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Zinc in PDB 8p4a: Structural Insights Into Human Co-Transcriptional Capping - Structure 1

Enzymatic activity of Structural Insights Into Human Co-Transcriptional Capping - Structure 1

All present enzymatic activity of Structural Insights Into Human Co-Transcriptional Capping - Structure 1:
2.7.7.50; 2.7.7.6; 3.6.1.74;

Other elements in 8p4a:

The structure of Structural Insights Into Human Co-Transcriptional Capping - Structure 1 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Insights Into Human Co-Transcriptional Capping - Structure 1 (pdb code 8p4a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structural Insights Into Human Co-Transcriptional Capping - Structure 1, PDB code: 8p4a:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8p4a

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Zinc binding site 1 out of 8 in the Structural Insights Into Human Co-Transcriptional Capping - Structure 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Insights Into Human Co-Transcriptional Capping - Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:230.2
occ:1.00
 CB A:CYS114 2.1 204.5 1.0
SG A:CYS111 2.3 194.1 1.0
SG A:CYS114 2.3 204.5 1.0
CA A:CYS114 3.2 204.5 1.0
N A:CYS114 3.3 204.5 1.0
CB A:CYS111 3.4 194.1 1.0
CE1 A:TYR187 3.6 197.9 1.0
CD1 A:TYR187 3.7 197.9 1.0
CB A:CYS184 4.0 197.8 1.0
N A:CYS184 4.0 197.8 1.0
C A:CYS114 4.1 204.5 1.0
CG A:LYS116 4.2 183.2 1.0
CB A:LYS116 4.4 183.2 1.0
N A:SER115 4.5 189.1 1.0
CZ A:TYR187 4.5 197.9 1.0
CA A:CYS184 4.5 197.8 1.0
C A:PHE113 4.5 190.9 1.0
CG A:TYR187 4.6 197.9 1.0
N A:LYS116 4.7 183.2 1.0
O A:CYS114 4.8 204.5 1.0
CA A:CYS111 4.8 194.1 1.0
C A:GLY183 5.0 189.5 1.0

Zinc binding site 2 out of 8 in 8p4a

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Zinc binding site 2 out of 8 in the Structural Insights Into Human Co-Transcriptional Capping - Structure 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Insights Into Human Co-Transcriptional Capping - Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:191.9
occ:1.00
 NE2 A:HIS84 2.0 145.5 1.0
SG A:CYS74 2.3 164.6 1.0
SG A:CYS81 2.3 154.1 1.0
SG A:CYS71 2.3 167.9 1.0
CD2 A:HIS84 2.8 145.5 1.0
CB A:CYS71 2.8 167.9 1.0
CE1 A:HIS84 3.2 145.5 1.0
CB A:CYS81 3.6 154.1 1.0
CB A:CYS74 3.7 164.6 1.0
N A:CYS74 3.8 164.6 1.0
CG A:HIS84 4.0 145.5 1.0
ND1 A:HIS84 4.1 145.5 1.0
CA A:CYS74 4.2 164.6 1.0
CA A:CYS81 4.3 154.1 1.0
CA A:CYS71 4.3 167.9 1.0
CB A:THR73 4.5 158.5 1.0
C A:CYS74 4.6 164.6 1.0
N A:GLY76 4.7 169.3 1.0
N A:GLY83 4.7 139.3 1.0
O A:CYS74 4.7 164.6 1.0
CA A:GLY63 4.7 157.7 1.0
CG2 A:VAL64 4.7 161.7 1.0
CD A:PRO82 4.8 142.4 1.0
C A:CYS81 4.8 154.1 1.0
C A:THR73 4.9 158.5 1.0
CA A:GLY76 4.9 169.3 1.0
N A:THR73 5.0 158.5 1.0

Zinc binding site 3 out of 8 in 8p4a

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Zinc binding site 3 out of 8 in the Structural Insights Into Human Co-Transcriptional Capping - Structure 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Insights Into Human Co-Transcriptional Capping - Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2000

