Atomistry » Iron » PDB 7o4j-7oqr » 7o6a
Atomistry »
  Iron »
    PDB 7o4j-7oqr »
      7o6a »

Iron in PDB 7o6a: Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment

Enzymatic activity of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment

All present enzymatic activity of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 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 5 Minutes Under Anaerobic Environment, PDB code: 7o6a 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) 106.04 / 1.40
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.675, 183.675, 183.675, 90, 90, 90
R / Rfree (%) 13.2 / 16.3

Other elements in 7o6a:

The structure of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Magnesium (Mg) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment (pdb code 7o6a). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment, PDB code: 7o6a:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in 7o6a

Go back to Iron Binding Sites List in 7o6a
Iron binding site 1 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:19.2
occ:0.25
O A:HOH498 2.1 25.8 0.2
NE2 A:HIS173 2.2 17.5 0.7
NE2 A:HIS173 2.3 16.1 0.3
O A:HOH517 2.5 10.7 0.2
CE1 A:HIS173 3.0 18.9 0.7
CE1 A:HIS173 3.2 16.7 0.3
CD2 A:HIS173 3.3 18.3 0.7
CD2 A:HIS173 3.4 16.2 0.3
ND1 A:HIS173 4.2 18.8 0.7
CG A:HIS173 4.4 17.8 0.7
ND1 A:HIS173 4.4 16.0 0.3
CG A:HIS173 4.5 15.9 0.3

Iron binding site 2 out of 9 in 7o6a

Go back to Iron Binding Sites List in 7o6a
Iron binding site 2 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:15.7
occ:0.80
OE1 A:GLU62 2.0 20.9 1.0
OE2 A:GLU27 2.0 16.4 1.0
O A:HOH314 2.1 22.5 1.0
ND1 A:HIS65 2.2 18.4 0.8
O A:HOH307 2.2 30.7 1.0
ND1 A:HIS65 2.4 13.2 0.2
O A:HOH484 2.7 24.0 1.0
CD A:GLU62 3.0 19.1 1.0
CE1 A:HIS65 3.0 19.9 0.8
CD A:GLU27 3.1 14.4 1.0
CG A:HIS65 3.3 17.8 0.8
CE1 A:HIS65 3.4 13.3 0.2
OE2 A:GLU62 3.4 21.4 1.0
CG A:HIS65 3.4 13.3 0.2
FE A:FE2203 3.5 19.6 0.4
OE1 A:GLU27 3.5 16.8 1.0
CB A:HIS65 3.6 13.3 0.2
CB A:HIS65 3.7 16.3 0.8
OE1 A:GLN141 3.7 31.0 1.0
O A:HOH499 4.0 25.4 0.8
CG1 A:VAL110 4.2 23.4 1.0
NE2 A:HIS65 4.2 19.8 0.8
CD2 A:HIS65 4.3 19.0 0.8
CG A:GLU62 4.4 17.2 1.0
CG A:GLU27 4.4 14.4 1.0
NE2 A:HIS65 4.5 13.3 0.2
O A:HOH316 4.5 11.1 0.2
CD2 A:HIS65 4.5 13.2 0.2
CA A:GLU62 4.6 13.8 1.0
CB A:GLU62 4.7 14.6 1.0
CD A:GLN141 4.7 20.6 1.0
CB A:GLU27 4.8 13.4 1.0
OE1 A:GLU140 4.8 26.1 0.7
OE1 A:GLU107 4.8 21.0 0.5

