Zinc in PDB 7w5a: The Cryo-Em Structure of Human Pre-C*-II Complex

Enzymatic activity of The Cryo-Em Structure of Human Pre-C*-II Complex

All present enzymatic activity of The Cryo-Em Structure of Human Pre-C*-II Complex:
2.3.2.27; 3.6.4.13; 5.2.1.8;

Other elements in 7w5a:

The structure of The Cryo-Em Structure of Human Pre-C*-II Complex also contains other interesting chemical elements:

Magnesium (Mg) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Cryo-Em Structure of Human Pre-C*-II Complex (pdb code 7w5a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the The Cryo-Em Structure of Human Pre-C*-II Complex, PDB code: 7w5a:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 7w5a

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Zinc binding site 1 out of 7 in the The Cryo-Em Structure of Human Pre-C*-II Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Cryo-Em Structure of Human Pre-C*-II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn201

b:77.6
occ:1.00
 SG N:CYS134 2.4 56.2 1.0
SG N:CYS105 2.4 47.3 1.0
SG N:CYS117 2.7 48.9 1.0
CB N:CYS119 2.9 50.5 1.0
CB N:CYS134 3.1 56.2 1.0
SG N:CYS119 3.3 50.5 1.0
CB N:CYS105 3.3 47.3 1.0
ZN N:ZN203 3.8 61.0 1.0
ZN N:ZN202 3.9 75.7 1.0
CB N:CYS137 4.2 54.9 1.0
CB N:CYS117 4.2 48.9 1.0
CA N:CYS105 4.2 47.3 1.0
CA N:CYS119 4.3 50.5 1.0
CB N:CYS139 4.3 58.8 1.0
CD2 N:HIS136 4.5 50.0 1.0
CA N:CYS134 4.5 56.2 1.0
N N:CYS119 4.6 50.5 1.0
CB N:HIS136 5.0 50.0 1.0

Zinc binding site 2 out of 7 in 7w5a

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Zinc binding site 2 out of 7 in the The Cryo-Em Structure of Human Pre-C*-II Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Cryo-Em Structure of Human Pre-C*-II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn202

b:75.7
occ:1.00
 SG N:CYS105 2.4 47.3 1.0
SG N:CYS137 2.4 54.9 1.0
SG N:CYS102 2.5 50.9 1.0
CB N:CYS137 2.6 54.9 1.0
CB N:CYS101 2.6 52.1 1.0
CB N:CYS102 2.9 50.9 1.0
N N:CYS102 3.1 50.9 1.0
CA N:CYS102 3.6 50.9 1.0
C N:CYS101 3.6 52.1 1.0
ZN N:ZN203 3.7 61.0 1.0
CB N:CYS105 3.7 47.3 1.0
SG N:CYS101 3.7 52.1 1.0
CA N:CYS101 3.8 52.1 1.0
ZN N:ZN201 3.9 77.6 1.0
CA N:CYS137 4.0 54.9 1.0
O N:CYS101 4.3 52.1 1.0
N N:CYS101 4.7 52.1 1.0
C N:CYS102 4.7 50.9 1.0
N N:CYS137 4.8 54.9 1.0
N N:CYS105 4.8 47.3 1.0
CA N:CYS105 4.8 47.3 1.0
C N:CYS137 4.9 54.9 1.0
CB N:CYS139 4.9 58.8 1.0

Zinc binding site 3 out of 7 in 7w5a

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Zinc binding site 3 out of 7 in the The Cryo-Em Structure of Human Pre-C*-II Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Cryo-Em Structure of Human Pre-C*-II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn203

b:61.0
occ:1.00
 SG N:CYS119 2.4 50.5 1.0
SG N:CYS142 2.5 54.5 1.0
CB N:CYS101 2.5 52.1 1.0
SG N:CYS101 2.6 52.1 1.0
CB N:CYS139 3.1 58.8 1.0
SG N:CYS139 3.2 58.8 1.0
N N:CYS101 3.6 52.1 1.0
CA N:CYS101 3.6 52.1 1.0
ZN N:ZN202 3.7 75.7 1.0
ZN N:ZN201 3.8 77.6 1.0
CB N:CYS142 3.9 54.5 1.0
CB N:CYS119 3.9 50.5 1.0
SG N:CYS105 4.0 47.3 1.0
CB N:CYS105 4.2 47.3 1.0
CA N:CYS139 4.5 58.8 1.0
SG N:CYS137 4.6 54.9 1.0
N N:CYS102 4.6 50.9 1.0
C N:CYS101 4.7 52.1 1.0
N N:CYS142 4.8 54.5 1.0
CA N:CYS142 4.8 54.5 1.0
C N:LEU100 4.8 45.1 1.0

Zinc binding site 4 out of 7 in 7w5a

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Zinc binding site 4 out of 7 in the The Cryo-Em Structure of Human Pre-C*-II Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Cryo-Em Structure of Human Pre-C*-II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn501

b:73.4
occ:1.00
 SG O:CYS81 2.4 54.1 1.0
SG O:CYS27 2.4 53.6 1.0
SG O:CYS84 2.4 55.9 1.0
CB O:CYS84 2.6 55.9 1.0
SG O:CYS24 2.6 55.6 1.0
CB O:CYS81 2.7 54.1 1.0
CB O:CYS24 3.1 55.6 1.0
N O:CYS84 3.3 55.9 1.0
CA O:CYS84 3.5 55.9 1.0
N O:CYS24 3.7 55.6 1.0
OG1 O:THR83 3.8 53.5 1.0
CB O:CYS27 3.8 53.6 1.0
CA O:CYS24 4.0 55.6 1.0
CA O:CYS81 4.2 54.1 1.0
C O:THR83 4.5 53.5 1.0
N O:CYS27 4.5 53.6 1.0
NH2 O:ARG159 4.6 61.3 1.0
OG1 O:THR26 4.6 56.0 1.0
N O:THR83 4.7 53.5 1.0
C O:CYS84 4.7 55.9 1.0
CA O:CYS27 4.8 53.6 1.0
C O:CYS81 4.9 54.1 1.0
C O:LEU23 4.9 48.0 1.0
N O:LEU85 4.9 52.8 1.0
CA O:THR83 4.9 53.5 1.0
CB O:THR83 5.0 53.5 1.0
N O:CYS81 5.0 54.1 1.0

