Zinc in PDB 8yhe: Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 2

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 2 (pdb code 8yhe). 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 Post-State 2, PDB code: 8yhe:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 8yhe

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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 Post-State 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:206.0
occ:1.00
 SG A:CYS84 2.3 151.0 1.0
SG A:CYS71 2.3 165.7 1.0
SG A:CYS81 2.3 164.2 1.0
SG A:CYS87 2.3 141.9 1.0
CB A:CYS84 3.1 149.3 1.0
CB A:CYS81 3.2 163.9 1.0
CB A:CYS71 3.2 162.8 1.0
N A:CYS81 3.2 164.1 1.0
N A:CYS84 3.6 148.8 1.0
CA A:CYS81 3.7 163.9 1.0
N A:GLY82 3.7 162.2 1.0
CB A:CYS87 3.8 142.5 1.0
CA A:CYS84 3.9 149.0 1.0
N A:CYS71 4.1 163.7 1.0
C A:CYS81 4.1 164.4 1.0
CA A:CYS71 4.2 163.3 1.0
N A:ARG83 4.2 154.8 1.0
C A:PRO80 4.4 160.1 1.0
C A:ARG83 4.6 152.4 1.0
CA A:PRO80 4.7 160.0 1.0
CA A:GLY82 4.8 161.7 1.0
CB A:PRO80 4.8 159.8 1.0
C A:GLY82 4.9 162.8 1.0
CA A:ARG83 4.9 153.2 1.0
CA A:CYS87 5.0 143.3 1.0

Zinc binding site 2 out of 9 in 8yhe

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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 Post-State 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:186.8
occ:1.00
 SG B:CYS84 1.8 133.8 1.0
SG B:CYS81 2.3 128.3 1.0
SG B:CYS87 2.3 110.2 1.0
SG B:CYS71 2.3 144.2 1.0
CB B:CYS87 2.9 109.8 1.0
CB B:CYS84 3.0 129.4 1.0
CB B:CYS71 3.7 141.1 1.0
N B:CYS81 3.8 120.5 1.0
CB B:CYS81 3.8 122.4 1.0
N B:CYS87 3.9 110.3 1.0
N B:CYS84 3.9 126.9 1.0
CA B:CYS87 3.9 109.4 1.0
N B:CYS71 4.0 140.9 1.0
CA B:CYS84 4.0 127.5 1.0
N B:GLY82 4.1 122.3 1.0
OG1 B:THR86 4.3 111.0 1.0
CA B:CYS81 4.3 121.6 1.0
CA B:CYS71 4.5 142.4 1.0
C B:CYS84 4.7 127.2 1.0
C B:CYS81 4.7 121.5 1.0
N B:ARG83 4.8 130.0 1.0
C B:PRO80 4.8 108.1 1.0
C B:THR86 5.0 108.3 1.0

Zinc binding site 3 out of 9 in 8yhe

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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 Post-State 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:110.4
occ:1.00
 SG C:CYS84 2.3 71.8 1.0
SG C:CYS87 2.3 75.6 1.0
SG C:CYS71 2.3 80.3 1.0
SG C:CYS81 2.3 81.5 1.0
CB C:CYS71 3.2 74.2 1.0
N C:CYS81 3.3 68.0 1.0
CB C:CYS87 3.6 60.3 1.0
CB C:CYS81 3.8 68.6 1.0
N C:CYS71 3.8 70.3 1.0
N C:GLY82 3.9 58.9 1.0
CA C:CYS81 4.0 67.0 1.0
CB C:CYS84 4.0 65.1 1.0
CA C:CYS71 4.1 74.0 1.0
N C:CYS84 4.2 63.5 1.0
C C:PRO80 4.3 66.0 1.0
C C:CYS81 4.4 67.9 1.0
CA C:PRO80 4.4 60.3 1.0
N C:ARG83 4.5 75.7 1.0
CA C:CYS87 4.6 49.7 1.0
N C:CYS87 4.6 53.4 1.0
CA C:CYS84 4.7 64.0 1.0
CB C:PRO80 4.7 56.2 1.0
CA C:GLY82 4.9 58.9 1.0
C C:VAL70 5.0 76.3 1.0

