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Zinc in PDB 7vd8: 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope

Enzymatic activity of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope

All present enzymatic activity of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope:
1.16.3.1;

Other elements in 7vd8:

The structure of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope also contains other interesting chemical elements:

Sodium (Na) 75 atoms

Zinc Binding Sites:

Zinc binding site 1 out of 254 in 7vd8

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Zinc binding site 1 out of 254 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:21.5
occ:1.00
CD2 A:HIS65 2.0 5.4 1.0
CG A:HIS65 2.1 4.5 1.0
NE2 A:HIS65 2.1 9.6 1.0
ND1 A:HIS65 2.3 7.6 1.0
CE1 A:HIS65 2.3 8.4 1.0
O A:HOH326 2.7 14.3 1.0
CB A:HIS65 3.2 3.2 1.0
CD2 A:TYR137 3.3 2.3 1.0
CE2 A:TYR137 3.3 3.0 1.0
ZN A:ZN214 3.5 32.5 1.0
O A:HIS136 3.6 6.9 1.0
O A:HOH333 4.0 13.2 1.0
CA A:HIS65 4.1 1.7 1.0
CG A:TYR137 4.1 2.4 1.0
CZ A:TYR137 4.1 1.9 1.0
CD A:GLU140 4.3 13.9 1.0
OE2 A:GLU140 4.4 15.8 1.0
OE1 A:GLU140 4.5 12.5 1.0
CA A:TYR137 4.6 2.4 1.0
CG A:GLU140 4.7 8.6 1.0
C A:HIS136 4.7 2.9 1.0
CD1 A:TYR137 4.8 2.3 1.0
OH A:TYR137 4.8 3.7 1.0
CB A:TYR137 4.8 2.0 1.0
CE1 A:TYR137 4.8 2.0 1.0
CB A:GLU140 4.9 6.1 1.0
N A:HIS65 4.9 1.5 1.0

Zinc binding site 2 out of 254 in 7vd8

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Zinc binding site 2 out of 254 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:12.3
occ:1.00
OD2 A:ASP44 2.3 6.8 1.0
O S:ASN74 2.8 0.6 1.0
N A:ASP44 2.8 1.5 1.0
NH1 S:ARG79 3.0 5.8 1.0
CG A:ASP44 3.1 3.0 1.0
CB A:ASP44 3.1 3.1 1.0
CA A:ASP44 3.6 1.9 1.0
C S:ASN74 3.7 0.6 1.0
NH2 S:ARG79 3.8 8.6 1.0
C A:ARG43 3.8 1.4 1.0
CZ S:ARG79 3.9 5.8 1.0
CA A:ARG43 3.9 1.4 1.0
CA S:GLY77 4.0 1.6 1.0
CA S:ASN74 4.0 0.7 1.0
CE M:LYS146 4.1 4.0 1.0
OD1 A:ASP44 4.3 3.1 1.0
CB A:ARG43 4.3 1.2 1.0
N S:GLY77 4.3 1.3 1.0
CB S:ASN74 4.4 0.6 1.0
OG S:SER6 4.5 6.4 1.0
OD1 S:ASN74 4.5 0.8 1.0
O S:GLY78 4.6 4.9 1.0
CG2 S:VAL8 4.6 1.5 1.0
C S:GLY77 4.6 2.1 1.0
CD M:LYS146 4.7 1.8 1.0
C A:ASP44 4.7 1.9 1.0
CG S:ASN74 4.7 0.6 1.0
N A:ASP45 4.8 1.6 1.0
CG A:ARG43 4.8 1.8 1.0
O A:ARG43 5.0 1.2 1.0
O S:GLY77 5.0 5.2 1.0
N S:GLN75 5.0 0.6 1.0
O A:ASP42 5.0 2.0 1.0

