Zinc in PDB 7zg7: Structure of Human Apoferritin Obtained From Ssdna Coated Grid

All present enzymatic activity of Structure of Human Apoferritin Obtained From Ssdna Coated Grid:
1.16.3.1;

The structure of Structure of Human Apoferritin Obtained From Ssdna Coated Grid also contains other interesting chemical elements:

Sodium

(Na)

112 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 160; Page 17, Binding sites: 161 - 170; Page 18, Binding sites: 171 - 180; Page 19, Binding sites: 181 - 190; Page 20, Binding sites: 191 - 200; Page 21, Binding sites: 201 - 210; Page 22, Binding sites: 211 - 220; Page 23, Binding sites: 221 - 230; Page 24, Binding sites: 231 - 240; Page 25, Binding sites: 241 - 250; Page 26, Binding sites: 251 - 260; Page 27, Binding sites: 261 - 270;

Binding sites:

The binding sites of Zinc atom in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid (pdb code 7zg7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 270 binding sites of Zinc where determined in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid, PDB code: 7zg7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 270 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:25.2 occ:1.00 NE2 A:HIS173 3.0 2.6 1.0 NE2 M:HIS173 3.0 3.4 1.0 NE2 E:HIS173 3.0 3.7 1.0 NE2 I:HIS173 3.0 4.2 1.0 CE1 A:HIS173 3.8 2.3 1.0 CE1 I:HIS173 3.8 4.4 1.0 CE1 M:HIS173 3.8 4.1 1.0 CE1 E:HIS173 3.8 3.8 1.0 CD2 A:LEU169 4.0 0.4 1.0 CD2 E:LEU169 4.0 0.0 1.0 CD2 M:LEU169 4.0 0.2 1.0 CD2 I:LEU169 4.0 0.1 1.0 CD2 A:HIS173 4.0 2.1 1.0 CD2 M:HIS173 4.0 1.5 1.0 CD2 E:HIS173 4.0 1.6 1.0 CD2 I:HIS173 4.1 1.8 1.0 CD1 E:LEU169 4.7 0.5 1.0 CD1 A:LEU169 4.7 0.0 1.0 CD1 I:LEU169 4.7 0.6 1.0 CD1 M:LEU169 4.7 1.6 1.0 CG A:LEU169 5.0 0.0 1.0 CG E:LEU169 5.0 0.0 1.0 CG M:LEU169 5.0 0.0 1.0 CG I:LEU169 5.0 0.0 1.0

Zinc binding site 2 out of 270 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:37.8 occ:1.00 OD1 A:ASP44 2.6 6.3 1.0 O S:ASN74 2.6 4.3 1.0 N A:ASP44 2.9 0.1 1.0 NH1 S:ARG79 3.0 7.5 1.0 CG A:ASP44 3.4 1.9 1.0 CB A:ASP44 3.4 3.5 1.0 C S:ASN74 3.5 4.4 1.0 CA S:ASN74 3.7 4.8 1.0 NH2 S:ARG79 3.7 8.1 1.0 CA A:ASP44 3.7 0.0 1.0 CA A:ARG43 3.8 1.4 1.0 C A:ARG43 3.8 0.0 1.0 CZ S:ARG79 3.8 7.9 1.0 CA S:GLY77 3.9 5.6 1.0 CE M:LYS146 4.0 1.4 1.0 CB S:ASN74 4.0 4.8 1.0 OD1 S:ASN74 4.2 6.5 1.0 CB A:ARG43 4.3 0.0 1.0 N S:GLY77 4.3 5.0 1.0 CG S:ASN74 4.4 5.6 1.0 CD M:LYS146 4.5 1.9 1.0 CG2 S:VAL8 4.6 5.3 1.0 OD2 A:ASP44 4.6 9.0 1.0 OG S:SER6 4.6 10.6 1.0 O S:GLY78 4.7 7.4 1.0 C S:GLY77 4.7 6.1 1.0 CG A:ARG43 4.7 1.6 1.0 N S:GLN75 4.8 4.6 1.0 C A:ASP44 4.8 0.0 1.0 O A:ASP42 4.8 0.8 1.0 N A:ASP45 4.9 0.0 1.0 O A:ARG43 5.0 2.0 1.0 NZ M:LYS146 5.0 3.4 1.0

Zinc binding site 3 out of 270 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:41.7 occ:1.00 OE1 A:GLU62 2.0 15.6 1.0 O A:HOH313 2.1 15.7 1.0 OE1 A:GLU27 2.2 12.1 1.0 O A:HOH306 2.3 17.9 1.0 ND1 A:HIS65 2.3 8.3 1.0 CD A:GLU62 3.0 5.4 1.0 CD A:GLU27 3.1 5.3 1.0 CE1 A:HIS65 3.2 7.4 1.0 CG A:HIS65 3.3 6.1 1.0 OE2 A:GLU27 3.3 11.3 1.0 OE2 A:GLU62 3.3 16.2 1.0 CB A:HIS65 3.6 4.2 1.0 OE1 A:GLN141 3.9 10.5 1.0 O A:HOH348 4.1 18.8 1.0 CG1 A:VAL110 4.3 0.0 1.0 CG A:GLU62 4.3 1.2 1.0 NE2 A:HIS65 4.4 7.8 1.0 CD2 A:HIS65 4.4 3.4 1.0 CG A:GLU27 4.4 0.0 1.0 CA A:GLU62 4.5 0.0 1.0 CB A:GLU62 4.6 4.9 1.0 CD A:GLN141 4.7 3.1 1.0 O A:HOH358 4.8 19.7 1.0 CB A:GLU27 4.8 0.0 1.0

