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Chlorine in PDB 5j9v: Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A

Enzymatic activity of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A

All present enzymatic activity of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A:
1.16.3.1;

Protein crystallography data

The structure of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A, PDB code: 5j9v 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) 42.15 / 1.16
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.744, 183.744, 183.744, 90.00, 90.00, 90.00
R / Rfree (%) 12.8 / 13.8

Other elements in 5j9v:

The structure of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms
Iron (Fe) 7 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Chlorine atom in the Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A (pdb code 5j9v). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 17 binding sites of Chlorine where determined in the Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A, PDB code: 5j9v:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 17 in 5j9v

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Chlorine binding site 1 out of 17 in the Ten Minutes Iron Loaded 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 Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl214

b:8.5
occ:0.25
 FE A:FE2203 2.4 8.1 0.2
NE2 A:HIS169 3.3 8.4 1.0
CE1 A:HIS169 3.4 8.4 1.0
CD2 A:LEU165 3.6 9.2 1.0
CD2 A:HIS169 4.5 8.1 1.0
ND1 A:HIS169 4.5 8.2 1.0
O A:HOH492 4.6 10.7 0.2

Chlorine binding site 2 out of 17 in 5j9v

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Chlorine binding site 2 out of 17 in the Ten Minutes Iron Loaded 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 Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl215

b:13.6
occ:0.90
 O A:HOH495 2.9 34.3 1.0
O A:HOH546 3.1 36.5 1.0
O A:HOH525 3.2 26.6 1.0
N A:TYR8 3.3 7.9 1.0
N A:ASN7 3.4 7.9 1.0
CD A:ARG5 3.5 9.9 1.0
O A:TYR8 3.5 9.3 1.0
CG A:ARG5 3.6 8.8 1.0
NE A:ARG5 3.6 9.8 1.0
O A:HOH485 3.9 21.3 1.0
C A:GLN6 4.0 7.7 1.0
CA A:GLN6 4.0 7.8 1.0
N A:GLN6 4.1 7.8 1.0
C A:TYR8 4.1 8.4 1.0
CA A:ASN7 4.1 7.8 1.0
CA A:TYR8 4.1 7.7 1.0
C A:ASN7 4.2 7.8 1.0
C A:ARG5 4.3 8.0 1.0
O A:HOH603 4.4 37.5 1.0
CB A:TYR8 4.5 8.4 1.0
CB A:ARG5 4.5 9.2 1.0
O A:ARG5 4.5 9.2 1.0
O A:GLN6 4.8 8.0 1.0
CZ A:ARG5 4.9 9.9 1.0
CA A:ARG5 5.0 8.3 1.0

Chlorine binding site 3 out of 17 in 5j9v

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Chlorine binding site 3 out of 17 in the Ten Minutes Iron Loaded 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 Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl216

b:13.1
occ:0.70
 O A:HOH583 3.0 27.3 1.0
O A:HOH394 3.1 12.6 0.8
N A:ALA136 3.2 11.0 1.0
C A:GLU132 3.3 9.7 1.0
N A:TYR133 3.4 8.8 1.0
N A:GLU135 3.4 9.4 1.0
O A:HOH475 3.5 30.4 1.0
O A:SER131 3.6 12.1 1.0
O A:GLU132 3.7 12.7 1.0
CB A:GLU135 3.7 11.7 1.0
C A:TYR133 3.7 9.1 1.0
C A:SER131 3.8 9.8 1.0
CA A:GLU135 3.8 10.1 1.0
CA A:GLU132 3.8 10.2 1.0
N A:GLU132 3.9 9.5 1.0
N A:LEU134 3.9 8.5 1.0
CA A:TYR133 3.9 8.9 1.0
C A:GLU135 3.9 9.9 1.0
CB A:ALA136 3.9 13.7 1.0
O A:HOH379 4.0 28.3 1.0
O A:GLU130 4.1 12.9 1.0
O A:TYR133 4.1 10.0 1.0
CA A:ALA136 4.1 11.8 1.0
C A:LEU134 4.4 8.6 1.0
CG A:GLU135 4.5 11.1 0.8
O A:HOH623 4.6 16.7 0.8
O A:HOH466 4.7 25.2 1.0
CA A:SER131 4.8 12.7 0.4
CA A:LEU134 4.8 8.8 1.0
CA A:SER131 4.8 10.5 0.6
O A:HOH425 4.8 14.3 0.8
C A:GLU130 4.9 10.1 1.0
MG A:MG208 4.9 11.9 0.8