Zinc binding site 3 out of 254 in 7vd8

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Zinc binding site 3 out of 254 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:2.1
occ:1.00
NE2 A:HIS173 2.9 3.0 1.0
NE2 E:HIS173 2.9 2.7 1.0
NE2 I:HIS173 2.9 2.8 1.0
NE2 M:HIS173 2.9 2.8 1.0
CE1 A:HIS173 3.7 2.8 1.0
CE1 I:HIS173 3.7 2.6 1.0
CE1 M:HIS173 3.7 2.5 1.0
CE1 E:HIS173 3.7 2.6 1.0
CD2 E:HIS173 4.0 1.5 1.0
CD2 A:HIS173 4.0 1.6 1.0
CD2 I:HIS173 4.0 1.5 1.0
CD2 M:HIS173 4.0 1.5 1.0
CD2 I:LEU169 4.1 0.6 1.0
CD2 A:LEU169 4.1 0.6 1.0
CD2 M:LEU169 4.1 0.5 1.0
CD2 E:LEU169 4.1 0.6 1.0
ND1 I:HIS173 4.9 2.4 1.0
ND1 A:HIS173 4.9 2.6 1.0
ND1 M:HIS173 4.9 2.4 1.0
ND1 E:HIS173 4.9 2.3 1.0
CD1 I:LEU169 5.0 1.3 1.0
CD1 A:LEU169 5.0 1.5 1.0
CD1 M:LEU169 5.0 1.1 1.0
CD1 E:LEU169 5.0 1.3 1.0

Zinc binding site 4 out of 254 in 7vd8

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Zinc binding site 4 out of 254 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:19.6
occ:1.00
NH2 A:ARG22 2.7 4.8 1.0
O A:ASP15 2.8 5.2 1.0
NH1 A:ARG22 3.5 3.1 1.0
C A:ASP15 3.5 6.4 1.0
CZ A:ARG22 3.5 5.0 1.0
CA A:ASP15 3.6 9.8 1.0
CB A:ASP15 3.8 11.3 1.0
N A:ALA19 3.8 2.0 1.0
CD2 A:LEU120 3.9 5.6 1.0
CB A:ALA18 3.9 2.8 1.0
CB A:ALA19 4.1 2.3 1.0
OD2 A:ASP15 4.1 30.7 1.0
CG A:ASP15 4.2 18.8 1.0
CA A:ALA19 4.3 2.3 1.0
C A:ALA18 4.4 1.8 1.0
CA A:ALA18 4.6 3.2 1.0
N A:SER16 4.8 5.5 1.0
NE A:ARG22 4.8 4.8 1.0
N A:ASP15 5.0 8.2 1.0
OD1 A:ASP15 5.0 21.0 1.0

Zinc binding site 5 out of 254 in 7vd8

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Zinc binding site 5 out of 254 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:13.4
occ:1.00
OD2 A:ASP91 2.2 37.8 1.0
O S:HOH388 2.4 0.0 1.0
CG A:ASP91 2.9 28.0 1.0
CB A:ASP91 3.0 21.5 1.0
NA A:NA206 3.1 9.6 1.0
N S:LEU82 3.2 2.2 1.0
CA A:ASP91 3.4 17.0 1.0
O S:HOH380 3.4 9.8 1.0
O S:ILE80 3.6 3.1 1.0
CA S:PHE81 3.7 3.0 1.0
C S:PHE81 3.9 3.0 1.0
CB S:LEU82 4.0 1.2 1.0
OD1 A:ASP91 4.0 35.7 1.0
O A:HOH305 4.1 9.9 1.0
CA S:LEU82 4.1 2.6 1.0
CG S:LEU82 4.2 2.3 1.0
N A:ASP91 4.2 16.0 1.0
C S:ILE80 4.3 2.5 1.0
O A:CYS90 4.4 14.4 1.0
N S:PHE81 4.4 1.8 1.0
CD1 S:PHE81 4.5 5.5 1.0
C A:ASP91 4.5 16.4 1.0
O S:LEU82 4.5 4.8 1.0
OG A:SER36 4.5 2.9 1.0
O A:ASP91 4.6 15.4 1.0
C A:CYS90 4.7 14.1 1.0
CD1 S:LEU82 4.7 1.5 1.0
CB S:PHE81 4.8 3.4 1.0
C S:LEU82 4.8 2.4 1.0

