Zinc in PDB 8z9c: Cryo-Em Structure of Ntr-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 Ntr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 1 (pdb code 8z9c). 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 Ntr-Bound Type 7 Crispr-Cas Complex at Substrate- Engaged State 1, PDB code: 8z9c:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 8z9c

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Zinc binding site 1 out of 9 in the Cryo-Em Structure of Ntr-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 Ntr-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:170.0
occ:1.00
 SG A:CYS84 2.3 119.2 1.0
SG A:CYS81 2.3 122.5 1.0
SG A:CYS87 2.3 113.9 1.0
SG A:CYS71 2.3 125.2 1.0
CB A:CYS87 3.1 111.2 1.0
CB A:CYS71 3.3 123.1 1.0
CB A:CYS84 3.5 114.6 1.0
N A:CYS81 3.8 119.9 1.0
OG1 A:THR86 3.9 106.9 1.0
CB A:CYS81 3.9 118.7 1.0
N A:CYS87 4.0 111.0 1.0
CA A:CYS87 4.1 111.1 1.0
N A:GLY82 4.3 107.2 1.0
N A:CYS84 4.3 114.9 1.0
N A:CYS71 4.3 123.5 1.0
NH2 A:ARG56 4.4 109.6 1.0
CA A:CYS71 4.4 122.7 1.0
CA A:CYS81 4.4 118.5 1.0
CA A:CYS84 4.4 115.3 1.0
C A:VAL70 4.6 119.0 1.0
C A:THR86 4.6 105.0 1.0
C A:PRO80 4.7 109.3 1.0
CA A:PRO80 4.7 108.1 1.0
O A:VAL70 4.8 117.9 1.0
CB A:PRO80 4.9 107.2 1.0
C A:CYS81 4.9 117.2 1.0
C A:CYS84 4.9 115.4 1.0
CB A:THR86 4.9 105.1 1.0

Zinc binding site 2 out of 9 in 8z9c

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Zinc binding site 2 out of 9 in the Cryo-Em Structure of Ntr-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 Ntr-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:127.7
occ:1.00
 SG B:CYS71 2.3 76.2 1.0
SG B:CYS87 2.3 61.0 1.0
SG B:CYS81 2.3 64.0 1.0
CB B:CYS84 2.7 52.1 1.0
CB B:CYS71 3.2 62.8 1.0
SG B:CYS84 3.2 65.5 1.0
N B:CYS71 3.5 63.1 1.0
CB B:CYS87 3.6 40.6 1.0
N B:CYS81 3.8 59.9 1.0
CB B:CYS81 3.8 59.1 1.0
CA B:CYS71 4.0 61.7 1.0
CA B:CYS84 4.1 51.1 1.0
N B:GLY82 4.2 53.8 1.0
CA B:CYS81 4.3 55.2 1.0
N B:CYS84 4.4 50.2 1.0
N B:CYS87 4.5 38.5 1.0
OG1 B:THR86 4.5 47.8 1.0
C B:VAL70 4.6 65.5 1.0
CA B:CYS87 4.7 39.2 1.0
CA B:VAL70 4.8 63.7 1.0
C B:PRO80 4.8 55.8 1.0
C B:CYS81 4.8 57.9 1.0
N B:ARG83 4.8 63.6 1.0
O B:ASN69 4.9 89.0 1.0
CA B:PRO80 4.9 45.1 1.0
C B:ARG83 5.0 66.5 1.0

Zinc binding site 3 out of 9 in 8z9c

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Zinc binding site 3 out of 9 in the Cryo-Em Structure of Ntr-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 Ntr-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:143.6
occ:1.00
 SG C:CYS84 2.3 65.6 1.0
SG C:CYS71 2.3 67.4 1.0
SG C:CYS81 2.3 64.9 1.0
SG C:CYS87 2.3 51.4 1.0
N C:CYS81 3.0 56.5 1.0
CB C:CYS81 3.3 56.6 1.0
CB C:CYS71 3.4 53.7 1.0
N C:GLY82 3.5 46.4 1.0
CB C:CYS84 3.5 50.4 1.0
CB C:CYS87 3.6 44.6 1.0
CA C:CYS81 3.6 55.5 1.0
C C:PRO80 3.9 55.5 1.0
C C:CYS81 4.1 58.3 1.0
N C:CYS71 4.1 46.1 1.0
N C:CYS84 4.1 54.7 1.0
CA C:PRO80 4.2 45.8 1.0
CA C:CYS71 4.4 45.3 1.0
CA C:CYS84 4.5 54.1 1.0
N C:ARG83 4.6 55.2 1.0
CA C:GLY82 4.6 42.7 1.0
CB C:PRO80 4.7 45.2 1.0
CA C:CYS87 4.7 36.8 1.0
N C:CYS87 4.9 39.8 1.0
C C:GLY82 5.0 49.2 1.0
O C:PRO80 5.0 60.4 1.0

