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Cobalt in PDB 3ka4: Frog M-Ferritin with Cobalt

Enzymatic activity of Frog M-Ferritin with Cobalt

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

Protein crystallography data

The structure of Frog M-Ferritin with Cobalt, PDB code: 3ka4 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 (°) 183.765, 183.765, 183.765, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 17.4

Other elements in 3ka4:

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

Magnesium (Mg) 6 atoms
Chlorine (Cl) 8 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Frog M-Ferritin with Cobalt (pdb code 3ka4). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Frog M-Ferritin with Cobalt, PDB code: 3ka4:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 3ka4

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Cobalt binding site 1 out of 8 in the Frog M-Ferritin 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 with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co176

b:14.0
occ:0.70
 OE1 A:GLU23 1.9 16.8 1.0
OE1 A:GLU58 2.0 20.3 1.0
O A:HOH341 2.1 22.1 1.0
O A:HOH335 2.1 20.2 1.0
ND1 A:HIS61 2.1 18.3 1.0
CD A:GLU23 2.9 17.5 1.0
CD A:GLU58 3.0 16.8 1.0
CE1 A:HIS61 3.0 21.9 1.0
OE2 A:GLU23 3.2 19.4 1.0
CG A:HIS61 3.3 18.0 1.0
O A:HOH354 3.4 31.7 1.0
OE2 A:GLU58 3.5 18.2 1.0
CB A:HIS61 3.6 14.5 1.0
CG1 A:VAL106 3.9 12.8 1.0
CO A:CO177 4.2 18.6 0.5
NE2 A:HIS61 4.2 20.4 1.0
OE1 A:GLN137 4.2 11.2 0.5
CG A:GLU58 4.3 18.6 1.0
CG A:GLU23 4.3 15.5 1.0
O A:HOH331 4.3 22.2 1.0
CD2 A:HIS61 4.3 18.3 1.0
CA A:GLU58 4.4 13.6 1.0
OE1 A:GLN137 4.5 19.0 0.5
CB A:GLU58 4.6 15.5 1.0
CB A:GLU23 4.7 11.6 1.0
CD A:GLN137 4.9 12.3 0.5
O A:GLU58 4.9 13.2 1.0
CA A:GLU23 4.9 9.8 1.0
OE2 A:GLU57 5.0 29.2 0.5

Cobalt binding site 2 out of 8 in 3ka4

Go back to Cobalt Binding Sites List in 3ka4
Cobalt binding site 2 out of 8 in the Frog M-Ferritin 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 with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co177

b:18.6
occ:0.50
 OE2 A:GLU58 1.8 18.2 1.0
O A:HOH354 1.9 31.7 1.0
OE2 A:GLU103 2.1 15.3 0.5
NE2 A:HIS54 2.1 17.0 0.5
OE1 A:GLU103 2.3 14.7 0.5
OE1 A:GLU103 2.3 19.0 0.5
OE2 A:GLU103 2.4 22.1 0.5
CD A:GLU103 2.5 14.3 0.5
CD A:GLU103 2.5 19.6 0.5
O A:HOH341 2.6 22.1 1.0
CD A:GLU58 2.9 16.8 1.0
CE1 A:HIS54 3.0 17.5 0.5
CO A:CO182 3.1 14.5 0.2
CD2 A:HIS54 3.2 20.3 0.5
OE2 A:GLU57 3.3 29.2 0.5
OE1 A:GLU58 3.6 20.3 1.0
CG A:GLU103 3.9 16.2 0.5
CE2 A:TYR30 3.9 8.3 0.5
CG A:GLU58 4.0 18.6 1.0
CG A:GLU103 4.0 13.6 0.5
CE2 A:TYR30 4.1 13.6 0.5
OE1 A:GLN137 4.1 19.0 0.5
ND1 A:HIS54 4.1 20.0 0.5
OE1 A:GLN137 4.1 11.2 0.5
CO A:CO176 4.2 14.0 0.7
CG A:HIS54 4.2 15.5 0.5
OH A:TYR30 4.3 13.7 0.5
NE2 A:GLN137 4.3 10.3 0.5
CD A:GLU57 4.4 24.6 0.5
NE2 A:GLN137 4.4 18.3 0.5
OD2 A:ASP140 4.5 21.5 0.5
OH A:TYR30 4.5 17.3 0.5
CZ A:TYR30 4.6 9.7 0.5
OD2 A:ASP140 4.6 15.6 0.5
CD A:GLN137 4.7 12.3 0.5
CD A:GLN137 4.7 14.4 0.5
CZ A:TYR30 4.7 15.0 0.5
ND1 A:HIS54 4.7 17.3 0.5
CB A:GLU103 4.8 13.0 0.5
CE1 A:HIS61 4.8 21.9 1.0
CB A:GLU103 4.8 11.9 0.5
OE1 A:GLU57 4.8 20.7 0.5
CD2 A:TYR30 4.9 9.2 0.5
CA A:GLU103 4.9 11.8 0.5
CA A:GLU103 4.9 11.3 0.5
CD2 A:TYR30 5.0 13.1 0.5

