Chlorine in PDB 7o6d: Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment

Enzymatic activity of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment

All present enzymatic activity of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment, PDB code: 7o6d was solved by C.Pozzi, S.Ciambellotti, G.Tassone, P.Turano, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.09 / 1.47
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.09, 184.09, 184.09, 90, 90, 90
R / Rfree (%) 14.6 / 15.7

Other elements in 7o6d:

The structure of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment also contains other interesting chemical elements:

Iron (Fe) 10 atoms
Magnesium (Mg) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment (pdb code 7o6d). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment, PDB code: 7o6d:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 7o6d

Go back to Chlorine Binding Sites List in 7o6d
Chlorine binding site 1 out of 6 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl214

b:22.9
occ:0.80
 O A:HOH523 3.0 34.2 0.5
O A:HOH491 3.1 16.0 0.3
O A:HOH537 3.2 32.1 1.0
N A:PHE12 3.2 15.1 1.0
O A:HOH600 3.4 34.5 0.6
N A:ASN11 3.4 15.1 1.0
O A:PHE12 3.5 16.3 1.0
CG A:ARG9 3.6 15.3 1.0
NE A:ARG9 3.6 16.7 1.0
CD A:ARG9 3.6 16.0 1.0
O A:HOH560 3.7 29.4 1.0
C A:GLN10 3.9 15.2 1.0
CA A:GLN10 4.0 14.2 1.0
C A:PHE12 4.0 15.1 1.0
CA A:PHE12 4.0 15.2 1.0
N A:GLN10 4.1 14.4 1.0
CA A:ASN11 4.1 14.8 1.0
O A:HOH491 4.1 21.4 0.7
C A:ASN11 4.1 14.6 1.0
CB A:PHE12 4.3 14.5 1.0
C A:ARG9 4.3 14.6 1.0
CB A:ARG9 4.5 15.5 1.0
O A:ARG9 4.6 16.4 1.0
O A:GLN10 4.7 14.6 1.0
CZ A:ARG9 4.8 15.6 1.0

Chlorine binding site 2 out of 6 in 7o6d

Go back to Chlorine Binding Sites List in 7o6d
Chlorine binding site 2 out of 6 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl215

b:24.3
occ:0.80
 O A:HOH382 2.9 22.6 1.0
NZ A:LYS86 3.1 19.5 0.5
O A:HOH381 3.1 13.1 1.0
O A:HOH585 3.1 39.4 0.3
O A:HOH558 3.4 40.5 1.0
O A:HOH327 3.8 29.6 1.0
O A:HOH612 3.9 34.8 1.0
CB A:ASP84 4.0 12.7 1.0
OD2 A:ASP84 4.1 14.4 1.0
CE A:LYS86 4.2 15.1 0.5
NZ A:LYS86 4.3 15.1 0.5
CG A:ASP84 4.3 13.0 1.0
N A:ASP84 4.4 12.2 1.0
CE A:LYS86 4.6 18.9 0.5
O A:ASP84 4.6 12.3 1.0
CB A:GLN83 4.7 15.8 1.0
O A:HOH580 4.7 28.8 1.0
CA A:ASP84 4.7 12.1 1.0
CD A:LYS86 4.8 14.9 0.5
O A:HOH526 4.8 37.2 0.6
O A:HOH653 4.8 34.0 0.5
OE1 A:GLN83 4.9 20.8 1.0

Chlorine binding site 3 out of 6 in 7o6d

Go back to Chlorine Binding Sites List in 7o6d
Chlorine binding site 3 out of 6 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl216

