Zinc in PDB 8z4l: Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 1

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 1 (pdb code 8z4l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 1, PDB code: 8z4l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 8z4l

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Zinc binding site 1 out of 9 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged 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 Substrate- Engaged State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:135.3
occ:1.00
 SG A:CYS84 2.2 77.0 1.0
SG A:CYS71 2.4 87.9 1.0
SG A:CYS81 2.5 78.2 1.0
CB A:CYS87 2.5 80.7 1.0
N A:CYS84 2.5 73.2 1.0
N A:ARG83 3.0 71.2 1.0
SG A:CYS87 3.1 84.5 1.0
CB A:CYS84 3.2 75.8 1.0
N A:GLY82 3.3 68.0 1.0
CA A:CYS84 3.3 74.2 1.0
C A:ARG83 3.5 69.8 1.0
C A:GLY82 3.7 68.2 1.0
O A:CYS84 3.7 74.2 1.0
CA A:GLY82 3.8 67.4 1.0
C A:CYS84 3.8 73.8 1.0
CA A:CYS87 3.8 79.9 1.0
CA A:ARG83 3.8 70.1 1.0
CB A:CYS71 4.0 78.5 1.0
N A:CYS87 4.0 79.6 1.0
CB A:CYS81 4.1 68.9 1.0
C A:CYS81 4.3 69.1 1.0
N A:CYS81 4.5 71.6 1.0
CA A:CYS81 4.5 70.1 1.0
C A:CYS87 4.6 81.1 1.0
N A:CYS71 4.6 79.3 1.0
O A:ARG83 4.7 71.5 1.0
O A:GLY82 4.7 67.0 1.0
CB A:ARG83 4.8 69.0 1.0
N A:VAL85 4.9 76.3 1.0
CA A:CYS71 5.0 79.0 1.0

Zinc binding site 2 out of 9 in 8z4l

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Zinc binding site 2 out of 9 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged 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 Substrate- Engaged State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:106.7
occ:1.00
 SG B:CYS81 2.3 62.7 1.0
SG B:CYS87 2.3 57.7 1.0
SG B:CYS71 2.3 75.0 1.0
SG B:CYS84 2.3 47.1 1.0
CB B:CYS71 3.2 61.6 1.0
N B:CYS81 3.3 51.9 1.0
CB B:CYS84 3.3 48.3 1.0
CB B:CYS81 3.3 51.5 1.0
CB B:CYS87 3.4 46.0 1.0
N B:CYS84 3.5 43.6 1.0
N B:GLY82 3.6 47.1 1.0
CA B:CYS81 3.7 49.2 1.0
N B:ARG83 3.9 49.2 1.0
CA B:CYS84 4.0 46.3 1.0
C B:CYS81 4.0 52.0 1.0
N B:CYS71 4.1 64.4 1.0
CA B:CYS71 4.2 60.1 1.0
C B:PRO80 4.3 52.0 1.0
N B:CYS87 4.4 42.0 1.0
CA B:CYS87 4.5 40.3 1.0
C B:ARG83 4.5 50.6 1.0
CA B:GLY82 4.6 47.4 1.0
CA B:PRO80 4.7 47.0 1.0
CA B:ARG83 4.7 49.8 1.0
C B:GLY82 4.8 49.1 1.0
C B:CYS84 4.8 44.1 1.0
OG1 B:THR86 5.0 44.1 1.0
O B:CYS84 5.0 44.8 1.0
C B:VAL70 5.0 55.8 1.0

Zinc binding site 3 out of 9 in 8z4l

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Zinc binding site 3 out of 9 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged 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 Substrate- Engaged State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:87.4
occ:1.00
 SG C:CYS87 2.3 39.4 1.0
SG C:CYS84 2.3 34.5 1.0
SG C:CYS71 2.3 52.9 1.0
SG C:CYS81 2.3 40.1 1.0
CB C:CYS84 3.4 36.4 1.0
CB C:CYS81 3.4 32.4 1.0
N C:CYS81 3.4 29.0 1.0
CB C:CYS87 3.5 22.6 1.0
CB C:CYS71 3.6 48.0 1.0
N C:GLY82 3.8 21.4 1.0
N C:CYS84 3.8 33.1 1.0
CA C:CYS81 3.8 26.5 1.0
N C:CYS71 3.9 42.0 1.0
CA C:CYS84 4.1 36.7 1.0
N C:CYS87 4.2 27.6 1.0
C C:CYS81 4.2 28.6 1.0
CA C:CYS71 4.3 43.3 1.0
CA C:CYS87 4.4 18.7 1.0
C C:PRO80 4.4 29.1 1.0
N C:ARG83 4.4 31.1 1.0
CA C:PRO80 4.7 21.4 1.0
C C:CYS84 4.8 37.1 1.0
CA C:GLY82 4.8 16.8 1.0
O C:CYS84 4.9 38.3 1.0
C C:VAL70 5.0 53.0 1.0
C C:ARG83 5.0 33.2 1.0
CB C:PRO80 5.0 21.4 1.0

