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Chlorine in PDB 5j8s: Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A

Enzymatic activity of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A

All present enzymatic activity of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A:
1.16.3.1;

Protein crystallography data

The structure of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A, PDB code: 5j8s was solved by C.Pozzi, F.Di Pisa, S.Mangani, C.Bernacchioni, P.Turano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.77 / 1.50
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 185.010, 185.010, 185.010, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 17.9

Other elements in 5j8s:

The structure of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Chlorine atom in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A (pdb code 5j8s). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 14 binding sites of Chlorine where determined in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A, PDB code: 5j8s:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 14 in 5j8s

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Chlorine binding site 1 out of 14 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl209

b:13.6
occ:0.25
 NE2 A:HIS169 3.1 15.7 1.0
CE1 A:HIS169 3.8 17.7 1.0
CD2 A:LEU165 3.9 13.9 1.0
CD2 A:HIS169 4.2 15.7 1.0

Chlorine binding site 2 out of 14 in 5j8s

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Chlorine binding site 2 out of 14 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl210

b:23.0
occ:0.70
 O A:HOH315 2.8 34.1 1.0
N A:ASP87 3.1 13.1 1.0
O A:HOH640 3.1 31.5 1.0
N A:GLU88 3.7 13.1 1.0
CA A:ARG86 3.7 13.1 1.0
CB A:ARG86 3.9 13.2 1.0
C A:ARG86 3.9 12.8 1.0
CA A:ASP87 3.9 14.0 1.0
CB A:ASP87 4.0 14.5 1.0
O A:HOH404 4.0 45.5 1.0
O A:GLU88 4.1 13.2 1.0
CG A:GLU88 4.2 16.4 1.0
CG A:ARG86 4.3 13.1 1.0
C A:ASP87 4.3 14.1 1.0
O A:HOH482 4.4 32.6 1.0
OD2 A:ASP87 4.5 18.3 1.0
CG A:ASP87 4.6 15.0 1.0
OE2 A:GLU88 4.6 22.6 1.0
CA A:GLU88 4.7 13.3 1.0
NE A:ARG86 4.7 15.7 1.0
O A:HOH585 4.8 31.0 1.0
CB A:GLU88 4.9 14.4 1.0
C A:GLU88 4.9 13.2 1.0
CD A:GLU88 4.9 18.5 1.0

Chlorine binding site 3 out of 14 in 5j8s

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Chlorine binding site 3 out of 14 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:20.7
occ:0.70
 O A:HOH598 2.8 29.9 1.0
OG1 A:THR105 3.1 13.2 1.0
O A:HOH401 3.1 16.4 1.0
NE2 A:GLN101 3.5 22.4 0.6
CG A:GLN101 3.6 17.7 0.6
CA A:LEU102 3.6 12.8 1.0
O A:GLN101 3.6 12.8 1.0
C A:GLN101 3.7 12.9 1.0
N A:LEU102 3.7 12.3 1.0
CB A:THR105 3.8 12.2 1.0
O A:HOH344 3.9 24.5 1.0
CD A:GLN101 4.1 20.3 0.6
CB A:GLN101 4.2 14.8 0.6
CB A:LEU102 4.3 13.9 1.0
CG2 A:THR105 4.4 12.9 1.0
CB A:GLN101 4.4 12.6 0.4
CD1 A:LEU102 4.4 16.4 1.0
CA A:GLN101 4.6 13.4 0.6
CA A:GLN101 4.7 12.6 0.4
O A:HOH639 4.7 19.8 1.0
O A:HOH352 4.7 42.4 1.0
O A:HOH459 4.8 24.3 1.0
C A:LEU102 4.8 12.5 1.0
O A:HOH557 4.9 51.2 1.0
O A:HOH504 4.9 22.8 1.0
O A:LEU102 5.0 11.7 1.0
CG A:LEU102 5.0 14.7 1.0

