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Chlorine in PDB 4lpn: Frog M-Ferritin with Cobalt, D127E Mutant

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

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

Protein crystallography data

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

Resolution Low / High (Å) 46.00 / 1.66
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.003, 184.003, 184.003, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 17.7

Other elements in 4lpn:

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

Cobalt (Co) 11 atoms
Magnesium (Mg) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Frog M-Ferritin with Cobalt, D127E Mutant (pdb code 4lpn). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Frog M-Ferritin with Cobalt, D127E Mutant, PDB code: 4lpn:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 4lpn

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Chlorine binding site 1 out of 9 in the Frog M-Ferritin with Cobalt, 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 Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl212

b:12.6
occ:0.25
 CO A:CO205 2.3 11.7 0.2
HE1 A:HIS169 2.9 14.1 1.0
NE2 A:HIS169 3.2 10.6 1.0
HD22 A:LEU165 3.2 19.1 1.0
CE1 A:HIS169 3.3 11.8 1.0
HD21 A:LEU165 3.5 19.1 1.0
CD2 A:LEU165 3.7 15.9 1.0
HD23 A:LEU165 3.8 19.1 1.0
ND1 A:HIS169 4.4 12.0 1.0
CD2 A:HIS169 4.4 13.1 1.0
O A:HOH317 4.6 17.3 0.2
HD1 A:HIS169 4.9 14.4 1.0
HD2 A:HIS169 4.9 15.7 1.0

Chlorine binding site 2 out of 9 in 4lpn

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Chlorine binding site 2 out of 9 in the Frog M-Ferritin with Cobalt, 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 Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl213

b:32.9
occ:1.00
 H A:GLU136 2.3 21.3 0.4
H A:GLU136 2.4 21.1 0.6
HB2 A:GLU136 3.0 27.4 0.6
HB3 A:GLU136 3.1 27.1 0.4
N A:GLU136 3.1 17.7 0.4
N A:GLU136 3.1 17.6 0.6
HB3 A:GLU135 3.2 31.1 1.0
HB2 A:GLU136 3.2 27.1 0.4
H A:GLU135 3.2 19.5 1.0
C A:GLU132 3.2 15.7 1.0
N A:TYR133 3.4 12.6 1.0
O A:GLU132 3.4 17.7 1.0
CB A:GLU136 3.5 22.6 0.4
HA A:GLU132 3.5 15.8 1.0
H A:TYR133 3.7 15.2 1.0
CB A:GLU136 3.7 22.8 0.6
HA A:TYR133 3.7 16.5 1.0
N A:GLU135 3.7 16.3 1.0
O A:SER131 3.7 19.9 1.0
HB3 A:GLU136 3.8 27.4 0.6
C A:TYR133 3.8 15.2 1.0
CA A:GLU132 3.8 13.2 1.0
CA A:TYR133 3.8 13.7 1.0
CA A:GLU136 3.8 19.2 0.4
CB A:GLU135 4.0 25.9 1.0
CA A:GLU136 4.0 19.1 0.6
C A:GLU135 4.0 18.8 1.0
O A:TYR133 4.0 16.0 1.0
CA A:GLU135 4.0 18.8 1.0
C A:SER131 4.1 17.8 1.0
N A:GLU132 4.1 14.1 1.0
N A:LEU134 4.2 14.1 1.0
HA A:GLU136 4.3 23.0 0.4
HG3 A:GLU135 4.3 41.0 1.0
H A:LEU134 4.3 16.9 1.0
HA A:GLU136 4.4 22.9 0.6
O A:HOH469 4.6 35.1 1.0
C A:LEU134 4.6 15.8 1.0
HB2 A:GLU135 4.7 31.1 1.0
CG A:GLU135 4.7 34.2 1.0
H A:GLU132 4.7 16.9 1.0
H A:GLN137 4.7 18.1 0.4
OE2 A:GLU136 4.7 27.5 0.6
CG A:GLU136 4.9 28.2 0.4
H A:GLN137 4.9 17.1 0.6
HG2 A:GLU135 4.9 41.0 1.0
HG2 A:GLU136 5.0 33.8 0.4

