Zinc in PDB 7qtt: Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)

Enzymatic activity of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)

All present enzymatic activity of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region):
2.3.2.27; 3.6.4.13; 5.2.1.8;

Other elements in 7qtt:

The structure of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) (pdb code 7qtt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region), PDB code: 7qtt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 7qtt

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Zinc binding site 1 out of 12 in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:269.4
occ:1.00
 SG D:CYS85 2.3 231.9 1.0
SG D:CYS11 2.3 231.6 1.0
SG D:CYS49 2.3 228.8 1.0
SG D:CYS46 2.3 230.6 1.0
CB D:CYS85 2.9 231.9 1.0
CB D:CYS11 3.4 231.6 1.0
CB D:CYS49 3.7 228.8 1.0
O D:ILE45 3.7 227.2 1.0
CB D:CYS46 4.0 230.6 1.0
C D:ILE45 4.3 227.2 1.0
CA D:CYS85 4.4 231.9 1.0
CD D:LYS13 4.5 225.2 1.0
CB D:LYS87 4.5 229.8 1.0
N D:ASP47 4.6 223.9 1.0
CA D:ILE45 4.9 227.2 1.0
CA D:CYS11 4.9 231.6 1.0
C D:CYS85 4.9 231.9 1.0
CA D:CYS46 4.9 230.6 1.0
N D:CYS46 4.9 230.6 1.0
CA D:CYS49 5.0 228.8 1.0

Zinc binding site 2 out of 12 in 7qtt

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Zinc binding site 2 out of 12 in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:209.6
occ:1.00
 SG D:CYS75 2.3 189.4 1.0
SG D:CYS72 2.3 191.2 1.0
SG D:CYS33 2.3 201.4 1.0
SG D:CYS30 2.3 196.5 1.0
CB D:CYS33 3.3 201.4 1.0
CB D:CYS30 3.4 196.5 1.0
CB D:CYS72 3.4 191.2 1.0
CB D:CYS75 3.5 189.4 1.0
N D:CYS33 3.6 201.4 1.0
CA D:CYS33 3.9 201.4 1.0
N D:CYS75 4.0 189.4 1.0
N D:CYS72 4.1 191.2 1.0
CA D:CYS72 4.3 191.2 1.0
CA D:CYS75 4.3 189.4 1.0
C D:CYS33 4.5 201.4 1.0
CB D:ILE32 4.6 198.2 1.0
C D:ILE32 4.7 198.2 1.0
N D:ASP34 4.7 196.0 1.0
CA D:CYS30 4.8 196.5 1.0
C D:CYS72 4.8 191.2 1.0
N D:ILE32 4.9 198.2 1.0
CB D:SER35 4.9 185.9 1.0
O D:CYS72 5.0 191.2 1.0
CA D:ILE32 5.0 198.2 1.0

Zinc binding site 3 out of 12 in 7qtt

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Zinc binding site 3 out of 12 in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn203

b:263.4
occ:1.00
 SG D:CYS23 2.3 220.4 1.0
SG D:CYS26 2.3 214.1 1.0
SG D:CYS58 2.3 232.4 1.0
SG D:CYS61 2.3 236.6 1.0
CB D:CYS23 3.6 220.4 1.0
CB D:CYS58 3.6 232.4 1.0
N D:CYS61 3.8 236.6 1.0
CB D:CYS26 3.8 214.1 1.0
CB D:CYS61 4.0 236.6 1.0
CB D:ILE60 4.1 230.0 1.0
C D:ILE60 4.2 230.0 1.0
N D:CYS23 4.2 220.4 1.0
N D:CYS26 4.3 214.1 1.0
N D:GLY62 4.3 231.3 1.0
CA D:CYS23 4.4 220.4 1.0
CA D:CYS61 4.4 236.6 1.0
N D:GLY63 4.5 227.6 1.0
CA D:ILE60 4.6 230.0 1.0
CA D:CYS26 4.6 214.1 1.0
O D:ILE60 4.6 230.0 1.0
O D:CYS23 4.7 220.4 1.0
C D:CYS23 4.8 220.4 1.0
CD2 D:LEU22 4.8 217.3 1.0
CG1 D:ILE60 4.9 230.0 1.0
C D:CYS61 4.9 236.6 1.0
N D:ILE60 4.9 230.0 1.0
CG2 D:ILE60 4.9 230.0 1.0
CA D:CYS58 5.0 232.4 1.0

