Sodium 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:

Chlorine	(Cl)	21 atoms
Iron	(Fe)	8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Sodium atom in the Dendrorhynchus Zhejiangensis Ferritin (pdb code 7emk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 17 binding sites of Sodium where determined in the Dendrorhynchus Zhejiangensis Ferritin, PDB code: 7emk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 17 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na209 b:54.8 occ:1.00 O A:HOH345 2.6 39.4 1.0 O A:ALA111 3.3 24.2 1.0 CB A:ASP114 3.8 29.2 1.0 N A:LEU115 3.8 25.4 1.0 NZ A:LYS20 4.0 94.1 1.0 CB A:LEU115 4.1 25.2 1.0 CA A:LEU115 4.1 25.5 1.0 C A:ALA111 4.2 23.9 1.0 C A:ASP114 4.2 26.0 1.0 CA A:ALA111 4.3 23.4 1.0 CB A:ALA111 4.4 23.9 1.0 CD1 A:LEU115 4.5 28.1 1.0 CA A:ASP114 4.6 26.3 1.0 OE1 A:GLN21 4.6 30.1 1.0 O A:ASP114 4.8 27.3 1.0 OD2 A:ASP114 4.8 40.9 1.0 CG A:ASP114 4.8 34.5 1.0 CG A:LEU115 4.9 26.2 1.0 CE A:LYS20 4.9 88.6 1.0 O A:GLY17 4.9 25.7 1.0

Sodium binding site 2 out of 17 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na210 b:51.6 occ:1.00 O A:GLY157 2.8 30.2 1.0 O A:LEU153 2.8 30.1 1.0 O A:HOH333 3.3 39.0 1.0 CD2 A:LEU153 3.5 29.0 1.0 C A:GLY157 3.5 28.4 1.0 C A:LEU153 3.6 27.8 1.0 CA A:LEU153 3.7 28.6 1.0 CA A:GLU162 3.7 31.6 1.0 CB A:GLU162 3.8 32.0 1.0 N A:GLY157 3.9 29.6 1.0 N A:GLU162 3.9 29.9 1.0 CB A:LEU153 4.0 30.1 1.0 CB A:CYS156 4.1 27.6 1.0 C A:GLY161 4.1 30.3 1.0 CA A:GLY157 4.2 29.2 1.0 OG1 A:THR95 4.2 31.2 1.0 N A:PRO158 4.4 28.6 1.0 O A:GLY161 4.4 29.9 1.0 CG A:LEU153 4.4 29.7 1.0 C A:CYS156 4.4 28.4 1.0 CG A:GLU162 4.4 37.3 1.0 CA A:PRO158 4.6 30.1 1.0 CA A:CYS156 4.7 29.0 1.0 N A:LYS154 4.9 30.7 1.0 CA A:GLY161 4.9 28.2 1.0

Sodium binding site 3 out of 17 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na211 b:40.7 occ:1.00 O A:HOH365 2.7 28.3 1.0 OD2 A:ASP40 2.8 28.6 1.0 CB A:ASP40 3.5 26.8 1.0 CG A:ASP40 3.6 28.0 1.0 CE1 A:HIS50 4.1 27.3 1.0 NA A:NA223 4.4 38.1 1.0 CA A:SER37 4.4 24.6 1.0 CB A:SER37 4.6 25.5 1.0 O A:HOH343 4.6 26.3 1.0 ND1 A:HIS50 4.8 27.6 1.0 OD1 A:ASP40 4.8 32.0 1.0 NE2 A:HIS50 4.8 28.0 1.0 CA A:ASP40 4.8 25.1 1.0 O A:SER37 4.8 25.1 1.0 O A:ASP40 4.9 25.9 1.0 O A:HOH350 5.0 30.1 1.0

Sodium binding site 4 out of 17 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na212 b:58.5 occ:1.00 O A:ALA16 2.9 26.5 1.0 NA A:NA213 2.9 48.8 1.0 NA A:NA215 3.7 51.0 1.0 C A:ALA16 3.7 26.1 1.0 CA A:ALA16 3.8 26.7 1.0 CB A:ALA16 3.9 26.3 1.0 CB A:ASN19 3.9 24.7 1.0 N A:LYS20 4.0 30.1 1.0 CD A:LYS20 4.4 77.8 1.0 CB A:LYS20 4.4 42.9 1.0 C A:ASN19 4.4 27.5 1.0 CA A:LYS20 4.5 32.1 1.0 CA A:ASN19 4.6 25.6 1.0 CG A:LYS20 4.8 58.9 1.0 O A:HOH360 4.9 40.4 1.0 N A:GLY17 4.9 24.3 1.0 CE A:LYS20 5.0 88.6 1.0

Sodium binding site 5 out of 17 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na213 b:48.8 occ:1.00 O A:HOH360 2.7 40.4 1.0 NA A:NA212 2.9 58.5 1.0 NA A:NA215 3.4 51.0 1.0 ND2 A:ASN19 3.7 24.5 1.0 CB A:ASN19 4.0 24.7 1.0 CB A:VAL79 4.2 29.9 1.0 CA A:ALA16 4.3 26.7 1.0 CG A:ASN19 4.3 25.5 1.0 CB A:ALA16 4.3 26.3 1.0 CG1 A:VAL79 4.5 31.4 1.0 CG2 A:VAL79 4.6 33.1 1.0 O A:HOH328 4.7 27.9 1.0 O A:ALA16 4.8 26.5 1.0 NA A:NA222 4.9 58.2 1.0