Cobalt binding site 3 out of 8 in 3ka4

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Cobalt binding site 3 out of 8 in the Frog M-Ferritin 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 with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co178

b:22.1
occ:0.50
 OE1 A:GLU57 1.9 27.0 0.5
OE2 A:GLU136 1.9 26.9 1.0
O A:HOH353 2.0 27.4 1.0
OD1 A:ASP140 2.2 18.9 0.5
O A:HOH304 2.2 43.5 1.0
OD1 A:ASP140 2.3 24.4 0.5
OD2 A:ASP140 2.3 15.6 0.5
OD2 A:ASP140 2.3 21.5 0.5
CG A:ASP140 2.5 14.9 0.5
CG A:ASP140 2.6 18.2 0.5
OE1 A:GLU57 2.8 20.7 0.5
CD A:GLU136 2.9 29.8 1.0
CD A:GLU57 3.0 27.5 0.5
OE2 A:GLU57 3.3 32.6 0.5
OE1 A:GLU136 3.3 32.7 1.0
CD A:GLU57 3.7 24.6 0.5
CO A:CO182 3.7 14.5 0.2
CB A:ASP140 4.0 12.4 0.5
CB A:ASP140 4.1 13.5 0.5
CE1 A:HIS54 4.2 17.5 0.5
CG A:GLU136 4.3 24.2 1.0
CE1 A:HIS54 4.3 17.5 0.5
CG A:GLU57 4.4 21.6 0.5
OE2 A:GLU57 4.4 29.2 0.5
ND1 A:HIS54 4.5 20.0 0.5
CG A:GLU57 4.5 20.7 0.5
ND1 A:HIS54 4.5 17.3 0.5
O A:HOH359 4.6 24.8 1.0
O A:GLU136 4.8 14.6 1.0
CA A:ASP140 4.9 12.2 0.5
CA A:ASP140 4.9 11.6 0.5

Cobalt binding site 4 out of 8 in 3ka4

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Cobalt binding site 4 out of 8 in the Frog M-Ferritin 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 with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co179

b:13.0
occ:0.25
 NE2 A:HIS169 2.2 12.1 1.0
CL A:CL195 2.3 14.9 0.2
O A:HOH345 2.4 14.6 0.2
CE1 A:HIS169 3.1 13.3 1.0
CD2 A:HIS169 3.3 12.8 1.0
ND1 A:HIS169 4.2 12.8 1.0
CG A:HIS169 4.4 12.5 1.0

Cobalt binding site 5 out of 8 in 3ka4

Go back to Cobalt Binding Sites List in 3ka4
Cobalt binding site 5 out of 8 in the Frog M-Ferritin 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 with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co180

b:22.7
occ:0.50
 OE2 A:GLU60 1.8 40.8 1.0
O A:HOH347 2.0 34.1 1.0
O A:HOH348 2.3 38.2 1.0
OE1 A:GLU63 2.5 27.0 1.0
CD A:GLU60 2.6 30.8 1.0
OE1 A:GLU60 2.7 35.6 1.0
OE2 A:GLU63 3.0 32.5 1.0
CD A:GLU63 3.1 24.7 1.0
O A:HOH346 3.8 48.5 1.0
CG A:GLU60 4.1 24.6 1.0
O A:HOH226 4.3 37.7 1.0
CG A:GLU63 4.5 21.8 1.0

Cobalt binding site 6 out of 8 in 3ka4

Go back to Cobalt Binding Sites List in 3ka4
Cobalt binding site 6 out of 8 in the Frog M-Ferritin 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 with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co181

b:22.8
occ:0.33
 O A:HOH212 2.0 11.5 1.0
O A:HOH232 2.0 13.8 1.0
OE2 A:GLU130 3.8 13.9 1.0
OE1 A:GLU130 4.2 17.4 1.0
O A:HOH291 4.3 21.3 1.0
O A:HOH247 4.3 16.0 1.0
CD A:GLU130 4.5 13.3 1.0