b:21.1
occ:0.80
 O A:HOH414 2.8 29.4 1.0
O A:HOH625 2.9 19.7 1.0
CA A:GLY125 3.6 14.9 1.0
CD A:PRO127 3.7 14.8 1.0
C A:GLY125 3.7 15.7 1.0
N A:PRO127 3.8 14.1 1.0
N A:ASP126 3.9 14.6 1.0
CB A:PRO127 4.0 14.8 1.0
CA A:PRO127 4.1 14.4 1.0
O A:GLY125 4.2 15.4 1.0
C A:ASP126 4.2 14.3 1.0
CG A:PRO127 4.3 15.1 1.0
O A:HOH562 4.4 30.2 0.5
O A:HOH631 4.5 34.3 0.5
O A:SER122 4.6 16.3 1.0
N A:GLY125 4.6 15.7 1.0
CA A:ASP126 4.7 14.1 1.0
O A:HOH631 4.7 25.5 0.5
O A:ASP126 4.8 14.8 1.0
O A:HOH446 4.8 29.5 1.0
CA A:SER122 5.0 16.1 1.0
O A:ALA121 5.0 15.8 1.0

Chlorine binding site 4 out of 6 in 7o6d

Go back to Chlorine Binding Sites List in 7o6d
Chlorine binding site 4 out of 6 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl217

b:35.3
occ:0.80
 ND1 A:HIS153 3.1 16.3 1.0
O A:HOH599 3.8 40.5 1.0
CA A:HIS153 4.0 15.5 1.0
CG A:HIS153 4.0 14.9 1.0
CE1 A:HIS153 4.0 16.2 1.0
CB A:HIS153 4.1 14.9 1.0
CG1 A:VAL156 4.4 17.6 1.0
CB A:VAL156 4.5 15.2 1.0
O A:HIS153 4.5 14.2 1.0
C A:HIS153 4.8 14.5 1.0
O A:HOH551 4.8 25.3 0.5
N A:HIS153 4.9 14.7 1.0
CG2 A:VAL156 4.9 16.6 1.0

Chlorine binding site 5 out of 6 in 7o6d

Go back to Chlorine Binding Sites List in 7o6d
Chlorine binding site 5 out of 6 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl218

b:22.5
occ:0.25
 FE A:FE2204 2.5 19.1 0.2
CE1 A:HIS173 3.3 19.8 1.0
NE2 A:HIS173 3.3 18.2 1.0
CD2 A:LEU169 3.8 18.5 1.0
ND1 A:HIS173 4.5 19.5 1.0
CD2 A:HIS173 4.5 19.2 1.0
O A:HOH503 4.6 22.4 0.2

Chlorine binding site 6 out of 6 in 7o6d

Go back to Chlorine Binding Sites List in 7o6d
Chlorine binding site 6 out of 6 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 3 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl219

b:23.5
occ:0.80
 ND1 A:HIS151 2.9 15.4 1.0
O A:HOH336 2.9 25.9 1.0
ND2 A:ASN154 3.3 15.2 1.0
O A:ASP150 3.5 14.4 1.0
C A:ASP150 3.5 14.7 1.0
CE1 A:HIS151 3.5 15.2 1.0
O A:HOH364 3.5 30.0 1.0
N A:HIS151 3.6 14.5 1.0
CB A:ASP150 3.7 14.4 1.0
CA A:HIS151 3.7 13.8 1.0
CG A:HIS151 4.1 14.3 1.0
CG2 A:THR174 4.1 16.5 1.0
CG A:ASN154 4.1 15.3 1.0
CE1 A:PHE170 4.2 16.1 1.0
CA A:ASP150 4.2 14.2 1.0
CZ A:PHE170 4.4 15.5 1.0
CB A:ASN154 4.4 14.7 1.0
O A:HOH619 4.4 29.6 0.5
CB A:HIS151 4.5 13.7 1.0
O A:HOH472 4.7 17.6 1.0
NE2 A:HIS151 4.8 15.8 1.0
CG A:ASP150 4.8 15.3 1.0
OG1 A:THR174 4.9 16.6 1.0
C A:HIS151 4.9 13.5 1.0

Reference:

S.Ciambellotti, A.Pratesi, G.Tassone, P.Turano, S.Mangani, C.Pozzi. Iron Binding in the Ferroxidase Site of Human Mitochondrial Ferritin. Chemistry 2021.
ISSN: ISSN 0947-6539
PubMed: 34343376
DOI: 10.1002/CHEM.202102270
Page generated: Tue Jul 30 01:17:27 2024

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