Chlorine binding site 4 out of 14 in 5j8s

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Chlorine binding site 4 out of 14 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl212

b:16.2
occ:0.70
 O A:HOH529 3.0 18.1 1.0
O A:HOH501 3.1 29.4 1.0
O A:HOH655 3.1 35.0 1.0
O A:HOH420 3.3 35.3 1.0
ND2 A:ASN17 3.3 11.4 1.0
CB A:ASN17 3.7 10.5 1.0
CA A:ALA14 4.0 11.1 1.0
CG A:ASN17 4.0 11.0 1.0
O A:HOH656 4.0 42.0 1.0
CB A:VAL77 4.0 12.6 1.0
CB A:ALA14 4.2 11.4 1.0
O A:ALA14 4.3 11.2 1.0
CG2 A:VAL77 4.4 13.3 1.0
CG1 A:VAL77 4.4 13.7 1.0
C A:ALA14 4.6 11.2 1.0
O A:HOH363 4.7 15.6 1.0

Chlorine binding site 5 out of 14 in 5j8s

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Chlorine binding site 5 out of 14 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl213

b:19.3
occ:1.00
 O A:HOH568 3.1 43.4 1.0
O A:HOH517 3.2 32.3 1.0
O A:HOH496 3.2 47.0 1.0
N A:TYR8 3.3 11.3 1.0
N A:ASN7 3.4 11.4 1.0
O A:TYR8 3.5 13.1 1.0
CD A:ARG5 3.5 12.1 1.0
CG A:ARG5 3.6 11.9 1.0
NE A:ARG5 3.6 12.4 1.0
O A:HOH485 3.8 21.5 1.0
C A:GLN6 3.9 11.7 1.0
CA A:GLN6 4.0 11.8 1.0
CA A:ASN7 4.0 11.4 1.0
C A:TYR8 4.1 11.8 1.0
N A:GLN6 4.1 11.3 1.0
CA A:TYR8 4.1 11.7 1.0
C A:ASN7 4.1 11.5 1.0
C A:ARG5 4.3 12.0 1.0
CB A:TYR8 4.4 11.6 1.0
O A:ARG5 4.5 12.8 1.0
O A:HOH632 4.5 28.6 1.0
CB A:ARG5 4.5 11.7 1.0
O A:GLN6 4.8 11.8 1.0
CZ A:ARG5 4.9 12.5 1.0

Chlorine binding site 6 out of 14 in 5j8s

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Chlorine binding site 6 out of 14 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl214

b:16.1
occ:0.20
 CE1 A:HIS169 3.7 17.7 1.0
ND1 A:HIS169 4.5 17.9 1.0
NE2 A:HIS169 4.6 15.7 1.0
O A:HOH417 5.0 30.0 1.0

Chlorine binding site 7 out of 14 in 5j8s

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Chlorine binding site 7 out of 14 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl215

b:22.6
occ:0.60
 O A:HOH580 2.9 41.0 1.0
O A:HOH555 3.0 43.8 1.0
O A:HOH596 3.0 31.9 1.0
N A:SER10 3.0 13.0 1.0
CB A:SER10 3.6 13.9 1.0
CA A:HIS9 3.8 12.9 1.0
CD2 A:HIS9 3.8 14.4 1.0
CG A:HIS9 3.8 14.0 1.0
C A:HIS9 3.9 13.3 1.0
O A:HOH517 3.9 32.3 1.0
ND1 A:HIS9 3.9 14.4 1.0
CA A:SER10 3.9 12.7 1.0
NE2 A:HIS9 3.9 15.3 1.0
CE1 A:HIS9 3.9 15.1 1.0
CB A:HIS9 4.4 12.9 1.0
O A:TYR8 4.4 13.1 1.0
O A:HOH568 4.5 43.4 1.0
N A:HIS9 4.9 12.4 1.0
O A:HOH534 4.9 42.5 1.0
OG A:SER10 4.9 14.5 0.8
O A:HOH556 4.9 35.4 1.0
O A:HOH565 5.0 43.1 1.0