Zinc binding site 6 out of 254 in 7vd8

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Zinc binding site 6 out of 254 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn207

b:14.8
occ:1.00
OE2 A:GLU17 2.4 7.1 1.0
O A:ARG79 2.6 2.8 1.0
CD A:GLU17 3.0 8.1 1.0
CE2 A:PHE81 3.0 4.9 1.0
O A:HOH380 3.1 7.9 1.0
CD2 A:PHE81 3.2 4.3 1.0
CG A:GLU17 3.4 4.9 1.0
C A:ARG79 3.6 2.4 1.0
ND2 A:ASN21 3.7 2.3 1.0
CB A:ARG79 3.7 2.9 1.0
N A:ARG79 3.7 3.2 1.0
OE1 A:GLU17 3.9 12.1 1.0
CA A:ARG79 3.9 3.4 1.0
O A:HOH320 3.9 9.2 1.0
O A:HOH367 4.1 8.1 1.0
CZ A:PHE81 4.3 5.0 1.0
CG A:PHE81 4.5 3.7 1.0
CB A:GLU17 4.5 4.2 1.0
N A:ILE80 4.8 2.4 1.0
O A:HOH386 4.8 6.5 1.0
CG A:ARG79 4.9 2.5 1.0
CG A:ASN21 4.9 1.9 1.0
C A:GLY78 5.0 2.7 1.0

Zinc binding site 7 out of 254 in 7vd8

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Zinc binding site 7 out of 254 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn208

b:19.5
occ:1.00
O A:HOH339 2.7 4.4 1.0
OE1 A:GLU134 3.0 12.2 1.0
OE1 F:GLU134 3.0 13.6 1.0
OE1 T:GLU134 3.0 13.4 1.0
OD1 T:ASP131 3.2 13.3 1.0
OD1 A:ASP131 3.2 13.7 1.0
OD1 F:ASP131 3.2 13.9 1.0
CD A:GLU134 4.1 11.0 1.0
CD F:GLU134 4.1 11.6 1.0
CD T:GLU134 4.1 11.5 1.0
CG T:ASP131 4.2 10.5 1.0
CG A:ASP131 4.2 10.2 1.0
CG F:ASP131 4.2 10.3 1.0
CB T:ASP131 4.6 3.2 1.0
CB F:ASP131 4.6 3.1 1.0
CB A:ASP131 4.6 3.1 1.0
OE2 F:GLU134 4.7 14.3 1.0
OE2 A:GLU134 4.7 13.5 1.0
OE2 T:GLU134 4.7 14.5 1.0
CB A:GLU134 4.8 4.2 1.0
CB T:GLU134 4.8 4.5 1.0
CB F:GLU134 4.8 4.3 1.0
CA T:ASP131 4.8 3.8 1.0
CA A:ASP131 4.8 3.7 1.0
CA F:ASP131 4.8 3.7 1.0
CG A:GLU134 5.0 6.3 1.0
CG T:GLU134 5.0 6.7 1.0

Zinc binding site 8 out of 254 in 7vd8

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Zinc binding site 8 out of 254 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn209