Chlorine binding site 4 out of 17 in 5j9v

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Chlorine binding site 4 out of 17 in the Ten Minutes Iron Loaded 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 Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl217

b:13.4
occ:0.80
 O A:HOH531 3.0 15.0 1.0
O A:HOH628 3.1 32.0 1.0
O A:HOH478 3.1 25.4 1.0
O A:HOH427 3.3 26.3 1.0
ND2 A:ASN17 3.3 8.1 1.0
CB A:ASN17 3.8 7.1 1.0
O A:HOH631 3.9 41.6 1.0
CA A:ALA14 4.0 8.1 1.0
CB A:VAL77 4.0 9.9 1.0
CG A:ASN17 4.0 7.7 1.0
CB A:ALA14 4.1 9.0 1.0
O A:ALA14 4.2 8.2 1.0
CG2 A:VAL77 4.3 11.0 1.0
CG1 A:VAL77 4.4 11.7 1.0
C A:ALA14 4.6 8.0 1.0
O A:HOH341 4.7 12.4 1.0
O A:HOH558 4.8 40.6 1.0
O A:HOH506 4.9 28.9 1.0

Chlorine binding site 5 out of 17 in 5j9v

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Chlorine binding site 5 out of 17 in the Ten Minutes Iron Loaded 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 Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl218

b:15.3
occ:0.60
 O A:HOH504 3.1 35.7 1.0
N A:ASP87 3.1 9.7 1.0
N A:GLU88 3.7 9.8 1.0
CA A:ARG86 3.8 10.2 1.0
CB A:ARG86 3.8 10.6 1.0
C A:ARG86 4.0 10.0 1.0
CA A:ASP87 4.0 10.6 1.0
CG A:GLU88 4.0 13.3 0.6
O A:GLU88 4.0 11.1 1.0
CB A:ASP87 4.1 12.0 1.0
OE2 A:GLU88 4.1 16.8 0.6
CG A:ARG86 4.2 12.9 1.0
C A:ASP87 4.3 11.0 1.0
CD A:GLU88 4.5 14.5 0.6
NE A:ARG86 4.6 15.3 0.7
CA A:GLU88 4.6 13.7 0.4
CB A:GLU88 4.6 14.7 0.4
CA A:GLU88 4.6 11.9 0.6
OD2 A:ASP87 4.6 17.1 0.9
CG A:ASP87 4.7 12.2 0.9
O A:HOH498 4.7 38.7 1.0
C A:GLU88 4.8 9.2 1.0
O A:HOH301 4.8 18.7 0.6
CB A:GLU88 4.8 12.6 0.6
O A:HOH497 4.9 46.2 1.0

Chlorine binding site 6 out of 17 in 5j9v

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Chlorine binding site 6 out of 17 in the Ten Minutes Iron Loaded 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 Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl219

b:18.3
occ:0.60
 O A:HOH506 2.8 28.9 1.0
O A:HOH594 2.8 27.7 1.0
O A:HOH385 3.1 11.2 0.4
CB A:ASN21 3.5 7.3 1.0
CG A:ASN21 3.7 7.6 1.0
CG A:GLN79 3.8 10.9 1.0
O A:HOH552 3.8 13.9 0.4
OD1 A:ASN21 4.0 8.4 1.0
CB A:GLN79 4.0 8.8 1.0
CA A:ARG18 4.0 7.7 1.0
CG A:ARG18 4.1 12.0 1.0
ND2 A:ASN21 4.2 8.0 1.0
O A:HOH558 4.2 40.6 1.0
CB A:ARG18 4.4 9.5 1.0
FE A:FE2207 4.5 13.2 0.3
O A:ARG18 4.6 8.1 1.0
O A:ASN17 4.6 7.6 1.0
O A:HOH478 4.7 25.4 1.0
O A:HOH377 4.8 17.1 1.0
C A:ARG18 4.8 7.9 1.0
N A:ARG18 4.8 7.6 1.0
CD A:ARG18 4.8 14.3 0.9
O A:HOH401 4.9 11.7 0.8
O A:HOH514 4.9 40.4 1.0
O A:HOH630 4.9 15.7 0.4

