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Zinc in PDB 6zym: Human C Complex Spliceosome - High-Resolution Core

Enzymatic activity of Human C Complex Spliceosome - High-Resolution Core

All present enzymatic activity of Human C Complex Spliceosome - High-Resolution Core:
3.6.4.13; 5.2.1.8;

Other elements in 6zym:

The structure of Human C Complex Spliceosome - High-Resolution Core also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human C Complex Spliceosome - High-Resolution Core (pdb code 6zym). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Human C Complex Spliceosome - High-Resolution Core, PDB code: 6zym:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6zym

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Zinc binding site 1 out of 7 in the Human C Complex Spliceosome - High-Resolution Core


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human C Complex Spliceosome - High-Resolution Core within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn301

b:75.8
occ:1.00
 NE2 P:HIS183 2.0 53.6 1.0
SG P:CYS179 2.2 55.8 1.0
SG P:CYS173 2.2 55.0 1.0
SG P:CYS165 2.3 50.6 1.0
CE1 P:HIS183 3.0 53.6 1.0
CD2 P:HIS183 3.0 53.6 1.0
CB P:CYS179 3.2 55.8 1.0
CB P:CYS173 3.2 55.0 1.0
CB P:CYS165 3.3 50.6 1.0
ND1 P:HIS183 4.1 53.6 1.0
CG P:HIS183 4.1 53.6 1.0
N6 6:A28 4.4 48.2 1.0
CB P:TRP168 4.4 53.7 1.0
CA P:CYS173 4.6 55.0 1.0
CA P:CYS179 4.6 55.8 1.0
N P:TRP168 4.7 53.7 1.0
CA P:CYS165 4.7 50.6 1.0
CD P:ARG175 4.8 53.6 1.0
CB P:ARG175 5.0 53.6 1.0

Zinc binding site 2 out of 7 in 6zym

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Zinc binding site 2 out of 7 in the Human C Complex Spliceosome - High-Resolution Core


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human C Complex Spliceosome - High-Resolution Core within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn302

b:95.4
occ:1.00
 SG P:CYS84 2.1 46.9 1.0
SG P:CYS81 2.3 42.8 1.0
SG P:CYS24 2.3 41.5 1.0
SG P:CYS27 2.3 45.0 1.0
CB P:CYS84 3.1 46.9 1.0
CB P:CYS24 3.3 41.5 1.0
CB P:CYS81 3.3 42.8 1.0
CB P:CYS27 3.3 45.0 1.0
N P:CYS84 3.8 46.9 1.0
N P:CYS24 4.0 41.5 1.0
CA P:CYS84 4.0 46.9 1.0
CA P:CYS24 4.2 41.5 1.0
N P:CYS27 4.3 45.0 1.0
CA P:CYS27 4.4 45.0 1.0
CG2 P:THR83 4.6 40.5 1.0
C P:CYS24 4.8 41.5 1.0
CA P:CYS81 4.8 42.8 1.0
C P:CYS84 4.9 46.9 1.0
NH2 P:ARG159 4.9 52.4 1.0
N P:LEU85 5.0 44.3 1.0

Zinc binding site 3 out of 7 in 6zym

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Zinc binding site 3 out of 7 in the Human C Complex Spliceosome - High-Resolution Core


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human C Complex Spliceosome - High-Resolution Core within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn303

b:0.9
occ:1.00
 SG P:CYS48 2.1 51.9 1.0
SG P:CYS45 2.2 47.1 1.0
SG P:CYS74 2.2 45.7 1.0
SG P:CYS71 2.3 42.5 1.0
CB P:CYS74 3.2 45.7 1.0
CB P:CYS48 3.2 51.9 1.0
CB P:CYS45 3.2 47.1 1.0
CB P:CYS71 3.3 42.5 1.0
N P:CYS71 3.9 42.5 1.0
CA P:CYS71 4.2 42.5 1.0
N P:CYS48 4.2 51.9 1.0
CA P:CYS48 4.2 51.9 1.0
CA P:CYS74 4.3 45.7 1.0
N P:CYS74 4.3 45.7 1.0
CG1 P:ILE47 4.3 49.6 1.0
CA P:CYS45 4.7 47.1 1.0
C P:CYS71 4.8 42.5 1.0
OG1 P:THR73 4.8 42.6 1.0
CD1 P:ILE47 4.8 49.6 1.0
O P:CYS71 4.9 42.5 1.0
C P:CYS48 4.9 51.9 1.0
CG1 P:VAL70 4.9 38.5 1.0

Zinc binding site 4 out of 7 in 6zym

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Zinc binding site 4 out of 7 in the Human C Complex Spliceosome - High-Resolution Core


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human C Complex Spliceosome - High-Resolution Core within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn201

b:47.9
occ:1.00
 SG Q:CYS101 2.0 36.4 1.0
SG Q:CYS102 2.3 32.3 1.0
SG Q:CYS137 2.4 36.5 1.0
SG Q:CYS105 2.4 35.4 1.0
CB Q:CYS101 3.0 36.4 1.0
CB Q:CYS137 3.2 36.5 1.0
CB Q:CYS102 3.3 32.3 1.0
CB Q:CYS105 3.6 35.4 1.0
N Q:CYS102 3.7 32.3 1.0
ZN Q:ZN202 3.8 51.7 1.0
CA Q:CYS101 4.0 36.4 1.0
C Q:CYS101 4.0 36.4 1.0
ZN Q:ZN203 4.0 67.2 1.0
CA Q:CYS102 4.1 32.3 1.0
N Q:CYS105 4.3 35.4 1.0
C Q:CYS102 4.4 32.3 1.0
CA Q:CYS137 4.4 36.5 1.0
N Q:CYS137 4.5 36.5 1.0
SG Q:CYS139 4.5 43.5 1.0
O Q:CYS102 4.5 32.3 1.0
CA Q:CYS105 4.5 35.4 1.0
SG Q:CYS119 4.6 41.9 1.0
CB Q:HIS136 4.7 32.5 1.0
N Q:CYS101 4.8 36.4 1.0
O Q:CYS101 4.9 36.4 1.0
SG Q:CYS134 4.9 38.4 1.0

