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Chlorine in PDB 4lyx: Five Minutes Iron Loaded Frog M Ferritin

Enzymatic activity of Five Minutes Iron Loaded Frog M Ferritin

All present enzymatic activity of Five Minutes Iron Loaded Frog M Ferritin:
1.16.3.1;

Protein crystallography data

The structure of Five Minutes Iron Loaded Frog M Ferritin, PDB code: 4lyx was solved by S.Mangani, F.Di Pisa, C.Pozzi, P.Turano, D.Lalli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.22 / 1.23
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.180, 184.180, 184.180, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 17.5

Other elements in 4lyx:

The structure of Five Minutes Iron Loaded Frog M Ferritin also contains other interesting chemical elements:

Magnesium (Mg) 11 atoms
Iron (Fe) 3 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Five Minutes Iron Loaded Frog M Ferritin (pdb code 4lyx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Five Minutes Iron Loaded Frog M Ferritin, PDB code: 4lyx:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 4lyx

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Chlorine binding site 1 out of 12 in the Five Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl215

b:17.0
occ:0.50
 O A:HOH367 2.3 22.7 1.0
OG A:SER170 2.7 14.3 1.0
O A:HOH317 3.2 11.1 1.0
ND2 A:ASN150 3.4 8.8 1.0
CG A:ASN150 3.5 9.1 1.0
CB A:SER170 3.5 12.4 1.0
CB A:ASN150 3.7 8.6 1.0
OD1 A:ASN150 4.1 9.1 1.0
CD1 A:PHE147 4.1 12.8 1.0
CE1 A:PHE147 4.3 15.4 1.0
CA A:SER170 4.3 12.7 1.0
CE1 A:PHE166 4.4 11.4 1.0
CD1 A:PHE166 4.8 10.6 1.0
O A:ASP146 4.9 8.6 1.0

Chlorine binding site 2 out of 12 in 4lyx

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Chlorine binding site 2 out of 12 in the Five Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

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

b:20.8
occ:0.40
 O A:HOH580 2.9 36.1 1.0
CG A:GLU94 3.0 12.8 0.6
O A:HOH644 3.1 36.5 1.0
OE1 A:GLU94 3.2 13.7 0.6
ND2 A:ASN91 3.3 11.9 1.0
CD A:GLU94 3.6 13.0 0.6
CB A:PRO157 3.7 14.9 1.0
OD1 A:ASN91 3.8 10.5 1.0
CG A:PRO157 3.9 15.9 1.0
CG A:ASN91 4.0 10.2 1.0
O A:HOH591 4.1 48.5 1.0
CD A:PRO157 4.3 14.1 1.0
CB A:GLU94 4.3 10.1 1.0
CD2 A:LEU93 4.3 11.8 1.0
N A:GLU94 4.4 9.1 1.0
CG A:LEU93 4.6 10.2 1.0
CB A:LEU93 4.7 9.4 1.0
CA A:GLU94 4.7 9.1 1.0
CA A:PRO157 4.8 12.4 1.0
NE2 A:GLN97 4.9 12.0 0.6
OE2 A:GLU94 4.9 12.7 0.6
N A:PRO157 4.9 12.1 1.0

Chlorine binding site 3 out of 12 in 4lyx

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Chlorine binding site 3 out of 12 in the Five Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl217

b:14.8
occ:1.00
 O A:HOH584 3.0 35.9 1.0
O A:HOH460 3.1 30.1 1.0
O A:HOH608 3.1 34.6 1.0
N A:TYR8 3.3 8.6 1.0
N A:ASN7 3.4 8.5 1.0
CD A:ARG5 3.5 10.8 1.0
O A:TYR8 3.5 10.0 1.0
CG A:ARG5 3.6 9.5 1.0
NE A:ARG5 3.6 10.4 1.0
O A:HOH388 3.9 21.4 1.0
C A:GLN6 4.0 8.5 1.0
CA A:GLN6 4.0 8.6 1.0
C A:TYR8 4.1 9.3 1.0
CA A:ASN7 4.1 8.7 1.0
N A:GLN6 4.1 8.6 1.0
CA A:TYR8 4.1 8.6 1.0
C A:ASN7 4.2 8.6 1.0
C A:ARG5 4.3 8.8 1.0
O A:HOH513 4.4 28.9 1.0
CB A:TYR8 4.5 8.8 1.0
CB A:ARG5 4.5 10.0 1.0
O A:ARG5 4.5 9.6 1.0
O A:GLN6 4.8 8.9 1.0
CZ A:ARG5 4.9 10.4 1.0

