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

Enzymatic activity of 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;

Other elements in 7k3w:

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

Zinc Binding Sites:

Zinc binding site 1 out of 270 in 7k3w

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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 7k3w

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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 7k3w

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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 7k3w

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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 7k3w

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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 7k3w

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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 7k3w

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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 7k3w

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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 7k3w

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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 7k3w

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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

Reference:

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
Page generated: Wed Dec 16 13:49:09 2020

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