Zinc binding site 4 out of 9 in 8yhe

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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 Post-State 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:137.0
occ:1.00
 SG D:CYS71 2.3 80.8 1.0
SG D:CYS84 2.3 83.9 1.0
SG D:CYS81 2.3 89.7 1.0
SG D:CYS87 2.3 66.6 1.0
CB D:CYS71 2.9 69.8 1.0
N D:CYS81 3.2 67.8 1.0
N D:GLY82 3.5 67.3 1.0
CB D:CYS84 3.5 67.8 1.0
CB D:CYS81 3.6 72.5 1.0
CB D:CYS87 3.7 56.3 1.0
CA D:CYS81 3.8 69.7 1.0
N D:CYS71 3.8 65.9 1.0
CA D:CYS71 4.0 65.2 1.0
N D:CYS84 4.0 63.9 1.0
C D:PRO80 4.1 69.7 1.0
C D:CYS81 4.2 75.0 1.0
CA D:PRO80 4.3 62.1 1.0
N D:ARG83 4.3 72.8 1.0
CA D:CYS84 4.4 65.0 1.0
CA D:GLY82 4.5 63.3 1.0
CB D:PRO80 4.5 67.1 1.0
C D:GLY82 4.9 70.1 1.0
CA D:CYS87 4.9 54.4 1.0
C D:CYS71 4.9 56.5 1.0

Zinc binding site 5 out of 9 in 8yhe

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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 Post-State 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:124.0
occ:1.00
 SG E:CYS84 2.3 89.2 1.0
SG E:CYS87 2.3 65.1 1.0
SG E:CYS81 2.3 84.2 1.0
SG E:CYS71 2.3 83.2 1.0
CB E:CYS71 3.1 76.2 1.0
CB E:CYS87 3.4 55.6 1.0
N E:CYS81 3.4 75.6 1.0
CB E:CYS81 3.7 76.0 1.0
N E:GLY82 3.7 73.9 1.0
CB E:CYS84 3.8 74.0 1.0
N E:CYS71 3.8 76.2 1.0
CA E:CYS81 4.0 73.5 1.0
CA E:CYS71 4.0 73.2 1.0
N E:CYS84 4.1 75.9 1.0
C E:CYS81 4.3 72.7 1.0
C E:PRO80 4.3 75.6 1.0
CA E:CYS87 4.4 47.3 1.0
N E:CYS87 4.4 55.5 1.0
N E:ARG83 4.4 83.6 1.0
CA E:CYS84 4.5 75.9 1.0
CA E:PRO80 4.5 66.8 1.0
CA E:GLY82 4.7 80.4 1.0
CB E:PRO80 4.8 69.8 1.0
C E:CYS71 4.8 68.8 1.0
O E:CYS71 4.9 75.6 1.0

Zinc binding site 6 out of 9 in 8yhe

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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 Post-State 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:176.5
occ:1.00
 SG F:CYS87 2.3 96.6 1.0
SG F:CYS84 2.3 107.5 1.0
SG F:CYS81 2.3 125.4 1.0
SG F:CYS71 2.3 111.4 1.0
CB F:CYS84 3.3 104.9 1.0
CB F:CYS71 3.3 106.4 1.0
N F:CYS81 3.6 123.5 1.0
CB F:CYS87 3.6 93.3 1.0
N F:CYS71 3.7 109.0 1.0
CB F:CYS81 3.9 124.1 1.0
OG1 F:THR86 4.0 85.5 1.0
N F:CYS87 4.1 89.8 1.0
CA F:CYS71 4.1 107.1 1.0
N F:CYS84 4.1 107.7 1.0
N F:GLY82 4.2 116.1 1.0
CA F:CYS81 4.2 123.9 1.0
CA F:CYS84 4.3 106.1 1.0
CA F:CYS87 4.4 87.7 1.0
C F:PRO80 4.6 114.5 1.0
CA F:PRO80 4.6 112.3 1.0
C F:CYS81 4.8 122.8 1.0
C F:VAL70 4.8 109.8 1.0
CB F:PRO80 4.9 110.8 1.0
C F:CYS84 4.9 102.2 1.0
CA F:VAL70 4.9 107.3 1.0