Zinc binding site 4 out of 9 in 8z9c

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Zinc binding site 4 out of 9 in the Cryo-Em Structure of Ntr-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 Ntr-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:146.4
occ:1.00
 SG D:CYS84 2.3 64.6 1.0
SG D:CYS71 2.3 66.7 1.0
SG D:CYS87 2.3 53.5 1.0
SG D:CYS81 2.3 69.7 1.0
CB D:CYS87 3.3 36.8 1.0
CB D:CYS71 3.4 52.9 1.0
N D:CYS81 3.5 59.1 1.0
N D:GLY82 3.7 67.6 1.0
CB D:CYS81 3.7 59.3 1.0
CB D:CYS84 3.9 60.4 1.0
CA D:CYS81 4.0 60.2 1.0
N D:CYS71 4.1 51.5 1.0
N D:CYS87 4.2 37.7 1.0
CA D:CYS87 4.3 33.0 1.0
CA D:CYS71 4.3 48.2 1.0
N D:CYS84 4.3 61.7 1.0
C D:PRO80 4.3 50.8 1.0
C D:CYS81 4.4 63.2 1.0
CA D:PRO80 4.5 38.5 1.0
N D:ARG83 4.6 77.3 1.0
OG1 D:THR86 4.6 45.5 1.0
CA D:CYS84 4.7 63.4 1.0
CA D:GLY82 4.7 63.3 1.0
CB D:PRO80 4.9 42.1 1.0
NH2 D:ARG56 4.9 55.0 1.0
C D:GLY82 5.0 69.3 1.0

Zinc binding site 5 out of 9 in 8z9c

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Zinc binding site 5 out of 9 in the Cryo-Em Structure of Ntr-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 Ntr-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:171.0
occ:1.00
 SG E:CYS71 2.3 80.6 1.0
SG E:CYS87 2.3 64.5 1.0
SG E:CYS81 2.3 98.2 1.0
SG E:CYS84 2.3 96.8 1.0
CB E:CYS84 2.5 84.8 1.0
CB E:CYS87 3.1 54.5 1.0
CB E:CYS71 3.3 75.5 1.0
N E:CYS71 3.5 72.4 1.0
N E:CYS87 3.6 52.8 1.0
CA E:CYS84 3.6 84.8 1.0
N E:CYS84 3.7 84.8 1.0
OG1 E:THR86 3.7 54.7 1.0
CA E:CYS87 3.9 52.5 1.0
CB E:CYS81 3.9 90.5 1.0
CA E:CYS71 4.1 72.3 1.0
N E:CYS81 4.1 91.5 1.0
C E:CYS84 4.2 83.8 1.0
N E:GLY82 4.5 89.8 1.0
CA E:CYS81 4.5 91.6 1.0
C E:THR86 4.5 52.7 1.0
C E:VAL70 4.6 72.4 1.0
O E:CYS84 4.6 87.3 1.0
CA E:VAL70 4.7 72.0 1.0
N E:ARG83 4.9 92.7 1.0
N E:THR86 4.9 52.1 1.0
N E:VAL85 4.9 57.5 1.0
CB E:THR86 4.9 47.9 1.0
C E:CYS71 4.9 72.6 1.0
O E:CYS71 5.0 74.4 1.0
NH2 E:ARG56 5.0 43.6 1.0
C E:ARG83 5.0 92.7 1.0

Zinc binding site 6 out of 9 in 8z9c

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Zinc binding site 6 out of 9 in the Cryo-Em Structure of Ntr-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 Ntr-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:179.2
occ:1.00
 CB F:CYS84 1.2 105.2 1.0
SG F:CYS71 2.3 109.0 1.0
SG F:CYS87 2.3 97.3 1.0
SG F:CYS84 2.4 105.0 1.0
CA F:CYS84 2.5 103.5 1.0
CB F:CYS87 2.9 91.3 1.0
N F:CYS84 3.0 104.3 1.0
CB F:CYS71 3.6 106.9 1.0
C F:CYS84 3.6 102.0 1.0
N F:CYS71 3.7 106.2 1.0
N F:CYS87 3.8 90.1 1.0
SG F:CYS81 3.8 112.9 1.0
CA F:CYS87 3.9 89.8 1.0
O F:CYS81 4.1 107.3 1.0
O F:CYS84 4.2 102.4 1.0
N F:VAL85 4.3 87.8 1.0
CA F:CYS71 4.3 107.0 1.0
C F:ARG83 4.3 98.9 1.0
OG1 F:THR86 4.5 78.1 1.0
C F:CYS81 4.5 107.4 1.0
N F:CYS81 4.6 107.4 1.0
C F:VAL70 4.6 97.1 1.0
CA F:VAL70 4.7 95.7 1.0
N F:ARG83 4.7 97.7 1.0
N F:THR86 4.9 83.0 1.0
CA F:CYS81 4.9 108.9 1.0
C F:THR86 5.0 80.5 1.0
CB F:CYS81 5.0 110.6 1.0

