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

Enzymatic activity of 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;

Other elements in 7zg7:

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

Sodium (Na) 112 atoms

Zinc Binding Sites:

Zinc binding site 1 out of 270 in 7zg7

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


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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 7zg7

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


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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 7zg7

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


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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 7zg7

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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 7zg7

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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 7zg7

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


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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 7zg7

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


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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 7zg7

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


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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 7zg7

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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 7zg7

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


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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

Reference:

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
Page generated: Fri Aug 22 07:29:59 2025

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