS54 4.7 24.2 0.5
CZ A:TYR30 4.8 15.9 1.0
O A:HOH386 4.8 16.2 1.0
CG A:ASP140 4.9 19.6 0.5

Cobalt binding site 4 out of 10 in 3ka6

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Cobalt binding site 4 out of 10 in the Frog M-Ferritin, Eed 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, Eed Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co179

b:20.1
occ:0.50
 OE2 A:GLU60 2.0 38.4 1.0
O A:HOH469 2.1 31.6 1.0
OE1 A:GLU63 2.3 23.3 1.0
OE1 A:GLU60 2.5 30.9 1.0
CD A:GLU60 2.5 29.2 1.0
CD A:GLU63 3.0 23.8 1.0
OE2 A:GLU63 3.2 27.6 1.0
CG A:GLU60 4.1 21.7 1.0
O A:HOH480 4.3 31.0 1.0
CG A:GLU63 4.5 19.8 1.0
CB A:GLU63 4.9 14.3 1.0
CA A:GLU60 4.9 13.7 1.0

Cobalt binding site 5 out of 10 in 3ka6

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Cobalt binding site 5 out of 10 in the Frog M-Ferritin, Eed 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, Eed Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co180

b:14.2
occ:0.20
 O A:HOH352 2.1 13.2 1.0
O A:HOH411 2.1 15.4 1.0
OE2 A:GLU130 3.9 13.5 1.0
OE1 A:GLU130 4.2 17.6 1.0
O A:HOH412 4.2 16.6 1.0
O A:HOH400 4.3 20.3 1.0
CD A:GLU130 4.5 14.6 1.0

Cobalt binding site 6 out of 10 in 3ka6

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Cobalt binding site 6 out of 10 in the Frog M-Ferritin, Eed 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, Eed Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co181

b:22.6
occ:0.50
 O A:HOH332 1.9 40.0 1.0
O A:HOH252 2.0 21.8 1.0
O A:HOH238 2.1 34.6 1.0
OD2 A:ASP41 2.1 15.8 1.0
CG A:ASP41 3.2 12.1 1.0
CB A:ASP41 3.7 10.8 1.0
NH2 A:ARG39 4.2 14.7 1.0
OD1 A:ASP41 4.3 11.8 1.0
O A:HOH436 4.3 19.4 1.0
O A:HOH414 4.5 21.0 1.0
O A:HOH285 4.5 38.1 1.0
MG A:MG192 4.9 35.5 1.0

Cobalt binding site 7 out of 10 in 3ka6

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Cobalt binding site 7 out of 10 in the Frog M-Ferritin, Eed 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, Eed Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co182

b:28.7
occ:0.50
 NE2 A:HIS45 1.8 20.4 0.5
OE2 A:GLU49 2.0 25.0 0.5
O A:HOH259 2.2 40.0 1.0
O A:HOH337 2.3 44.9 1.0
CE1 A:HIS45 2.5 18.5 0.5
CD A:GLU49 2.9 21.8 0.5
CD2 A:HIS45 3.0 20.1 0.5
OE2 A:GLU49 3.3 28.5 0.5
CG A:GLU49 3.4 15.4 0.5
CD A:GLU49 3.5 22.6 0.5
CG A:GLU49 3.5 18.0 0.5
ND1 A:HIS45 3.8 21.1 0.5
CG A:HIS45 4.0 16.0 0.5
OE1 A:GLU49 4.1 25.2 0.5
OE1 A:GLU49 4.2 27.2 0.5
O A:HOH204 4.6 33.9 1.0
O A:HOH213 4.7 32.6 1.0
CB A:GLU49 4.8 12.2 0.5
CB A:GLU49 4.9 13.1 0.5

Cobalt binding site 8 out of 10 in 3ka6

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Cobalt binding site 8 out of 10 in the Frog M-Ferritin, Eed Mutant, with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Frog M-Ferritin, Eed Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co183

