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Chlorine in PDB 4ykh: Thirty Minutes Iron Loaded Human H Ferritin

Enzymatic activity of Thirty Minutes Iron Loaded Human H Ferritin

All present enzymatic activity of Thirty Minutes Iron Loaded Human H Ferritin:
1.16.3.1;

Protein crystallography data

The structure of Thirty Minutes Iron Loaded Human H Ferritin, PDB code: 4ykh 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) 28.07 / 1.52
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.050, 184.050, 184.050, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.7

Other elements in 4ykh:

The structure of Thirty Minutes Iron Loaded Human H Ferritin also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Iron (Fe) 7 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Thirty Minutes Iron Loaded Human H Ferritin (pdb code 4ykh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Thirty Minutes Iron Loaded Human H Ferritin, PDB code: 4ykh:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 4ykh

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Chlorine binding site 1 out of 12 in the Thirty Minutes 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 Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl213

b:16.3
occ:0.70
 NE2 A:GLN83 2.7 15.1 0.6
N A:ASP84 3.1 9.7 1.0
CG A:ASP84 3.5 9.6 1.0
OD1 A:ASP84 3.5 9.6 1.0
CB A:GLN83 3.7 12.1 1.0
OD2 A:ASP84 3.8 10.0 1.0
CA A:GLN83 3.8 11.1 1.0
CD A:GLN83 3.9 14.4 0.6
CB A:ASP84 3.9 9.3 1.0
C A:GLN83 3.9 10.3 1.0
CA A:ASP84 4.1 9.2 1.0
CG A:GLN83 4.3 13.9 1.0
O A:HOH311 4.4 10.6 0.8
O A:HOH305 4.5 11.7 0.4
O A:HOH343 4.8 17.8 1.0
OE1 A:GLN83 4.9 15.0 0.6

Chlorine binding site 2 out of 12 in 4ykh

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Chlorine binding site 2 out of 12 in the Thirty Minutes 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 Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl214

b:10.3
occ:0.25
 FE A:FE2206 2.4 8.8 0.2
NE2 A:HIS173 3.3 9.4 1.0
CE1 A:HIS173 3.4 9.4 1.0
CD2 A:LEU169 4.0 9.9 1.0
ND1 A:HIS173 4.5 9.6 1.0
CD2 A:HIS173 4.5 9.4 1.0
O A:HOH386 4.6 13.0 0.2

Chlorine binding site 3 out of 12 in 4ykh

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Chlorine binding site 3 out of 12 in the Thirty Minutes 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 Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl215

b:21.6
occ:0.80
 O A:HOH611 3.1 48.4 1.0
O A:HOH548 3.1 32.8 1.0
O A:HOH573 3.1 39.6 1.0
N A:GLN14 3.2 11.8 1.0
CG A:GLN14 3.6 13.0 0.5
CD2 A:HIS13 3.7 12.8 0.9
CG A:HIS13 3.7 12.2 0.9
NE2 A:HIS13 3.8 12.8 0.9
O A:HOH551 3.8 34.2 1.0
CA A:HIS13 3.8 11.3 1.0
CB A:GLN14 3.8 12.4 0.5
ND1 A:HIS13 3.9 12.3 0.9
CE1 A:HIS13 3.9 12.4 0.9
CG A:GLN14 3.9 14.9 0.5
CB A:GLN14 3.9 13.4 0.5
C A:HIS13 4.0 11.6 1.0
CA A:GLN14 4.1 11.9 0.5
CA A:GLN14 4.1 12.2 0.5
NE2 A:GLN14 4.3 16.6 0.5
CB A:HIS13 4.4 11.7 1.0
CD A:GLN14 4.6 15.9 0.5
O A:TYR12 4.6 11.2 1.0
O A:HOH555 4.6 40.8 1.0
CD A:GLN14 4.9 13.3 0.3
N A:HIS13 5.0 10.9 1.0

