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Chlorine in PDB 3ka8: Frog M-Ferritin, Eqh Mutant, with Cobalt

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

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

Protein crystallography data

The structure of Frog M-Ferritin, Eqh Mutant, with Cobalt, PDB code: 3ka8 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 / 1.35
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.490, 183.490, 183.490, 90.00, 90.00, 90.00
R / Rfree (%) 13 / 15.3

Other elements in 3ka8:

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

Cobalt (Co) 5 atoms
Magnesium (Mg) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Frog M-Ferritin, Eqh Mutant, with Cobalt (pdb code 3ka8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Frog M-Ferritin, Eqh Mutant, with Cobalt, PDB code: 3ka8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 3ka8

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Frog M-Ferritin, Eqh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl184

b:11.1
occ:0.25
 CO A:CO176 2.3 11.6 0.2
NE2 A:HIS169 3.2 11.6 1.0
CE1 A:HIS169 3.3 11.8 1.0
CD2 A:LEU165 3.6 12.6 1.0
CD2 A:HIS169 4.4 10.6 1.0
ND1 A:HIS169 4.5 11.0 1.0
O A:HOH342 4.7 13.7 0.2

Chlorine binding site 2 out of 7 in 3ka8

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Frog M-Ferritin, Eqh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl186

b:18.8
occ:1.00
 O A:HOH256 2.9 40.5 1.0
O A:HOH294 3.0 41.3 1.0
O A:HOH201 3.2 31.7 1.0
N A:TYR8 3.2 10.6 1.0
N A:ASN7 3.4 9.8 1.0
O A:TYR8 3.5 11.1 1.0
CG A:ARG5 3.6 11.7 1.0
CD A:ARG5 3.6 13.6 1.0
NE A:ARG5 3.7 12.1 1.0
O A:HOH389 3.8 19.9 1.0
C A:GLN6 3.9 8.7 1.0
CA A:GLN6 4.0 8.9 1.0
C A:TYR8 4.0 9.6 1.0
N A:GLN6 4.1 9.3 1.0
CA A:TYR8 4.1 9.7 1.0
CA A:ASN7 4.1 9.7 1.0
C A:ASN7 4.1 9.5 1.0
C A:ARG5 4.3 10.1 1.0
CB A:ARG5 4.4 10.5 1.0
CB A:TYR8 4.4 9.5 1.0
O A:ARG5 4.5 11.2 1.0
O A:GLN6 4.8 9.8 1.0
CZ A:ARG5 4.9 11.0 1.0
CA A:ARG5 5.0 10.8 1.0

Chlorine binding site 3 out of 7 in 3ka8

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Frog M-Ferritin, Eqh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl187

b:28.4
occ:1.00
 O A:HOH302 2.9 50.3 1.0
N A:SER10 3.1 11.0 1.0
O A:HOH312 3.1 39.8 1.0
O A:HOH307 3.2 39.5 1.0
CB A:SER10 3.7 12.6 1.0
CA A:HIS9 3.8 9.9 1.0
CD2 A:HIS9 3.8 16.0 1.0
CG A:HIS9 3.9 14.2 1.0
C A:HIS9 3.9 9.6 1.0
O A:HOH201 3.9 31.7 1.0
NE2 A:HIS9 4.0 18.8 1.0
CA A:SER10 4.0 10.8 1.0
ND1 A:HIS9 4.0 15.7 1.0
CE1 A:HIS9 4.1 9.4 1.0
O A:HOH294 4.1 41.3 1.0
CB A:HIS9 4.4 11.1 1.0
O A:TYR8 4.4 11.1 1.0
O A:HOH224 4.8 35.9 1.0
N A:HIS9 4.9 9.7 1.0
O A:HOH251 5.0 41.8 1.0

Chlorine binding site 4 out of 7 in 3ka8

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Chlorine binding site 4 out of 7 in the Frog M-Ferritin, Eqh Mutant, with Cobalt


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Frog M-Ferritin, Eqh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl188

b:21.9
occ:1.00
 N A:ASP87 3.2 11.6 1.0
N A:GLU88 3.6 10.9 0.5
N A:GLU88 3.7 11.4 0.5
CA A:ARG86 3.8 11.5 0.5
CA A:ARG86 3.8 11.3 0.5
CB A:ARG86 3.8 12.2 0.5
CB A:ARG86 3.9 11.5 0.5
CG A:GLU88 3.9 11.2 0.5
CA A:ASP87 3.9 11.9 1.0
C A:ARG86 4.0 11.1 1.0
O A:GLU88 4.0 10.8 0.5
O A:GLU88 4.0 13.1 0.5
CB A:ASP87 4.0 12.7 1.0
CG A:ARG86 4.2 15.2 0.5
C A:ASP87 4.3 12.3 1.0
OE2 A:GLU88 4.3 20.4 0.5
CG A:ARG86 4.4 13.5 0.5
O A:HOH292 4.5 34.3 1.0
NE A:ARG86 4.5 14.3 0.5
CA A:GLU88 4.5 12.3 0.5
CB A:GLU88 4.5 13.9 0.5
CA A:GLU88 4.6 10.9 0.5
OD2 A:ASP87 4.6 21.1 1.0
CG A:ASP87 4.7 14.4 1.0
CD A:GLU88 4.7 14.7 0.5
CB A:GLU88 4.7 12.3 0.5
C A:GLU88 4.7 10.3 0.5
C A:GLU88 4.7 11.4 0.5
CG A:GLU88 5.0 15.2 0.5

