Zinc in PDB 8p4f: Structural Insights Into Human Co-Transcriptional Capping - Structure 6

Enzymatic activity of Structural Insights Into Human Co-Transcriptional Capping - Structure 6

All present enzymatic activity of Structural Insights Into Human Co-Transcriptional Capping - Structure 6:
2.1.1.57; 2.7.7.6;

Other elements in 8p4f:

The structure of Structural Insights Into Human Co-Transcriptional Capping - Structure 6 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 6 (pdb code 8p4f). 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 6, PDB code: 8p4f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8p4f

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


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

b:112.1
occ:1.00
 SG A:CYS81 2.2 162.1 1.0
SG A:CYS71 2.3 174.4 1.0
SG A:CYS74 2.4 166.8 1.0
NE2 A:HIS84 2.8 138.0 1.0
CD2 A:HIS84 3.0 138.0 1.0
OG1 A:THR73 3.2 159.3 1.0
CB A:CYS71 3.7 174.4 1.0
CB A:CYS81 3.8 162.1 1.0
CB A:CYS74 4.0 166.8 1.0
CE1 A:HIS84 4.0 138.0 1.0
N A:CYS74 4.2 168.3 1.0
CG A:HIS84 4.3 138.0 1.0
CB A:THR73 4.4 159.3 1.0
C A:THR73 4.5 162.9 1.0
CA A:CYS81 4.5 150.3 1.0
CA A:CYS74 4.5 168.3 1.0
O A:CYS74 4.5 168.3 1.0
C A:CYS74 4.8 168.3 1.0
ND1 A:HIS84 4.8 138.0 1.0
CA A:THR73 4.8 162.9 1.0
N A:THR73 4.8 162.9 1.0
CA A:GLY76 4.9 173.4 1.0
N A:GLY83 4.9 137.6 1.0

Zinc binding site 2 out of 8 in 8p4f

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


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

b:112.1
occ:1.00
 SG A:CYS111 2.3 183.1 1.0
SG A:CYS114 2.3 182.3 1.0
CB A:CYS184 2.4 191.0 1.0
SG A:CYS184 2.5 191.0 1.0
O A:CYS184 3.1 183.9 1.0
SG A:CYS154 3.4 192.6 1.0
O A:GLY183 3.4 186.6 1.0
CB A:CYS111 3.5 183.1 1.0
CA A:CYS184 3.6 183.9 1.0
CB A:CYS114 3.6 182.3 1.0
C A:CYS184 3.8 183.9 1.0
CB A:CYS154 3.8 192.6 1.0
N A:CYS114 4.1 169.3 1.0
C A:GLY183 4.2 186.6 1.0
N A:CYS184 4.3 183.9 1.0
NE2 A:GLN188 4.4 176.1 1.0
CA A:CYS114 4.5 169.3 1.0
CA A:CYS111 4.9 169.3 1.0

Zinc binding site 3 out of 8 in 8p4f

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Zinc binding site 3 out of 8 in the Structural Insights Into Human Co-Transcriptional Capping - Structure 6


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

b:112.1
occ:1.00
 SG B:CYS1122 2.3 143.3 1.0
SG B:CYS1140 2.4 167.2 1.0
SG B:CYS1119 2.4 148.1 1.0
SG B:CYS1137 2.4 165.8 1.0
CB B:CYS1140 2.7 167.2 1.0
CB B:CYS1119 3.4 148.1 1.0
CB B:CYS1122 3.6 143.3 1.0
CB B:CYS1137 3.6 165.8 1.0
N B:CYS1122 3.6 131.6 1.0
CA B:CYS1140 4.0 160.7 1.0
CA B:CYS1122 4.2 131.6 1.0
N B:CYS1140 4.2 160.7 1.0
CB B:LEU1121 4.3 129.2 1.0
CB B:ASN1142 4.6 156.9 1.0
O B:CYS1122 4.6 131.6 1.0
C B:LEU1121 4.7 125.7 1.0
N B:LEU1121 4.7 125.7 1.0
C B:CYS1122 4.8 131.6 1.0
CA B:LEU1121 4.8 125.7 1.0
CA B:CYS1119 4.9 132.6 1.0
ND2 B:ASN1142 4.9 156.9 1.0
C B:CYS1140 4.9 160.7 1.0
CA B:CYS1137 5.0 158.0 1.0

Zinc binding site 4 out of 8 in 8p4f

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Zinc binding site 4 out of 8 in the Structural Insights Into Human Co-Transcriptional Capping - Structure 6


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

b:112.1
occ:1.00
 SG I:CYS17 2.3 155.5 1.0
SG I:CYS42 2.4 157.7 1.0
SG I:CYS20 2.5 158.6 1.0
SG I:CYS39 2.7 159.2 1.0
CB I:CYS39 2.7 159.2 1.0
CB I:CYS17 3.0 155.5 1.0
CB I:CYS42 4.0 157.7 1.0
N I:CYS20 4.0 146.9 1.0
CB I:CYS20 4.1 158.6 1.0
CA I:CYS39 4.3 148.1 1.0
CB I:TYR44 4.4 149.7 1.0
CA I:CYS17 4.5 146.2 1.0
N I:CYS42 4.6 149.9 1.0
CA I:CYS20 4.6 146.9 1.0
CB I:GLU19 4.8 150.1 1.0
CA I:CYS42 4.8 149.9 1.0
N I:GLU19 4.9 148.2 1.0
N I:ASN22 4.9 141.5 1.0
CB I:ASN22 4.9 140.3 1.0
N I:ASN21 4.9 141.9 1.0
N I:CYS39 4.9 148.1 1.0
CD2 I:TYR44 5.0 149.7 1.0
C I:CYS39 5.0 148.1 1.0
C I:CYS20 5.0 146.9 1.0