Zinc binding site 4 out of 9 in 8z4l

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Zinc binding site 4 out of 9 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged 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 Substrate- Engaged State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:113.4
occ:1.00
 SG D:CYS84 2.3 63.8 1.0
SG D:CYS71 2.3 48.9 1.0
SG D:CYS81 2.3 54.4 1.0
SG D:CYS87 2.3 27.8 1.0
N D:CYS81 2.9 33.3 1.0
CB D:CYS81 3.2 44.2 1.0
N D:GLY82 3.4 41.9 1.0
CA D:CYS81 3.5 36.5 1.0
CB D:CYS71 3.7 49.5 1.0
CB D:CYS84 3.7 45.5 1.0
CB D:CYS87 3.8 24.6 1.0
C D:CYS81 3.9 41.6 1.0
N D:CYS84 4.0 46.5 1.0
C D:PRO80 4.0 33.9 1.0
N D:ARG83 4.2 50.2 1.0
N D:CYS71 4.2 45.5 1.0
CA D:PRO80 4.3 25.9 1.0
CA D:GLY82 4.4 36.4 1.0
CA D:CYS84 4.5 46.5 1.0
CA D:CYS71 4.6 47.5 1.0
CB D:PRO80 4.7 26.1 1.0
C D:GLY82 4.7 40.7 1.0
CA D:CYS87 4.9 19.6 1.0
N D:CYS87 4.9 33.0 1.0
C D:ARG83 5.0 54.4 1.0

Zinc binding site 5 out of 9 in 8z4l

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Zinc binding site 5 out of 9 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged 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 Substrate- Engaged State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:150.3
occ:1.00
 SG E:CYS84 2.3 79.6 1.0
SG E:CYS71 2.3 69.7 1.0
SG E:CYS81 2.3 58.5 1.0
SG E:CYS87 2.3 38.8 1.0
N E:CYS81 3.3 57.8 1.0
CB E:CYS71 3.4 71.1 1.0
CB E:CYS81 3.5 58.8 1.0
N E:GLY82 3.5 55.4 1.0
CB E:CYS87 3.6 41.8 1.0
CB E:CYS84 3.6 64.9 1.0
CA E:CYS81 3.8 57.0 1.0
N E:CYS71 3.9 69.6 1.0
N E:CYS84 4.0 64.5 1.0
C E:CYS81 4.1 58.9 1.0
N E:ARG83 4.3 67.7 1.0
CA E:CYS71 4.3 69.4 1.0
C E:PRO80 4.3 61.9 1.0
CA E:CYS84 4.4 66.4 1.0
CA E:PRO80 4.5 59.8 1.0
CA E:GLY82 4.5 54.1 1.0
CA E:CYS87 4.6 36.3 1.0
N E:CYS87 4.7 45.0 1.0
C E:GLY82 4.9 61.5 1.0
CB E:PRO80 5.0 57.3 1.0

Zinc binding site 6 out of 9 in 8z4l

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Zinc binding site 6 out of 9 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged 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 Substrate- Engaged State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:133.4
occ:1.00
 SG F:CYS81 2.3 87.0 1.0
SG F:CYS87 2.3 78.9 1.0
SG F:CYS84 2.3 79.0 1.0
SG F:CYS71 2.3 79.2 1.0
CB F:CYS71 3.0 74.1 1.0
CB F:CYS84 3.3 78.0 1.0
N F:CYS81 3.5 78.0 1.0
CB F:CYS87 3.6 72.4 1.0
CB F:CYS81 3.6 77.8 1.0
N F:CYS71 3.7 73.5 1.0
N F:CYS84 3.8 77.9 1.0
CA F:CYS81 4.0 76.9 1.0
CA F:CYS71 4.0 75.0 1.0
CA F:CYS84 4.1 76.8 1.0
C F:CYS81 4.2 78.0 1.0
O F:CYS81 4.3 74.9 1.0
N F:CYS87 4.4 71.9 1.0
C F:VAL70 4.5 68.9 1.0
C F:CYS84 4.6 75.7 1.0
C F:PRO80 4.6 83.4 1.0
CA F:CYS87 4.6 71.6 1.0
N F:ARG83 4.7 75.1 1.0
CB F:PRO80 4.8 81.7 1.0
CA F:VAL70 4.8 67.8 1.0
O F:CYS84 4.8 75.1 1.0
N F:GLY82 4.8 78.5 1.0
CA F:PRO80 4.9 82.2 1.0