Sodium binding site 6 out of 17 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na214 b:59.6 occ:1.00 CL A:CL242 2.9 80.7 1.0 ND1 A:HIS122 3.0 31.9 1.0 O A:HIS122 3.6 25.8 1.0 CA A:HIS122 3.7 28.1 1.0 CB A:HIS122 3.7 29.0 1.0 CD2 A:HIS11 3.8 29.0 1.0 CG A:HIS122 3.8 29.6 1.0 C A:HIS122 4.0 25.8 1.0 CE1 A:HIS122 4.0 32.8 1.0 O A:HOH323 4.3 30.7 1.0 CG A:HIS11 4.5 29.6 1.0 NE2 A:HIS11 4.5 26.3 1.0 CB A:HIS11 4.7 27.7 1.0 O A:LYS121 5.0 27.7 1.0 CD2 A:HIS122 5.0 30.4 1.0 N A:HIS122 5.0 29.2 1.0

Sodium binding site 7 out of 17 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na215 b:51.0 occ:1.00 O A:VAL79 3.0 28.1 1.0 NE2 A:GLN81 3.3 27.9 1.0 NA A:NA213 3.4 48.8 1.0 CG A:GLN81 3.4 28.2 1.0 CG1 A:VAL79 3.7 31.4 1.0 NA A:NA212 3.7 58.5 1.0 C A:VAL79 3.7 26.7 1.0 CB A:VAL79 3.8 29.9 1.0 CB A:ASN19 3.8 24.7 1.0 CD A:GLN81 3.9 33.5 1.0 CA A:VAL79 4.3 27.6 1.0 O A:HOH320 4.4 29.8 1.0 CG A:ASN19 4.5 25.5 1.0 C A:TYR80 4.6 25.2 1.0 N A:TYR80 4.6 24.5 1.0 ND2 A:ASN19 4.7 24.5 1.0 O A:ASN19 4.7 26.8 1.0 O A:TYR80 4.7 24.0 1.0 CB A:GLN81 4.7 25.7 1.0 C A:ASN19 4.7 27.5 1.0 N A:GLN81 4.8 23.4 1.0 CA A:ASN19 4.8 25.6 1.0 CA A:TYR80 4.9 25.1 1.0

Sodium binding site 8 out of 17 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na216 b:63.2 occ:1.00 NE2 A:GLN73 2.8 38.0 1.0 CL A:CL233 3.2 77.4 1.0 CG A:GLN73 3.2 31.1 1.0 CD A:GLN73 3.4 41.8 1.0 CB A:GLN73 4.2 27.4 1.0 OE1 A:GLN73 4.6 40.7 1.0 CL A:CL229 4.7 85.7 1.0 CE A:LYS69 4.7 44.6 1.0 CA A:GLN73 4.8 24.8 1.0

Sodium binding site 9 out of 17 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na217 b:43.7 occ:1.00 OE1 A:GLN73 2.9 40.7 1.0 OE1 A:GLN126 3.2 25.6 1.0 CD A:GLN73 3.5 41.8 1.0 CL A:CL229 3.5 85.7 1.0 NE2 A:GLN73 3.6 38.0 1.0 CD1 A:PHE70 3.7 20.5 1.0 CD1 A:PHE130 4.0 29.4 1.0 CE1 A:PHE70 4.2 22.9 1.0 CD A:GLN126 4.2 25.3 1.0 CE1 A:PHE130 4.4 28.5 1.0 NE2 A:GLN126 4.5 21.9 1.0 CL A:CL226 4.6 73.9 1.0 CG A:PHE130 4.7 28.4 1.0 CB A:GLN73 4.7 27.4 1.0 CG A:GLN73 4.7 31.1 1.0 CG A:PHE70 4.8 21.3 1.0 CB A:PHE130 4.9 26.2 1.0

Sodium binding site 10 out of 17 in the Dendrorhynchus Zhejiangensis Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Dendrorhynchus Zhejiangensis Ferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na218 b:52.2 occ:1.00 O A:LYS85 2.9 24.6 1.0 CL A:CL232 2.9 72.8 1.0 O A:HOH314 3.1 30.9 1.0 CG A:LYS85 3.7 40.6 1.0 CB A:LYS84 3.8 36.4 1.0 N A:LYS85 3.9 31.1 1.0 C A:LYS85 3.9 28.9 1.0 OE2 A:GLU87 4.0 47.3 1.0 CA A:LYS85 4.3 32.1 1.0 CL A:CL237 4.4 73.7 1.0 C A:LYS84 4.4 30.4 1.0 CA A:LYS84 4.6 32.6 1.0 CG A:LYS84 4.6 39.8 1.0 CB A:LYS85 4.6 35.7 1.0 O A:PRO86 4.7 28.2 1.0 CE A:LYS85 4.7 55.2 1.0 CD A:LYS84 4.8 45.1 1.0 CD A:LYS85 4.8 51.9 1.0 C A:PRO86 4.9 28.2 1.0 N A:PRO86 5.0 27.4 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