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Chlorine in PDB 9eq8: Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes

Enzymatic activity of Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes

All present enzymatic activity of Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes:
1.16.3.1;

Protein crystallography data

The structure of Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes, PDB code: 9eq8 was solved by Z.Bugg, J.M.Bradley, N.E.Le Brun, A.M.Hemmings, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.87 / 1.48
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 182.77, 182.77, 182.77, 90, 90, 90
R / Rfree (%) 16.5 / 18.2

Other elements in 9eq8:

The structure of Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes also contains other interesting chemical elements:

Magnesium (Mg) 10 atoms
Iron (Fe) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes (pdb code 9eq8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes, PDB code: 9eq8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 9eq8

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Chlorine binding site 1 out of 8 in the Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl215

b:21.1
occ:0.70
 H A:ASP84 2.3 19.2 1.0
HB3 A:GLN83 2.8 26.0 1.0
N A:ASP84 3.2 16.0 1.0
HA A:GLN83 3.2 20.8 1.0
CG A:ASP84 3.6 16.4 1.0
OD1 A:ASP84 3.6 17.2 1.0
CB A:GLN83 3.7 21.6 1.0
CA A:GLN83 3.7 17.3 1.0
HB2 A:ASP84 3.7 19.7 1.0
OD2 A:ASP84 3.9 18.3 1.0
C A:GLN83 3.9 16.6 1.0
CB A:ASP84 4.0 16.4 1.0
CA A:ASP84 4.2 15.2 1.0
HB2 A:GLN83 4.2 26.0 1.0
HE21 A:GLN83 4.3 47.1 1.0
HG2 A:GLN83 4.3 36.3 1.0
O A:HOH332 4.6 20.0 1.0
O A:HOH323 4.6 22.9 0.5
CG A:GLN83 4.6 30.3 1.0
HA A:ASP84 4.7 18.2 1.0
O A:HOH376 4.8 26.4 1.0
MG A:MG207 4.8 19.2 0.5
HB3 A:ASP84 5.0 19.7 1.0

Chlorine binding site 2 out of 8 in 9eq8

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Chlorine binding site 2 out of 8 in the Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl216

b:36.3
occ:0.72
 O A:HOH425 2.1 32.6 1.0
HG A:SER95 2.7 25.1 1.0
HG3 A:PRO161 2.9 31.1 1.0
HB2 A:HIS98 3.0 23.6 1.0
OG A:SER95 3.0 20.9 1.0
O A:HOH454 3.1 44.1 1.0
HB3 A:SER95 3.2 22.2 1.0
HB3 A:GLU94 3.3 33.7 1.0
HB2 A:GLU94 3.6 33.7 1.0
CB A:SER95 3.6 18.5 1.0
CG A:PRO161 3.8 25.9 1.0
OE1 A:GLU94 3.9 42.9 1.0
CB A:GLU94 3.9 28.1 1.0
CB A:HIS98 3.9 19.7 1.0
HB3 A:HIS98 4.0 23.6 1.0
H A:HIS98 4.2 21.0 1.0
HG2 A:PRO161 4.2 31.1 1.0
HB3 A:PRO161 4.2 32.8 1.0
O A:HOH312 4.2 46.3 1.0
HB2 A:SER95 4.3 22.2 1.0
C A:GLU94 4.4 21.4 1.0
N A:SER95 4.4 20.9 1.0
CB A:PRO161 4.5 27.3 1.0
HD3 A:PRO161 4.5 29.7 1.0
O A:GLU94 4.6 19.9 1.0
CG A:HIS98 4.6 21.0 1.0
H A:SER95 4.6 25.1 1.0
CA A:SER95 4.7 19.1 1.0
HB2 A:PRO161 4.7 32.8 1.0
HD1 A:HIS98 4.7 29.1 1.0
N A:HIS98 4.8 17.5 1.0
CD A:PRO161 4.8 24.8 1.0
CA A:GLU94 4.8 23.8 1.0
CD A:GLU94 4.8 42.3 1.0
HB3 A:LEU97 4.8 23.0 1.0
CA A:HIS98 4.9 18.0 1.0
ND1 A:HIS98 4.9 24.3 1.0
CG A:GLU94 4.9 33.9 1.0

