Zinc in PDB 8yhd: Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1

Zinc Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1 (pdb code 8yhd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1, PDB code: 8yhd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 8yhd

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Zinc binding site 1 out of 11 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:120.1
occ:1.00
 SG A:CYS84 2.3 97.2 1.0
SG A:CYS71 2.3 97.1 1.0
SG A:CYS81 2.3 98.1 1.0
SG A:CYS87 2.3 102.1 1.0
CB A:CYS71 3.2 95.9 1.0
N A:CYS81 3.2 91.9 1.0
CB A:CYS81 3.3 95.1 1.0
CB A:CYS84 3.6 87.8 1.0
N A:GLY82 3.6 84.9 1.0
CA A:CYS81 3.7 92.5 1.0
N A:CYS84 3.8 86.0 1.0
CB A:CYS87 3.8 94.8 1.0
N A:ARG83 4.1 86.4 1.0
C A:CYS81 4.1 91.6 1.0
N A:CYS71 4.1 99.0 1.0
CA A:CYS71 4.2 97.7 1.0
C A:PRO80 4.2 87.7 1.0
CA A:CYS84 4.3 86.6 1.0
CA A:PRO80 4.5 83.5 1.0
CA A:GLY82 4.6 90.8 1.0
CB A:PRO80 4.7 87.3 1.0
C A:ARG83 4.8 89.0 1.0
C A:GLY82 4.8 91.3 1.0
CA A:ARG83 5.0 87.8 1.0

Zinc binding site 2 out of 11 in 8yhd

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Zinc binding site 2 out of 11 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:113.0
occ:1.00
 SG B:CYS84 2.3 63.9 1.0
SG B:CYS87 2.3 81.0 1.0
SG B:CYS71 2.3 80.4 1.0
SG B:CYS81 2.3 86.1 1.0
CB B:CYS87 3.2 67.7 1.0
N B:CYS81 3.6 65.7 1.0
CB B:CYS81 3.7 69.3 1.0
CB B:CYS84 3.7 61.8 1.0
CB B:CYS71 3.8 70.4 1.0
N B:CYS84 4.0 63.9 1.0
N B:CYS71 4.2 71.0 1.0
N B:GLY82 4.2 64.8 1.0
CA B:CYS81 4.2 68.7 1.0
N B:CYS87 4.3 64.4 1.0
CA B:CYS87 4.4 64.0 1.0
CA B:CYS84 4.5 59.2 1.0
N B:ARG83 4.6 61.4 1.0
CA B:CYS71 4.6 73.1 1.0
C B:PRO80 4.7 64.8 1.0
C B:CYS81 4.7 71.9 1.0
CA B:PRO80 4.8 56.0 1.0
C B:VAL70 4.9 74.9 1.0
CB B:PRO80 5.0 55.8 1.0

Zinc binding site 3 out of 11 in 8yhd

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Zinc binding site 3 out of 11 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:110.5
occ:1.00
 SG C:CYS84 2.3 66.7 1.0
SG C:CYS87 2.3 64.7 1.0
SG C:CYS81 2.3 66.2 1.0
SG C:CYS71 2.3 75.5 1.0
N C:CYS81 3.3 52.7 1.0
CB C:CYS87 3.3 45.7 1.0
CB C:CYS71 3.4 59.3 1.0
CB C:CYS81 3.5 47.7 1.0
N C:GLY82 3.7 49.1 1.0
CB C:CYS84 3.8 56.5 1.0
CA C:CYS81 3.8 46.5 1.0
N C:CYS71 4.0 52.0 1.0
N C:CYS84 4.0 46.6 1.0
C C:CYS81 4.3 52.8 1.0
CA C:CYS71 4.3 55.6 1.0
CA C:CYS87 4.3 41.5 1.0
N C:CYS87 4.3 51.4 1.0
C C:PRO80 4.3 54.1 1.0
N C:ARG83 4.4 48.1 1.0
CA C:CYS84 4.5 50.1 1.0
CA C:PRO80 4.6 46.2 1.0
CA C:GLY82 4.8 48.5 1.0
CB C:PRO80 4.8 45.0 1.0
C C:VAL70 5.0 58.0 1.0