Chlorine binding site 3 out of 9 in 4lpn

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Chlorine binding site 3 out of 9 in the Frog M-Ferritin with Cobalt, 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 Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl214

b:30.6
occ:1.00
 H A:SER10 2.2 14.8 1.0
HA A:HIS9 3.0 16.1 1.0
N A:SER10 3.1 12.3 1.0
HB2 A:SER10 3.3 20.3 1.0
HB3 A:SER10 3.4 20.3 1.0
CB A:SER10 3.7 16.9 1.0
CD2 A:HIS9 3.8 29.7 1.0
CA A:HIS9 3.8 13.4 1.0
CG A:HIS9 3.9 28.1 1.0
C A:HIS9 3.9 15.5 1.0
NE2 A:HIS9 3.9 32.3 1.0
CA A:SER10 4.0 12.9 1.0
ND1 A:HIS9 4.0 23.9 1.0
O A:HOH488 4.0 32.8 1.0
HD2 A:HIS9 4.1 35.7 1.0
CE1 A:HIS9 4.1 15.4 1.0
HE2 A:HIS9 4.3 38.7 1.0
O A:TYR8 4.4 14.3 1.0
HD1 A:HIS9 4.4 28.7 1.0
CB A:HIS9 4.5 15.1 1.0
HA A:SER10 4.5 15.5 1.0
HE1 A:HIS9 4.5 18.5 1.0
HH21 A:ARG5 4.6 18.7 1.0
H A:ASP11 4.8 16.8 1.0
O A:HOH437 4.8 31.2 1.0
N A:HIS9 4.9 13.5 1.0
HB2 A:HIS9 4.9 18.2 1.0

Chlorine binding site 4 out of 9 in 4lpn

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Chlorine binding site 4 out of 9 in the Frog M-Ferritin with Cobalt, 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 Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl215

b:23.4
occ:1.00
 H A:TYR8 2.4 17.4 1.0
HG2 A:ARG5 2.8 14.6 1.0
HE A:ARG5 3.1 19.7 1.0
H A:ASN7 3.1 15.3 1.0
HD3 A:ARG5 3.1 18.2 1.0
O A:HOH488 3.2 32.8 1.0
N A:TYR8 3.3 14.5 1.0
N A:ASN7 3.4 12.8 1.0
O A:TYR8 3.5 14.3 1.0
HA A:GLN6 3.6 14.8 1.0
CG A:ARG5 3.6 12.2 1.0
CD A:ARG5 3.6 15.2 1.0
NE A:ARG5 3.7 16.4 1.0
O A:HOH364 3.9 22.9 1.0
HB3 A:TYR8 3.9 16.4 1.0
C A:GLN6 4.0 13.2 1.0
HA A:ASN7 4.0 16.2 1.0
CA A:GLN6 4.0 12.3 1.0
C A:TYR8 4.1 12.2 1.0
N A:GLN6 4.1 12.0 1.0
CA A:ASN7 4.1 13.5 1.0
CA A:TYR8 4.1 11.9 1.0
C A:ASN7 4.2 14.6 1.0
HG3 A:ARG5 4.2 14.6 1.0
HB3 A:ARG5 4.2 17.4 1.0
H A:GLN6 4.3 14.4 1.0
C A:ARG5 4.3 11.9 1.0
CB A:TYR8 4.4 13.7 1.0
CB A:ARG5 4.5 14.5 1.0
O A:ARG5 4.5 14.7 1.0
HD2 A:ARG5 4.5 18.2 1.0
HB2 A:TYR8 4.6 16.4 1.0
O A:GLN6 4.8 13.8 1.0
CZ A:ARG5 4.9 16.7 1.0
HH21 A:ARG5 4.9 18.7 1.0
HA A:TYR8 5.0 14.3 1.0