Chlorine binding site 3 out of 8 in 9eq8

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Chlorine binding site 3 out of 8 in the Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl217

b:97.8
occ:1.00
 O A:HOH312 2.7 46.3 1.0
O A:HOH305 2.9 54.0 1.0
HD1 A:HIS98 3.7 29.1 1.0
OE1 A:GLU101 4.0 37.6 1.0
ND1 A:HIS98 4.5 24.3 1.0
HE1 A:HIS98 4.7 30.5 1.0
O A:HOH425 4.9 32.6 1.0
CE1 A:HIS98 5.0 25.4 1.0
CD A:GLU101 5.0 32.0 1.0

Chlorine binding site 4 out of 8 in 9eq8

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Chlorine binding site 4 out of 8 in the Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl218

b:65.3
occ:1.00
 HD21 A:ASN74 2.5 31.6 1.0
HA A:ARG71 2.8 25.6 1.0
HG3 A:ARG71 3.1 29.8 1.0
HB2 A:ASN74 3.3 27.8 1.0
ND2 A:ASN74 3.4 26.3 1.0
HB2 A:ARG71 3.6 27.2 1.0
CA A:ARG71 3.7 21.3 1.0
HB3 A:ASN74 3.7 27.8 1.0
CB A:ASN74 3.8 23.2 1.0
CG A:ARG71 3.9 24.8 1.0
CB A:ARG71 3.9 22.7 1.0
HD22 A:ASN74 3.9 31.6 1.0
CG A:ASN74 4.1 27.8 1.0
HH11 A:ARG71 4.3 58.2 1.0
HD2 A:ARG71 4.4 34.5 1.0
O A:ARG71 4.4 17.9 1.0
HG2 A:ARG71 4.5 29.8 1.0
C A:ARG71 4.6 16.7 1.0
N A:ARG71 4.6 17.7 1.0
CD A:ARG71 4.7 28.8 1.0
O A:MET70 4.8 17.9 1.0
HB3 A:ARG71 4.8 27.2 1.0
HG3 A:GLN75 4.9 34.2 1.0
NH1 A:ARG71 5.0 48.5 1.0

Chlorine binding site 5 out of 8 in 9eq8

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Chlorine binding site 5 out of 8 in the Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl219

b:105.4
occ:1.00
 O A:HOH415 2.7 40.8 1.0
HA A:GLN90 2.8 41.2 1.0
HB3 A:GLN90 3.1 44.3 1.0
HG2 A:GLN90 3.2 48.9 1.0
HE21 A:GLN90 3.4 54.8 1.0
CB A:GLN90 3.6 36.9 1.0
CA A:GLN90 3.6 34.4 1.0
CG A:GLN90 3.8 40.7 1.0
H A:ASP91 3.9 47.6 1.0
O A:GLU89 3.9 39.7 1.0
NE2 A:GLN90 3.9 45.7 1.0
CD A:GLN90 4.2 43.8 1.0
H A:ASP92 4.3 48.2 1.0
N A:ASP91 4.5 39.7 1.0
HE22 A:GLN90 4.5 54.8 1.0
HB2 A:GLN90 4.5 44.3 1.0
N A:GLN90 4.6 34.4 1.0
C A:GLN90 4.6 34.3 1.0
C A:GLU89 4.6 41.0 1.0
HG3 A:GLN90 4.6 48.9 1.0
O A:HOH348 4.7 62.8 1.0
O A:ASP92 4.8 33.3 1.0
HB3 A:ASP92 4.8 42.2 1.0

Chlorine binding site 6 out of 8 in 9eq8

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Chlorine binding site 6 out of 8 in the Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl220