Zinc binding site 4 out of 11 in 8yhd

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Zinc binding site 4 out of 11 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:124.7
occ:1.00
 SG D:CYS84 2.3 80.9 1.0
SG D:CYS81 2.3 65.3 1.0
SG D:CYS71 2.3 73.6 1.0
SG D:CYS87 2.3 62.6 1.0
CB D:CYS84 2.9 48.9 1.0
CB D:CYS71 3.4 58.1 1.0
N D:CYS81 3.5 47.8 1.0
CB D:CYS81 3.7 57.6 1.0
N D:GLY82 3.8 57.0 1.0
CB D:CYS87 3.8 50.3 1.0
N D:CYS71 3.9 46.1 1.0
CA D:CYS81 4.0 52.8 1.0
CA D:CYS84 4.1 53.5 1.0
N D:CYS84 4.1 62.4 1.0
CA D:CYS71 4.3 53.1 1.0
C D:CYS81 4.4 56.3 1.0
C D:PRO80 4.4 48.7 1.0
CA D:PRO80 4.6 33.8 1.0
N D:ARG83 4.7 54.8 1.0
CB D:PRO80 4.7 43.5 1.0
CA D:GLY82 4.8 57.8 1.0
CA D:CYS87 4.8 42.5 1.0
N D:CYS87 4.9 52.1 1.0
C D:ARG83 5.0 65.9 1.0

Zinc binding site 5 out of 11 in 8yhd

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Zinc binding site 5 out of 11 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:117.2
occ:1.00
 SG E:CYS87 2.3 61.9 1.0
SG E:CYS84 2.3 63.4 1.0
SG E:CYS71 2.3 52.5 1.0
SG E:CYS81 2.3 62.0 1.0
CB E:CYS71 3.2 46.6 1.0
CB E:CYS87 3.3 41.5 1.0
N E:CYS81 3.4 42.7 1.0
CB E:CYS84 3.5 43.8 1.0
CB E:CYS81 3.6 51.1 1.0
N E:GLY82 3.6 48.2 1.0
N E:CYS71 3.9 43.2 1.0
CA E:CYS81 3.9 44.3 1.0
N E:CYS84 4.1 41.7 1.0
CA E:CYS71 4.2 44.6 1.0
N E:CYS87 4.2 39.4 1.0
C E:CYS81 4.3 46.8 1.0
CA E:CYS87 4.3 37.8 1.0
CA E:CYS84 4.4 43.1 1.0
C E:PRO80 4.5 46.8 1.0
N E:ARG83 4.5 58.6 1.0
CA E:GLY82 4.6 51.4 1.0
CA E:PRO80 4.7 38.3 1.0
CB E:PRO80 4.7 39.5 1.0
CG2 E:THR86 4.8 45.9 1.0
C E:GLY82 4.9 59.4 1.0
C E:CYS71 4.9 53.3 1.0

Zinc binding site 6 out of 11 in 8yhd

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Zinc binding site 6 out of 11 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:100.5
occ:1.00
 SG F:CYS71 2.3 69.8 1.0
SG F:CYS84 2.3 71.0 1.0
SG F:CYS87 2.3 63.6 1.0
SG F:CYS81 2.3 69.8 1.0
CB F:CYS71 3.4 59.0 1.0
CB F:CYS84 3.4 59.1 1.0
N F:CYS81 3.5 64.8 1.0
CB F:CYS87 3.6 54.0 1.0
O F:CYS81 3.8 72.3 1.0
CB F:CYS81 3.8 62.9 1.0
N F:CYS71 3.9 57.6 1.0
CA F:CYS81 4.0 62.1 1.0
C F:CYS81 4.1 68.3 1.0
CA F:CYS71 4.3 57.7 1.0
C F:PRO80 4.5 67.4 1.0
CA F:CYS84 4.5 50.9 1.0
N F:CYS84 4.6 56.7 1.0
CA F:PRO80 4.6 57.0 1.0
CA F:CYS87 4.8 48.9 1.0
N F:CYS87 4.8 49.1 1.0
CB F:PRO80 4.9 61.7 1.0
C F:VAL70 4.9 56.4 1.0
N F:GLY82 4.9 67.6 1.0
C F:ARG83 5.0 70.5 1.0
NH2 F:ARG56 5.0 43.2 1.0

Zinc binding site 7 out of 11 in 8yhd

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Zinc binding site 7 out of 11 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:30.0
occ:1.00
 SG G:CYS88 1.6 30.0 1.0
SG G:CYS85 1.8 30.0 1.0
SG G:CYS70 2.1 30.0 1.0
CB G:CYS70 2.3 30.0 1.0
CB G:CYS85 2.3 30.0 1.0
CB G:CYS88 3.4 30.0 1.0
N G:CYS88 3.5 125.6 1.0
CA G:CYS70 3.6 117.9 1.0
OG G:SER68 3.7 108.5 1.0
CB G:SER87 3.7 122.4 1.0
N G:CYS70 3.8 119.2 1.0
CA G:CYS85 3.8 116.5 1.0
CB G:SER68 3.8 107.2 1.0
CA G:CYS88 4.0 124.7 1.0
C G:SER87 4.2 122.9 1.0
C G:CYS85 4.3 115.1 1.0
CA G:SER87 4.3 122.0 1.0
O G:CYS85 4.4 114.7 1.0
O G:CYS88 4.4 123.0 1.0
N G:SER87 4.5 121.3 1.0
OG G:SER87 4.6 123.7 1.0
C G:CYS70 4.6 115.2 1.0
C G:CYS88 4.8 123.8 1.0
CB G:LYS72 4.8 94.9 1.0
N G:CYS85 4.8 115.8 1.0
N G:GLY71 4.9 100.7 1.0
CA G:SER68 5.0 108.0 1.0
N G:LYS72 5.0 95.2 1.0