Cobalt binding site 7 out of 8 in 3ka4

Go back to Cobalt Binding Sites List in 3ka4
Cobalt binding site 7 out of 8 in the Frog M-Ferritin 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 with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co182

b:14.5
occ:0.25
 CE1 A:HIS54 0.8 17.5 0.5
NE2 A:HIS54 1.5 17.0 0.5
ND1 A:HIS54 1.6 20.0 0.5
ND1 A:HIS54 2.1 17.3 0.5
OD2 A:ASP140 2.1 15.6 0.5
OE2 A:GLU57 2.3 29.2 0.5
OE1 A:GLU57 2.4 20.7 0.5
CD2 A:HIS54 2.4 20.3 0.5
CG A:HIS54 2.4 15.5 0.5
OE1 A:GLU103 2.6 19.0 0.5
CE1 A:HIS54 2.7 17.5 0.5
CD A:GLU57 2.7 24.6 0.5
OD2 A:ASP140 2.9 21.5 0.5
CO A:CO177 3.1 18.6 0.5
CG A:ASP140 3.3 14.9 0.5
CG A:HIS54 3.4 12.8 0.5
OE1 A:GLU103 3.4 14.7 0.5
CG A:ASP140 3.5 18.2 0.5
OE1 A:GLU57 3.6 27.0 0.5
CD A:GLU103 3.7 19.6 0.5
CO A:CO178 3.7 22.1 0.5
CB A:HIS54 3.8 13.2 0.5
CD A:GLU57 3.9 27.5 0.5
OE2 A:GLU58 3.9 18.2 1.0
CD A:GLU103 3.9 14.3 0.5
OE2 A:GLU103 3.9 15.3 0.5
NE2 A:HIS54 3.9 18.1 0.5
OE2 A:GLU136 4.0 26.9 1.0
CB A:ASP140 4.0 12.4 0.5
OE2 A:GLU103 4.0 22.1 0.5
CB A:HIS54 4.1 12.1 0.5
OE2 A:GLU57 4.1 32.6 0.5
CB A:ASP140 4.1 13.5 0.5
OH A:TYR30 4.3 13.7 0.5
O A:HOH353 4.3 27.4 1.0
OD1 A:ASP140 4.3 24.4 0.5
CD2 A:HIS54 4.3 15.8 0.5
CG A:GLU57 4.3 20.7 0.5
OD1 A:ASP140 4.4 18.9 0.5
CE2 A:TYR30 4.4 8.3 0.5
CA A:HIS54 4.4 12.1 0.5
CA A:HIS54 4.5 11.6 0.5
CZ A:TYR30 4.6 9.7 0.5
CB A:GLU57 4.6 16.3 0.5
CG A:GLU57 4.8 21.6 0.5
O A:HIS54 4.8 13.2 1.0
CD A:GLU58 4.8 16.8 1.0
O A:HOH354 4.9 31.7 1.0
CG A:GLU103 5.0 16.2 0.5

Cobalt binding site 8 out of 8 in 3ka4

Go back to Cobalt Binding Sites List in 3ka4
Cobalt binding site 8 out of 8 in the Frog M-Ferritin 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 with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co183

b:27.8
occ:0.50
 NE2 A:HIS45 2.0 16.7 0.5
O A:HOH349 2.0 43.2 1.0
O A:HOH350 2.1 41.0 1.0
OE2 A:GLU49 2.1 27.6 0.5
O A:HOH351 2.2 42.2 1.0
CE1 A:HIS45 2.9 18.3 0.5
CD2 A:HIS45 3.0 19.6 0.5
CD A:GLU49 3.1 23.9 0.5
OE2 A:GLU49 3.3 27.9 0.5
CD A:GLU49 3.4 19.3 0.5
CG A:GLU49 3.5 16.0 0.5
CG A:GLU49 3.5 17.4 0.5
ND1 A:HIS45 4.0 17.3 0.5
OE1 A:GLU49 4.1 26.1 0.5
CG A:HIS45 4.1 16.3 0.5
OE1 A:GLU49 4.2 21.8 0.5
O A:HOH357 4.6 30.6 1.0
CB A:GLU49 4.8 11.4 0.5
O A:HOH306 4.8 26.0 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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