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Chlorine in PDB 4lpm: Frog M-Ferritin with Magnesium, D127E Mutant

Enzymatic activity of Frog M-Ferritin with Magnesium, D127E Mutant

All present enzymatic activity of Frog M-Ferritin with Magnesium, D127E Mutant:
1.16.3.1;

Protein crystallography data

The structure of Frog M-Ferritin with Magnesium, D127E Mutant, PDB code: 4lpm was solved by R.Torres, R.Behera, C.W.Goulding, E.C.Theil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.98 / 1.65
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.913, 183.913, 183.913, 90.00, 90.00, 90.00
R / Rfree (%) 12.6 / 16.4

Other elements in 4lpm:

The structure of Frog M-Ferritin with Magnesium, D127E Mutant also contains other interesting chemical elements:

Magnesium (Mg) 11 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Frog M-Ferritin with Magnesium, D127E Mutant (pdb code 4lpm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Frog M-Ferritin with Magnesium, D127E Mutant, PDB code: 4lpm:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4lpm

Go back to Chlorine Binding Sites List in 4lpm
Chlorine binding site 1 out of 6 in the Frog M-Ferritin with Magnesium, D127E Mutant


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, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:11.2
occ:0.25
 HE2 A:HIS169 2.4 17.1 1.0
NE2 A:HIS169 3.2 14.3 1.0
HD22 A:LEU165 3.4 18.4 1.0
HD21 A:LEU165 3.7 18.4 1.0
HE1 A:HIS169 3.8 20.8 1.0
CE1 A:HIS169 3.9 17.3 1.0
CD2 A:LEU165 3.9 15.3 1.0
HD23 A:LEU165 4.1 18.4 1.0
CD2 A:HIS169 4.3 12.7 1.0
HD2 A:HIS169 4.5 15.2 1.0
CL A:CL203 4.8 22.1 0.2

Chlorine binding site 2 out of 6 in 4lpm

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Chlorine binding site 2 out of 6 in the Frog M-Ferritin with Magnesium, D127E Mutant


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, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:22.1
occ:0.25
 HE1 A:HIS169 2.8 20.8 1.0
CE1 A:HIS169 3.7 17.3 1.0
HE2 A:HIS169 4.5 17.1 1.0
NE2 A:HIS169 4.5 14.3 1.0
ND1 A:HIS169 4.6 16.8 1.0
HD1 A:HIS169 4.6 20.2 1.0
CL A:CL201 4.8 11.2 0.2

Chlorine binding site 3 out of 6 in 4lpm

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Chlorine binding site 3 out of 6 in the Frog M-Ferritin with Magnesium, D127E Mutant


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, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:29.0
occ:1.00
 H A:SER10 2.3 12.8 1.0
HA A:HIS9 2.9 12.6 1.0
O A:HOH492 3.1 38.8 1.0
O A:HOH441 3.1 33.0 1.0
N A:SER10 3.1 10.7 1.0
HB2 A:SER10 3.3 15.5 1.0
HB3 A:SER10 3.5 15.5 1.0
O A:HOH514 3.6 29.9 1.0
CB A:SER10 3.7 12.9 1.0
CA A:HIS9 3.8 10.5 1.0
CD2 A:HIS9 3.8 15.5 1.0
CG A:HIS9 3.8 13.5 1.0
C A:HIS9 3.9 10.2 1.0
NE2 A:HIS9 3.9 16.0 1.0
ND1 A:HIS9 4.0 13.1 1.0
CA A:SER10 4.0 10.4 1.0
CE1 A:HIS9 4.1 15.4 1.0
HD2 A:HIS9 4.1 18.6 1.0
HE2 A:HIS9 4.3 19.1 1.0
O A:TYR8 4.4 10.9 1.0
HD1 A:HIS9 4.4 15.8 1.0
CB A:HIS9 4.4 12.1 1.0
HH11 A:ARG5 4.5 14.6 1.0
HA A:SER10 4.5 12.5 1.0
HE1 A:HIS9 4.5 18.5 1.0
H A:ASP11 4.7 12.4 1.0
O A:HOH425 4.8 31.4 1.0
N A:HIS9 4.9 10.2 1.0
O A:HOH501 4.9 34.1 1.0
HB2 A:HIS9 4.9 14.6 1.0
NH1 A:ARG5 5.0 12.2 1.0

Chlorine binding site 4 out of 6 in 4lpm

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Chlorine binding site 4 out of 6 in the Frog M-Ferritin with Magnesium, D127E Mutant