Iron binding site 3 out of 9 in 7o6a

Go back to Iron Binding Sites List in 7o6a
Iron binding site 3 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:19.6
occ:0.40
O A:HOH307 1.8 30.7 1.0
OE1 A:GLU107 1.9 21.0 0.5
OE2 A:GLU62 2.0 21.4 1.0
OE1 A:GLU107 2.0 16.8 0.5
OE2 A:GLU107 2.1 16.0 0.5
OE2 A:GLU107 2.2 25.3 0.5
O A:HOH316 2.3 24.4 0.4
CD A:GLU107 2.3 16.7 0.5
CD A:GLU107 2.3 23.7 0.5
O A:HOH484 2.4 24.0 1.0
O A:HOH316 2.6 11.1 0.2
CD A:GLU62 3.0 19.1 1.0
OE1 A:GLU62 3.4 20.9 1.0
FE A:FE2202 3.5 15.7 0.8
OE1 A:GLN141 3.5 31.0 1.0
O A:HOH352 3.7 14.9 0.2
O A:HOH385 3.8 28.2 1.0
CG A:GLU107 3.8 21.3 0.5
CG A:GLU107 3.8 15.7 0.5
NE2 A:GLN141 4.0 28.0 1.0
O A:HOH514 4.2 23.2 0.5
CD A:GLN141 4.2 20.6 1.0
CE1 A:HIS65 4.3 19.9 0.8
FE A:FE2209 4.3 19.6 0.2
CG A:GLU62 4.3 17.2 1.0
OE1 A:GLU140 4.3 26.1 0.7
CE2 A:TYR34 4.5 16.8 0.5
OH A:TYR34 4.5 20.2 0.5
ND1 A:HIS65 4.5 18.4 0.8
O A:HOH314 4.5 22.5 1.0
CE2 A:TYR34 4.6 13.2 0.5
CB A:GLU107 4.6 14.3 0.5
CB A:GLU107 4.7 19.2 0.5
O A:HOH320 4.7 19.9 0.4
OH A:TYR34 4.8 13.9 0.5
OG A:SER144 4.9 23.9 1.0
CA A:GLU107 4.9 14.3 0.5
CA A:GLU107 4.9 18.8 0.5
CB A:SER144 5.0 18.6 1.0
CZ A:TYR34 5.0 17.5 0.5

Iron binding site 4 out of 9 in 7o6a

Go back to Iron Binding Sites List in 7o6a
Iron binding site 4 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:42.0
occ:0.20
O A:HOH440 2.0 38.2 1.0
O A:HOH306 2.1 46.5 1.0
OD1 A:ASP131 3.4 23.9 1.0
O A:HOH614 3.6 37.8 0.3
OG1 A:THR135 4.2 24.6 1.0
OE1 A:GLU134 4.4 27.7 1.0
CG A:ASP131 4.5 20.8 1.0

Iron binding site 5 out of 9 in 7o6a

Go back to Iron Binding Sites List in 7o6a
Iron binding site 5 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe205

b:18.2
occ:0.40
O A:HOH320 2.0 19.9 0.4
O A:HOH429 2.0 33.6 1.0
O A:HOH476 2.0 20.5 0.5
OE1 A:GLU61 2.1 31.6 1.0
O A:HOH504 2.1 30.9 1.0
OE1 A:GLN58 2.1 23.9 1.0
CD A:GLN58 3.1 22.4 1.0
CD A:GLU61 3.1 28.9 1.0
O A:HOH476 3.1 19.5 0.4
FE A:FE2209 3.1 19.6 0.2
O A:HOH418 3.3 21.6 0.3
O A:HOH352 3.3 14.9 0.2
NE2 A:GLN58 3.3 27.9 1.0
OE2 A:GLU61 3.5 36.8 1.0
O A:HOH385 4.0 28.2 1.0
OE2 A:GLU140 4.1 31.3 0.7
O A:HOH506 4.1 30.5 1.0
O A:HOH418 4.2 18.9 0.3
O A:HOH563 4.2 37.1 1.0
OG A:SER144 4.3 23.9 1.0
CG A:GLU61 4.4 17.8 1.0
O A:HOH329 4.5 33.5 1.0
O A:HOH514 4.5 23.2 0.5
CG A:GLN58 4.5 18.4 1.0
O A:HOH442 4.5 24.4 0.4
O A:HOH316 4.6 24.4 0.4
CD2 A:HIS57 4.8 28.3 1.0
OE1 A:GLU147 4.8 24.8 1.0
CB A:GLU61 4.8 16.1 1.0
CA A:GLN58 4.9 13.6 1.0
CB A:GLN58 5.0 14.8 1.0

Iron binding site 6 out of 9 in 7o6a

Go back to Iron Binding Sites List in 7o6a
Iron binding site 6 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe206

b:17.8
occ:0.20
O A:HOH661 2.1 22.6 1.0
O A:HOH472 2.1 20.6 1.0
OE2 A:GLU134 3.9 18.2 1.0
O A:HOH435 4.2 33.1 1.0
O A:HOH628 4.2 20.6 1.0
OE1 A:GLU134 4.3 27.7 1.0
CD A:GLU134 4.5 18.3 1.0

