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Zinc in PDB 6ff4: Human Bact Spliceosome Core Structure

Enzymatic activity of Human Bact Spliceosome Core Structure

All present enzymatic activity of Human Bact Spliceosome Core Structure:
5.2.1.8;

Other elements in 6ff4:

The structure of Human Bact Spliceosome Core Structure also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Bact Spliceosome Core Structure (pdb code 6ff4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Human Bact Spliceosome Core Structure, PDB code: 6ff4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 6ff4

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Zinc binding site 1 out of 10 in the Human Bact Spliceosome Core Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Bact Spliceosome Core Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn501

b:69.8
occ:1.00
 SG P:CYS27 2.4 41.9 1.0
SG P:CYS81 2.4 46.7 1.0
SG P:CYS84 2.5 47.2 1.0
SG P:CYS24 2.5 41.6 1.0
CB P:CYS84 3.2 47.2 1.0
N P:CYS84 3.2 47.2 1.0
CB P:CYS81 3.3 46.7 1.0
CB P:CYS27 3.7 41.9 1.0
CA P:CYS84 3.7 47.2 1.0
CB P:CYS24 3.9 41.6 1.0
CG2 P:THR83 4.1 44.5 1.0
N P:CYS24 4.2 41.6 1.0
N P:THR83 4.3 44.5 1.0
C P:THR83 4.4 44.5 1.0
C P:CYS84 4.4 47.2 1.0
N P:LEU85 4.4 48.0 1.0
O P:CYS24 4.5 41.6 1.0
CA P:CYS24 4.6 41.6 1.0
N P:GLN82 4.6 41.6 1.0
CA P:CYS81 4.7 46.7 1.0
CA P:THR83 4.7 44.5 1.0
C P:CYS81 4.8 46.7 1.0
C P:CYS24 4.9 41.6 1.0
CA P:CYS27 4.9 41.9 1.0
CG2 P:THR26 4.9 42.5 1.0
N P:CYS27 4.9 41.9 1.0

Zinc binding site 2 out of 10 in 6ff4

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Zinc binding site 2 out of 10 in the Human Bact Spliceosome Core Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Bact Spliceosome Core Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn502

b:62.5
occ:1.00
 SG P:CYS173 2.4 58.0 1.0
SG P:CYS179 2.5 54.0 1.0
SG P:CYS165 2.6 58.2 1.0
CB P:CYS173 3.1 58.0 1.0
CB P:CYS179 3.3 54.0 1.0
CB P:CYS165 3.8 58.2 1.0
CB P:TRP168 3.9 62.0 1.0
O P:ARG182 4.0 55.5 1.0
O P:SER166 4.1 61.9 1.0
N P:TRP168 4.2 62.0 1.0
CA P:TRP168 4.6 62.0 1.0
CA P:CYS173 4.6 58.0 1.0
C P:PHE167 4.7 62.3 1.0
CA P:CYS179 4.8 54.0 1.0
N6 6:A27 4.8 52.1 1.0
CG P:TRP168 5.0 62.0 1.0

Zinc binding site 3 out of 10 in 6ff4

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Zinc binding site 3 out of 10 in the Human Bact Spliceosome Core Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Bact Spliceosome Core Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn503

b:52.4
occ:1.00
 SG P:CYS71 2.4 43.8 1.0
SG P:CYS48 2.4 45.7 1.0
SG P:CYS45 2.4 45.5 1.0
SG P:CYS74 2.5 43.7 1.0
CB P:CYS45 2.9 45.5 1.0
NE2 P:GLN119 3.2 52.5 1.0
CB P:CYS74 3.3 43.7 1.0
CB P:CYS71 3.4 43.8 1.0
N P:CYS71 3.8 43.8 1.0
CB P:CYS48 4.0 45.7 1.0
CA P:CYS71 4.2 43.8 1.0
N P:CYS74 4.3 43.7 1.0
CA P:CYS45 4.4 45.5 1.0
CB P:ARG50 4.4 47.8 1.0
CD P:GLN119 4.4 52.5 1.0
CA P:CYS74 4.4 43.7 1.0
N P:CYS48 4.4 45.7 1.0
CA P:CYS48 4.7 45.7 1.0
OE1 P:GLN119 4.8 52.5 1.0
C P:VAL70 4.9 42.0 1.0
CB P:VAL70 4.9 42.0 1.0
C P:CYS71 4.9 43.8 1.0
N P:ARG50 5.0 47.8 1.0

Zinc binding site 4 out of 10 in 6ff4

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Zinc binding site 4 out of 10 in the Human Bact Spliceosome Core Structure