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, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:18.8
occ:1.00
 H A:TYR8 2.4 11.7 1.0
O A:HOH462 2.8 39.2 1.0
HG2 A:ARG5 2.8 12.6 1.0
HE A:ARG5 3.0 13.2 1.0
H A:ASN7 3.1 12.3 1.0
HD3 A:ARG5 3.1 13.4 1.0
O A:HOH514 3.2 29.9 1.0
N A:TYR8 3.3 9.8 1.0
N A:ASN7 3.4 10.3 1.0
O A:TYR8 3.5 10.9 1.0
CD A:ARG5 3.6 11.2 1.0
HA A:GLN6 3.6 12.0 1.0
CG A:ARG5 3.6 10.5 1.0
NE A:ARG5 3.6 11.0 1.0
HB3 A:TYR8 3.9 10.8 1.0
O A:HOH397 3.9 22.4 1.0
C A:GLN6 4.0 9.2 1.0
HA A:ASN7 4.0 11.7 1.0
C A:TYR8 4.1 9.4 1.0
CA A:GLN6 4.1 10.0 1.0
N A:GLN6 4.1 10.0 1.0
CA A:TYR8 4.1 9.2 1.0
CA A:ASN7 4.1 9.8 1.0
C A:ASN7 4.2 9.2 1.0
HB3 A:ARG5 4.2 12.8 1.0
HG3 A:ARG5 4.3 12.6 1.0
H A:GLN6 4.3 12.0 1.0
C A:ARG5 4.4 9.8 1.0
CB A:TYR8 4.4 9.0 1.0
CB A:ARG5 4.5 10.7 1.0
HD2 A:ARG5 4.5 13.4 1.0
O A:HOH455 4.6 36.5 1.0
O A:ARG5 4.6 10.5 1.0
HB2 A:TYR8 4.6 10.8 1.0
O A:GLN6 4.8 10.3 1.0
HH11 A:ARG5 4.8 14.6 1.0
CZ A:ARG5 4.8 10.6 1.0
HA A:TYR8 5.0 11.1 1.0

Chlorine binding site 5 out of 6 in 4lpm

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Chlorine binding site 5 out of 6 in the Frog M-Ferritin with Magnesium, D127E Mutant


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, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl214

b:22.2
occ:0.33
 MG A:MG213 2.3 2.9 0.3
OE1 A:GLU127 3.4 16.8 1.0
O A:HOH529 3.4 37.3 1.0
HB2 A:SER131 3.7 21.3 1.0
HB3 A:SER131 3.8 21.3 1.0
O A:HOH396 3.8 23.9 1.0
O A:HOH583 3.9 51.2 1.0
CB A:SER131 4.2 17.8 1.0
O A:HOH489 4.4 34.4 1.0
CD A:GLU127 4.6 14.1 1.0
MG A:MG212 4.7 29.9 0.8
HA A:SER131 4.9 18.2 1.0

Chlorine binding site 6 out of 6 in 4lpm

Go back to Chlorine Binding Sites List in 4lpm
Chlorine binding site 6 out of 6 in the Frog M-Ferritin with Magnesium, D127E Mutant


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, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl215

b:24.6
occ:1.00
 H A:ASP87 2.3 16.7 1.0
O A:HOH523 2.8 35.9 1.0
H A:GLU88 2.9 13.9 1.0
HG3 A:GLU88 3.0 25.1 1.0
O A:HOH591 3.1 39.4 1.0
N A:ASP87 3.1 13.9 1.0
HA A:ARG86 3.2 16.5 1.0
HB3 A:ARG86 3.3 16.3 1.0
HB2 A:ASP87 3.3 17.4 1.0
O A:HOH587 3.6 46.6 1.0
N A:GLU88 3.7 11.6 1.0
HG2 A:ARG86 3.8 17.9 1.0
CA A:ARG86 3.8 13.8 1.0
CB A:ARG86 3.9 13.6 1.0
HE A:ARG86 3.9 24.4 1.0
C A:ARG86 3.9 12.6 1.0
CA A:ASP87 4.0 13.5 1.0
CG A:GLU88 4.0 20.9 1.0
CB A:ASP87 4.0 14.4 1.0
O A:GLU88 4.1 13.7 1.0
HG2 A:GLU88 4.3 25.1 1.0
C A:ASP87 4.3 12.6 1.0
CG A:ARG86 4.3 14.9 1.0
OE2 A:GLU88 4.6 28.9 1.0
OD2 A:ASP87 4.6 22.2 1.0
CG A:ASP87 4.6 17.2 1.0
CA A:GLU88 4.6 13.2 1.0
O A:HOH589 4.7 41.6 1.0
NE A:ARG86 4.7 20.3 1.0
O A:HOH570 4.7 41.9 1.0
HB2 A:ARG86 4.8 16.3 1.0
CB A:GLU88 4.8 16.6 1.0
HB3 A:ASP87 4.8 17.4 1.0
CD A:GLU88 4.8 25.3 1.0
C A:GLU88 4.8 12.6 1.0
HA A:ASP87 4.8 16.2 1.0
HB3 A:GLU88 4.9 19.9 1.0

Reference:

R.Behera, R.Torres, T.Takehiko, J.Bradley, C.W.Goulding, E.C.Theil. D127E Ion Channel Exit Modification in Ferritin Nanocages Entraps Fe(II) and Impairs Its Distribution to Diiron Catalytic Centers To Be Published.
Page generated: Fri Jul 11 18:39:12 2025

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