Zinc binding site 8 out of 11 in 8yhd

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Zinc binding site 8 out of 11 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn701

b:145.5
occ:1.00
 CE1 H:HIS148 1.8 83.6 1.0
ND1 H:HIS64 2.1 89.2 1.0
NE2 H:HIS62 2.2 72.0 1.0
ND1 H:HIS148 2.3 80.7 1.0
CD2 H:HIS62 2.5 71.1 1.0
NE2 H:HIS148 3.0 81.4 1.0
CE1 H:HIS64 3.0 89.5 1.0
CG H:HIS64 3.1 89.0 1.0
CE1 H:HIS62 3.2 70.8 1.0
CB H:HIS64 3.5 87.2 1.0
CG H:HIS148 3.5 75.2 1.0
OD2 H:ASP169 3.5 77.1 1.0
CG H:HIS62 3.6 68.5 1.0
CD2 H:HIS148 3.8 77.2 1.0
ND1 H:HIS62 3.9 69.1 1.0
NE2 H:HIS64 4.1 92.1 1.0
CD2 H:HIS64 4.2 90.5 1.0
CG H:ASP169 4.2 80.5 1.0
CD1 H:ILE149 4.2 77.0 1.0
CB H:ASP169 4.4 77.7 1.0
OD1 H:ASP66 4.5 92.4 1.0
CB H:HIS148 4.6 73.2 1.0
NE2 H:HIS373 4.7 89.2 1.0
CB H:HIS62 4.7 68.2 1.0
CG1 H:ILE149 4.8 79.5 1.0
CA H:HIS64 4.8 88.1 1.0
OD2 H:ASP66 4.8 86.2 1.0

Zinc binding site 9 out of 11 in 8yhd

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Zinc binding site 9 out of 11 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn702

b:167.5
occ:1.00
 NE2 H:HIS67 2.4 85.3 1.0
OD1 H:ASP169 2.9 82.4 1.0
OD2 H:ASP169 2.9 77.1 1.0
CE1 H:HIS67 3.2 82.6 1.0
CG H:ASP169 3.3 80.5 1.0
CD2 H:HIS67 3.4 82.1 1.0
OD2 H:ASP66 4.2 86.2 1.0
OG1 H:THR197 4.3 83.9 1.0
ND1 H:HIS67 4.4 81.3 1.0
OE2 H:GLU195 4.5 78.7 1.0
CG H:HIS67 4.5 80.8 1.0
CG H:ASP66 4.6 88.2 1.0
CB H:ASP169 4.8 77.7 1.0
CB H:HIS397 4.8 57.4 1.0
CE1 H:HIS62 4.9 70.8 1.0

Zinc binding site 10 out of 11 in 8yhd

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Zinc binding site 10 out of 11 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn301

b:99.3
occ:1.00
 SG J:CYS87 2.3 63.3 1.0
SG J:CYS71 2.3 67.5 1.0
SG J:CYS81 2.3 67.1 1.0
SG J:CYS84 2.3 72.2 1.0
CB J:CYS84 3.2 49.2 1.0
CB J:CYS71 3.3 53.2 1.0
CB J:CYS87 3.3 46.7 1.0
N J:CYS81 3.5 44.9 1.0
N J:CYS71 3.7 51.3 1.0
CB J:CYS81 3.7 50.0 1.0
N J:CYS84 3.9 51.0 1.0
N J:GLY82 3.9 44.5 1.0
N J:CYS87 4.0 46.7 1.0
CA J:CYS84 4.1 43.8 1.0
OG1 J:THR86 4.1 53.1 1.0
CA J:CYS81 4.1 43.8 1.0
CA J:CYS71 4.1 49.5 1.0
CA J:CYS87 4.2 38.5 1.0
C J:CYS81 4.5 48.8 1.0
C J:PRO80 4.5 42.0 1.0
C J:CYS84 4.6 44.8 1.0
N J:ARG83 4.6 48.1 1.0
CA J:PRO80 4.7 37.1 1.0
CB J:PRO80 4.7 47.5 1.0
O J:CYS84 4.8 54.3 1.0
C J:VAL70 4.8 59.2 1.0
CA J:GLY82 4.9 44.1 1.0
CA J:VAL70 5.0 58.7 1.0
C J:CYS71 5.0 55.3 1.0
C J:THR86 5.0 47.1 1.0

Reference:

X.Li, Z.Deng, H.Zhang. Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 1 To Be Published.
Page generated: Thu Oct 31 14:01:54 2024

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