b:233.0
occ:1.00
 SG B:CYS1122 2.3 150.2 1.0
SG B:CYS1137 2.3 164.5 1.0
SG B:CYS1119 2.3 160.4 1.0
CB B:CYS1140 2.6 177.2 1.0
CB B:CYS1137 3.0 164.5 1.0
SG B:CYS1140 3.3 177.2 1.0
CB B:CYS1119 3.5 160.4 1.0
CB B:CYS1122 4.0 150.2 1.0
CA B:CYS1140 4.0 177.2 1.0
N B:CYS1140 4.2 177.2 1.0
ND2 B:ASN1142 4.2 172.9 1.0
N B:CYS1122 4.3 150.2 1.0
O B:CYS1137 4.4 164.5 1.0
CA B:CYS1137 4.4 164.5 1.0
OD1 B:ASN1142 4.5 172.9 1.0
CG B:ASN1142 4.5 172.9 1.0
O B:CYS1122 4.6 150.2 1.0
CA B:CYS1122 4.6 150.2 1.0
C B:CYS1137 4.6 164.5 1.0
CG1 B:ILE1124 4.8 151.7 1.0
C B:CYS1140 4.8 177.2 1.0
CA B:CYS1119 4.9 160.4 1.0
CB B:LEU1121 5.0 151.5 1.0
CD1 B:ILE1124 5.0 151.7 1.0

Zinc binding site 4 out of 8 in 8p4a

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Zinc binding site 4 out of 8 in the Structural Insights Into Human Co-Transcriptional Capping - Structure 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Insights Into Human Co-Transcriptional Capping - Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:231.7
occ:1.00
 SG C:CYS94 2.3 161.9 1.0
SG C:CYS90 2.3 189.6 1.0
SG C:CYS97 2.3 161.1 1.0
SG C:CYS88 2.3 180.6 1.0
CB C:CYS90 2.8 189.6 1.0
CB C:CYS88 3.0 180.6 1.0
CB C:CYS97 3.4 161.1 1.0
CB C:CYS94 3.5 161.9 1.0
N C:CYS94 3.8 161.9 1.0
N C:CYS97 4.0 161.1 1.0
CA C:CYS90 4.0 189.6 1.0
N C:CYS90 4.1 189.6 1.0
CA C:CYS94 4.1 161.9 1.0
C C:PHE93 4.2 166.1 1.0
CA C:CYS97 4.3 161.1 1.0
O C:CYS94 4.4 161.9 1.0
CA C:CYS88 4.4 180.6 1.0
C C:CYS94 4.6 161.9 1.0
CA C:PHE93 4.7 166.1 1.0
C C:GLU96 4.7 159.7 1.0
C C:CYS88 4.7 180.6 1.0
O C:PHE93 4.8 166.1 1.0
N C:PHE93 4.8 166.1 1.0
CB C:GLU96 4.9 159.7 1.0
C C:CYS90 4.9 189.6 1.0

Zinc binding site 5 out of 8 in 8p4a

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Zinc binding site 5 out of 8 in the Structural Insights Into Human Co-Transcriptional Capping - Structure 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Insights Into Human Co-Transcriptional Capping - Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn200

b:246.3
occ:1.00
 SG I:CYS20 2.3 199.2 1.0
SG I:CYS42 2.3 205.0 1.0
SG I:CYS17 2.3 197.0 1.0
SG I:CYS39 2.3 196.0 1.0
CB I:CYS39 3.2 196.0 1.0
CB I:CYS17 3.3 197.0 1.0
CB I:CYS42 3.7 205.0 1.0
CB I:CYS20 3.8 199.2 1.0
N I:CYS42 3.9 205.0 1.0
N I:CYS20 4.0 199.2 1.0
CA I:CYS42 4.2 205.0 1.0
CA I:CYS20 4.4 199.2 1.0
C I:CYS42 4.5 205.0 1.0
O I:CYS42 4.6 205.0 1.0
OE1 I:GLU19 4.6 205.1 1.0
CB I:TYR44 4.6 193.8 1.0
CA I:CYS39 4.7 196.0 1.0
CA I:CYS17 4.7 197.0 1.0
ND2 I:ASN22 4.8 188.4 1.0
CB I:ASN41 4.9 195.5 1.0
CB I:ASN22 4.9 188.4 1.0
C I:CYS20 4.9 199.2 1.0
CB I:GLU19 5.0 205.1 1.0
N I:ASN21 5.0 193.4 1.0