b:28.5
occ:0.25
 O A:HOH345 1.8 36.1 1.0
O A:HOH338 2.1 23.8 1.0
OD2 A:ASP140 2.2 16.8 0.5
O A:HOH294 2.3 49.1 1.0
OD1 A:ASP140 2.4 14.2 0.5
CO A:CO184 2.5 19.4 0.2
O A:HOH349 2.6 42.7 1.0
CG A:ASP140 2.6 11.1 0.5
O A:HOH507 2.9 33.2 1.0
OE2 A:GLU136 3.1 26.8 0.5
OE1 A:GLU57 3.2 36.5 1.0
CG A:GLU136 3.7 17.6 0.5
CD A:GLU136 3.8 21.4 0.5
O A:HOH486 3.9 37.7 1.0
O A:HOH344 4.0 27.0 1.0
O A:HOH347 4.0 38.7 1.0
CD A:GLU57 4.1 32.8 1.0
CB A:ASP140 4.1 11.1 0.5
CG A:ASP140 4.1 19.6 0.5
NH1 A:ARG143 4.1 30.7 0.5
CB A:ASP140 4.1 13.4 0.5
O A:HOH491 4.2 33.9 1.0
NH2 A:ARG143 4.3 27.5 0.5
O A:HOH322 4.4 33.8 1.0
OD1 A:ASP140 4.4 24.2 0.5
CE1 A:HIS54 4.4 21.0 0.5
OE2 A:GLU57 4.5 35.2 1.0
OD2 A:ASP140 4.5 24.0 0.5
O A:GLU136 4.6 13.4 1.0
OE1 A:GLU136 4.6 30.5 0.5
CE1 A:HIS54 4.6 20.8 0.5
CZ A:ARG143 4.7 29.4 0.5
NE2 A:HIS54 4.8 18.2 0.5
ND1 A:HIS54 4.9 24.2 0.5
OE1 A:GLU136 5.0 22.5 0.5

Cobalt binding site 9 out of 10 in 3ka6

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Cobalt binding site 9 out of 10 in the Frog M-Ferritin, Eed Mutant, with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Frog M-Ferritin, Eed Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co184

b:19.4
occ:0.25
 OD2 A:ASP140 1.6 16.8 0.5
O A:HOH349 1.9 42.7 1.0
O A:HOH347 1.9 38.7 1.0
O A:HOH491 2.0 33.9 1.0
O A:HOH345 2.2 36.1 1.0
CO A:CO183 2.5 28.5 0.2
CG A:ASP140 2.8 11.1 0.5
NE2 A:HIS54 2.8 18.2 0.5
O A:HOH344 3.0 27.0 1.0
CE1 A:HIS54 3.1 20.8 0.5
OD2 A:ASP140 3.2 24.0 0.5
CO A:CO178 3.3 16.9 0.5
OD1 A:ASP140 3.6 14.2 0.5
CG A:ASP140 3.6 19.6 0.5
CD2 A:HIS54 3.8 19.1 0.5
CE1 A:HIS61 3.8 9.8 0.5
OE1 A:GLU57 3.8 36.5 1.0
CB A:ASP140 3.8 11.1 0.5
CB A:ASP140 3.9 13.4 0.5
ND1 A:HIS54 3.9 24.2 0.5
CE1 A:HIS54 3.9 21.0 0.5
O A:HOH294 4.0 49.1 1.0
ND1 A:HIS54 4.0 22.1 0.5
OE2 A:GLU58 4.1 21.4 1.0
O A:HOH338 4.1 23.8 1.0
NE2 A:HIS61 4.3 10.7 0.5
CG A:HIS54 4.4 15.9 0.5
OD1 A:ASP140 4.4 24.2 0.5
OE2 A:GLU136 4.5 26.8 0.5
CG A:GLU136 4.5 17.6 0.5
OE2 A:GLU103 4.5 19.1 1.0
O A:HOH387 4.5 21.1 1.0
OE1 A:GLU103 4.6 21.1 1.0
O A:HOH507 4.7 33.2 1.0
CE1 A:HIS61 4.8 22.9 0.5
CD A:GLU136 4.8 21.4 0.5
CD A:GLU103 4.8 17.5 1.0
ND1 A:HIS61 4.9 9.2 0.5
CD A:GLU57 4.9 32.8 1.0
O A:GLU136 4.9 13.4 1.0
CD A:GLU58 4.9 14.9 1.0
CB A:GLU57 5.0 17.1 1.0

Cobalt binding site 10 out of 10 in 3ka6

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Cobalt binding site 10 out of 10 in the Frog M-Ferritin, Eed Mutant, with Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Frog M-Ferritin, Eed Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co185

b:19.1
occ:0.16
 O A:HOH342 1.9 27.5 1.0
O A:HOH250 1.9 27.5 1.0
OD1 A:ASP127 3.9 19.5 1.0
OE1 A:GLU130 4.4 17.6 1.0
OG A:SER131 4.5 20.6 1.0
O A:HOH262 4.5 34.3 1.0
O A:HOH473 4.9 22.1 1.0
CG A:ASP127 5.0 14.9 1.0

Reference:

T.Tosha, H.L.Ng, O.Bhattasali, T.Alber, E.C.Theil. Moving Metal Ions Through Ferritin-Protein Nanocages From Three-Fold Pores to Catalytic Sites. J.Am.Chem.Soc. V. 132 14562 2010.
ISSN: ISSN 0002-7863
PubMed: 20866049
DOI: 10.1021/JA105583D
Page generated: Tue Jul 30 16:12:08 2024

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