Chlorine binding site 5 out of 7 in 3ka8

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Frog M-Ferritin, Eqh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl190

b:18.4
occ:1.00
 O A:HOH281 3.2 18.0 1.0
N A:GLU136 3.2 10.8 1.0
C A:GLU132 3.3 11.7 1.0
N A:TYR133 3.4 9.3 1.0
N A:GLU135 3.5 9.6 1.0
O A:HOH475 3.5 26.7 1.0
CB A:GLU135 3.6 12.8 1.0
O A:GLU132 3.6 13.8 1.0
O A:SER131 3.7 13.3 1.0
C A:TYR133 3.7 9.3 1.0
CA A:GLU135 3.8 10.3 1.0
O A:HOH263 3.9 31.1 1.0
CA A:GLU132 3.9 11.2 1.0
CA A:TYR133 3.9 9.2 1.0
C A:GLU135 3.9 10.3 1.0
C A:SER131 4.0 13.1 1.0
N A:LEU134 4.0 9.2 1.0
N A:GLU132 4.0 11.2 1.0
CB A:GLU136 4.0 12.5 1.0
O A:HOH265 4.0 36.2 1.0
O A:TYR133 4.2 11.0 1.0
CA A:GLU136 4.2 10.8 1.0
O A:GLU130 4.2 13.9 1.0
CG A:GLU135 4.4 13.1 1.0
C A:LEU134 4.5 8.9 1.0
O A:HOH335 4.6 22.1 1.0
CA A:LEU134 4.8 9.2 1.0
CA A:SER131 4.9 12.1 1.0
MG A:MG193 5.0 14.2 1.0
O A:HOH314 5.0 18.9 1.0

Chlorine binding site 6 out of 7 in 3ka8

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Frog M-Ferritin, Eqh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl191

b:21.8
occ:1.00
 OG A:SER31 3.1 10.4 0.5
NZ A:LYS52 3.3 24.9 1.0
CB A:SER31 3.5 10.6 0.5
CB A:SER31 3.8 9.3 0.5
OG A:SER55 3.8 11.9 1.0
CA A:SER31 3.9 9.3 0.5
NH2 A:ARG59 4.0 15.8 0.5
CG A:LYS52 4.0 12.6 1.0
CB A:SER55 4.0 8.9 1.0
CA A:SER31 4.0 8.7 0.5
CE1 A:HIS56 4.2 15.8 1.0
CE A:LYS52 4.2 22.6 1.0
CD2 A:TYR34 4.3 13.3 1.0
CA A:LYS52 4.5 9.3 1.0
CB A:LYS52 4.5 10.8 1.0
ND1 A:HIS56 4.5 16.2 1.0
CD A:LYS52 4.7 17.1 1.0
O A:LYS52 4.7 9.7 1.0
CG A:TYR34 4.7 11.4 1.0
CB A:TYR34 4.8 10.2 1.0
OG A:SER31 4.8 13.9 0.5
N A:SER31 4.8 8.1 1.0
CE2 A:TYR34 4.9 16.7 1.0
O A:SER31 5.0 9.7 1.0
C A:SER31 5.0 9.4 1.0

Chlorine binding site 7 out of 7 in 3ka8

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Frog M-Ferritin, Eqh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl192

b:38.2
occ:1.00
 CG A:GLU94 2.9 13.9 0.5
OE1 A:GLU94 3.1 15.6 0.5
ND2 A:ASN91 3.2 14.3 1.0
O A:HOH269 3.3 42.9 1.0
CD A:GLU94 3.5 13.8 0.5
CB A:PRO157 3.7 15.8 1.0
CG A:PRO157 3.8 17.5 1.0
OD1 A:ASN91 3.9 11.2 1.0
CG A:ASN91 4.0 10.8 1.0
CB A:GLU94 4.1 11.9 0.5
CB A:GLU94 4.2 11.8 0.5
CD A:PRO157 4.4 15.0 1.0
N A:GLU94 4.4 10.0 1.0
CD2 A:LEU93 4.6 12.3 1.0
CA A:GLU94 4.6 9.8 0.5
CA A:GLU94 4.7 9.7 0.5
OE2 A:GLU94 4.8 18.0 0.5
OE1 A:GLU94 4.8 25.9 0.5
O A:HOH266 4.8 34.5 1.0
CG A:LEU93 4.8 9.6 1.0
CA A:PRO157 4.9 14.2 1.0
CB A:LEU93 4.9 10.7 1.0
NE2 A:GLN97 4.9 20.6 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: Sat Jul 20 22:31:47 2024

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