Zinc binding site 6 out of 8 in 8p4a

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Zinc binding site 6 out of 8 in the Structural Insights Into Human Co-Transcriptional Capping - Structure 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Insights Into Human Co-Transcriptional Capping - Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:218.3
occ:1.00
 SG I:CYS89 2.3 178.3 1.0
SG I:CYS119 2.3 182.0 1.0
SG I:CYS86 2.3 168.4 1.0
SG I:CYS114 2.8 176.3 1.0
CB I:CYS114 2.9 176.3 1.0
CB I:CYS119 3.3 182.0 1.0
CB I:CYS86 3.4 168.4 1.0
CB I:HIS121 3.5 166.6 1.0
CB I:CYS89 3.6 178.3 1.0
N I:HIS121 3.8 166.6 1.0
N I:CYS89 4.2 178.3 1.0
CA I:HIS121 4.2 166.6 1.0
CA I:CYS114 4.4 176.3 1.0
N I:GLY120 4.4 169.3 1.0
C I:CYS119 4.5 182.0 1.0
CA I:CYS89 4.6 178.3 1.0
CA I:CYS119 4.6 182.0 1.0
CG I:HIS121 4.6 166.6 1.0
O I:HIS121 4.6 166.6 1.0
CB I:ALA116 4.6 170.8 1.0
CA I:CYS86 4.8 168.4 1.0
C I:HIS121 4.9 166.6 1.0
C I:CYS114 4.9 176.3 1.0
C I:GLY120 4.9 169.3 1.0
CB I:HIS91 5.0 164.8 1.0
CD2 I:HIS121 5.0 166.6 1.0
O I:CYS114 5.0 176.3 1.0

Zinc binding site 7 out of 8 in 8p4a

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Zinc binding site 7 out of 8 in the Structural Insights Into Human Co-Transcriptional Capping - Structure 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural Insights Into Human Co-Transcriptional Capping - Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:184.9
occ:1.00
 SG J:CYS45 2.3 136.7 1.0
SG J:CYS44 2.3 137.2 1.0
SG J:CYS10 2.3 133.9 1.0
SG J:CYS7 2.3 127.1 1.0
CB J:CYS10 2.8 133.9 1.0
OG1 J:THR9 3.1 131.1 1.0
N J:CYS45 3.3 136.7 1.0
CB J:CYS7 3.5 127.1 1.0
CB J:CYS45 3.6 136.7 1.0
N J:CYS10 3.6 133.9 1.0
CB J:CYS44 3.7 137.2 1.0
C J:CYS44 3.7 137.2 1.0
CA J:CYS45 3.7 136.7 1.0
CA J:CYS10 3.8 133.9 1.0
NE J:ARG42 3.9 130.9 1.0
O J:CYS44 4.2 137.2 1.0
CA J:CYS44 4.3 137.2 1.0
CB J:THR9 4.5 131.1 1.0
CB J:ARG42 4.5 130.9 1.0
CD J:ARG42 4.6 130.9 1.0
NH2 J:ARG42 4.7 130.9 1.0
C J:THR9 4.7 131.1 1.0
CZ J:ARG42 4.8 130.9 1.0
CB J:LYS12 4.9 125.4 1.0
CA J:CYS7 4.9 127.1 1.0
N J:CYS44 4.9 137.2 1.0

Zinc binding site 8 out of 8 in 8p4a

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Zinc binding site 8 out of 8 in the Structural Insights Into Human Co-Transcriptional Capping - Structure 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural Insights Into Human Co-Transcriptional Capping - Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:213.1
occ:1.00
 CB L:CYS22 1.9 175.1 1.0
SG L:CYS22 2.3 175.1 1.0
SG L:CYS36 2.3 175.6 1.0
CB L:CYS19 2.5 184.4 1.0
CG2 L:THR24 3.0 184.4 1.0
SG L:CYS19 3.4 184.4 1.0
CA L:CYS22 3.4 175.1 1.0
O L:CYS19 3.4 184.4 1.0
CB L:GLU38 3.7 188.2 1.0
CG L:GLU38 3.7 188.2 1.0
CB L:CYS36 3.8 175.6 1.0
CA L:CYS19 3.9 184.4 1.0
N L:CYS22 4.1 175.1 1.0
C L:CYS22 4.1 175.1 1.0
C L:CYS19 4.1 184.4 1.0
CB L:THR24 4.4 184.4 1.0
N L:GLU38 4.4 188.2 1.0
N L:THR24 4.4 184.4 1.0
N L:HIS23 4.5 174.5 1.0
CA L:GLU38 4.6 188.2 1.0
O L:CYS22 4.6 175.1 1.0
N L:CYS19 4.8 184.4 1.0
N L:CYS39 4.9 181.0 1.0
CA L:THR24 4.9 184.4 1.0
O L:THR24 5.0 184.4 1.0
CA L:CYS36 5.0 175.6 1.0

Reference:

G.Garg, C.Dienemann, L.Farnung, J.Schwarz, A.Linden, H.Urlaub, P.Cramer. Structural Insights Into Human Co-Transcriptional Capping. Mol.Cell V. 83 2464 2023.
ISSN: ISSN 1097-2765
PubMed: 37369200
DOI: 10.1016/J.MOLCEL.2023.06.002
Page generated: Thu Oct 31 09:05:15 2024

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