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Chlorine in PDB 3ka3: Frog M-Ferritin with Magnesium

Enzymatic activity of Frog M-Ferritin with Magnesium

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

Protein crystallography data

The structure of Frog M-Ferritin with Magnesium, PDB code: 3ka3 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 (°) 183.886, 183.886, 183.886, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 15.9

Other elements in 3ka3:

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

Magnesium (Mg) 10 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Frog M-Ferritin with Magnesium (pdb code 3ka3). 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 with Magnesium, PDB code: 3ka3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 3ka3

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Chlorine binding site 1 out of 7 in the Frog M-Ferritin with Magnesium


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 with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl181

b:29.4
occ:1.00
 N A:SER10 3.1 11.5 1.0
O A:HOH230 3.2 39.4 1.0
O A:HOH276 3.3 43.2 1.0
O A:HOH484 3.6 30.8 1.0
CB A:SER10 3.7 14.3 1.0
CA A:HIS9 3.8 11.4 1.0
CG A:HIS9 3.8 11.4 1.0
CD2 A:HIS9 3.9 15.1 1.0
C A:HIS9 3.9 11.0 1.0
ND1 A:HIS9 4.0 12.4 1.0
CA A:SER10 4.0 11.6 1.0
CE1 A:HIS9 4.0 14.7 1.0
NE2 A:HIS9 4.0 16.4 1.0
O A:TYR8 4.3 11.9 1.0
CB A:HIS9 4.4 12.6 1.0
N A:HIS9 4.8 11.3 1.0
O A:HOH452 4.9 34.9 1.0
NH1 A:ARG5 5.0 13.3 1.0
O A:HOH247 5.0 35.9 1.0

Chlorine binding site 2 out of 7 in 3ka3

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Chlorine binding site 2 out of 7 in the Frog M-Ferritin with Magnesium


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 with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl182

b:18.9
occ:1.00
 O A:HOH241 2.6 37.6 1.0
O A:HOH484 3.2 30.8 1.0
N A:TYR8 3.3 10.9 1.0
N A:ASN7 3.5 11.2 1.0
O A:TYR8 3.5 11.9 1.0
CD A:ARG5 3.5 11.9 1.0
NE A:ARG5 3.6 12.7 1.0
CG A:ARG5 3.6 11.9 1.0
O A:HOH382 3.8 22.5 1.0
C A:GLN6 3.9 10.4 1.0
CA A:GLN6 4.0 10.4 1.0
C A:TYR8 4.0 10.5 1.0
CA A:TYR8 4.1 10.7 1.0
N A:GLN6 4.1 11.0 1.0
CA A:ASN7 4.1 10.9 1.0
C A:ASN7 4.2 10.3 1.0
O A:HOH205 4.3 40.2 1.0
C A:ARG5 4.4 11.2 1.0
CB A:TYR8 4.4 11.0 1.0
CB A:ARG5 4.5 10.8 1.0
O A:ARG5 4.6 11.9 1.0
O A:GLN6 4.8 11.1 1.0
CZ A:ARG5 4.8 12.9 1.0

Chlorine binding site 3 out of 7 in 3ka3

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Chlorine binding site 3 out of 7 in the Frog M-Ferritin with Magnesium


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 with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl184

b:25.4
occ:1.00
 O A:HOH281 2.7 36.9 1.0
N A:ASP87 3.1 12.5 1.0
N A:GLU88 3.7 12.5 1.0
CA A:ARG86 3.8 13.5 1.0
CB A:ARG86 3.8 13.5 1.0
C A:ARG86 3.9 11.7 1.0
CA A:ASP87 3.9 13.6 1.0
CB A:ASP87 4.0 15.0 1.0
O A:GLU88 4.1 14.6 1.0
CG A:GLU88 4.1 12.7 0.5
CG A:ARG86 4.3 16.4 1.0
C A:ASP87 4.3 13.2 1.0
CB A:GLU88 4.4 15.3 0.5
CA A:GLU88 4.5 13.3 0.5
CA A:GLU88 4.6 12.1 0.5
CG A:ASP87 4.6 15.6 1.0
NE A:ARG86 4.7 20.1 1.0
OD2 A:ASP87 4.7 23.2 1.0
OE2 A:GLU88 4.7 20.8 0.5
O A:HOH295 4.7 40.1 1.0
O A:HOH306 4.7 42.0 1.0
C A:GLU88 4.8 12.8 1.0
CB A:GLU88 4.8 12.6 0.5