Chlorine binding site 5 out of 9 in 4lpn

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Chlorine binding site 5 out of 9 in the Frog M-Ferritin with Cobalt, 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 Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl216

b:30.8
occ:1.00
 HZ2 A:LYS82 1.9 43.6 1.0
NZ A:LYS82 2.7 36.4 1.0
HZ3 A:LYS82 3.2 43.6 1.0
HZ1 A:LYS82 3.2 43.6 1.0
HE3 A:LYS82 3.2 30.8 1.0
HE2 A:LYS82 3.3 30.8 1.0
CE A:LYS82 3.3 25.7 1.0
O A:HOH470 4.7 29.1 1.0
CD A:LYS82 4.8 23.9 1.0

Chlorine binding site 6 out of 9 in 4lpn

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Chlorine binding site 6 out of 9 in the Frog M-Ferritin with Cobalt, 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 Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl217

b:29.3
occ:1.00
 H A:ASP87 2.3 19.7 1.0
HG3 A:GLU88 2.9 35.2 1.0
H A:GLU88 2.9 18.7 1.0
N A:ASP87 3.1 16.4 1.0
HB3 A:ARG86 3.1 19.7 1.0
HA A:ARG86 3.2 18.7 1.0
HB2 A:ASP87 3.3 24.4 1.0
HE A:ARG86 3.6 38.2 1.0
N A:GLU88 3.6 15.6 1.0
CG A:GLU88 3.8 29.4 1.0
CA A:ARG86 3.8 15.6 1.0
CB A:ARG86 3.8 16.4 1.0
HG2 A:ARG86 3.9 23.5 1.0
CA A:ASP87 4.0 15.7 1.0
C A:ARG86 4.0 14.2 1.0
CB A:ASP87 4.0 20.3 1.0
O A:GLU88 4.1 17.7 1.0
HG2 A:GLU88 4.1 35.2 1.0
C A:ASP87 4.3 17.8 1.0
OE2 A:GLU88 4.3 44.9 1.0
CG A:ARG86 4.4 19.6 1.0
NE A:ARG86 4.5 31.8 1.0
OD2 A:ASP87 4.5 32.7 1.0
CD A:GLU88 4.6 45.6 1.0
CG A:ASP87 4.6 33.6 1.0
HH21 A:ARG86 4.6 48.1 1.0
CA A:GLU88 4.6 16.4 1.0
HB2 A:ARG86 4.7 19.7 1.0
CB A:GLU88 4.7 22.6 1.0
C A:GLU88 4.8 18.4 1.0
HB3 A:ASP87 4.8 24.4 1.0
HB3 A:GLU88 4.8 27.1 1.0
HA A:ASP87 4.8 18.8 1.0

Chlorine binding site 7 out of 9 in 4lpn

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Chlorine binding site 7 out of 9 in the Frog M-Ferritin with Cobalt, D127E Mutant


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 Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl218

b:33.4
occ:1.00
 HG2 A:GLN101 2.6 15.0 0.5
HA A:LEU102 2.8 15.7 1.0
OG1 A:THR105 3.1 16.0 1.0
HG1 A:THR105 3.1 19.2 1.0
O A:HOH336 3.3 19.4 1.0
CG A:GLN101 3.6 12.5 0.5
O A:GLN101 3.6 15.4 0.6
CA A:LEU102 3.6 13.1 1.0
HB A:THR105 3.6 15.5 1.0
N A:LEU102 3.7 13.9 1.0
C A:GLN101 3.7 15.1 0.6
HE21 A:GLN101 3.7 36.0 0.5
HB3 A:GLN101 3.8 19.1 0.6
O A:GLN101 3.8 14.9 0.5
C A:GLN101 3.8 15.1 0.5
HD12 A:LEU102 3.8 24.2 1.0
HG21 A:THR105 3.9 19.2 1.0
HB2 A:LEU102 3.9 16.3 1.0
CB A:THR105 3.9 12.9 1.0
HB3 A:GLN101 3.9 18.0 0.5
HD13 A:LEU102 4.0 24.2 1.0
NE2 A:GLN101 4.1 30.0 0.5
CD A:GLN101 4.1 25.8 0.5
HG3 A:GLN101 4.2 15.0 0.5
H A:LEU102 4.2 16.7 1.0
CB A:GLN101 4.2 15.0 0.5
CB A:LEU102 4.3 13.6 1.0
HB2 A:GLN101 4.3 19.1 0.6
CD1 A:LEU102 4.4 20.2 1.0
CB A:GLN101 4.4 15.9 0.6
CG2 A:THR105 4.4 16.0 1.0
CA A:GLN101 4.7 13.4 0.5
CA A:GLN101 4.7 13.5 0.6
HE22 A:GLN101 4.7 36.0 0.5
H A:THR105 4.8 14.0 1.0
C A:LEU102 4.8 13.8 1.0
O A:HOH408 4.8 27.6 1.0
O A:HOH375 4.8 26.2 1.0
HG23 A:THR105 4.9 19.2 1.0
HE2 A:TYR25 5.0 18.3 1.0
O A:LEU102 5.0 13.9 1.0
CG A:LEU102 5.0 18.8 1.0
OE1 A:GLN101 5.0 34.8 0.5

