Chlorine in PDB 4y08: One Minute Iron Loaded Human H Ferritin

Enzymatic activity of One Minute Iron Loaded Human H Ferritin

All present enzymatic activity of One Minute Iron Loaded Human H Ferritin:
1.16.3.1;

Protein crystallography data

The structure of One Minute Iron Loaded Human H Ferritin, PDB code: 4y08 was solved by C.Pozzi, F.Di Pisa, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.76 / 1.34
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.140, 184.140, 184.140, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 17.3

Other elements in 4y08:

The structure of One Minute Iron Loaded Human H Ferritin also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Iron (Fe) 5 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the One Minute Iron Loaded Human H Ferritin (pdb code 4y08). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the One Minute Iron Loaded Human H Ferritin, PDB code: 4y08:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 4y08

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Chlorine binding site 1 out of 9 in the One Minute Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of One Minute Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:11.2
occ:0.70
 O A:HOH394 2.9 30.5 1.0
O A:HOH392 3.2 19.9 1.0
O A:HOH516 3.2 26.3 1.0
NE2 A:GLN75 3.2 7.8 1.0
O A:HOH402 4.0 20.2 1.0
CE A:LYS71 4.1 8.0 0.5
NZ A:LYS71 4.2 8.8 0.5
CD A:GLN75 4.2 7.7 1.0
O A:HOH522 4.3 24.0 1.0
CE A:LYS71 4.3 8.4 0.5
OE1 A:GLN75 4.3 8.0 1.0
O A:HOH563 4.6 36.6 1.0
O A:HOH451 4.7 9.4 1.0

Chlorine binding site 2 out of 9 in 4y08

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Chlorine binding site 2 out of 9 in the One Minute Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of One Minute Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:15.2
occ:0.80
 NE2 A:GLN83 2.6 12.8 0.7
N A:ASP84 3.1 7.8 1.0
CG A:ASP84 3.5 7.6 1.0
OD1 A:ASP84 3.5 7.5 1.0
CB A:GLN83 3.6 10.1 1.0
CA A:GLN83 3.7 9.1 1.0
O A:HOH407 3.8 45.8 1.0
OD2 A:ASP84 3.8 8.3 1.0
CD A:GLN83 3.8 12.1 0.7
CB A:ASP84 3.9 7.6 1.0
C A:GLN83 3.9 8.3 1.0
CA A:ASP84 4.1 7.5 1.0
CG A:GLN83 4.3 11.4 1.0
O A:HOH319 4.5 9.0 0.8
O A:HOH307 4.5 12.1 0.4
O A:HOH336 4.9 14.9 1.0
OE1 A:GLN83 4.9 12.9 0.7

Chlorine binding site 3 out of 9 in 4y08

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Chlorine binding site 3 out of 9 in the One Minute Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of One Minute Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:16.4
occ:0.70
 O A:HOH570 2.9 36.0 1.0
O A:HOH539 3.1 28.0 1.0
N A:GLN14 3.2 8.5 1.0
O A:HOH616 3.2 37.5 1.0
CD2 A:HIS13 3.7 9.8 1.0
CG A:HIS13 3.8 9.3 1.0
CA A:HIS13 3.8 8.5 1.0
NE2 A:HIS13 3.8 10.1 1.0
ND1 A:HIS13 3.9 9.4 1.0
CB A:GLN14 3.9 9.1 1.0
O A:HOH529 4.0 28.2 1.0
CE1 A:HIS13 4.0 9.7 1.0
C A:HIS13 4.0 8.5 1.0
O A:HOH559 4.0 33.4 1.0
CA A:GLN14 4.1 8.7 1.0
CB A:HIS13 4.4 9.0 1.0
O A:TYR12 4.5 8.3 1.0
N A:HIS13 4.9 8.1 1.0

Chlorine binding site 4 out of 9 in 4y08

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Chlorine binding site 4 out of 9 in the One Minute Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of One Minute Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:8.7
occ:0.25
 FE A:FE2204 2.5 13.8 0.1
NE2 A:HIS173 3.2 14.0 1.0
CD2 A:LEU169 4.0 8.2 1.0
CE1 A:HIS173 4.1 13.2 1.0
CD2 A:HIS173 4.1 13.0 1.0
CD1 A:LEU169 4.9 8.4 1.0