Zinc binding site 4 out of 12 in 7qtt

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Zinc binding site 4 out of 12 in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn600

b:200.0
occ:1.00
 CE1 I:HIS78 2.0 174.5 1.0
NE2 I:HIS72 2.0 178.8 1.0
ND1 I:HIS78 2.1 174.5 1.0
NE2 I:HIS78 2.1 174.5 1.0
CG I:HIS78 2.2 174.5 1.0
CD2 I:HIS78 2.3 174.5 1.0
SG I:CYS56 2.3 176.1 1.0
SG I:CYS59 2.3 176.5 1.0
CD2 I:HIS72 2.4 178.8 1.0
CB I:CYS59 3.1 176.5 1.0
CE1 I:HIS72 3.2 178.8 1.0
CB I:HIS78 3.4 174.5 1.0
CG I:HIS72 3.6 178.8 1.0
CB I:CYS56 3.7 176.1 1.0
N I:CYS59 3.8 176.5 1.0
ND1 I:HIS72 3.9 178.8 1.0
CA I:HIS78 4.0 174.5 1.0
CA I:CYS59 4.0 176.5 1.0
O I:HIS72 4.5 178.8 1.0
C I:LEU58 4.6 163.5 1.0
CB I:LEU58 4.6 163.5 1.0
O I:HIS78 4.8 174.5 1.0
CB I:HIS72 4.9 178.8 1.0
C I:HIS78 4.9 174.5 1.0

Zinc binding site 5 out of 12 in 7qtt

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Zinc binding site 5 out of 12 in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1401

b:295.9
occ:1.00
 ND1 J:HIS425 2.2 254.4 1.0
ND1 J:HIS431 2.2 271.4 1.0
SG J:CYS408 2.3 260.7 1.0
SG J:CYS411 2.3 262.2 1.0
CE1 J:HIS431 2.5 271.4 1.0
CB J:CYS408 2.8 260.7 1.0
CG J:HIS425 2.9 254.4 1.0
CG J:HIS431 2.9 271.4 1.0
CE1 J:HIS425 3.0 254.4 1.0
CB J:HIS425 3.2 254.4 1.0
NE2 J:HIS431 3.2 271.4 1.0
CD2 J:HIS431 3.5 271.4 1.0
CB J:CYS411 3.6 262.2 1.0
CD2 J:HIS425 3.8 254.4 1.0
CB J:HIS431 3.8 271.4 1.0
NE2 J:HIS425 3.8 254.4 1.0
CA J:CYS408 4.3 260.7 1.0
N J:CYS411 4.5 262.2 1.0
CA J:HIS425 4.6 254.4 1.0
CA J:CYS411 4.7 262.2 1.0
C J:CYS408 4.8 260.7 1.0
O J:CYS408 5.0 260.7 1.0

Zinc binding site 6 out of 12 in 7qtt

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Zinc binding site 6 out of 12 in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1000

b:151.8
occ:1.00
 SG T:CYS105 2.3 124.4 1.0
SG T:CYS117 2.3 125.4 1.0
SG T:CYS134 2.3 121.2 1.0
SG T:CYS119 2.3 123.9 1.0
CB T:CYS117 2.9 125.4 1.0
CB T:CYS134 3.0 121.2 1.0
CB T:CYS119 3.5 123.9 1.0
ZN T:ZN1002 3.6 142.9 1.0
CB T:CYS105 4.0 124.4 1.0
N T:CYS119 4.0 123.9 1.0
ZN T:ZN1001 4.1 133.0 1.0
SG T:CYS137 4.2 120.6 1.0
CA T:CYS134 4.3 121.2 1.0
CA T:CYS117 4.3 125.4 1.0
CA T:CYS119 4.3 123.9 1.0
CB T:CYS139 4.6 122.7 1.0
SG T:CYS101 4.6 122.8 1.0
C T:CYS117 4.7 125.4 1.0
N T:ILE118 4.7 122.8 1.0
O T:CYS105 4.9 124.4 1.0
CA T:CYS105 4.9 124.4 1.0
C T:CYS119 5.0 123.9 1.0

Zinc binding site 7 out of 12 in 7qtt

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Zinc binding site 7 out of 12 in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1001

b:133.0
occ:1.00
 SG T:CYS101 2.3 122.8 1.0
SG T:CYS142 2.3 125.3 1.0
SG T:CYS139 2.3 122.7 1.0
SG T:CYS119 2.3 123.9 1.0
CB T:CYS142 2.8 125.3 1.0
CB T:CYS139 2.9 122.7 1.0
CB T:CYS101 3.1 122.8 1.0
CB T:CYS119 3.4 123.9 1.0
N T:CYS142 3.8 125.3 1.0
CA T:CYS142 3.9 125.3 1.0
ZN T:ZN1002 3.9 142.9 1.0
O T:CYS119 4.0 123.9 1.0
N T:CYS101 4.1 122.8 1.0
ZN T:ZN1000 4.1 151.8 1.0
SG T:CYS105 4.2 124.4 1.0
CA T:CYS101 4.3 122.8 1.0
C T:CYS119 4.3 123.9 1.0
CA T:CYS139 4.3 122.7 1.0
CA T:CYS119 4.5 123.9 1.0
SG T:CYS137 4.5 120.6 1.0
C T:CYS139 4.9 122.7 1.0
CD T:ARG120 4.9 125.9 1.0
C T:CYS142 4.9 125.3 1.0
N T:ARG120 4.9 125.9 1.0