Zinc binding site 5 out of 7 in 6zym

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Zinc binding site 5 out of 7 in the Human C Complex Spliceosome - High-Resolution Core


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human C Complex Spliceosome - High-Resolution Core within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn202

b:51.7
occ:1.00
 SG Q:CYS119 1.9 41.9 1.0
SG Q:CYS139 2.3 43.5 1.0
SG Q:CYS101 2.7 36.4 1.0
SG Q:CYS142 2.7 43.1 1.0
CB Q:CYS119 3.0 41.9 1.0
CB Q:CYS101 3.1 36.4 1.0
CB Q:CYS139 3.3 43.5 1.0
ZN Q:ZN203 3.4 67.2 1.0
CB Q:CYS142 3.6 43.1 1.0
ZN Q:ZN201 3.8 47.9 1.0
N Q:CYS101 4.1 36.4 1.0
CA Q:CYS101 4.2 36.4 1.0
SG Q:CYS134 4.3 38.4 1.0
CA Q:CYS119 4.4 41.9 1.0
SG Q:CYS105 4.4 35.4 1.0
SG Q:CYS137 4.5 36.5 1.0
C Q:CYS119 4.5 41.9 1.0
CA Q:CYS139 4.6 43.5 1.0
O Q:CYS119 4.7 41.9 1.0
CA Q:CYS142 4.8 43.1 1.0
CB Q:CYS105 4.8 35.4 1.0
N Q:CYS142 4.8 43.1 1.0
N Q:CYS139 4.8 43.5 1.0
C Q:CYS139 4.9 43.5 1.0

Zinc binding site 6 out of 7 in 6zym

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Zinc binding site 6 out of 7 in the Human C Complex Spliceosome - High-Resolution Core


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human C Complex Spliceosome - High-Resolution Core within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn203

b:67.2
occ:1.00
 SG Q:CYS134 2.3 38.4 1.0
SG Q:CYS117 2.3 39.3 1.0
SG Q:CYS119 2.3 41.9 1.0
SG Q:CYS105 2.6 35.4 1.0
CB Q:CYS105 3.1 35.4 1.0
CB Q:CYS119 3.2 41.9 1.0
CB Q:CYS134 3.2 38.4 1.0
CB Q:CYS117 3.3 39.3 1.0
ZN Q:ZN202 3.4 51.7 1.0
N Q:CYS119 4.0 41.9 1.0
ZN Q:ZN201 4.0 47.9 1.0
SG Q:CYS139 4.1 43.5 1.0
CA Q:CYS119 4.1 41.9 1.0
SG Q:CYS101 4.5 36.4 1.0
CA Q:CYS134 4.6 38.4 1.0
CA Q:CYS117 4.6 39.3 1.0
CA Q:CYS105 4.6 35.4 1.0
ND1 Q:HIS136 4.6 32.5 1.0
C Q:CYS119 4.9 41.9 1.0
SG Q:CYS137 4.9 36.5 1.0
N Q:ARG120 4.9 40.4 1.0
C Q:CYS134 4.9 38.4 1.0
N Q:ILE118 5.0 40.1 1.0

Zinc binding site 7 out of 7 in 6zym

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Zinc binding site 7 out of 7 in the Human C Complex Spliceosome - High-Resolution Core


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human C Complex Spliceosome - High-Resolution Core within 5.0Å range:
probe atom residue distance (Å) B Occ
u:Zn1001

b:0.7
occ:1.00
 SG u:CYS83 1.5 68.5 1.0
SG u:CYS80 2.0 64.7 1.0
SG u:CYS43 2.3 60.1 1.0
SG u:CYS46 2.3 66.0 1.0
CB u:CYS83 2.8 68.5 1.0
CB u:CYS80 3.2 64.7 1.0
CB u:CYS43 3.3 60.1 1.0
CB u:CYS46 3.5 66.0 1.0
CA u:CYS83 3.8 68.5 1.0
N u:CYS83 3.9 68.5 1.0
O u:CYS83 4.0 68.5 1.0
OE2 u:GLU48 4.2 67.7 1.0
C u:CYS83 4.2 68.5 1.0
CG u:GLU48 4.2 67.7 1.0
N u:CYS46 4.2 66.0 1.0
CA u:CYS46 4.4 66.0 1.0
CA u:CYS80 4.7 64.7 1.0
CD u:GLU48 4.7 67.7 1.0
CA u:CYS43 4.7 60.1 1.0
CG2 u:THR45 4.8 56.0 1.0
C u:CYS46 4.9 66.0 1.0
C u:ARG82 4.9 69.6 1.0
CB u:ARG82 5.0 69.6 1.0

Reference:

K.Bertram, L.El Ayoubi, O.Dybkov, D.E.Agafonov, C.L.Will, K.Hartmuth, H.Urlaub, B.Kastner, H.Stark, R.Luhrmann. Structural Insights Into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome. Mol.Cell V. 80 127 2020.
ISSN: ISSN 1097-2765
PubMed: 33007253
DOI: 10.1016/J.MOLCEL.2020.09.012
Page generated: Tue Oct 29 16:09:23 2024

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