Chlorine binding site 5 out of 9 in 4y08

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Chlorine binding site 5 out of 9 in the One Minute Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of One Minute Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl209

b:12.4
occ:0.80
 O A:HOH400 2.9 32.2 1.0
O A:HOH529 3.1 28.2 1.0
O A:HOH539 3.2 28.0 1.0
N A:TYR12 3.3 7.8 1.0
N A:ASN11 3.4 8.1 1.0
O A:TYR12 3.5 8.3 1.0
CD A:ARG9 3.6 9.4 1.0
CG A:ARG9 3.7 9.0 1.0
NE A:ARG9 3.7 9.4 1.0
C A:GLN10 3.9 8.2 1.0
O A:HOH390 4.0 17.9 1.0
CA A:GLN10 4.0 8.5 1.0
C A:TYR12 4.1 8.0 1.0
N A:GLN10 4.1 8.4 1.0
CA A:ASN11 4.1 8.0 1.0
CA A:TYR12 4.1 7.9 1.0
C A:ASN11 4.2 7.9 1.0
O A:HOH598 4.3 40.0 1.0
C A:ARG9 4.4 8.6 1.0
CB A:TYR12 4.4 7.9 1.0
CB A:ARG9 4.6 8.8 1.0
O A:ARG9 4.6 9.1 1.0
O A:GLN10 4.8 7.9 1.0
CZ A:ARG9 4.9 9.4 1.0

Chlorine binding site 6 out of 9 in 4y08

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Chlorine binding site 6 out of 9 in the One Minute Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of One Minute Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl210

b:15.7
occ:0.15
 FE A:FE2204 3.1 13.8 0.1
O A:HOH387 3.5 35.4 1.0
CE1 A:HIS173 3.6 13.2 1.0
ND1 A:HIS173 4.2 13.1 1.0
NE2 A:HIS173 4.6 14.0 1.0

Chlorine binding site 7 out of 9 in 4y08

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Chlorine binding site 7 out of 9 in the One Minute Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of One Minute Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:18.9
occ:0.70
 O A:HOH553 2.9 31.6 1.0
O A:HOH512 2.9 27.5 1.0
O A:HOH603 3.1 12.0 0.5
CB A:ASN25 3.5 6.8 1.0
CG A:GLN83 3.8 11.4 1.0
CG A:ASN25 3.8 6.9 1.0
O A:HOH564 3.9 16.0 0.5
CA A:ARG22 4.0 7.8 1.0
OD1 A:ASN25 4.1 7.1 1.0
CB A:GLN83 4.1 10.1 1.0
CG A:ARG22 4.3 10.7 1.0
ND2 A:ASN25 4.4 7.2 1.0
MG A:MG218 4.5 12.7 0.5
CB A:ARG22 4.5 9.0 1.0
O A:ASN21 4.5 7.1 1.0
O A:ARG22 4.5 7.3 1.0
N A:ARG22 4.7 7.3 1.0
C A:ARG22 4.8 7.4 1.0
O A:HOH608 4.8 15.7 0.5
C A:ASN21 4.9 7.1 1.0
O A:HOH602 4.9 22.2 1.0
CA A:ASN25 5.0 6.8 1.0

Chlorine binding site 8 out of 9 in 4y08

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Chlorine binding site 8 out of 9 in the One Minute Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of One Minute Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl212

b:15.2
occ:0.80
 O A:HOH381 2.8 13.8 1.0
O A:HOH522 3.0 24.0 1.0
NE2 A:GLN75 3.1 7.8 1.0
CG A:GLN75 3.7 7.5 1.0
CD A:GLN75 3.9 7.7 1.0
NZ A:LYS71 4.2 8.2 0.5
CE A:LYS71 4.5 8.4 0.5
CE A:LYS71 4.6 8.0 0.5
CB A:GLN75 4.9 7.2 1.0

Chlorine binding site 9 out of 9 in 4y08

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Chlorine binding site 9 out of 9 in the One Minute Iron Loaded Human H Ferritin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of One Minute Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl213

b:13.4
occ:0.70
 O A:HOH360 2.8 26.5 1.0
O A:HOH433 2.9 10.8 1.0
CA A:ASN125 3.5 9.5 1.0
C A:ASN125 3.7 8.8 1.0
CD A:PRO127 3.7 7.2 1.0
N A:ASP126 3.8 8.0 1.0
N A:PRO127 3.8 7.1 1.0
O A:HOH416 4.0 18.1 1.0
CB A:PRO127 4.0 7.3 1.0
CA A:PRO127 4.1 7.2 1.0
CB A:ASN125 4.2 11.0 1.0
O A:ASN125 4.2 8.4 1.0
CG A:PRO127 4.3 7.2 1.0
C A:ASP126 4.3 7.5 1.0
OD1 A:ASN125 4.6 14.4 1.0
N A:ASN125 4.7 9.3 1.0
CA A:ASP126 4.7 7.6 1.0
O A:THR122 4.7 9.5 1.0
CG A:ASN125 4.9 12.4 1.0
O A:ASP126 4.9 7.3 1.0

Reference:

C.Pozzi, F.Di Pisa, C.Bernacchioni, S.Ciambellotti, P.Turano, S.Mangani. Iron Binding to Human Heavy-Chain Ferritin. Acta Crystallogr.,Sect.D V. 71 1909 2015.
ISSN: ESSN 1399-0047
PubMed: 26327381
DOI: 10.1107/S1399004715013073
Page generated: Sat Dec 12 11:21:59 2020

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