Chlorine binding site 8 out of 9 in 4lpn

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Chlorine binding site 8 out of 9 in the Frog M-Ferritin with Cobalt, D127E Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Frog M-Ferritin with Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl219

b:18.8
occ:0.33
 CO A:CO206 2.1 13.0 0.3
OE2 A:GLU127 3.2 14.2 1.0
O A:HOH361 3.3 30.0 1.0
HB3 A:SER131 3.6 21.0 1.0
HB2 A:SER131 3.7 21.0 1.0
O A:HOH366 3.8 21.5 1.0
CB A:SER131 4.1 17.5 1.0
CD A:GLU127 4.4 13.0 1.0
O A:HOH397 4.6 25.1 1.0
CO A:CO210 4.7 33.9 0.6
HA A:SER131 4.9 19.7 1.0
OE1 A:GLU127 5.0 14.0 1.0

Chlorine binding site 9 out of 9 in 4lpn

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Chlorine binding site 9 out of 9 in the Frog M-Ferritin with Cobalt, D127E Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Frog M-Ferritin with Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl222

b:64.5
occ:1.00
 HE2 A:HIS61 2.4 32.7 1.0
OE2 A:GLU136 2.7 27.5 0.6
OE1 A:GLU136 2.8 31.6 0.6
HG3 A:GLU57 3.0 36.1 0.6
NE2 A:HIS61 3.1 27.2 1.0
CD A:GLU136 3.1 32.3 0.6
HD2 A:HIS61 3.4 30.7 1.0
O A:HOH484 3.4 28.2 1.0
CD2 A:HIS61 3.6 25.6 1.0
HG2 A:GLU136 3.8 33.8 0.4
CG A:GLU57 3.9 30.1 0.6
HG2 A:GLU57 4.1 36.1 0.6
O A:HOH469 4.1 35.1 1.0
HB3 A:GLU57 4.2 28.4 0.4
CE1 A:HIS61 4.3 32.0 1.0
HG2 A:GLU57 4.3 28.2 0.4
OE2 A:GLU136 4.4 25.7 0.4
CD A:GLU57 4.5 35.9 0.6
CD A:GLU136 4.5 28.5 0.4
CG A:GLU136 4.6 28.2 0.4
CG A:GLU136 4.6 23.5 0.6
HE1 A:HIS61 4.6 38.4 1.0
OE1 A:GLU57 4.7 29.9 0.6
HA A:GLU57 4.8 19.7 0.6
HB2 A:GLU60 4.8 22.0 1.0
CG A:HIS61 4.9 20.2 1.0
O A:GLU57 4.9 16.6 1.0
CB A:GLU57 4.9 23.6 0.4
HB2 A:GLU136 4.9 27.1 0.4
CB A:GLU57 5.0 23.6 0.6
HG2 A:GLU136 5.0 28.2 0.6

Reference:

R.Torres, R.Behera, 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: Sat Dec 12 10:53:26 2020

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