Zinc binding site 4 out of 270 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:43.0 occ:1.00 OD1 A:ASP126 2.6 2.6 1.0 O A:HOH403 2.8 5.7 1.0 ND2 A:ASN11 3.0 0.0 1.0 N A:HIS128 3.3 0.0 1.0 CD A:PRO127 3.4 0.5 1.0 CD2 F:LEU115 3.5 4.0 1.0 CB A:HIS128 3.5 0.0 1.0 CG A:ASP126 3.6 3.8 1.0 NH2 A:ARG76 3.6 0.0 1.0 N A:PRO127 3.6 0.0 1.0 CA A:ASP126 3.8 0.5 1.0 C A:ASP126 3.8 0.0 1.0 CG A:PRO127 4.0 1.1 1.0 CG A:ASN11 4.0 0.0 1.0 NH1 A:ARG76 4.0 3.1 1.0 CA A:HIS128 4.0 0.0 1.0 CZ A:ARG76 4.1 0.0 1.0 CB A:ASN11 4.2 0.5 1.0 O A:ASN11 4.2 4.6 1.0 CB A:ASP126 4.3 0.0 1.0 OD2 A:ASP126 4.3 3.3 1.0 C A:PRO127 4.4 0.0 1.0 CA A:PRO127 4.5 0.0 1.0 CD1 F:LEU115 4.5 4.7 1.0 O A:ASP126 4.6 0.2 1.0 CG F:LEU115 4.6 4.5 1.0 N A:LEU129 4.7 0.0 1.0 O A:ASN125 4.7 10.9 1.0 CG A:HIS128 4.9 2.8 1.0 CB A:PRO127 4.9 1.6 1.0 C A:HIS128 4.9 0.0 1.0 O F:HOH321 4.9 4.6 1.0

Zinc binding site 5 out of 270 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:51.2 occ:1.00 OD2 A:ASP131 2.4 19.7 1.0 O A:HIS128 3.0 0.0 1.0 CD2 A:HIS128 3.1 0.1 1.0 O F:HOH380 3.3 15.7 1.0 NE2 A:HIS128 3.3 2.7 1.0 CG A:ASP131 3.4 9.4 1.0 N A:PHE132 3.4 0.0 1.0 CB A:ASP131 3.6 2.7 1.0 CG A:HIS128 3.7 2.8 1.0 CA A:PHE132 3.8 0.0 1.0 C A:HIS128 3.9 0.0 1.0 CB A:PHE132 3.9 0.0 1.0 C A:ASP131 3.9 0.9 1.0 CB F:ASN139 3.9 8.2 1.0 CE1 A:HIS128 4.0 0.6 1.0 CA A:HIS128 4.1 0.0 1.0 ND1 A:HIS128 4.2 0.0 1.0 OD1 F:ASN139 4.3 9.5 1.0 CG F:ASN139 4.3 8.7 1.0 CA A:ASP131 4.3 0.9 1.0 CB A:HIS128 4.5 0.0 1.0 OD1 A:ASP131 4.5 13.6 1.0 O A:ASP131 4.6 7.8 1.0 CA F:ASN139 4.6 6.2 1.0 N F:ASN139 4.7 5.9 1.0 N A:ASP131 4.9 0.0 1.0 O F:HOH315 4.9 12.7 1.0

Zinc binding site 6 out of 270 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:58.0 occ:1.00 OE2 A:GLU17 2.5 9.2 1.0 CD A:GLU17 3.2 7.7 1.0 OE1 A:GLU17 3.3 14.6 1.0 NH1 A:ARG9 3.3 5.9 1.0 CG A:ARG79 3.8 2.0 1.0 N A:ARG79 4.0 9.1 1.0 CB A:ARG79 4.0 4.7 1.0 O A:HOH316 4.2 14.3 1.0 CA A:GLY78 4.4 1.2 1.0 C A:GLY78 4.5 1.9 1.0 CZ A:ARG9 4.5 2.7 1.0 O A:GLY77 4.6 0.2 1.0 CA A:ARG79 4.6 0.6 1.0 CG A:GLU17 4.7 6.2 1.0 NH2 A:ARG9 5.0 4.2 1.0