b:23.0
occ:1.00
O A:HIS60 2.7 3.4 1.0
NH1 S:ARG63 3.0 16.8 1.0
C A:HIS60 3.4 2.3 1.0
CG A:GLU64 3.4 3.9 0.5
CA A:HIS60 3.5 2.5 1.0
CB A:HIS60 3.7 1.9 1.0
CB A:ARG63 3.9 2.9 1.0
N A:GLU64 3.9 1.9 1.0
CZ S:ARG63 3.9 19.0 1.0
CD A:GLU64 4.1 5.9 0.5
NH2 S:ARG63 4.2 22.3 1.0
CD A:ARG63 4.2 14.7 1.0
CG A:HIS60 4.3 2.8 1.0
CG A:ARG63 4.3 8.5 1.0
CD2 A:HIS60 4.3 4.6 1.0
CB A:GLU64 4.4 3.6 0.5
CB A:GLU64 4.4 3.6 0.5
C A:ARG63 4.5 2.1 1.0
CA A:GLU64 4.5 3.0 1.0
OE2 A:GLU64 4.6 7.7 0.5
OE1 A:GLU64 4.6 6.6 0.5
N A:GLU61 4.6 2.2 1.0
CA A:ARG63 4.7 2.3 1.0
N A:HIS60 4.9 1.0 1.0
N A:ARG63 5.0 1.5 1.0

Zinc binding site 9 out of 254 in 7vd8

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Zinc binding site 9 out of 254 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn211

b:23.2
occ:1.00
OD1 A:ASP84 2.1 13.8 1.0
CG A:ASP84 2.8 10.6 1.0
OD2 A:ASP84 2.8 24.9 1.0
CG S:LYS87 2.9 5.6 1.0
O A:HOH400 3.1 28.4 1.0
N S:LYS87 3.3 2.6 1.0
CD S:LYS87 3.3 13.1 1.0
CB S:LYS87 3.9 5.6 1.0
CB S:LYS86 4.0 2.2 1.0
CD S:LYS86 4.0 8.7 1.0
CA S:LYS86 4.0 2.7 1.0
C S:LYS86 4.1 1.9 1.0
CA S:LYS87 4.2 3.5 1.0
CB A:ASP84 4.2 5.6 1.0
CE S:LYS87 4.3 10.4 1.0
O A:HOH338 4.4 6.9 1.0
O S:LYS87 4.4 2.9 1.0
CG S:LYS86 4.4 3.9 1.0
CE S:LYS86 4.5 8.4 1.0
C S:LYS87 4.8 2.6 1.0
CA A:ASP84 4.8 2.9 1.0
N A:ASP84 4.9 2.5 1.0

Zinc binding site 10 out of 254 in 7vd8

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Zinc binding site 10 out of 254 in the 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of 1.96 A Structure of Human Apoferritin Obtained From Talos Arctica Microscope within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn212

b:21.2
occ:1.00
O A:HOH357 2.4 0.0 1.0
NZ A:LYS71 2.5 11.8 1.0
O F:HOH370 2.5 0.0 1.0
O A:HOH379 3.1 10.5 1.0
CE A:LYS71 3.5 5.8 1.0
CG A:GLN75 3.6 1.9 1.0
CG A:LYS71 3.8 1.8 1.0
NE2 A:GLN75 4.1 7.7 1.0
CD A:GLN75 4.1 7.3 1.0
OD2 S:ASP42 4.1 20.0 1.0
CD A:LYS71 4.3 4.4 1.0
OD1 S:ASP42 4.3 9.6 1.0
NZ F:LYS146 4.4 4.0 1.0
CG F:LYS146 4.5 1.0 1.0
CE F:LYS146 4.5 4.0 1.0
O A:LYS71 4.6 0.6 1.0
CG S:ASP42 4.7 9.1 1.0
CB A:GLN75 4.9 0.9 1.0
O F:HOH322 5.0 0.0 1.0

Reference:

H.Fan, B.Wang, Y.Zhang, Y.Zhu, B.Song, H.Xu, Y.Zhai, M.Qiao, F.Sun. A Cryo-Electron Microscopy Support Film Formed By 2D Crystals of Hydrophobin Hfbi. Nat Commun V. 12 7257 2021.
ISSN: ESSN 2041-1723
PubMed: 34907237
DOI: 10.1038/S41467-021-27596-8
Page generated: Thu Mar 31 05:24:39 2022

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