Iron in PDB 7emk: Dendrorhynchus Zhejiangensis Ferritin

The structure of Dendrorhynchus Zhejiangensis Ferritin, PDB code: 7emk was solved by H.S.Huan, T.H.Ming, X.R.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 2.30
Space group	I 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	151.79, 151.79, 151.79, 90, 90, 90
R / Rfree (%)	15.2 / 18.8

The structure of Dendrorhynchus Zhejiangensis Ferritin also contains other interesting chemical elements:

Sodium	(Na)	17 atoms
Chlorine	(Cl)	21 atoms

The binding sites of Iron atom in the Dendrorhynchus Zhejiangensis Ferritin (pdb code 7emk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Dendrorhynchus Zhejiangensis Ferritin, PDB code: 7emk:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:62.4 occ:1.00 O A:HOH347 2.5 45.4 1.0 OE2 A:GLU60 2.5 42.6 1.0 O A:HOH315 2.6 40.9 1.0 O A:HOH361 2.6 38.4 1.0 OE2 A:GLU105 2.7 36.4 1.0 O A:HOH321 2.8 33.1 1.0 CD A:GLU105 3.3 34.8 1.0 OE1 A:GLU105 3.3 34.7 1.0 O A:HOH305 3.6 41.4 1.0 CD A:GLU60 3.7 32.3 1.0 CB A:ALA142 4.2 26.3 1.0 CE1 A:HIS63 4.2 40.8 1.0 OE1 A:GLU138 4.4 51.9 1.0 CG A:GLU60 4.5 28.9 1.0 CE2 A:TYR32 4.5 25.8 1.0 OH A:TYR32 4.5 32.6 1.0 O A:HOH334 4.5 34.4 1.0 OE2 A:GLU59 4.6 44.1 1.0 CG A:GLU105 4.6 30.1 1.0 OE1 A:GLU60 4.7 35.2 1.0 OE2 A:GLU138 4.8 59.3 1.0 FE A:FE204 4.8 40.7 1.0 OE1 A:GLN139 4.9 40.8 1.0 ND1 A:HIS63 4.9 37.4 1.0 CZ A:TYR32 4.9 30.7 1.0

Iron binding site 2 out of 8 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:86.0 occ:1.00 N A:TYR10 3.3 23.0 1.0 O A:TYR10 3.5 22.0 1.0 N A:ASN9 3.5 23.9 1.0 C A:TYR10 4.0 25.2 1.0 NE A:ARG7 4.0 27.3 1.0 CG A:ARG7 4.0 28.1 1.0 C A:GLN8 4.1 24.8 1.0 CA A:ASN9 4.1 26.9 1.0 CA A:TYR10 4.1 24.1 1.0 CA A:GLN8 4.2 25.9 1.0 C A:ASN9 4.2 25.8 1.0 N A:GLN8 4.3 26.2 1.0 CD A:ARG7 4.3 29.1 1.0 CB A:TYR10 4.6 23.2 1.0 C A:ARG7 4.7 27.2 1.0 CB A:ARG7 4.9 28.2 1.0 O A:ARG7 5.0 27.2 1.0 N A:HIS11 5.0 24.2 1.0 O A:GLN8 5.0 24.9 1.0

Iron binding site 3 out of 8 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:93.1 occ:1.00 OE1 A:GLU162 3.1 35.8 1.0 OE2 A:GLU162 3.4 37.2 1.0 CD A:GLU162 3.6 40.2 1.0 CA A:THR93 4.0 29.1 1.0 CG2 A:THR93 4.2 33.6 1.0 CB A:THR93 4.2 33.1 1.0 CL A:CL231 4.3 72.8 1.0 CD1 A:LEU46 4.6 30.0 1.0 N A:LEU94 4.7 24.7 1.0 O A:GLY92 4.7 30.2 1.0 C A:THR93 4.8 25.1 1.0 N A:THR93 4.8 28.4 1.0 CG1 A:VAL44 5.0 27.0 1.0

Iron binding site 4 out of 8 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe204 b:40.7 occ:1.00 OE1 A:GLU25 2.2 30.7 1.0 OE1 A:GLU60 2.2 35.2 1.0 ND1 A:HIS63 2.2 37.4 1.0 O A:HOH308 2.3 36.6 1.0 O A:HOH305 2.3 41.4 1.0 CD A:GLU60 2.9 32.3 1.0 OE2 A:GLU60 3.0 42.6 1.0 CD A:GLU25 3.1 29.0 1.0 CE1 A:HIS63 3.1 40.8 1.0 CG A:HIS63 3.3 34.9 1.0 OE2 A:GLU25 3.3 28.0 1.0 CB A:HIS63 3.6 27.7 1.0 OE1 A:GLN139 3.8 40.8 1.0 O A:HOH315 3.9 40.9 1.0 CG1 A:VAL108 4.2 29.5 1.0 NE2 A:HIS63 4.3 40.1 1.0 CG A:GLU60 4.4 28.9 1.0 CD2 A:HIS63 4.4 38.1 1.0 CG A:GLU25 4.4 27.1 1.0 CA A:GLU60 4.6 24.8 1.0 FE A:FE201 4.8 62.4 1.0 CB A:GLU60 4.8 24.7 1.0 CB A:GLU25 4.9 24.8 1.0 OE1 A:GLU105 5.0 34.7 1.0

Iron binding site 5 out of 8 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe205 b:61.7 occ:0.33 OE1 A:GLU132 2.5 37.0 1.0 FE A:FE207 3.0 112.3 0.3 OD1 A:ASP129 3.0 33.8 1.0 CD A:GLU132 3.8 35.4 1.0 O A:HOH338 3.9 38.8 1.0 CG A:ASP129 4.2 33.8 1.0 O A:HOH354 4.4 65.8 1.0 OE2 A:GLU132 4.5 37.1 1.0 CB A:ASP129 4.6 30.7 1.0 CA A:ASP129 4.8 29.2 1.0 CB A:GLU132 4.8 31.6 1.0 CG A:GLU132 4.8 33.8 1.0

Iron binding site 6 out of 8 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe206 b:94.9 occ:0.33 FE A:FE207 3.1 112.3 0.3 O A:HOH354 3.7 65.8 1.0 O A:HOH371 4.0 39.8 1.0 OE2 A:GLU132 4.8 37.1 1.0

Iron binding site 7 out of 8 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe207 b:112.3 occ:0.33 O A:HOH354 2.7 65.8 1.0 FE A:FE205 3.0 61.7 0.3 OE1 A:GLU132 3.1 37.0 1.0 FE A:FE206 3.1 94.9 0.3 OE2 A:GLU132 3.5 37.1 1.0 CD A:GLU132 3.6 35.4 1.0

Iron binding site 8 out of 8 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe208 b:87.8 occ:0.33 O A:HOH338 2.9 38.8 1.0 OD1 A:ASN133 3.4 57.2 1.0 CG A:ASN133 4.4 47.7 1.0 OD1 A:ASP129 4.7 33.8 1.0 O A:HOH359 4.8 46.2 1.0 CB A:ASN133 4.8 38.6 1.0

H.S.Huan, Q.Q.Jiang, Y.Wu, X.T.Qiu, C.Y.Lu, C.Su, J.Zhou, Y.Li, T.H.Ming, X.R.Su. Structure Determination of Ferritin From Dendrorhynchus Zhejiangensis Biochemical and Biophysical V. 531 195 2020RESEARCH Communications.
ISSN: ISSN 0006-291X
PubMed: 32792196
DOI: 10.1016/J.BBRC.2020.07.069