Mono view


Stereo pair view

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

b:69.2
occ:1.00
 N Q:CYS102 2.2 36.5 1.0
SG Q:CYS137 2.4 32.2 1.0
CB Q:CYS137 2.5 32.2 1.0
SG Q:CYS101 2.5 39.2 1.0
C Q:CYS101 2.7 39.2 1.0
CB Q:CYS101 2.8 39.2 1.0
CB Q:CYS102 2.9 36.5 1.0
CA Q:CYS102 2.9 36.5 1.0
SG Q:CYS102 3.0 36.5 1.0
CA Q:CYS101 3.3 39.2 1.0
C Q:CYS102 3.5 36.5 1.0
O Q:CYS101 3.5 39.2 1.0
O Q:CYS102 3.5 36.5 1.0
CA Q:CYS137 3.8 32.2 1.0
N Q:CYS101 4.3 39.2 1.0
N Q:LEU103 4.5 30.6 1.0
C Q:CYS137 4.6 32.2 1.0
SG Q:CYS105 4.7 28.9 1.0
O Q:CYS137 4.7 32.2 1.0
N Q:CYS137 4.8 32.2 1.0
N Q:ARG104 4.9 27.2 1.0
ZN Q:ZN202 4.9 60.4 1.0
CZ2 E:TRP196 4.9 43.3 1.0
N Q:CYS105 5.0 28.9 1.0

Zinc binding site 5 out of 10 in 6ff4

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Zinc binding site 5 out of 10 in the Human Bact Spliceosome Core Structure


Mono view


Stereo pair view

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

b:60.4
occ:1.00
 NH2 Q:ARG140 2.2 44.6 1.0
SG Q:CYS119 2.4 37.2 1.0
CB Q:CYS101 2.5 39.2 1.0
SG Q:CYS101 2.6 39.2 1.0
N Q:CYS101 2.7 39.2 1.0
CZ Q:ARG140 2.9 44.6 1.0
CA Q:CYS101 3.1 39.2 1.0
NH1 Q:ARG140 3.6 44.6 1.0
NE Q:ARG140 3.6 44.6 1.0
C Q:LEU100 3.7 37.2 1.0
CB Q:CYS119 3.9 37.2 1.0
CD Q:ARG120 4.2 40.2 1.0
CA Q:LEU100 4.2 37.2 1.0
O Q:CYS139 4.4 40.7 1.0
C Q:CYS101 4.4 39.2 1.0
O Q:ASN99 4.5 47.9 1.0
O Q:LEU100 4.6 37.2 1.0
O Q:CYS119 4.6 37.2 1.0
CG Q:ARG120 4.7 40.2 1.0
C Q:CYS119 4.7 37.2 1.0
N Q:CYS102 4.7 36.5 1.0
CD Q:ARG140 4.9 44.6 1.0
CG E:PRO195 4.9 46.0 1.0
ZN Q:ZN201 4.9 69.2 1.0
CA Q:CYS119 4.9 37.2 1.0
CB E:PRO195 4.9 46.0 1.0

Zinc binding site 6 out of 10 in 6ff4

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Zinc binding site 6 out of 10 in the Human Bact Spliceosome Core Structure


Mono view


Stereo pair view

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

b:34.2
occ:1.00
 SG Q:CYS105 2.4 28.9 1.0
SG Q:CYS134 2.4 33.6 1.0
SG Q:CYS117 2.5 32.5 1.0
CB Q:CYS119 2.5 37.2 1.0
CB Q:CYS134 2.6 33.6 1.0
N Q:CYS119 3.3 37.2 1.0
CB Q:CYS117 3.4 32.5 1.0
CA Q:CYS119 3.5 37.2 1.0
SG Q:CYS119 3.8 37.2 1.0
CA Q:CYS134 3.9 33.6 1.0
CB Q:CYS105 3.9 28.9 1.0
N Q:ILE118 4.5 36.2 1.0
C Q:CYS117 4.5 32.5 1.0
C Q:ILE118 4.6 36.2 1.0
C Q:CYS119 4.6 37.2 1.0
CA Q:CYS117 4.6 32.5 1.0
SG Q:CYS101 4.7 39.2 1.0
SG Q:CYS137 4.7 32.2 1.0
CB Q:CYS137 4.7 32.2 1.0
C Q:CYS134 4.8 33.6 1.0
N Q:CYS134 4.8 33.6 1.0
N Q:ARG120 4.8 40.2 1.0
O Q:CYS117 4.9 32.5 1.0
CA Q:CYS105 5.0 28.9 1.0
N Q:CYS137 5.0 32.2 1.0

Zinc binding site 7 out of 10 in 6ff4

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Zinc binding site 7 out of 10 in the Human Bact Spliceosome Core Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human Bact Spliceosome Core Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
t:Zn401

b:30.0
occ:1.00
 SG t:CYS202 2.4 18.1 1.0
SG t:CYS211 2.4 20.9 1.0
SG t:CYS217 2.5 17.5 1.0
CE1 t:HIS221 2.6 15.6 1.0
CB t:CYS211 2.6 20.9 1.0
ND1 t:HIS221 3.1 15.6 1.0
NE2 t:HIS221 3.2 15.6 1.0
CB t:CYS217 3.3 17.5 1.0
CB t:CYS202 3.4 18.1 1.0
CG t:HIS221 3.9 15.6 1.0
CD2 t:HIS221 3.9 15.6 1.0
CA t:CYS211 4.1 20.9 1.0
CB t:TYR205 4.2 17.4 1.0
O t:GLY214 4.2 21.0 1.0
CA t:CYS217 4.8 17.5 1.0
N t:CYS211 4.8 20.9 1.0
CG t:TYR205 4.8 17.4 1.0
CA t:CYS202 4.9 18.1 1.0
N2 Z:G243 4.9 22.0 1.0