Chlorine binding site 8 out of 14 in 5j8s

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Chlorine binding site 8 out of 14 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl216

b:18.8
occ:0.70
 O A:HOH320 3.0 21.9 1.0
NE2 A:GLN108 3.2 15.2 1.0
NZ A:LYS115 3.2 13.1 0.2
O A:HOH511 3.2 53.9 1.0
CE A:LYS115 3.6 13.3 0.2
NZ A:LYS115 3.9 23.1 0.5
CD A:GLN108 4.1 14.4 1.0
OE1 A:GLN108 4.1 16.2 1.0
O A:HOH573 4.1 34.7 1.0
CD1 A:LEU111 4.3 12.9 1.0
CB A:LEU111 4.3 12.0 1.0
OD1 A:ASP112 4.7 14.8 1.0
CE A:LYS115 4.8 20.9 0.5
CG A:LEU111 4.8 12.3 1.0

Chlorine binding site 9 out of 14 in 5j8s

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Chlorine binding site 9 out of 14 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl217

b:23.6
occ:0.70
 O A:HOH582 2.9 40.7 1.0
O A:HOH430 3.2 21.9 0.8
N A:ALA136 3.2 14.8 1.0
C A:GLU132 3.3 14.2 1.0
N A:TYR133 3.4 12.5 1.0
N A:GLU135 3.4 12.8 1.0
O A:SER131 3.4 15.9 1.0
CB A:GLU135 3.6 14.6 1.0
O A:GLU132 3.6 15.4 1.0
C A:SER131 3.7 14.4 1.0
C A:TYR133 3.7 12.8 1.0
CA A:GLU135 3.8 14.2 1.0
CA A:GLU132 3.8 14.4 1.0
N A:LEU134 3.8 12.4 1.0
N A:GLU132 3.8 14.5 1.0
CA A:TYR133 3.8 12.5 1.0
O A:GLU130 3.9 15.1 1.0
C A:GLU135 3.9 14.1 1.0
O A:HOH440 4.0 37.2 1.0
CB A:ALA136 4.1 16.1 1.0
O A:TYR133 4.2 13.0 1.0
CA A:ALA136 4.2 14.4 1.0
C A:LEU134 4.4 12.4 1.0
CG A:GLU135 4.4 15.6 1.0
O A:HOH410 4.5 31.3 1.0
CA A:SER131 4.6 14.2 0.5
CA A:SER131 4.6 14.2 0.5
CA A:LEU134 4.7 12.5 1.0
C A:GLU130 4.7 14.1 1.0
O A:HOH636 4.8 27.3 0.8
O A:HOH439 4.8 38.8 1.0
O A:LEU129 4.9 11.9 1.0
O A:HOH483 5.0 20.4 0.8

Chlorine binding site 10 out of 14 in 5j8s

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Chlorine binding site 10 out of 14 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl218

b:50.8
occ:1.00
 O A:HOH576 3.1 41.4 1.0
O A:HOH435 3.2 23.7 1.0
CD A:LYS64 3.6 19.4 0.5
O A:HOH507 3.7 33.6 1.0
CE1 A:PHE128 3.7 12.4 1.0
O A:HOH462 3.9 18.0 1.0
CD A:GLU132 3.9 19.4 1.0
CG A:GLU132 3.9 17.2 1.0
CD A:LYS64 4.0 12.3 0.5
CG A:LYS64 4.0 17.0 0.5
OE2 A:GLU132 4.2 22.9 1.0
CE A:LYS64 4.2 13.1 0.5
CD1 A:PHE128 4.2 11.9 1.0
CG A:LYS64 4.2 12.3 0.5
OE1 A:GLU132 4.2 19.6 1.0
O A:HOH308 4.6 45.9 1.0
CE A:LYS64 4.7 19.4 0.5
CZ A:PHE128 4.9 12.5 1.0
NZ A:LYS64 4.9 14.3 0.5

Reference:

C.Bernacchioni, C.Pozzi, F.Di Pisa, S.Mangani, P.Turano. Ferroxidase Activity in Eukaryotic Ferritin Is Controlled By Accessory-Iron-Binding Sites in the Catalytic Cavity. Chemistry V. 22 16213 2016.
ISSN: ISSN 0947-6539
PubMed: 27650996
DOI: 10.1002/CHEM.201602842
Page generated: Fri Jul 26 09:49:45 2024

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