Zinc binding site 7 out of 270 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn207 b:58.4 occ:1.00 OD2 A:ASP89 2.2 21.0 1.0 N A:ASP89 2.8 13.2 1.0 CG A:ASP89 3.0 16.8 1.0 CB A:ASP89 3.1 15.5 1.0 OH A:TYR29 3.2 8.7 1.0 CA A:ASP89 3.5 15.3 1.0 CH2 A:TRP93 3.8 7.2 1.0 C A:PRO88 3.9 7.0 1.0 CG2 A:VAL33 4.0 0.0 1.0 CA A:PRO88 4.0 3.4 1.0 CB A:PRO88 4.2 5.0 1.0 OD1 A:ASP89 4.2 21.8 1.0 CG1 A:VAL33 4.2 0.0 1.0 CZ A:TYR29 4.3 0.0 1.0 N A:CYS90 4.4 18.7 1.0 C A:ASP89 4.4 14.5 1.0 CZ3 A:TRP93 4.5 6.7 1.0 CZ2 A:TRP93 4.6 7.0 1.0 SG A:CYS102 4.7 16.1 0.5 CB A:VAL33 4.7 0.0 1.0 CE2 A:TYR29 4.8 0.0 1.0 O A:HOH329 4.9 18.4 1.0 O A:HOH334 5.0 12.9 1.0 O A:PRO88 5.0 11.7 1.0

Zinc binding site 8 out of 270 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn210 b:63.6 occ:1.00 OH A:TYR40 2.6 13.8 1.0 OD2 A:ASP92 2.9 16.4 1.0 OD1 A:ASP92 3.0 16.9 1.0 CG A:ASP92 3.3 11.5 1.0 CE1 A:TYR40 3.3 0.0 1.0 CZ A:TYR40 3.4 2.4 1.0 O A:HOH383 4.2 18.1 1.0 NH2 A:ARG43 4.3 14.4 1.0 CG2 A:VAL46 4.4 0.0 1.0 CA A:GLU94 4.5 2.0 1.0 CZ A:ARG43 4.5 7.0 1.0 NH1 A:ARG43 4.5 10.1 1.0 N A:GLU94 4.7 8.7 1.0 CD1 A:TYR40 4.7 2.1 1.0 CE2 A:TYR40 4.7 0.5 1.0 CB A:ASP92 4.8 10.0 1.0 O A:GLU94 4.8 12.9 1.0 C A:GLU94 4.9 5.0 1.0

Zinc binding site 9 out of 270 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn211 b:54.7 occ:1.00 O A:HOH353 2.5 9.4 1.0 OD2 A:ASP45 2.9 14.6 1.0 NH2 S:ARG79 3.5 8.1 1.0 CG A:ASP45 3.5 7.5 1.0 CB A:ASP45 3.5 4.8 1.0 CA S:SER6 3.7 12.3 1.0 CB S:SER6 4.1 11.5 1.0 O S:HOH407 4.2 12.8 1.0 N S:SER6 4.3 16.1 1.0 O S:THR5 4.3 26.4 1.0 OD1 A:ASP45 4.5 9.8 1.0 C S:THR5 4.5 23.8 1.0 OD2 A:ASP44 4.5 9.0 1.0 OG S:SER6 4.6 10.6 1.0 CZ S:ARG79 4.6 7.9 1.0 N S:GLN7 4.6 8.7 1.0 OD1 A:ASP44 4.7 6.3 1.0 C S:SER6 4.7 10.8 1.0 NE S:ARG79 4.8 8.1 1.0 CA A:ASP45 4.9 5.7 1.0 NH2 A:ARG43 5.0 14.4 1.0

Zinc binding site 10 out of 270 in the Structure of Human Apoferritin Obtained From Ssdna Coated Grid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Human Apoferritin Obtained From Ssdna Coated Grid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn213 b:60.3 occ:1.00 NZ A:LYS87 2.2 16.8 1.0 CE A:LYS87 2.4 6.5 1.0 O S:LEU82 2.6 6.2 1.0 OD1 A:ASP91 2.8 22.4 1.0 C S:LEU82 3.8 5.9 1.0 CG A:ASP91 3.8 15.9 1.0 O A:HOH303 3.8 14.2 1.0 CD A:LYS87 3.8 10.5 1.0 N S:LEU82 3.9 5.8 1.0 OD2 A:ASP91 4.0 19.5 1.0 NE2 S:GLN83 4.1 9.0 1.0 CA S:LEU82 4.4 5.7 1.0 C S:PHE81 4.5 6.2 1.0 CD S:GLN83 4.5 8.3 1.0 OE1 S:GLN83 4.6 11.4 1.0 CD1 S:PHE81 4.6 10.0 1.0 CA S:PHE81 4.7 6.7 1.0 CB S:PHE81 4.7 7.3 1.0 CG A:LYS87 4.8 1.8 1.0 CB A:LYS87 4.8 2.9 1.0 N S:GLN83 4.9 5.9 1.0 CB S:LEU82 4.9 5.3 1.0

D.Hrebik, M.Gondova, L.Valentova, T.Fuzik, A.Pridal, J.Novacek, P.Plevka. Polyelectrolyte Coating of Cryo-Em Grids Improves Lateral Distribution and Prevents Aggregation of Macromolecules. Acta Crystallogr D Struct V. 78 1337 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 36322417
DOI: 10.1107/S2059798322009299