Chlorine binding site 4 out of 12 in 4lyx

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Chlorine binding site 4 out of 12 in the Five Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl218

b:17.2
occ:0.80
 O A:HOH556 3.0 37.5 1.0
N A:ASP87 3.1 10.3 1.0
O A:HOH565 3.1 35.6 1.0
O A:HOH634 3.2 40.4 1.0
O A:HOH626 3.5 48.4 1.0
N A:GLU88 3.7 10.0 1.0
CA A:ARG86 3.8 10.4 1.0
CB A:ARG86 3.8 10.8 1.0
C A:ARG86 4.0 10.0 1.0
CA A:ASP87 4.0 10.4 1.0
CG A:GLU88 4.0 12.8 0.5
CB A:ASP87 4.0 11.5 1.0
O A:GLU88 4.0 10.7 1.0
CG A:ARG86 4.2 13.5 1.0
C A:ASP87 4.3 11.1 1.0
O A:HOH547 4.3 42.9 1.0
OE2 A:GLU88 4.4 15.1 0.5
O A:HOH611 4.4 46.9 1.0
CA A:GLU88 4.6 10.2 1.0
NE A:ARG86 4.6 13.8 0.6
OD2 A:ASP87 4.6 16.7 1.0
CG A:ASP87 4.6 12.4 1.0
CD A:GLU88 4.7 14.0 0.5
CB A:GLU88 4.8 12.4 1.0
C A:GLU88 4.8 9.3 1.0
O A:HOH484 4.8 33.6 1.0

Chlorine binding site 5 out of 12 in 4lyx

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Chlorine binding site 5 out of 12 in the Five Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl219

b:17.6
occ:0.20
 FE A:FE2203 3.5 13.4 0.1
CE1 A:HIS169 3.6 12.8 0.5
CE1 A:HIS169 4.3 15.1 0.5
NE2 A:HIS169 4.5 11.2 0.5
ND1 A:HIS169 4.5 11.5 0.5
ND1 A:HIS169 4.6 17.6 0.5
O A:HOH568 4.9 46.2 1.0

Chlorine binding site 6 out of 12 in 4lyx

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Chlorine binding site 6 out of 12 in the Five Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl220

b:11.4
occ:0.20
 FE A:FE2203 1.6 13.4 0.1
CE1 A:HIS169 3.1 15.1 0.5
NE2 A:HIS169 3.2 11.2 0.5
NE2 A:HIS169 3.3 18.4 0.5
CD2 A:LEU165 3.9 14.7 1.0
CE1 A:HIS169 4.0 12.8 0.5
CD2 A:HIS169 4.2 8.6 0.5
ND1 A:HIS169 4.4 17.6 0.5
CD2 A:HIS169 4.6 17.6 0.5

Chlorine binding site 7 out of 12 in 4lyx

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Chlorine binding site 7 out of 12 in the Five Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl221

b:16.0
occ:0.70
 O A:HOH549 3.0 31.2 1.0
N A:GLU136 3.2 13.8 1.0
C A:GLU132 3.4 11.9 1.0
N A:GLU135 3.4 11.5 1.0
N A:TYR133 3.4 10.7 1.0
O A:SER131 3.5 14.8 1.0
CB A:GLU135 3.7 14.5 1.0
O A:GLU132 3.7 13.9 1.0
C A:TYR133 3.7 10.7 1.0
CA A:GLU135 3.8 12.4 1.0
C A:SER131 3.8 12.6 1.0
CA A:GLU132 3.9 11.8 1.0
N A:LEU134 3.9 10.7 1.0
CA A:TYR133 3.9 10.4 1.0
N A:GLU132 3.9 11.8 1.0
C A:GLU135 4.0 12.6 1.0
CB A:GLU136 4.0 18.7 1.0
O A:GLU130 4.0 15.3 1.0
O A:HOH573 4.0 37.6 1.0
O A:HOH533 4.1 31.7 1.0
O A:TYR133 4.1 12.1 1.0
CG A:GLU136 4.1 15.0 0.5
CA A:GLU136 4.2 14.2 1.0
C A:LEU134 4.4 10.7 1.0
CG A:GLU135 4.5 14.5 1.0
CA A:LEU134 4.7 10.8 1.0
CA A:SER131 4.7 13.9 0.5
CA A:SER131 4.8 13.3 0.5
C A:GLU130 4.8 12.3 1.0