Zinc binding site 8 out of 12 in 7qtt

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Zinc binding site 8 out of 12 in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Zn1002

b:142.9
occ:1.00
 CB T:CYS105 2.2 124.4 1.0
SG T:CYS101 2.3 122.8 1.0
SG T:CYS137 2.3 120.6 1.0
SG T:CYS102 2.3 121.6 1.0
SG T:CYS105 2.4 124.4 1.0
CB T:CYS101 3.5 122.8 1.0
CA T:CYS105 3.6 124.4 1.0
ZN T:ZN1000 3.6 151.8 1.0
CB T:CYS137 3.7 120.6 1.0
N T:CYS102 3.8 121.6 1.0
CB T:CYS102 3.8 121.6 1.0
ZN T:ZN1001 3.9 133.0 1.0
N T:CYS105 4.1 124.4 1.0
SG T:CYS134 4.2 121.2 1.0
SG T:CYS119 4.2 123.9 1.0
CA T:CYS102 4.3 121.6 1.0
C T:CYS101 4.4 122.8 1.0
O T:CYS102 4.4 121.6 1.0
CA T:CYS101 4.5 122.8 1.0
CB T:CYS139 4.6 122.7 1.0
C T:CYS105 4.7 124.4 1.0
CB T:HIS136 4.7 122.4 1.0
C T:CYS102 4.8 121.6 1.0
N T:CYS137 4.8 120.6 1.0
CA T:CYS137 4.9 120.6 1.0
N T:CYS101 5.0 122.8 1.0

Zinc binding site 9 out of 12 in 7qtt

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Zinc binding site 9 out of 12 in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Zn501

b:178.2
occ:1.00
 SG U:CYS81 2.3 163.5 1.0
SG U:CYS84 2.3 159.7 1.0
SG U:CYS27 2.3 149.9 1.0
SG U:CYS24 2.3 153.5 1.0
CB U:CYS24 3.0 153.5 1.0
CB U:CYS81 3.0 163.5 1.0
CB U:CYS84 3.1 159.7 1.0
CB U:CYS27 3.2 149.9 1.0
N U:CYS24 3.3 153.5 1.0
OG1 U:THR83 3.4 155.8 1.0
N U:CYS84 3.6 159.7 1.0
CA U:CYS24 3.7 153.5 1.0
CA U:CYS84 4.0 159.7 1.0
N U:CYS27 4.4 149.9 1.0
CA U:CYS27 4.4 149.9 1.0
C U:LEU23 4.4 148.5 1.0
CA U:CYS81 4.5 163.5 1.0
C U:CYS24 4.6 153.5 1.0
OG1 U:THR26 4.6 144.4 1.0
CA U:LEU23 4.7 148.5 1.0
CB U:THR83 4.7 155.8 1.0
C U:THR83 4.8 155.8 1.0
NH2 U:ARG159 4.8 145.4 1.0
N U:THR83 4.8 155.8 1.0
O U:CYS24 4.9 153.5 1.0
CB U:LEU23 4.9 148.5 1.0

Zinc binding site 10 out of 12 in 7qtt

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Zinc binding site 10 out of 12 in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Zn502

b:168.0
occ:1.00
 SG U:CYS48 2.3 152.4 1.0
SG U:CYS71 2.3 155.8 1.0
SG U:CYS45 2.3 147.8 1.0
SG U:CYS74 2.3 172.5 1.0
CB U:CYS48 3.2 152.4 1.0
CB U:CYS71 3.2 155.8 1.0
CB U:CYS45 3.3 147.8 1.0
CB U:CYS74 3.5 172.5 1.0
N U:CYS48 3.7 152.4 1.0
N U:CYS71 3.8 155.8 1.0
CA U:CYS48 4.0 152.4 1.0
CA U:CYS71 4.0 155.8 1.0
NH1 U:ARG50 4.1 150.2 1.0
N U:CYS74 4.2 172.5 1.0
CA U:CYS74 4.5 172.5 1.0
C U:CYS71 4.6 155.8 1.0
C U:CYS48 4.6 152.4 1.0
O U:CYS71 4.7 155.8 1.0
CA U:CYS45 4.8 147.8 1.0
CG U:ARG50 4.8 150.2 1.0
C U:ILE47 4.9 152.2 1.0
CB U:ILE47 4.9 152.2 1.0
N U:ALA49 4.9 145.3 1.0
C U:VAL70 5.0 152.5 1.0

Reference:

J.Schmitzova, C.Cretu, C.Dienemann, H.Urlaub, V.Pena. Structural Basis of Catalytic Activation in Human Splicing Nature 2023.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-06049-W
Page generated: Wed Oct 30 10:03:28 2024

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