Zinc binding site 7 out of 9 in 8z4l

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Zinc binding site 7 out of 9 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged 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 Substrate- Engaged State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:134.3
occ:1.00
 O G:SER87 2.3 83.3 1.0
SG G:CYS70 2.3 94.3 1.0
SG G:CYS88 2.3 95.3 1.0
SG G:CYS85 2.3 98.8 1.0
C G:SER87 3.3 81.0 1.0
OG G:SER68 3.4 82.5 1.0
CB G:CYS70 3.5 91.5 1.0
CB G:CYS85 3.7 91.9 1.0
CB G:GLU90 3.7 77.2 1.0
CB G:CYS88 3.7 91.7 1.0
N G:CYS88 4.0 90.3 1.0
C G:CYS88 4.1 91.1 1.0
CA G:CYS88 4.1 91.2 1.0
O G:ASN89 4.1 89.8 1.0
CB G:SER68 4.1 81.2 1.0
C G:ASN89 4.3 92.6 1.0
N G:ASN89 4.3 94.9 1.0
CA G:SER87 4.4 79.6 1.0
CB G:SER87 4.4 77.4 1.0
N G:GLU90 4.5 80.1 1.0
O G:CYS88 4.6 89.1 1.0
N G:CYS70 4.7 91.5 1.0
CA G:GLU90 4.7 79.7 1.0
CA G:CYS70 4.8 92.9 1.0
CA G:CYS85 4.8 92.9 1.0
CA G:ASN89 4.8 95.4 1.0
N G:SER87 4.8 80.5 1.0
O G:CYS85 4.8 92.0 1.0
C G:CYS85 4.9 92.4 1.0

Zinc binding site 8 out of 9 in 8z4l

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Zinc binding site 8 out of 9 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged 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 Substrate- Engaged State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn701

b:93.6
occ:1.00
 OD2 H:ASP169 2.1 63.8 1.0
ND1 H:HIS64 2.3 70.9 1.0
NE2 H:HIS148 2.3 62.4 1.0
NE2 H:HIS62 2.3 58.0 1.0
CD2 H:HIS62 2.5 53.9 1.0
CD2 H:HIS148 2.7 55.6 1.0
CE1 H:HIS64 3.1 68.8 1.0
CG H:ASP169 3.2 61.9 1.0
CG H:HIS64 3.3 68.3 1.0
CE1 H:HIS148 3.5 63.6 1.0
CE1 H:HIS62 3.6 57.9 1.0
CB H:HIS64 3.7 64.9 1.0
CG H:HIS62 3.8 49.3 1.0
NE2 H:HIS373 3.8 81.4 1.0
CB H:ASP169 3.9 59.0 1.0
OP1 N:A-15 3.9 114.0 1.0
CG H:HIS148 4.0 55.0 1.0
OD1 H:ASP169 4.1 61.0 1.0
OP2 N:A-15 4.2 114.3 1.0
ND1 H:HIS62 4.3 55.0 1.0
NE2 H:HIS64 4.3 67.0 1.0
ND1 H:HIS148 4.3 62.8 1.0
CD2 H:HIS64 4.4 68.7 1.0
P N:A-15 4.6 116.8 1.0
CD2 H:HIS373 4.7 81.2 1.0
CE1 H:HIS373 4.8 80.7 1.0
CB H:HIS62 5.0 52.7 1.0

Zinc binding site 9 out of 9 in 8z4l

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Zinc binding site 9 out of 9 in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged 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 Substrate- Engaged State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn301

b:84.2
occ:1.00
 SG J:CYS87 2.3 31.0 1.0
SG J:CYS84 2.3 44.8 1.0
SG J:CYS71 2.3 48.5 1.0
SG J:CYS81 2.3 45.0 1.0
CB J:CYS87 3.3 15.9 1.0
CB J:CYS84 3.3 38.0 1.0
CB J:CYS71 3.5 37.8 1.0
CB J:CYS81 3.5 35.5 1.0
N J:CYS81 3.5 31.4 1.0
N J:GLY82 3.7 32.8 1.0
N J:CYS71 3.8 36.7 1.0
N J:CYS84 3.8 36.0 1.0
CA J:CYS81 3.9 29.3 1.0
N J:CYS87 4.1 24.4 1.0
CA J:CYS84 4.1 37.4 1.0
CA J:CYS87 4.2 10.3 1.0
CA J:CYS71 4.3 36.9 1.0
C J:CYS81 4.3 35.3 1.0
N J:ARG83 4.4 41.8 1.0
C J:PRO80 4.6 26.6 1.0
CA J:GLY82 4.7 25.5 1.0
C J:CYS84 4.7 37.3 1.0
O J:CYS84 4.8 41.7 1.0
CA J:PRO80 4.8 24.7 1.0
C J:VAL70 4.9 38.1 1.0
CB J:PRO80 5.0 23.0 1.0

Reference:

X.Li, Z.Deng, H.Zhang. Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Substrate-Engaged State 1 To Be Published.
Page generated: Thu Oct 31 14:09:18 2024

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