Zinc binding site 5 out of 7 in 7w5a

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Zinc binding site 5 out of 7 in the The Cryo-Em Structure of Human Pre-C*-II Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Cryo-Em Structure of Human Pre-C*-II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn502

b:79.0
occ:1.00
 SG O:CYS71 2.4 51.0 1.0
SG O:CYS48 2.5 52.7 1.0
SG O:CYS45 2.5 50.4 1.0
SG O:CYS74 2.6 50.0 1.0
CB O:CYS71 3.1 51.0 1.0
CB O:CYS45 3.4 50.4 1.0
CB O:CYS74 3.4 50.0 1.0
N O:CYS71 3.6 51.0 1.0
CB O:CYS48 3.7 52.7 1.0
N O:CYS48 3.7 52.7 1.0
CA O:CYS71 3.9 51.0 1.0
CA O:CYS48 4.2 52.7 1.0
CB O:ILE47 4.4 54.6 1.0
O O:CYS71 4.4 51.0 1.0
N O:CYS74 4.4 50.0 1.0
CA O:CYS74 4.5 50.0 1.0
C O:CYS71 4.5 51.0 1.0
C O:VAL70 4.7 46.2 1.0
C O:ILE47 4.8 54.6 1.0
CA O:CYS45 4.8 50.4 1.0
C O:CYS48 4.9 52.7 1.0
CG2 O:ILE47 4.9 54.6 1.0
CA O:ILE47 5.0 54.6 1.0
N O:ALA49 5.0 49.9 1.0
N O:ILE47 5.0 54.6 1.0

Zinc binding site 6 out of 7 in 7w5a

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Zinc binding site 6 out of 7 in the The Cryo-Em Structure of Human Pre-C*-II Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Cryo-Em Structure of Human Pre-C*-II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn503

b:90.0
occ:1.00
 NE2 O:HIS183 2.2 83.5 1.0
SG O:CYS179 2.4 81.0 1.0
SG O:CYS173 2.4 90.2 1.0
SG O:CYS165 2.4 86.5 1.0
CD2 O:HIS183 3.1 83.5 1.0
CE1 O:HIS183 3.2 83.5 1.0
CB O:CYS179 3.3 81.0 1.0
CB O:CYS165 3.3 86.5 1.0
CB O:CYS173 3.5 90.2 1.0
CG O:HIS183 4.3 83.5 1.0
ND1 O:HIS183 4.3 83.5 1.0
CB O:TRP168 4.3 94.1 1.0
N O:TRP168 4.5 94.1 1.0
N6 F:A28 4.6 93.6 1.0
CB O:TYR181 4.7 82.6 1.0
CA O:CYS165 4.7 86.5 1.0
CA O:CYS179 4.7 81.0 1.0
CA O:CYS173 4.8 90.2 1.0
CA O:TRP168 5.0 94.1 1.0

Zinc binding site 7 out of 7 in 7w5a

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Zinc binding site 7 out of 7 in the The Cryo-Em Structure of Human Pre-C*-II Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Cryo-Em Structure of Human Pre-C*-II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Zn601

b:29.7
occ:1.00
 SG 1:CYS120 2.0 32.5 1.0
SG 1:CYS133 2.3 20.8 1.0
CD2 1:HIS128 2.3 26.1 1.0
NE2 1:HIS128 2.4 26.1 1.0
CB 1:CYS120 3.1 32.5 1.0
CB 1:CYS133 3.2 20.8 1.0
SG 1:CYS123 3.4 29.6 1.0
CG 1:HIS128 3.6 26.1 1.0
O 1:LYS129 3.7 26.1 1.0
CE1 1:HIS128 3.7 26.1 1.0
CA 1:CYS133 3.8 20.8 1.0
N 1:CYS123 4.2 29.6 1.0
ND1 1:HIS128 4.3 26.1 1.0
C 1:LYS129 4.4 26.1 1.0
CB 1:ASN122 4.4 28.4 1.0
ND2 1:ASN122 4.5 28.4 1.0
CA 1:CYS120 4.6 32.5 1.0
N 1:PHE134 4.6 18.7 1.0
CA 1:LYS130 4.7 26.2 1.0
CB 1:HIS128 4.7 26.1 1.0
N 1:CYS133 4.7 20.8 1.0
O 1:HIS128 4.7 26.1 1.0
CB 1:CYS123 4.7 29.6 1.0
O 1:CYS123 4.8 29.6 1.0
C 1:CYS133 4.8 20.8 1.0
N 1:LYS130 4.8 26.2 1.0
C 1:HIS128 4.9 26.1 1.0
CA 1:CYS123 4.9 29.6 1.0
N 1:ASN122 4.9 28.4 1.0
C 1:CYS123 4.9 29.6 1.0
CG 1:ASN122 5.0 28.4 1.0

Reference:

X.Zhan, Y.Lu, X.Zhang, C.Yan, Y.Shi. Mechanism of Exon Ligation By Human Spliceosome. Mol.Cell V. 82 2769 2022.
ISSN: ISSN 1097-2765
PubMed: 35705093
DOI: 10.1016/J.MOLCEL.2022.05.021
Page generated: Wed Oct 30 13:39:39 2024

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