Iron binding site 7 out of 9 in 7o6a

Go back to Iron Binding Sites List in 7o6a
Iron binding site 7 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe207

b:22.8
occ:0.40
OE2 A:GLU61 2.0 36.8 1.0
NE2 A:HIS57 2.1 32.2 1.0
O A:HOH497 2.1 27.4 0.4
O A:HOH442 2.1 24.4 0.4
O A:HOH502 2.2 31.4 0.5
O A:HOH382 2.2 22.3 0.4
CE1 A:HIS57 2.9 35.2 1.0
CD A:GLU61 3.1 28.9 1.0
CD2 A:HIS57 3.2 28.3 1.0
CG A:GLU61 3.7 17.8 1.0
O A:HOH476 4.0 19.5 0.4
O A:HOH476 4.0 20.5 0.5
OE1 A:GLU61 4.1 31.6 1.0
ND1 A:HIS57 4.1 29.9 1.0
O A:HOH360 4.1 38.5 0.5
CG A:HIS57 4.3 24.1 1.0
O A:HOH547 4.3 37.4 0.6
O A:HOH312 4.7 35.0 0.6
O A:HOH429 4.9 33.6 1.0

Iron binding site 8 out of 9 in 7o6a

Go back to Iron Binding Sites List in 7o6a
Iron binding site 8 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe208

b:23.4
occ:0.35
O A:HOH395 2.0 20.9 0.5
O A:HOH663 2.1 16.9 1.0
O A:HOH658 2.2 19.6 1.0
OD1 A:ASP84 4.2 12.6 1.0
OD2 A:ASP84 4.2 14.8 1.0
CG A:ASP84 4.6 12.4 1.0
CL A:CL215 4.8 17.9 0.6

Iron binding site 9 out of 9 in 7o6a

Go back to Iron Binding Sites List in 7o6a
Iron binding site 9 out of 9 in the Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Human Mitochondrial Ferritin (Hmtf) Fe(II)-Loaded For 5 Minutes Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe209

b:19.6
occ:0.20
O A:HOH320 1.5 19.9 0.4
OE2 A:GLU140 1.7 31.3 0.7
O A:HOH352 2.0 14.9 0.2
OG A:SER144 2.0 23.9 1.0
O A:HOH316 2.2 11.1 0.2
O A:HOH316 2.3 24.4 0.4
CD A:GLU140 2.7 27.7 0.7
O A:HOH429 2.8 33.6 1.0
OE1 A:GLU140 3.1 26.1 0.7
FE A:FE2205 3.1 18.2 0.4
CB A:SER144 3.3 18.6 1.0
O A:HOH329 3.4 33.5 1.0
O A:HOH504 3.4 30.9 1.0
O A:HOH385 3.5 28.2 1.0
OE1 A:GLU61 3.7 31.6 1.0
O A:HOH514 4.0 23.2 0.5
OE1 A:GLN58 4.0 23.9 1.0
CG A:GLU140 4.1 25.7 0.7
O A:GLU140 4.1 17.8 0.3
OE2 A:GLU107 4.2 25.3 0.5
O A:GLU140 4.3 17.7 0.7
FE A:FE2203 4.3 19.6 0.4
CE1 A:HIS65 4.3 19.9 0.8
CA A:SER144 4.3 15.5 1.0
O A:HOH307 4.4 30.7 1.0
OE1 A:GLU107 4.4 16.8 0.5
O A:HOH563 4.5 37.1 1.0
O A:HOH506 4.5 30.5 1.0
O A:HOH468 4.6 33.4 0.6
CD A:GLU61 4.8 28.9 1.0
NE2 A:HIS65 4.8 19.8 0.8
OE2 A:GLU62 4.8 21.4 1.0
N A:SER144 4.9 15.4 1.0
C A:GLU140 4.9 17.5 0.3
CD A:GLU107 4.9 23.7 0.5
OE1 A:GLU140 4.9 21.8 0.3
C A:GLU140 5.0 18.0 0.7

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: Thu Aug 8 14:03:08 2024

Last articles

Cl in 5L5P
Cl in 5L5O
Cl in 5L5J
Cl in 5L5I
Cl in 5L5F
Cl in 5L5H
Cl in 5L5E
Cl in 5L5B
Cl in 5L5D
Cl in 5L4R
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy