Zinc in PDB 7k3w: Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector

All present enzymatic activity of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector:
1.16.3.1;

The structure of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector 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 Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector (pdb code 7k3w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 270 binding sites of Zinc where determined in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector, PDB code: 7k3w:
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 Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:2.0 occ:1.00 NE2 E:HIS173 3.1 5.0 1.0 NE2 A:HIS173 3.1 5.0 1.0 NE2 I:HIS173 3.1 5.0 1.0 NE2 M:HIS173 3.1 5.0 1.0 CE1 E:HIS173 3.9 6.0 1.0 CE1 A:HIS173 3.9 6.0 1.0 CE1 I:HIS173 3.9 6.0 1.0 CE1 M:HIS173 3.9 6.0 1.0 CD2 E:LEU169 4.0 6.0 1.0 CD2 A:LEU169 4.0 6.0 1.0 CD2 I:LEU169 4.0 6.0 1.0 CD2 M:LEU169 4.0 6.0 1.0 CD2 A:HIS173 4.1 5.0 1.0 CD2 E:HIS173 4.1 5.0 1.0 CD2 M:HIS173 4.1 5.0 1.0 CD2 I:HIS173 4.1 5.0 1.0 CD1 E:LEU169 4.7 3.0 1.0 CD1 A:LEU169 4.7 3.0 1.0 CD1 I:LEU169 4.7 3.0 1.0 CD1 M:LEU169 4.7 3.0 1.0 CG E:LEU169 4.9 6.0 1.0 CG A:LEU169 4.9 6.0 1.0 CG I:LEU169 4.9 6.0 1.0 CG M:LEU169 4.9 6.0 1.0

Zinc binding site 2 out of 270 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:4.0 occ:1.00 O S:ASN74 2.6 3.0 1.0 OD1 A:ASP44 2.6 4.0 1.0 N A:ASP44 2.9 5.0 1.0 NH1 S:ARG79 3.0 7.0 1.0 CG A:ASP44 3.5 4.0 1.0 CB A:ASP44 3.5 5.0 1.0 C S:ASN74 3.5 6.0 1.0 CA S:ASN74 3.7 10.0 1.0 NH2 S:ARG79 3.7 6.0 1.0 CA A:ARG43 3.8 10.0 1.0 CA A:ASP44 3.8 11.0 1.0 CZ S:ARG79 3.8 6.0 1.0 C A:ARG43 3.8 8.0 1.0 CA S:GLY77 3.9 6.0 1.0 CB S:ASN74 4.0 6.0 1.0 CE M:LYS146 4.0 7.0 1.0 OD1 S:ASN74 4.1 6.0 1.0 N S:GLY77 4.2 6.0 1.0 CB A:ARG43 4.3 5.0 1.0 CG S:ASN74 4.3 8.0 1.0 CD M:LYS146 4.5 5.0 1.0 CG2 S:VAL8 4.5 4.0 1.0 C S:GLY77 4.6 6.0 1.0 OG S:SER6 4.6 6.0 1.0 O S:GLY78 4.6 7.0 1.0 OD2 A:ASP44 4.7 7.0 1.0 CG A:ARG43 4.7 5.0 1.0 N S:GLN75 4.8 4.0 1.0 O A:ASP42 4.8 4.0 1.0 C A:ASP44 4.9 6.0 1.0 O S:GLN73 4.9 6.0 1.0 N A:ASP45 5.0 5.0 1.0 NZ M:LYS146 5.0 5.0 1.0

Zinc binding site 3 out of 270 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:3.0 occ:1.00 OE2 A:GLU62 2.0 11.0 1.0 O A:HOH307 2.1 11.0 1.0 O A:HOH303 2.1 5.0 1.0 OE2 A:GLU27 2.1 7.0 1.0 ND1 A:HIS65 2.2 15.0 1.0 CD A:GLU62 3.0 21.0 1.0 CD A:GLU27 3.1 16.0 1.0 CE1 A:HIS65 3.1 6.0 1.0 CG A:HIS65 3.3 6.0 1.0 OE1 A:GLU27 3.4 5.0 1.0 OE1 A:GLU62 3.4 25.0 1.0 CB A:HIS65 3.6 4.0 1.0 OE1 A:GLN141 4.0 11.0 1.0 O A:HOH335 4.1 4.0 1.0 NE2 A:HIS65 4.3 5.0 1.0 CG A:GLU62 4.4 6.0 1.0 CD2 A:HIS65 4.4 12.0 1.0 CG1 A:VAL110 4.4 3.0 1.0 CG A:GLU27 4.4 6.0 1.0 CA A:GLU62 4.5 12.0 1.0 CB A:GLU62 4.7 3.0 1.0 CD A:GLN141 4.8 6.0 1.0 CB A:GLU27 4.8 5.0 1.0 O A:HOH317 5.0 9.0 1.0

Zinc binding site 4 out of 270 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:3.0 occ:1.00 OD2 A:ASP126 2.5 6.0 1.0 O A:HOH403 2.7 5.0 1.0 ND2 A:ASN11 3.1 4.0 1.0 N A:HIS128 3.3 5.0 1.0 CB A:HIS128 3.4 6.0 1.0 CG A:ASP126 3.5 6.0 1.0 CD A:PRO127 3.5 4.0 1.0 CD2 F:LEU115 3.6 6.0 1.0 NH2 A:ARG76 3.6 5.0 1.0 N A:PRO127 3.6 8.0 1.0 CA A:ASP126 3.8 10.0 1.0 C A:ASP126 3.8 5.0 1.0 CA A:HIS128 4.0 9.0 1.0 NH1 A:ARG76 4.0 4.0 1.0 CG A:PRO127 4.0 4.0 1.0 CZ A:ARG76 4.1 5.0 1.0 CG A:ASN11 4.1 5.0 1.0 CB A:ASP126 4.2 6.0 1.0 CB A:ASN11 4.3 6.0 1.0 OD1 A:ASP126 4.3 6.0 1.0 O A:ASN11 4.3 7.0 1.0 C A:PRO127 4.4 7.0 1.0 CA A:PRO127 4.5 10.0 1.0 CD1 F:LEU115 4.5 3.0 1.0 O A:ASP126 4.6 5.0 1.0 N A:LEU129 4.6 4.0 1.0 CG F:LEU115 4.7 5.0 1.0 CG A:HIS128 4.7 5.0 1.0 O F:HOH325 4.7 3.0 1.0 O A:ASN125 4.8 4.0 1.0 C A:HIS128 4.9 6.0 1.0 CB A:PRO127 4.9 6.0 1.0

Zinc binding site 5 out of 270 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:6.0 occ:1.00 OD2 A:ASP131 2.3 14.0 1.0 O A:HIS128 2.7 5.0 1.0 O F:HOH398 2.8 7.0 1.0 CD2 A:HIS128 3.2 5.0 1.0 CG A:ASP131 3.2 11.0 1.0 N A:PHE132 3.3 4.0 1.0 CB A:ASP131 3.4 4.0 1.0 NE2 A:HIS128 3.4 5.0 1.0 C A:HIS128 3.7 6.0 1.0 CG A:HIS128 3.7 5.0 1.0 CA A:PHE132 3.7 9.0 1.0 C A:ASP131 3.7 6.0 1.0 CB A:PHE132 3.9 3.0 1.0 CA A:HIS128 4.0 9.0 1.0 CE1 A:HIS128 4.0 5.0 1.0 CA A:ASP131 4.1 10.0 1.0 ND1 A:HIS128 4.1 6.0 1.0 CB F:ASN139 4.2 6.0 1.0 OD1 A:ASP131 4.4 10.0 1.0 O A:ASP131 4.4 4.0 1.0 CB A:HIS128 4.4 6.0 1.0 OD1 F:ASN139 4.6 6.0 1.0 CG F:ASN139 4.6 7.0 1.0 N A:ASP131 4.7 4.0 1.0 CA F:ASN139 4.9 9.0 1.0 N A:LEU129 4.9 4.0 1.0 N F:ASN139 4.9 4.0 1.0 O A:PRO127 5.0 6.0 1.0

Zinc binding site 6 out of 270 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:5.0 occ:1.00 OE1 A:GLU17 2.5 5.0 1.0 CD A:GLU17 3.3 7.0 1.0 OE2 A:GLU17 3.4 11.0 1.0 NH1 A:ARG9 3.5 5.0 1.0 CG A:ARG79 3.6 7.0 1.0 CB A:ARG79 3.8 6.0 1.0 N A:ARG79 3.9 4.0 1.0 O A:HOH309 4.0 4.0 1.0 CA A:GLY78 4.4 8.0 1.0 C A:GLY78 4.5 6.0 1.0 CA A:ARG79 4.5 10.0 1.0 O A:GLY77 4.6 5.0 1.0 CZ A:ARG9 4.7 8.0 1.0 CG A:GLU17 4.7 7.0 1.0

Zinc binding site 7 out of 270 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn207 b:5.0 occ:1.00 OD2 A:ASP89 2.3 46.0 1.0 OH A:TYR29 2.7 3.0 1.0 N A:ASP89 2.8 3.0 1.0 CG A:ASP89 3.2 30.0 1.0 CB A:ASP89 3.4 14.0 1.0 CG2 A:VAL33 3.4 2.0 1.0 CA A:PRO88 3.6 8.0 1.0 CA A:ASP89 3.7 13.0 1.0 C A:PRO88 3.7 7.0 1.0 CZ A:TYR29 3.7 6.0 1.0 CB A:PRO88 3.9 5.0 1.0 CH2 A:TRP93 3.9 5.0 1.0 CG1 A:VAL33 4.1 4.0 1.0 O A:HOH324 4.2 6.0 1.0 OD1 A:ASP89 4.3 30.0 1.0 CB A:VAL33 4.4 6.0 1.0 CE1 A:TYR29 4.4 5.0 1.0 CE2 A:TYR29 4.6 3.0 1.0 CZ2 A:TRP93 4.6 4.0 1.0 N A:CYS90 4.7 6.0 1.0 C A:ASP89 4.7 9.0 1.0 CZ3 A:TRP93 4.9 8.0 1.0 O A:PRO88 4.9 6.0 1.0

Zinc binding site 8 out of 270 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn210 b:8.0 occ:1.00 OH A:TYR40 2.4 2.0 1.0 OD2 A:ASP92 2.8 6.0 1.0 OD1 A:ASP92 3.0 14.0 1.0 CG A:ASP92 3.3 17.0 1.0 CZ A:TYR40 3.3 7.0 1.0 CE1 A:TYR40 3.4 4.0 1.0 CA A:GLU94 4.1 11.0 1.0 N A:GLU94 4.3 5.0 1.0 O A:GLU94 4.3 7.0 1.0 O A:HOH380 4.3 5.0 1.0 C A:GLU94 4.5 5.0 1.0 CG2 A:VAL46 4.6 3.0 1.0 CE2 A:TYR40 4.7 6.0 1.0 NH2 A:ARG43 4.7 7.0 1.0 CB A:ASP92 4.8 6.0 1.0 CD1 A:TYR40 4.8 5.0 1.0 CZ A:ARG43 4.8 4.0 1.0 NH1 A:ARG43 4.8 4.0 1.0

Zinc binding site 9 out of 270 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn211 b:6.0 occ:1.00 O A:HOH319 2.6 4.0 1.0 OD2 A:ASP45 2.7 8.0 1.0 NH2 S:ARG79 3.2 6.0 1.0 CG A:ASP45 3.3 6.0 1.0 CB A:ASP45 3.5 4.0 1.0 CA S:SER6 3.7 9.0 1.0 CB S:SER6 4.0 5.0 1.0 N S:SER6 4.3 4.0 1.0 CZ S:ARG79 4.3 6.0 1.0 OD1 A:ASP45 4.3 8.0 1.0 O S:HOH409 4.3 6.0 1.0 O S:THR5 4.4 8.0 1.0 OG S:SER6 4.5 6.0 1.0 OD2 A:ASP44 4.5 7.0 1.0 NE S:ARG79 4.5 9.0 1.0 OD1 A:ASP44 4.5 4.0 1.0 C S:THR5 4.6 9.0 1.0 N S:GLN7 4.7 3.0 1.0 C S:SER6 4.8 7.0 1.0 CA A:ASP45 4.9 12.0 1.0 CG A:ASP44 4.9 4.0 1.0 NH2 A:ARG43 4.9 7.0 1.0

Zinc binding site 10 out of 270 in the Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Apoferritin Structure at 1.36 Angstrom Resolution Determined From A 300 Kv Titan Krios G3I Electron Microscope with FALCON4 Detector within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn213 b:5.0 occ:1.00 OD1 A:ASP91 2.7 16.0 1.0 O S:LEU82 2.7 5.0 1.0 NZ A:LYS87 3.1 50.0 1.0 CE A:LYS87 3.2 23.0 1.0 N S:LEU82 3.5 3.0 1.0 CG A:ASP91 3.5 19.0 1.0 O A:HOH310 3.6 5.0 1.0 CB S:PHE81 3.7 4.0 1.0 CD2 S:PHE81 3.7 8.0 1.0 NE2 S:GLN83 3.8 6.0 1.0 C S:LEU82 3.8 5.0 1.0 C S:PHE81 3.8 6.0 1.0 OD2 A:ASP91 3.8 12.0 1.0 CA S:PHE81 3.9 10.0 1.0 CA S:LEU82 4.2 9.0 1.0 CG S:PHE81 4.2 8.0 1.0 CD S:GLN83 4.4 10.0 1.0 O S:PHE81 4.6 5.0 1.0 CD A:LYS87 4.7 31.0 1.0 OE1 S:GLN83 4.7 8.0 1.0 CB A:ASP91 4.7 7.0 1.0 CE2 S:PHE81 4.9 7.0 1.0 CB S:LEU82 4.9 3.0 1.0 N S:GLN83 5.0 4.0 1.0

K.Zhang, G.D.Pintilie, S.Li, M.F.Schmid, W.Chiu. Resolving Individual Atoms of Protein Complex By Cryo-Electron Microscopy. Cell Res. 2020.
ISSN: ISSN 1001-0602
PubMed: 33139928
DOI: 10.1038/S41422-020-00432-2