Zinc in PDB 8p4b: Structural Insights Into Human Co-Transcriptional Capping - Structure 2

Enzymatic activity of Structural Insights Into Human Co-Transcriptional Capping - Structure 2

All present enzymatic activity of Structural Insights Into Human Co-Transcriptional Capping - Structure 2:
2.7.7.50; 2.7.7.6; 3.6.1.74;

Other elements in 8p4b:

The structure of Structural Insights Into Human Co-Transcriptional Capping - Structure 2 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 2 (pdb code 8p4b). 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 2, PDB code: 8p4b:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8p4b

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


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:110.1
occ:1.00
 SG A:CYS74 2.3 95.8 1.0
SG A:CYS71 2.3 99.8 1.0
NE2 A:HIS84 2.3 83.0 1.0
CB A:CYS71 2.6 99.8 1.0
CD2 A:HIS84 2.8 83.0 1.0
SG A:CYS81 3.3 92.4 1.0
CB A:CYS81 3.4 92.4 1.0
CE1 A:HIS84 3.6 83.0 1.0
O A:PRO82 3.7 82.6 1.0
O A:CYS74 3.7 95.8 1.0
CB A:CYS74 3.9 95.8 1.0
CG A:HIS84 4.1 83.0 1.0
OG1 A:THR73 4.1 97.2 1.0
CA A:CYS71 4.1 99.8 1.0
N A:CYS74 4.2 95.8 1.0
CA A:CYS74 4.4 95.8 1.0
ND1 A:HIS84 4.4 83.0 1.0
CA A:GLY63 4.4 92.5 1.0
C A:CYS74 4.4 95.8 1.0
O A:GLN62 4.6 87.8 1.0
C A:CYS71 4.7 99.8 1.0
CA A:CYS81 4.8 92.4 1.0
N A:CYS71 4.9 99.8 1.0
C A:PRO82 4.9 82.6 1.0
C A:GLY63 4.9 92.5 1.0
O A:ARG61 5.0 92.8 1.0

Zinc binding site 2 out of 8 in 8p4b

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


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:153.2
occ:1.00
 SG A:CYS114 2.3 130.9 1.0
SG A:CYS111 2.3 132.7 1.0
CB A:CYS114 3.1 130.9 1.0
CE1 A:TYR187 3.3 139.1 1.0
SG A:CYS184 3.4 140.0 1.0
CD1 A:TYR187 3.4 139.1 1.0
N A:CYS184 3.5 140.0 1.0
CZ A:TYR187 3.9 139.1 1.0
CB A:CYS111 3.9 132.7 1.0
CA A:GLY183 4.0 139.0 1.0
CG A:TYR187 4.1 139.1 1.0
CB A:CYS184 4.2 140.0 1.0
C A:GLY183 4.3 139.0 1.0
CD A:LYS116 4.3 128.9 1.0
CE2 A:TYR187 4.4 139.1 1.0
CA A:CYS184 4.5 140.0 1.0
O A:GLY182 4.5 135.6 1.0
OH A:TYR187 4.5 139.1 1.0
CD2 A:TYR187 4.5 139.1 1.0
CA A:CYS114 4.6 130.9 1.0
O A:PHE112 4.6 125.8 1.0
CB A:LYS116 4.8 128.9 1.0
NZ A:LYS116 4.9 128.9 1.0
CB A:TYR187 4.9 139.1 1.0
N A:GLY185 4.9 140.5 1.0
CG A:LYS116 4.9 128.9 1.0

Zinc binding site 3 out of 8 in 8p4b

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Zinc binding site 3 out of 8 in the Structural Insights Into Human Co-Transcriptional Capping - Structure 2