Zinc binding site 7 out of 9 in 8yhe

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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 Post-State 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn701

b:136.3
occ:1.00
 OD1 H:ASP169 2.1 97.6 1.0
NE2 H:HIS67 3.1 100.5 1.0
CG H:ASP169 3.2 96.8 1.0
NE2 H:HIS397 3.6 113.3 1.0
CE1 H:HIS62 3.6 87.9 1.0
CD2 H:HIS67 3.7 100.9 1.0
OD2 H:ASP66 3.7 105.2 1.0
OD2 H:ASP169 3.7 94.5 1.0
NE2 H:HIS62 3.9 87.2 1.0
CE1 H:HIS67 4.0 98.2 1.0
CE1 H:HIS397 4.1 113.8 1.0
CE1 H:HIS148 4.2 101.2 1.0
CE1 H:HIS373 4.3 124.8 1.0
CB H:ASP66 4.3 98.6 1.0
ZN H:ZN702 4.3 30.0 1.0
CB H:ASP169 4.4 92.6 1.0
CG H:ASP66 4.4 104.8 1.0
CD2 H:HIS397 4.7 113.9 1.0
CG H:HIS67 4.8 96.6 1.0
ND1 H:HIS62 4.9 88.0 1.0
NE2 H:HIS148 4.9 102.1 1.0
ND1 H:HIS148 4.9 99.9 1.0
ND1 H:HIS67 4.9 94.0 1.0

Zinc binding site 8 out of 9 in 8yhe

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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 Post-State 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn702

b:30.0
occ:1.00
 CE1 H:HIS148 1.7 101.2 1.0
ND1 H:HIS62 1.8 88.0 1.0
ND1 H:HIS148 2.0 99.9 1.0
CE1 H:HIS62 2.0 87.9 1.0
ND1 H:HIS64 2.2 109.3 1.0
CE1 H:HIS64 2.6 106.8 1.0
CG H:HIS64 2.8 104.2 1.0
NE2 H:HIS148 3.0 102.1 1.0
CG H:HIS62 3.0 84.3 1.0
NE2 H:HIS64 3.2 105.7 1.0
NE2 H:HIS62 3.2 87.2 1.0
CG H:HIS148 3.3 97.8 1.0
CD2 H:HIS64 3.3 103.3 1.0
CB H:HIS64 3.5 98.2 1.0
CD2 H:HIS62 3.7 87.2 1.0
CD2 H:HIS148 3.7 100.5 1.0
OD1 H:ASP169 3.9 97.6 1.0
CB H:HIS62 4.0 82.5 1.0
ZN H:ZN701 4.3 136.3 1.0
CB H:HIS148 4.4 93.4 1.0
N H:HIS64 4.6 100.8 1.0
CD1 H:ILE149 4.6 85.2 1.0
CA H:HIS64 4.7 98.5 1.0
CB H:ASP169 4.7 92.6 1.0
CG H:ASP169 4.7 96.8 1.0
CG1 H:ILE149 4.8 87.8 1.0
OD2 H:ASP66 4.9 105.2 1.0

Zinc binding site 9 out of 9 in 8yhe

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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 Post-State 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn301

b:110.4
occ:1.00
 SG J:CYS87 2.3 74.1 1.0
SG J:CYS84 2.3 63.8 1.0
SG J:CYS81 2.3 83.4 1.0
SG J:CYS71 2.3 84.0 1.0
CB J:CYS71 3.0 67.6 1.0
CB J:CYS84 3.3 62.3 1.0
CB J:CYS87 3.4 61.0 1.0
N J:CYS71 3.4 68.3 1.0
N J:CYS81 3.5 72.7 1.0
CA J:CYS71 3.8 65.5 1.0
CB J:CYS81 3.8 73.5 1.0
N J:CYS84 4.0 61.6 1.0
N J:GLY82 4.1 59.5 1.0
N J:CYS87 4.1 50.3 1.0
CA J:CYS81 4.1 69.8 1.0
CA J:CYS87 4.2 51.1 1.0
CA J:CYS84 4.2 61.5 1.0
OG1 J:THR86 4.3 53.0 1.0
C J:PRO80 4.5 60.8 1.0
CA J:PRO80 4.6 53.6 1.0
C J:VAL70 4.6 78.9 1.0
C J:CYS81 4.6 73.1 1.0
CB J:PRO80 4.7 59.1 1.0
C J:CYS71 4.7 64.7 1.0
N J:ARG83 4.8 69.8 1.0
CA J:VAL70 4.8 77.0 1.0
C J:CYS84 4.8 59.9 1.0
O J:CYS71 4.9 66.3 1.0
NH2 J:ARG56 4.9 40.7 1.0

Reference:

H.Zhang, Z.Deng, X.Li. Cryo-Em Structure of Ctr-Bound Type 7 Crispr-Cas Complex at Post-State 2 To Be Published.
Page generated: Thu Oct 31 14:06:18 2024

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