Chlorine binding site 8 out of 12 in 4lyx

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Chlorine binding site 8 out of 12 in the Five Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl222

b:14.2
occ:0.80
 O A:HOH398 3.0 15.6 1.0
O A:HOH577 3.1 31.4 1.0
O A:HOH383 3.1 24.1 1.0
O A:HOH474 3.3 29.4 1.0
ND2 A:ASN17 3.3 9.0 1.0
CB A:ASN17 3.8 7.9 1.0
CA A:ALA14 4.0 8.8 1.0
CG A:ASN17 4.0 8.0 1.0
CB A:VAL77 4.0 10.0 1.0
O A:HOH499 4.1 34.7 1.0
CB A:ALA14 4.1 9.7 1.0
O A:ALA14 4.3 8.7 1.0
CG2 A:VAL77 4.3 11.6 1.0
CG1 A:VAL77 4.5 11.9 1.0
C A:ALA14 4.7 8.3 1.0
O A:HOH315 4.7 12.4 1.0
O A:HOH647 4.9 43.8 1.0
O A:HOH539 4.9 34.4 1.0

Chlorine binding site 9 out of 12 in 4lyx

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Chlorine binding site 9 out of 12 in the Five Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl223

b:16.9
occ:0.80
 NZ A:LYS82 2.9 10.8 0.5
NZ A:LYS82 3.2 11.3 0.5
CE A:LYS82 3.4 11.0 0.5
CE A:LYS82 3.5 10.8 0.5
O A:HOH595 3.8 45.6 1.0
O A:HOH470 3.8 24.9 1.0
O A:HOH419 4.8 22.9 1.0
CD A:LYS82 5.0 9.9 0.5

Chlorine binding site 10 out of 12 in 4lyx

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Chlorine binding site 10 out of 12 in the Five Minutes Iron Loaded Frog M Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl224

b:17.1
occ:0.70
 O A:HOH523 2.8 29.1 1.0
OG1 A:THR105 3.1 11.2 1.0
O A:HOH319 3.1 13.2 1.0
CA A:LEU102 3.6 9.6 1.0
O A:GLN101 3.6 10.4 1.0
CG A:GLN101 3.7 16.4 1.0
N A:LEU102 3.7 9.2 1.0
C A:GLN101 3.7 9.7 1.0
CB A:THR105 3.8 10.4 1.0
O A:HOH464 3.9 22.7 1.0
CD A:GLN101 4.2 21.6 0.5
CB A:GLN101 4.3 11.3 1.0
CB A:LEU102 4.3 10.4 1.0
CG2 A:THR105 4.4 11.7 1.0
CD1 A:LEU102 4.5 13.0 1.0
OE1 A:GLN101 4.5 24.0 0.5
CA A:GLN101 4.6 9.9 1.0
O A:HOH487 4.7 30.8 1.0
O A:HOH413 4.7 19.3 1.0
C A:LEU102 4.8 9.3 1.0
O A:HOH370 4.8 20.9 1.0
O A:HOH587 4.8 37.0 1.0
NE2 A:GLN101 4.9 22.0 0.5
O A:LEU102 4.9 9.3 1.0

Reference:

S.Mangani, F.Di Pisa, C.Pozzi, P.Turano, D.Lalli. Crystallographic Snapshots of Iron in Frog M Ferritin To Be Published.
Page generated: Sun Jul 21 19:24:47 2024

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