Zinc binding site 8 out of 10 in 6ff4

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Zinc binding site 8 out of 10 in the Human Bact Spliceosome Core Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human Bact Spliceosome Core Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
y:Zn201

b:36.7
occ:1.00
 SG y:CYS46 2.4 17.9 1.0
SG y:CYS49 2.4 21.4 1.0
SG y:CYS85 2.5 17.9 1.0
SG y:CYS11 2.5 17.7 1.0
CB y:CYS49 2.8 21.4 1.0
CB y:CYS11 3.1 17.7 1.0
CB y:CYS46 3.7 17.9 1.0
NZ y:LYS13 3.8 17.4 1.0
N y:CYS49 4.0 21.4 1.0
CB y:LYS87 4.0 19.5 1.0
CA y:CYS49 4.0 21.4 1.0
CB y:CYS85 4.1 17.9 1.0
N y:CYS46 4.2 17.9 1.0
CA y:CYS46 4.5 17.9 1.0
CA y:CYS11 4.6 17.7 1.0
CG y:LYS87 4.7 19.5 1.0
CE y:LYS13 4.9 17.4 1.0
O y:CYS46 4.9 17.9 1.0
C y:CYS46 4.9 17.9 1.0
O y:CYS85 5.0 17.9 1.0

Zinc binding site 9 out of 10 in 6ff4

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Zinc binding site 9 out of 10 in the Human Bact Spliceosome Core Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Human Bact Spliceosome Core Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
y:Zn202

b:51.6
occ:1.00
 SG y:CYS23 2.4 23.9 1.0
SG y:CYS26 2.5 23.7 1.0
SG y:CYS61 2.7 25.8 1.0
SG y:CYS58 2.7 23.3 1.0
CB y:CYS26 2.8 23.7 1.0
CB y:CYS61 3.0 25.8 1.0
N y:CYS61 3.3 25.8 1.0
CA y:CYS61 3.7 25.8 1.0
CB y:CYS23 3.8 23.9 1.0
CB y:ILE60 4.0 20.8 1.0
CA y:CYS26 4.1 23.7 1.0
N y:CYS23 4.1 23.9 1.0
CB y:CYS58 4.2 23.3 1.0
N y:CYS26 4.2 23.7 1.0
C y:ILE60 4.3 20.8 1.0
CA y:CYS23 4.5 23.9 1.0
CA y:ILE60 4.6 20.8 1.0
N y:ILE60 4.6 20.8 1.0
CG2 y:ILE60 4.7 20.8 1.0
CD1 y:ILE60 4.8 20.8 1.0
CG1 y:ILE60 4.8 20.8 1.0
C y:CYS61 4.9 25.8 1.0

Zinc binding site 10 out of 10 in 6ff4

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Zinc binding site 10 out of 10 in the Human Bact Spliceosome Core Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Human Bact Spliceosome Core Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
y:Zn203

b:20.4
occ:1.00
 SG y:CYS75 2.4 15.4 1.0
CB y:CYS33 2.5 17.0 1.0
SG y:CYS30 2.5 17.6 1.0
SG y:CYS72 2.5 15.0 1.0
CB y:CYS72 3.0 15.0 1.0
N y:CYS33 3.1 17.0 1.0
CA y:CYS33 3.2 17.0 1.0
CB y:CYS30 3.3 17.6 1.0
SG y:CYS33 3.5 17.0 1.0
N y:CYS72 3.7 15.0 1.0
CB y:CYS75 3.7 15.4 1.0
C y:CYS33 3.9 17.0 1.0
N y:ASP34 3.9 18.3 1.0
CA y:CYS72 4.0 15.0 1.0
N y:CYS75 4.2 15.4 1.0
C y:ILE32 4.3 18.1 1.0
CA y:CYS75 4.5 15.4 1.0
N y:ILE32 4.7 18.1 1.0
OG y:SER35 4.7 16.1 1.0
O y:CYS33 4.8 17.0 1.0
CA y:CYS30 4.8 17.6 1.0
C y:TYR71 4.8 14.0 1.0
CA y:ILE32 4.9 18.1 1.0
CB y:ILE32 4.9 18.1 1.0
N y:SER35 5.0 16.1 1.0

Reference:

D.Haselbach, I.Komarov, D.E.Agafonov, K.Hartmuth, B.Graf, O.Dybkov, H.Urlaub, B.Kastner, R.Luhrmann, H.Stark. Structure and Conformational Dynamics of the Human Spliceosomal Bactcomplex. Cell V. 172 454 2018.
ISSN: ISSN 1097-4172
PubMed: 29361316
DOI: 10.1016/J.CELL.2018.01.010
Page generated: Mon Oct 28 20:56:22 2024

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