Chlorine binding site 4 out of 7 in 3ka3

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Chlorine binding site 4 out of 7 in the Frog M-Ferritin with Magnesium


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 with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl187

b:24.1
occ:1.00
 O A:HOH458 3.0 32.2 1.0
O A:HOH426 3.2 24.2 1.0
N A:GLU136 3.2 16.4 1.0
N A:TYR133 3.4 13.5 1.0
N A:GLU135 3.4 14.7 1.0
C A:GLU132 3.4 14.4 1.0
O A:SER131 3.5 18.5 1.0
CB A:GLU135 3.6 17.8 1.0
C A:TYR133 3.7 13.1 1.0
C A:SER131 3.8 16.4 1.0
CA A:GLU135 3.8 16.1 1.0
O A:GLU132 3.8 16.7 1.0
CA A:TYR133 3.8 14.4 1.0
N A:GLU132 3.9 15.1 1.0
N A:LEU134 3.9 13.8 1.0
CA A:GLU132 3.9 14.1 1.0
C A:GLU135 3.9 16.0 1.0
O A:GLU130 3.9 19.8 1.0
CB A:GLU136 4.0 21.2 0.5
CB A:GLU136 4.0 18.6 0.5
CG A:GLU136 4.0 16.3 0.5
O A:TYR133 4.1 14.6 1.0
CA A:GLU136 4.1 16.9 0.5
CA A:GLU136 4.2 15.3 0.5
CG A:GLU136 4.2 24.9 0.5
C A:LEU134 4.4 13.6 1.0
CG A:GLU135 4.5 18.3 1.0
O A:HOH471 4.6 28.2 1.0
CA A:SER131 4.7 16.9 0.5
CA A:SER131 4.7 15.8 0.5
CA A:LEU134 4.7 13.5 1.0
C A:GLU130 4.8 16.6 1.0
O A:HOH238 4.8 42.3 1.0
O A:HOH415 4.9 24.6 1.0

Chlorine binding site 5 out of 7 in 3ka3

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Chlorine binding site 5 out of 7 in the Frog M-Ferritin with Magnesium


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 with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl188

b:12.0
occ:0.25
 NE2 A:HIS169 3.2 12.7 1.0
CD2 A:LEU165 3.9 14.3 1.0
CE1 A:HIS169 3.9 15.0 1.0
CD2 A:HIS169 4.3 11.6 1.0
CL A:CL189 4.9 18.9 0.2

Chlorine binding site 6 out of 7 in 3ka3

Go back to Chlorine Binding Sites List in 3ka3
Chlorine binding site 6 out of 7 in the Frog M-Ferritin with Magnesium


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 with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl189

b:18.9
occ:0.25
 CE1 A:HIS169 3.7 15.0 1.0
NE2 A:HIS169 4.5 12.7 1.0
ND1 A:HIS169 4.6 15.9 1.0
CL A:CL188 4.9 12.0 0.2

Chlorine binding site 7 out of 7 in 3ka3

Go back to Chlorine Binding Sites List in 3ka3
Chlorine binding site 7 out of 7 in the Frog M-Ferritin with Magnesium


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 with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl191

b:38.9
occ:1.00
 O A:HOH266 2.6 34.5 1.0
NH2 A:ARG5 3.0 13.2 1.0
N A:SER2 3.0 14.2 1.0
CB A:VAL1 3.2 26.1 1.0
O A:GLY73 3.3 13.1 1.0
CA A:VAL1 3.5 24.0 1.0
CD A:ARG5 3.5 11.9 1.0
CB A:SER2 3.6 12.3 1.0
CG1 A:VAL1 3.7 31.8 1.0
C A:VAL1 3.8 18.8 1.0
CA A:SER2 3.9 12.4 1.0
CZ A:ARG5 4.0 12.9 1.0
NE A:ARG5 4.1 12.7 1.0
O A:HOH372 4.2 22.3 1.0
CG A:ARG5 4.2 11.9 1.0
CB A:ARG5 4.3 10.8 1.0
C A:GLY73 4.3 10.8 1.0
CG2 A:VAL1 4.4 23.6 1.0
O A:HOH452 4.8 34.9 1.0
O A:HOH371 4.8 31.6 1.0
N A:VAL1 4.8 26.9 1.0
O A:SER2 4.8 11.9 1.0
OG A:SER2 4.9 13.4 1.0
C A:SER2 4.9 12.4 1.0
O A:VAL1 5.0 21.2 1.0
O A:HOH222 5.0 36.0 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: Sat Jul 20 22:30:42 2024

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