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Iron in PDB 8xwb: Crystal Structure of Dinitrosyl Iron Units Binding with Human Heavy Chain Ferritin

Enzymatic activity of Crystal Structure of Dinitrosyl Iron Units Binding with Human Heavy Chain Ferritin

All present enzymatic activity of Crystal Structure of Dinitrosyl Iron Units Binding with Human Heavy Chain Ferritin:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of Dinitrosyl Iron Units Binding with Human Heavy Chain Ferritin, PDB code: 8xwb was solved by W.J.Gong, W.M.Wang, H.F.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.14 / 1.69
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.68, 183.68, 183.68, 90, 90, 90
R / Rfree (%) 15.9 / 19.5

Other elements in 8xwb:

The structure of Crystal Structure of Dinitrosyl Iron Units Binding with Human Heavy Chain Ferritin also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Dinitrosyl Iron Units Binding with Human Heavy Chain Ferritin (pdb code 8xwb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Dinitrosyl Iron Units Binding with Human Heavy Chain Ferritin, PDB code: 8xwb:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8xwb

Go back to Iron Binding Sites List in 8xwb
Iron binding site 1 out of 4 in the Crystal Structure of Dinitrosyl Iron Units Binding with Human Heavy Chain Ferritin


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 Dinitrosyl Iron Units Binding with Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:55.5
occ:0.59
 N A:NO211 1.7 46.4 1.0
N A:NO212 1.7 49.7 1.0
SG A:CYS102 2.2 25.9 0.5
SG A:CYS102 2.4 25.9 0.5
CB A:CYS102 2.8 22.1 0.5
CB A:CYS102 2.8 22.0 0.5
O A:NO211 2.8 51.1 1.0
O A:NO212 2.9 48.3 1.0
CA A:CYS102 3.7 19.4 0.5
CA A:CYS102 3.7 19.3 0.5
O A:HOH413 3.7 34.6 1.0
CZ3 A:TRP93 3.8 18.2 1.0
C A:CYS102 4.6 20.7 0.5
CE3 A:TRP93 4.6 32.2 1.0
CH2 A:TRP93 4.6 32.2 1.0
C A:CYS102 4.6 20.7 0.5
O A:CYS102 4.7 20.7 0.5
N A:CYS102 4.7 17.4 0.5
N A:CYS102 4.7 17.4 0.5
O A:CYS102 4.8 20.7 0.5
O A:ASP89 4.8 52.2 1.0

Iron binding site 2 out of 4 in 8xwb

Go back to Iron Binding Sites List in 8xwb
Iron binding site 2 out of 4 in the Crystal Structure of Dinitrosyl Iron Units Binding with Human Heavy Chain Ferritin


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 Dinitrosyl Iron Units Binding with Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:31.6
occ:0.31
 OE1 A:GLN58 2.1 36.6 1.0
O A:HOH334 2.2 26.4 1.0
O A:HOH345 2.2 34.9 1.0
O A:HOH482 2.3 46.4 1.0
OE1 A:GLU61 2.8 44.0 1.0
CD A:GLN58 3.3 33.5 1.0
OE2 A:GLU107 3.6 37.6 1.0
O A:HOH402 3.7 43.0 1.0
O A:HOH447 3.8 40.1 1.0
CD A:GLU61 4.1 38.1 1.0
NE2 A:GLN58 4.2 40.7 1.0
OE2 A:GLU62 4.2 31.8 1.0
O A:HOH465 4.3 29.0 1.0
CG A:GLN58 4.3 18.2 1.0
CB A:GLN58 4.4 16.2 1.0
CB A:ALA144 4.4 19.6 1.0
CD A:GLU107 4.5 38.0 1.0
CB A:GLU61 4.6 21.1 1.0
CA A:GLN58 4.6 17.3 1.0
OE2 A:GLU61 4.8 51.8 1.0
O A:GLN58 4.9 18.9 1.0
OE1 A:GLU107 4.9 33.9 1.0
CE1 A:HIS65 5.0 30.0 1.0
CG A:GLU61 5.0 23.1 1.0
OH A:TYR34 5.0 24.5 1.0

Iron binding site 3 out of 4 in 8xwb

Go back to Iron Binding Sites List in 8xwb
Iron binding site 3 out of 4 in the Crystal Structure of Dinitrosyl Iron Units Binding with Human Heavy Chain Ferritin


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 Dinitrosyl Iron Units Binding with Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe203

b:16.5
occ:0.40
 OE1 A:GLU62 2.1 24.1 1.0
O A:HOH337 2.1 20.7 1.0
OE1 A:GLU27 2.1 22.3 1.0
O A:HOH312 2.2 29.8 1.0
ND1 A:HIS65 2.2 26.1 1.0
CD A:GLU62 3.0 30.2 1.0
CE1 A:HIS65 3.0 30.0 1.0
CD A:GLU27 3.2 21.5 1.0
CG A:HIS65 3.3 24.5 1.0
OE2 A:GLU62 3.4 31.8 1.0
OE2 A:GLU27 3.5 21.0 1.0
CB A:HIS65 3.7 19.0 1.0
OE1 A:GLN141 4.0 29.3 1.0
O A:HOH403 4.0 30.1 1.0
NE2 A:HIS65 4.2 30.4 1.0
CG1 A:VAL110 4.3 21.2 1.0
CG A:GLU62 4.3 17.6 1.0
CD2 A:HIS65 4.4 25.3 1.0
CG A:GLU27 4.5 18.1 1.0
CA A:GLU62 4.5 17.1 1.0
CB A:GLU62 4.6 17.9 1.0
CB A:GLU27 4.8 15.1 1.0
CD A:GLN141 4.8 25.1 1.0
OE1 A:GLU107 4.9 33.9 1.0

Iron binding site 4 out of 4 in 8xwb

Go back to Iron Binding Sites List in 8xwb
Iron binding site 4 out of 4 in the Crystal Structure of Dinitrosyl Iron Units Binding with Human Heavy Chain Ferritin


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 Dinitrosyl Iron Units Binding with Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe204

b:33.0
occ:0.35
 O A:HOH318 2.2 34.6 1.0
OD1 A:ASP131 2.6 26.8 1.0
CG A:ASP131 3.5 20.7 1.0
CB A:ASP131 3.6 15.8 1.0
OE1 A:GLU134 3.8 26.7 1.0
CA A:ASP131 3.9 17.4 1.0
O A:HOH324 4.2 20.4 1.0
CD A:GLU134 4.4 24.4 1.0
OE2 A:GLU134 4.7 20.8 1.0
OD2 A:ASP131 4.7 28.8 1.0
N A:ASP131 4.8 16.4 1.0
OG1 A:THR135 4.8 26.8 1.0
O A:ASP131 4.9 18.4 1.0
O A:HOH418 4.9 32.5 1.0
C A:ASP131 4.9 18.7 1.0
CB A:GLU134 4.9 16.4 1.0

Reference:

W.Gong, T.Wu, Y.Liu, S.Jiao, W.Wang, W.Yan, Y.Li, Y.Liu, Y.Zhang, H.Wang. Insight Into the Photodynamic Mechanism and Protein Binding of A Nitrosyl Iron-Sulfur [Fe 2 S 2 (No) 4 ] 2- Cluster. Spectrochim Acta A Mol V. 320 24603 2024BIOMOL Spectrosc.
ISSN: ISSN 1873-3557
PubMed: 38878720
DOI: 10.1016/J.SAA.2024.124603
Page generated: Sun Dec 15 10:44:08 2024

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