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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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:124.0
occ:1.00
 SG B:CYS1122 2.3 93.7 1.0
SG B:CYS1119 2.3 93.3 1.0
SG B:CYS1137 2.3 102.5 1.0
CB B:CYS1119 2.5 93.3 1.0
SG B:CYS1140 2.7 106.3 1.0
CB B:CYS1137 3.4 102.5 1.0
CB B:CYS1140 3.6 106.3 1.0
CB B:CYS1122 3.7 93.7 1.0
N B:CYS1122 3.7 93.7 1.0
O B:CYS1122 3.9 93.7 1.0
CA B:CYS1119 4.0 93.3 1.0
CA B:CYS1122 4.1 93.7 1.0
ND2 B:ASN1142 4.3 105.5 1.0
O B:CYS1137 4.4 102.5 1.0
C B:CYS1122 4.4 93.7 1.0
CB B:LEU1121 4.6 92.0 1.0
C B:CYS1119 4.7 93.3 1.0
CA B:CYS1137 4.7 102.5 1.0
N B:CYS1119 4.7 93.3 1.0
C B:LEU1121 4.8 92.0 1.0
C B:CYS1137 4.8 102.5 1.0
N B:LEU1121 4.9 92.0 1.0
CA B:CYS1140 4.9 106.3 1.0
CG B:ASN1142 5.0 105.5 1.0

Zinc binding site 4 out of 8 in 8p4b

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Zinc binding site 4 out of 8 in the Structural Insights Into Human Co-Transcriptional Capping - Structure 2


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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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:130.6
occ:1.00
 SG C:CYS94 2.3 89.9 1.0
SG C:CYS90 2.3 101.4 1.0
SG C:CYS88 2.3 94.9 1.0
SG C:CYS97 2.3 85.0 1.0
CB C:CYS88 3.1 94.9 1.0
CB C:CYS97 3.2 85.0 1.0
CB C:CYS90 3.5 101.4 1.0
CB C:CYS94 3.7 89.9 1.0
N C:CYS97 3.9 85.0 1.0
N C:CYS94 4.0 89.9 1.0
CA C:CYS97 4.2 85.0 1.0
CA C:CYS94 4.3 89.9 1.0
N C:CYS90 4.4 101.4 1.0
CA C:CYS88 4.5 94.9 1.0
CA C:CYS90 4.5 101.4 1.0
C C:GLU96 4.6 86.4 1.0
O C:CYS94 4.6 89.9 1.0
CB C:GLU96 4.7 86.4 1.0
C C:CYS94 4.8 89.9 1.0
C C:CYS88 4.8 94.9 1.0
C C:PHE93 4.8 86.7 1.0
O C:GLU91 4.8 100.4 1.0

Zinc binding site 5 out of 8 in 8p4b

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Zinc binding site 5 out of 8 in the Structural Insights Into Human Co-Transcriptional Capping - Structure 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:161.8
occ:1.00
 SG I:CYS42 2.3 137.6 1.0
SG I:CYS20 2.3 127.8 1.0
SG I:CYS39 2.3 137.5 1.0
SG I:CYS17 2.3 128.6 1.0
CB I:CYS39 3.3 137.5 1.0
CB I:CYS17 3.3 128.6 1.0
CB I:CYS42 3.8 137.6 1.0
CB I:CYS20 3.9 127.8 1.0
N I:CYS20 4.0 127.8 1.0
N I:CYS42 4.0 137.6 1.0
CB I:GLU19 4.3 129.2 1.0
CA I:CYS42 4.4 137.6 1.0
CA I:CYS20 4.5 127.8 1.0
CB I:ASN41 4.5 131.9 1.0
CA I:CYS39 4.7 137.5 1.0
O I:CYS42 4.8 137.6 1.0
CA I:CYS17 4.8 128.6 1.0
CB I:TYR44 4.9 135.8 1.0
ND2 I:ASN22 4.9 123.9 1.0
C I:CYS42 4.9 137.6 1.0
CG I:GLU19 4.9 129.2 1.0
C I:CYS20 4.9 127.8 1.0
C I:GLU19 5.0 129.2 1.0
CB I:ASN22 5.0 123.9 1.0