Chlorine binding site 4 out of 12 in 4ykh

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Chlorine binding site 4 out of 12 in the Thirty Minutes 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 Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl216

b:18.2
occ:0.80
 O A:HOH542 3.2 31.2 1.0
NE2 A:GLN75 3.2 11.7 1.0
CE A:LYS71 4.0 10.5 0.4
NZ A:LYS71 4.1 11.4 0.6
CD A:GLN75 4.2 11.2 1.0
OE1 A:GLN75 4.3 11.7 1.0
O A:HOH315 4.3 25.7 1.0
CE A:LYS71 4.4 10.9 0.6
O A:HOH394 4.5 30.4 1.0
O A:HOH447 4.6 14.3 1.0
O A:HOH605 4.7 43.3 1.0
O A:HOH623 4.8 37.0 1.0
CD A:LYS71 5.0 10.1 0.4

Chlorine binding site 5 out of 12 in 4ykh

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Chlorine binding site 5 out of 12 in the Thirty Minutes 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 Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl217

b:13.1
occ:0.70
 O A:HOH426 3.1 12.7 1.0
ND2 A:ASN125 3.4 14.6 1.0
CA A:ASN125 3.5 11.3 1.0
C A:ASN125 3.8 10.7 1.0
CB A:ASN125 3.9 12.7 1.0
CD A:PRO127 4.0 9.0 1.0
N A:ASP126 4.0 9.9 1.0
CG A:ASN125 4.1 13.9 1.0
N A:PRO127 4.2 9.0 1.0
CB A:PRO127 4.3 9.0 1.0
O A:ASN125 4.3 10.3 1.0
CA A:PRO127 4.4 8.9 1.0
CG A:PRO127 4.6 8.9 1.0
C A:ASP126 4.6 9.3 1.0
N A:ASN125 4.6 11.4 1.0
O A:THR122 4.7 11.1 1.0
CA A:ASP126 4.9 9.5 1.0
O A:HOH450 5.0 14.9 1.0

Chlorine binding site 6 out of 12 in 4ykh

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Chlorine binding site 6 out of 12 in the Thirty Minutes 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 Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl218

b:27.9
occ:0.80
 NZ A:LYS124 3.2 15.7 1.0
O A:HOH566 3.3 35.2 1.0
CB A:ASP123 3.8 13.2 1.0
CE A:LYS124 3.8 14.3 1.0
CD A:LYS124 4.0 13.5 1.0
O A:ASP123 4.0 12.3 1.0
C A:ASP123 4.3 12.2 1.0
O A:HOH587 4.4 51.6 1.0
O A:HOH547 4.5 42.1 1.0
CG A:ASP123 4.6 14.2 1.0
CA A:ASP123 4.7 12.2 1.0
O A:HOH459 4.7 45.6 1.0
OD2 A:ASP123 4.8 16.4 1.0
CG A:LYS124 5.0 12.6 1.0

Chlorine binding site 7 out of 12 in 4ykh

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Chlorine binding site 7 out of 12 in the Thirty Minutes 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 Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl219

b:13.4
occ:0.60
 ND2 A:ASN154 2.6 10.4 0.5
ND1 A:HIS151 2.9 9.6 1.0
O A:HOH434 3.1 30.3 1.0
O A:HOH303 3.2 19.3 1.0
ND2 A:ASN154 3.3 9.8 0.5
C A:ASP150 3.4 9.1 1.0
O A:ASP150 3.5 9.2 1.0
CE1 A:HIS151 3.5 9.6 1.0
N A:HIS151 3.5 9.0 1.0
CB A:ASP150 3.6 9.6 1.0
CG A:ASN154 3.6 10.5 0.5
CA A:HIS151 3.7 9.0 1.0
O A:HOH452 4.0 17.4 1.0
CG A:HIS151 4.0 9.4 1.0
O A:HOH381 4.1 38.9 1.0
CA A:ASP150 4.1 9.2 1.0
CG2 A:THR174 4.2 10.6 1.0
CG A:ASN154 4.2 10.0 0.5
OD1 A:ASN154 4.3 10.9 0.5
CE1 A:PHE170 4.3 9.7 1.0
CB A:ASN154 4.4 10.3 0.5
CB A:HIS151 4.5 9.2 1.0
O A:HOH510 4.5 34.1 1.0
CB A:ASN154 4.5 9.9 0.5
CZ A:PHE170 4.6 9.6 1.0
O A:HOH346 4.6 20.9 1.0
NE2 A:HIS151 4.8 9.8 1.0
CG A:ASP150 4.8 10.1 1.0
O A:GLU147 4.8 9.5 1.0
C A:HIS151 4.9 9.0 1.0
OG1 A:THR174 5.0 11.2 1.0

