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Chlorine in PDB 6ftv: X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A

Enzymatic activity of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A

All present enzymatic activity of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A:
1.16.3.1;

Protein crystallography data

The structure of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A, PDB code: 6ftv was solved by A.Merlino, G.Ferraro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 105.30 / 1.58
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 182.380, 182.380, 182.380, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 18.3

Other elements in 6ftv:

The structure of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A also contains other interesting chemical elements:

Ruthenium (Ru) 2 atoms
Magnesium (Mg) 10 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A (pdb code 6ftv). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A, PDB code: 6ftv:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 6ftv

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Chlorine binding site 1 out of 7 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:19.2
occ:0.25
 NE2 A:HIS173 3.1 23.9 1.0
CE1 A:HIS173 3.9 24.1 1.0
CD2 A:LEU169 4.0 18.7 1.0
CD2 A:HIS173 4.2 20.8 1.0
CD1 A:LEU169 4.9 20.8 1.0

Chlorine binding site 2 out of 7 in 6ftv

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Chlorine binding site 2 out of 7 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:25.5
occ:0.75
 NE2 A:GLN83 3.0 39.8 0.7
O A:HOH579 3.0 29.5 1.0
N A:ASP84 3.1 16.1 1.0
CD A:GLN83 3.5 45.0 0.7
OD1 A:ASP84 3.5 18.9 1.0
CG A:ASP84 3.6 20.0 1.0
CA A:GLN83 3.7 17.5 1.0
CB A:GLN83 3.7 22.9 1.0
C A:GLN83 3.9 17.2 1.0
OD2 A:ASP84 3.9 21.7 1.0
CB A:ASP84 3.9 18.1 1.0
OE1 A:GLN83 4.0 59.2 0.7
CA A:ASP84 4.1 16.9 1.0
CG A:GLN83 4.2 31.2 1.0
O A:HOH337 4.4 25.5 1.0
O A:HOH329 4.5 26.4 0.5
O A:HOH380 4.7 26.2 1.0

Chlorine binding site 3 out of 7 in 6ftv

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Chlorine binding site 3 out of 7 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:26.4
occ:0.80
 O A:HOH399 2.7 24.2 1.0
O A:HOH459 3.5 24.3 0.7
CG A:LYS146 4.0 17.4 1.0
CG A:LYS143 4.1 21.9 1.0
CA A:LYS143 4.3 19.4 1.0
CB A:LYS146 4.4 16.1 1.0
CB A:LYS143 4.4 19.4 1.0
O A:HOH415 4.4 31.5 1.0
O A:HOH525 4.5 49.6 1.0
O A:LYS143 4.7 18.0 1.0
CD A:LYS143 4.9 26.9 1.0

Chlorine binding site 4 out of 7 in 6ftv

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Chlorine binding site 4 out of 7 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:22.5
occ:0.75
 O A:HOH557 3.2 47.0 1.0
O A:HOH518 3.2 49.4 1.0
N A:TYR12 3.3 17.6 1.0
N A:ASN11 3.4 19.2 1.0
O A:HOH492 3.5 65.5 1.0
O A:TYR12 3.5 21.0 1.0
CG A:ARG9 3.6 20.9 1.0
NE A:ARG9 3.7 22.8 1.0
CD A:ARG9 3.8 24.8 1.0
O A:HOH484 3.8 31.5 1.0
C A:GLN10 3.9 19.8 1.0
C A:TYR12 4.0 19.1 1.0
CA A:GLN10 4.0 18.9 1.0
N A:GLN10 4.0 18.7 1.0
CA A:TYR12 4.1 18.1 1.0
CA A:ASN11 4.2 18.4 1.0
C A:ASN11 4.2 18.0 1.0
C A:ARG9 4.3 19.2 1.0
CB A:TYR12 4.4 18.9 1.0
O A:ARG9 4.5 20.8 1.0
CB A:ARG9 4.5 19.1 1.0
O A:GLN10 4.8 19.5 1.0
CZ A:ARG9 5.0 21.7 1.0

Chlorine binding site 5 out of 7 in 6ftv

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Chlorine binding site 5 out of 7 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:29.9
occ:0.70
 O A:HOH518 3.1 49.4 1.0
N A:GLN14 3.2 20.1 1.0
CG A:GLN14 3.3 40.3 1.0
O A:HOH568 3.4 58.3 1.0
CG A:HIS13 3.7 22.9 1.0
O A:HOH557 3.7 47.0 1.0
CA A:HIS13 3.8 18.9 1.0
CD2 A:HIS13 3.8 27.2 1.0
NE2 A:HIS13 3.8 27.5 1.0
ND1 A:HIS13 3.9 25.3 1.0
CB A:GLN14 3.9 28.9 1.0
C A:HIS13 3.9 21.6 1.0
CE1 A:HIS13 3.9 25.8 1.0
O A:HOH456 4.0 51.2 1.0
CA A:GLN14 4.1 20.6 1.0
CB A:HIS13 4.3 19.6 1.0
CD A:GLN14 4.4 63.3 1.0
O A:TYR12 4.6 21.0 1.0
N A:HIS13 4.9 19.8 1.0
O A:HOH622 5.0 64.7 1.0

Chlorine binding site 6 out of 7 in 6ftv

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Chlorine binding site 6 out of 7 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:36.8
occ:0.75
 O A:HOH580 3.1 31.2 0.6
O A:HOH498 3.1 53.1 1.0
OE2 A:GLU140 3.2 62.0 1.0
O A:HOH491 3.2 22.3 1.0
ND2 A:ASN139 3.3 20.7 1.0
NZ A:LYS143 3.5 45.8 1.0
O A:HOH514 3.7 46.1 1.0
CB A:ASN139 3.7 21.2 1.0
CE A:LYS143 3.8 35.3 1.0
N A:GLU140 3.9 20.3 1.0
CD A:GLU140 3.9 51.4 1.0
CG A:GLU140 3.9 33.1 1.0
CG A:ASN139 4.0 22.5 1.0
O A:HOH478 4.2 27.0 0.6
C A:ASN139 4.2 20.1 1.0
O A:HOH408 4.4 23.0 0.6
CA A:ASN139 4.5 19.9 1.0
CA A:GLU140 4.5 20.8 1.0
O A:THR135 4.6 25.2 1.0
O A:ASN139 4.8 18.6 1.0
CD A:LYS143 4.8 26.9 1.0
CB A:GLU140 4.9 25.7 1.0

Chlorine binding site 7 out of 7 in 6ftv

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Chlorine binding site 7 out of 7 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:25.7
occ:0.70
 ND2 A:ASN139 3.4 20.7 1.0
O A:HOH514 3.7 46.1 1.0
CD A:LYS143 3.8 26.9 1.0
O A:HOH355 3.9 28.5 1.0
CG A:LYS143 4.1 21.9 1.0
OD1 A:ASN139 4.2 22.7 1.0
CG A:ASN139 4.2 22.5 1.0
CE A:LYS143 4.9 35.3 1.0

Reference:

S.Ciambellotti, A.Pratesi, M.Severi, G.Ferraro, E.Alessio, A.Merlino, L.Messori. The Nami A - Human Ferritin System: A Biophysical Characterization. Dalton Trans V. 47 11429 2018.
ISSN: ESSN 1477-9234
PubMed: 30063237
DOI: 10.1039/C8DT00860D
Page generated: Sat Jul 27 23:33:05 2024

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