b:34.0
occ:0.53
 H A:GLU167 2.2 22.4 1.0
O A:ALA163 2.5 30.6 1.0
HG3 A:GLU167 2.7 26.6 1.0
HB3 A:ALA166 2.7 23.8 1.0
HB2 A:GLU167 3.0 23.3 1.0
N A:GLU167 3.0 18.7 1.0
H A:ALA166 3.2 22.4 1.0
HA A:ALA160 3.2 23.8 1.0
HA A:PRO161 3.2 32.6 1.0
O A:PRO161 3.2 31.4 1.0
CG A:GLU167 3.4 22.1 1.0
CB A:GLU167 3.6 19.4 1.0
C A:ALA163 3.6 27.9 1.0
O A:HOH339 3.6 24.4 1.0
CB A:ALA166 3.6 19.8 1.0
N A:ALA166 3.6 18.6 1.0
C A:PRO161 3.7 30.3 1.0
HA2 A:GLY164 3.8 30.8 1.0
CA A:ALA166 3.9 17.7 1.0
CA A:PRO161 3.9 27.1 1.0
CA A:GLU167 3.9 17.6 1.0
C A:ALA166 3.9 19.3 1.0
HB2 A:ALA160 4.0 23.1 1.0
CA A:ALA160 4.1 19.8 1.0
CD A:GLU167 4.1 25.2 1.0
HB2 A:ALA166 4.1 23.8 1.0
C A:GLY164 4.2 25.0 1.0
HB1 A:ALA160 4.2 23.1 1.0
HG2 A:GLU167 4.2 26.6 1.0
HB1 A:ALA166 4.3 23.8 1.0
O A:GLY164 4.3 25.1 1.0
CA A:GLY164 4.3 25.7 1.0
H A:ALA163 4.3 29.1 1.0
CB A:ALA160 4.3 19.2 1.0
H A:TYR168 4.3 21.0 1.0
HB3 A:ALA163 4.4 30.1 1.0
N A:ALA163 4.4 24.3 1.0
N A:GLY164 4.4 27.5 1.0
HB3 A:GLU167 4.5 23.3 1.0
HA A:GLU167 4.5 21.2 1.0
OE1 A:GLU167 4.5 27.5 1.0
C A:LEU165 4.6 19.7 1.0
N A:ASP162 4.6 30.1 1.0
CA A:ALA163 4.6 26.2 1.0
N A:LEU165 4.6 21.4 1.0
OE2 A:GLU167 4.7 25.8 1.0
N A:ALA160 4.8 19.6 1.0
C A:ASP162 4.9 29.4 1.0
HA A:ALA166 4.9 21.2 1.0
H A:LEU165 4.9 25.7 1.0
N A:PRO161 4.9 24.1 1.0
N A:TYR168 5.0 17.4 1.0
CB A:ALA163 5.0 25.0 1.0

Chlorine binding site 7 out of 8 in 9eq8

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Chlorine binding site 7 out of 8 in the Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl221

b:46.6
occ:0.25
 FE A:FE203 2.2 40.2 0.2
NE2 A:HIS173 3.2 20.6 1.0
HD2 A:HIS173 3.6 25.8 1.0
CD2 A:HIS173 3.8 21.5 1.0
O A:HOH477 4.3 54.6 1.0
CE1 A:HIS173 4.3 29.1 1.0
CL A:CL222 4.4 37.7 0.2
O A:HOH475 4.5 47.3 1.0
HE1 A:HIS173 4.6 34.9 1.0

Chlorine binding site 8 out of 8 in 9eq8

Go back to Chlorine Binding Sites List in 9eq8
Chlorine binding site 8 out of 8 in the Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Iron Loaded Mitochondrial Ferritin Exposed to Oxygen For 2 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl222

b:37.7
occ:0.25
 FE A:FE203 2.2 40.2 0.2
HE1 A:HIS173 2.4 34.9 1.0
CE1 A:HIS173 3.0 29.1 1.0
NE2 A:HIS173 3.2 20.6 1.0
HD22 A:LEU169 3.4 25.6 1.0
HD21 A:LEU169 3.8 25.6 1.0
CD2 A:LEU169 4.0 21.4 1.0
ND1 A:HIS173 4.2 30.5 1.0
HD23 A:LEU169 4.3 25.6 1.0
CL A:CL221 4.4 46.6 0.2
CD2 A:HIS173 4.5 21.5 1.0
HD1 A:HIS173 4.6 36.6 1.0
CG A:HIS173 5.0 23.8 1.0

Reference:

J.M.Bradley, Z.Bugg, G.R.Moore, A.M.Hemmings, N.Le-Brun. The Core Nucleation Site of Human Mitochondrial Ferritin: Observation of the Nascent Mineral To Be Published.
Page generated: Sun Jul 13 16:32:43 2025

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