Chlorine binding site 7 out of 17 in 5j9v

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Chlorine binding site 7 out of 17 in the Ten Minutes Iron Loaded 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 Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl220

b:16.0
occ:0.50
 OG A:SER170 2.8 13.7 1.0
CL A:CL230 2.9 18.9 0.5
CG A:ASN150 3.4 8.1 1.0
ND2 A:ASN150 3.4 8.8 1.0
O A:HOH408 3.4 12.1 1.0
CB A:SER170 3.5 10.8 1.0
CB A:ASN150 3.5 7.8 1.0
CD1 A:PHE147 3.9 11.7 1.0
CE2 A:PHE166 3.9 9.6 1.0
OD1 A:ASN150 4.0 8.5 1.0
CE1 A:PHE147 4.2 13.6 1.0
CD2 A:PHE166 4.4 9.1 1.0
CA A:SER170 4.6 10.9 1.0
CA A:PHE147 4.8 7.5 1.0
O A:ASP146 4.8 7.7 1.0
CZ A:PHE166 4.9 9.6 1.0
CA A:ASN150 5.0 7.7 1.0

Chlorine binding site 8 out of 17 in 5j9v

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Chlorine binding site 8 out of 17 in the Ten Minutes Iron Loaded 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 Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl221

b:15.9
occ:0.60
 O A:HOH575 2.7 28.7 1.0
OG1 A:THR105 3.1 10.9 1.0
O A:HOH400 3.2 12.8 1.0
O A:GLN101 3.6 9.6 1.0
CA A:LEU102 3.6 9.0 1.0
N A:LEU102 3.7 8.6 1.0
C A:GLN101 3.7 9.0 1.0
CG A:GLN101 3.7 13.6 0.5
CB A:THR105 3.8 9.5 1.0
O A:HOH328 4.0 23.4 1.0
CD A:GLN101 4.2 15.2 0.5
CB A:GLN101 4.2 12.2 0.5
CB A:GLN101 4.2 12.2 0.4
CG2 A:THR105 4.4 11.1 1.0
CB A:LEU102 4.4 9.9 1.0
NE2 A:GLN101 4.6 16.6 0.5
CA A:GLN101 4.6 11.3 0.5
CD1 A:LEU102 4.6 13.0 1.0
CA A:GLN101 4.6 11.5 0.4
O A:HOH473 4.7 31.8 1.0
O A:HOH381 4.7 30.3 1.0
OE1 A:GLN101 4.7 17.1 0.5
O A:HOH468 4.8 19.4 1.0
C A:LEU102 4.8 8.4 1.0
O A:HOH610 4.8 19.1 1.0
O A:LEU102 4.9 8.8 1.0
O A:HOH308 5.0 17.6 0.5

Chlorine binding site 9 out of 17 in 5j9v

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Chlorine binding site 9 out of 17 in the Ten Minutes Iron Loaded 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 Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl222

b:15.5
occ:0.80
 O A:HOH618 2.8 25.7 0.5
O A:HOH442 3.1 14.3 1.0
O A:HOH342 3.4 27.7 1.0
OD1 A:ASN7 3.5 10.5 1.0
CG A:ASN7 3.6 8.4 1.0
CB A:ASN7 4.0 8.3 1.0
ND2 A:ASN7 4.1 8.8 1.0
O A:HOH388 4.4 19.3 1.0
CA A:ASN7 5.0 7.8 1.0

Chlorine binding site 10 out of 17 in 5j9v

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Chlorine binding site 10 out of 17 in the Ten Minutes Iron Loaded 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 Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl223

b:15.6
occ:0.70
 O A:HOH377 2.9 17.1 1.0
O A:HOH438 3.1 13.4 1.0
NZ A:LYS82 3.1 12.0 0.5
O A:HOH514 3.4 40.4 1.0
O A:HOH594 3.7 27.7 1.0
O A:HOH330 3.9 26.9 1.0
CB A:ASP80 4.0 6.9 1.0
CE A:LYS82 4.0 10.2 0.5
NZ A:LYS82 4.2 10.4 0.5
OD2 A:ASP80 4.2 8.6 1.0
N A:ASP80 4.3 6.4 1.0
CG A:ASP80 4.3 7.2 1.0
CE A:LYS82 4.5 11.6 0.5
CB A:GLN79 4.5 8.8 1.0
O A:ASP80 4.6 6.8 1.0
CA A:ASP80 4.7 6.4 1.0
O A:HOH548 4.7 22.4 1.0
CD A:LYS82 4.8 9.8 0.5
OE1 A:GLN79 4.9 12.6 0.8

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 09:51:17 2024

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