Zinc binding site 7 out of 9 in 8z9c

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Zinc binding site 7 out of 9 in the Cryo-Em Structure of Ntr-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 Ntr-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:175.1
occ:1.00
 SG G:CYS85 2.0 30.0 1.0
CB G:CYS88 2.1 119.0 1.0
SG G:CYS70 2.3 124.5 1.0
SG G:CYS88 2.6 121.9 1.0
O G:SER87 2.9 118.3 1.0
CB G:CYS70 3.0 120.4 1.0
CB G:CYS85 3.1 30.0 1.0
CA G:CYS88 3.2 119.4 1.0
C G:CYS88 3.3 119.2 1.0
CG G:GLU90 3.4 121.5 1.0
OE1 G:GLU90 3.4 121.3 1.0
N G:ASN89 3.5 121.9 1.0
CD G:GLU90 3.5 121.8 1.0
N G:GLU90 3.7 122.3 1.0
C G:SER87 3.7 118.9 1.0
N G:CYS88 3.9 118.9 1.0
O G:CYS88 3.9 118.1 1.0
CB G:GLU90 4.1 121.4 1.0
OE2 G:GLU90 4.3 121.5 1.0
CA G:CYS70 4.3 120.7 1.0
OG G:SER68 4.3 111.6 1.0
CA G:ASN89 4.4 122.4 1.0
C G:ASN89 4.4 122.1 1.0
N G:CYS70 4.5 120.0 1.0
CA G:CYS85 4.5 127.9 1.0
CA G:GLU90 4.5 122.4 1.0
CB G:SER68 4.8 110.1 1.0
O G:GLU90 4.9 121.1 1.0
C G:CYS85 5.0 128.6 1.0
N G:CYS85 5.0 129.0 1.0

Zinc binding site 8 out of 9 in 8z9c

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Zinc binding site 8 out of 9 in the Cryo-Em Structure of Ntr-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 Ntr-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:107.3
occ:1.00
 OD2 H:ASP169 2.1 74.6 1.0
ND1 H:HIS64 2.3 80.2 1.0
NE2 H:HIS148 2.3 73.7 1.0
NE2 H:HIS62 2.3 70.3 1.0
CD2 H:HIS62 2.4 64.7 1.0
OP2 N:A-15 2.8 127.8 1.0
CD2 H:HIS148 2.9 68.9 1.0
CE1 H:HIS64 3.0 77.6 1.0
CG H:ASP169 3.2 76.3 1.0
CG H:HIS64 3.4 80.1 1.0
CE1 H:HIS148 3.4 75.7 1.0
CE1 H:HIS62 3.5 69.9 1.0
CG H:HIS62 3.6 57.3 1.0
CB H:HIS64 3.9 79.2 1.0
CB H:ASP169 3.9 74.1 1.0
NE2 H:HIS373 4.1 106.6 1.0
CG H:HIS148 4.1 66.0 1.0
ND1 H:HIS62 4.1 64.9 1.0
P N:A-15 4.1 130.7 1.0
CE1 H:HIS373 4.2 105.5 1.0
NE2 H:HIS64 4.2 76.7 1.0
OD1 H:ASP169 4.2 76.3 1.0
ND1 H:HIS148 4.3 72.3 1.0
CD2 H:HIS64 4.4 79.0 1.0
OP1 N:A-15 4.7 128.0 1.0
CB H:HIS62 4.7 60.5 1.0
O5' N:A-15 4.9 129.7 1.0

Zinc binding site 9 out of 9 in 8z9c

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Zinc binding site 9 out of 9 in the Cryo-Em Structure of Ntr-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 Ntr-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:96.0
occ:1.00
 SG J:CYS87 2.3 59.6 1.0
SG J:CYS84 2.3 69.1 1.0
SG J:CYS71 2.3 51.3 1.0
SG J:CYS81 2.3 63.4 1.0
CB J:CYS87 3.1 36.8 1.0
CB J:CYS84 3.2 50.2 1.0
CB J:CYS71 3.5 52.3 1.0
CB J:CYS81 3.5 45.9 1.0
N J:CYS81 3.5 48.2 1.0
N J:GLY82 3.7 47.0 1.0
N J:CYS87 4.0 41.1 1.0
CA J:CYS81 4.0 43.5 1.0
N J:CYS71 4.1 50.6 1.0
CA J:CYS87 4.1 37.3 1.0
N J:CYS84 4.2 53.4 1.0
CA J:CYS84 4.2 50.3 1.0
C J:CYS81 4.4 49.6 1.0
CA J:CYS71 4.4 51.6 1.0
N J:ARG83 4.6 57.9 1.0
NH2 J:ARG56 4.6 48.4 1.0
C J:PRO80 4.6 45.4 1.0
CA J:GLY82 4.7 43.1 1.0
C J:CYS84 4.8 55.3 1.0
CA J:PRO80 4.9 38.5 1.0
CB J:PRO80 4.9 39.6 1.0
O J:CYS84 5.0 59.2 1.0
C J:THR86 5.0 40.2 1.0

Reference:

H.Zhang, Z.Deng, X.Li. Cryo-Em Structure of Ntr-Bound Type 7 Crispr-Cas Complex at Substrate-Engaged State 1. To Be Published.
Page generated: Thu Oct 31 14:11:10 2024

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