Chlorine binding site 8 out of 12 in 4ykh

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Chlorine binding site 8 out of 12 in the Thirty Minutes 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 Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl220

b:22.0
occ:0.60
 O A:HOH527 2.8 32.8 1.0
O A:HOH570 3.0 40.6 1.0
O A:HOH612 3.1 15.6 0.6
CB A:ASN25 3.5 8.6 1.0
CG A:GLN83 3.8 13.9 1.0
CG A:ASN25 3.8 8.8 1.0
O A:HOH536 3.8 21.9 0.6
CA A:ARG22 4.0 10.1 1.0
OD1 A:ASN25 4.1 9.1 1.0
CB A:GLN83 4.1 12.1 1.0
CG A:ARG22 4.3 12.7 1.0
MG A:MG211 4.4 14.0 0.6
ND2 A:ASN25 4.4 8.8 1.0
O A:ASN21 4.5 8.9 1.0
O A:ARG22 4.5 9.8 1.0
CB A:ARG22 4.5 11.2 1.0
N A:ARG22 4.7 9.5 1.0
C A:ARG22 4.8 9.6 1.0
O A:HOH607 4.8 21.2 0.6
C A:ASN21 4.9 9.2 1.0
CA A:ASN25 5.0 8.6 1.0
O A:HOH454 5.0 15.6 1.0

Chlorine binding site 9 out of 12 in 4ykh

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Chlorine binding site 9 out of 12 in the Thirty Minutes 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 Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl221

b:14.8
occ:0.80
 O A:HOH397 3.0 37.7 1.0
O A:HOH551 3.2 34.2 1.0
O A:HOH548 3.2 32.8 1.0
N A:TYR12 3.3 9.9 1.0
N A:ASN11 3.4 9.7 1.0
O A:TYR12 3.5 11.2 1.0
CG A:ARG9 3.7 10.8 1.0
CD A:ARG9 3.7 11.0 1.0
NE A:ARG9 3.7 11.2 1.0
O A:HOH602 3.8 46.5 1.0
C A:GLN10 3.9 9.9 1.0
CA A:GLN10 4.0 9.9 1.0
O A:HOH387 4.0 21.5 1.0
N A:GLN10 4.1 9.9 1.0
C A:TYR12 4.1 10.5 1.0
CA A:TYR12 4.1 10.2 1.0
CA A:ASN11 4.1 9.8 1.0
C A:ASN11 4.2 9.7 1.0
C A:ARG9 4.3 10.3 1.0
CB A:TYR12 4.4 10.3 1.0
O A:ARG9 4.6 10.9 1.0
CB A:ARG9 4.6 10.4 1.0
O A:GLN10 4.8 9.6 1.0
CZ A:ARG9 4.9 11.2 1.0

Chlorine binding site 10 out of 12 in 4ykh

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Chlorine binding site 10 out of 12 in the Thirty Minutes 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 10 of Thirty Minutes Iron Loaded Human H Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl222

b:18.3
occ:0.80
 O A:HOH390 2.8 18.1 1.0
O A:HOH394 3.0 30.4 1.0
NE2 A:GLN75 3.1 11.7 1.0
CG A:GLN75 3.7 10.8 1.0
CD A:GLN75 3.9 11.2 1.0
NZ A:LYS71 4.4 10.8 0.4
CE A:LYS71 4.6 10.9 0.6
CE A:LYS71 4.6 10.5 0.4
CB A:GLN75 4.9 9.9 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: Fri Jul 26 04:09:02 2024

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