Zinc binding site 6 out of 8 in 8p4b

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Zinc binding site 6 out of 8 in the Structural Insights Into Human Co-Transcriptional Capping - Structure 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:142.5
occ:1.00
 SG I:CYS119 2.3 119.3 1.0
SG I:CYS86 2.3 117.5 1.0
SG I:CYS114 2.3 113.3 1.0
SG I:CYS89 2.3 122.4 1.0
CB I:CYS86 2.8 117.5 1.0
CB I:CYS114 3.2 113.3 1.0
CB I:CYS119 3.6 119.3 1.0
CB I:CYS89 3.8 122.4 1.0
CB I:HIS91 4.1 116.6 1.0
N I:CYS89 4.3 122.4 1.0
CA I:CYS86 4.3 117.5 1.0
CB I:HIS121 4.4 112.9 1.0
O I:THR115 4.5 112.2 1.0
CA I:CYS89 4.5 122.4 1.0
N I:HIS91 4.5 116.6 1.0
CA I:CYS114 4.7 113.3 1.0
N I:GLY90 4.9 120.3 1.0
CE I:LYS88 4.9 117.5 1.0
CA I:CYS119 4.9 119.3 1.0
C I:CYS89 4.9 122.4 1.0
C I:CYS86 4.9 117.5 1.0
CA I:HIS91 5.0 116.6 1.0

Zinc binding site 7 out of 8 in 8p4b

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Zinc binding site 7 out of 8 in the Structural Insights Into Human Co-Transcriptional Capping - Structure 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:87.8
occ:1.00
 SG J:CYS7 2.3 60.4 1.0
SG J:CYS44 2.3 69.3 1.0
SG J:CYS45 2.3 67.3 1.0
N J:CYS45 2.5 67.3 1.0
CB J:CYS10 2.8 63.6 1.0
C J:CYS44 2.9 69.3 1.0
CA J:CYS45 2.9 67.3 1.0
CB J:CYS45 3.1 67.3 1.0
CB J:CYS44 3.1 69.3 1.0
CB J:CYS7 3.2 60.4 1.0
O J:CYS44 3.4 69.3 1.0
N J:CYS10 3.6 63.6 1.0
CA J:CYS44 3.6 69.3 1.0
CA J:CYS10 3.8 63.6 1.0
SG J:CYS10 4.1 63.6 1.0
C J:CYS45 4.4 67.3 1.0
N J:CYS44 4.5 69.3 1.0
CA J:CYS7 4.7 60.4 1.0
CB J:THR9 4.7 60.7 1.0
C J:THR9 4.8 60.7 1.0
N J:GLY11 4.8 61.5 1.0
C J:CYS10 4.9 63.6 1.0
NE J:ARG42 4.9 67.9 1.0

Zinc binding site 8 out of 8 in 8p4b

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


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:147.1
occ:1.00
 SG L:CYS19 2.3 105.7 1.0
SG L:CYS22 2.3 107.7 1.0
SG L:CYS39 2.3 120.5 1.0
SG L:CYS36 2.3 116.3 1.0
CB L:CYS19 3.1 105.7 1.0
CB L:CYS36 3.3 116.3 1.0
O L:GLU38 3.5 123.8 1.0
CB L:CYS22 3.5 107.7 1.0
N L:CYS22 3.9 107.7 1.0
CB L:CYS39 4.0 120.5 1.0
CA L:CYS22 4.3 107.7 1.0
C L:GLU38 4.3 123.8 1.0
CB L:TYR41 4.4 106.6 1.0
CA L:CYS19 4.5 105.7 1.0
CA L:CYS36 4.7 116.3 1.0
C L:CYS22 4.8 107.7 1.0
OG1 L:THR24 4.9 107.5 1.0
N L:TYR41 4.9 106.6 1.0
CB L:GLU21 4.9 108.7 1.0
CA L:CYS39 4.9 120.5 1.0
CB L:THR24 4.9 107.5 1.0
N L:HIS23 4.9 105.2 1.0
N L:CYS39 5.0 120.5 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 09:05:49 2024

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