Zinc binding site 5 out of 8 in 8p4f

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Zinc binding site 5 out of 8 in the Structural Insights Into Human Co-Transcriptional Capping - Structure 6


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

b:112.1
occ:1.00
 SG I:CYS119 2.2 147.9 1.0
SG I:CYS86 2.3 154.4 1.0
SG I:CYS89 2.3 162.9 1.0
SG I:CYS114 2.4 146.8 1.0
CB I:CYS86 3.0 154.4 1.0
CB I:CYS119 3.4 147.9 1.0
CB I:CYS114 3.5 146.8 1.0
CB I:CYS89 3.9 162.9 1.0
CB I:HIS91 3.9 136.2 1.0
N I:CYS89 4.0 149.9 1.0
CA I:CYS89 4.5 149.9 1.0
CA I:CYS86 4.5 144.2 1.0
N I:HIS91 4.5 141.6 1.0
O I:THR115 4.6 133.6 1.0
CA I:CYS119 4.8 139.4 1.0
CB I:HIS121 4.8 127.9 1.0
N I:GLY90 4.8 145.9 1.0
C I:CYS89 4.9 149.9 1.0
CA I:HIS91 4.9 141.6 1.0
CA I:CYS114 4.9 129.7 1.0
CG I:HIS91 5.0 136.2 1.0
CB I:LYS88 5.0 135.3 1.0

Zinc binding site 6 out of 8 in 8p4f

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


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

b:112.1
occ:1.00
 SG J:CYS10 2.1 78.1 1.0
SG J:CYS7 2.3 75.7 1.0
SG J:CYS44 2.3 83.7 1.0
SG J:CYS45 2.4 86.5 1.0
CB J:CYS7 3.2 75.7 1.0
N J:CYS45 3.2 72.0 1.0
CB J:CYS10 3.3 78.1 1.0
CB J:CYS44 3.4 83.7 1.0
C J:CYS44 3.5 75.6 1.0
CA J:CYS45 3.6 72.0 1.0
CB J:CYS45 3.6 86.5 1.0
N J:CYS10 3.7 72.3 1.0
O J:CYS44 3.9 75.6 1.0
CA J:CYS10 4.1 72.3 1.0
CA J:CYS44 4.1 75.6 1.0
N J:GLY11 4.4 71.7 1.0
CA J:CYS7 4.6 66.3 1.0
C J:CYS10 4.7 72.3 1.0
NH2 J:ARG42 4.7 77.0 1.0
CB J:LYS12 4.8 68.2 1.0
C J:CYS7 4.8 66.3 1.0
N J:LYS12 4.8 71.0 1.0
CB J:THR9 4.8 71.2 1.0
C J:THR9 4.9 67.8 1.0
N J:CYS44 4.9 75.6 1.0
O J:CYS7 4.9 66.3 1.0

Zinc binding site 7 out of 8 in 8p4f

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Zinc binding site 7 out of 8 in the Structural Insights Into Human Co-Transcriptional Capping - Structure 6


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

b:112.1
occ:1.00
 SG L:CYS22 2.2 137.8 1.0
SG L:CYS39 2.2 145.8 1.0
SG L:CYS36 2.3 146.2 1.0
SG L:CYS19 2.4 138.0 1.0
CB L:CYS36 2.7 146.2 1.0
CB L:CYS19 3.0 138.0 1.0
CB L:CYS39 3.3 145.8 1.0
O L:ARG37 3.7 140.3 1.0
CB L:CYS22 3.9 137.8 1.0
OG1 L:THR24 3.9 131.1 1.0
CA L:CYS36 4.0 132.4 1.0
N L:CYS39 4.2 138.8 1.0
C L:CYS36 4.2 132.4 1.0
N L:CYS22 4.3 132.2 1.0
O L:CYS36 4.3 132.4 1.0
CA L:CYS39 4.4 138.8 1.0
CA L:CYS19 4.4 127.3 1.0
CA L:CYS22 4.6 132.2 1.0
C L:ARG37 4.7 140.3 1.0
C L:GLU38 4.7 144.1 1.0
CB L:TYR41 4.9 126.1 1.0
N L:ARG37 4.9 140.3 1.0
N L:CYS36 4.9 132.4 1.0
N L:GLY40 4.9 128.0 1.0
CE L:MET44 5.0 120.6 1.0

Zinc binding site 8 out of 8 in 8p4f

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


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Zn201

b:112.1
occ:1.00
 SG Y:CYS33 2.3 506.4 1.0
SG Y:CYS16 2.4 484.9 1.0
SG Y:CYS36 2.4 521.2 1.0
SG Y:CYS19 2.4 462.5 1.0
CB Y:CYS16 3.2 484.9 1.0
CB Y:CYS19 3.2 462.5 1.0
CB Y:CYS36 3.3 521.2 1.0
CB Y:CYS33 3.5 506.4 1.0
N Y:CYS19 3.7 443.2 1.0
N Y:CYS36 3.9 520.6 1.0
CA Y:CYS19 4.0 443.2 1.0
CB Y:ASN35 4.3 431.1 1.0
CA Y:CYS36 4.3 520.6 1.0
CA Y:CYS16 4.6 465.5 1.0
CB Y:LEU18 4.6 484.9 1.0
CD1 Y:LEU40 4.6 536.6 1.0
C Y:LEU18 4.7 463.2 1.0
C Y:ASN35 4.8 475.1 1.0
CB Y:LEU21 4.8 434.6 1.0
ND2 Y:ASN35 4.8 431.1 1.0
C Y:CYS19 4.8 443.2 1.0
CA Y:CYS33 4.9 495.9 1.0
CA Y:ASN35 4.9 475.1 1.0
N Y:ASN35 4.9 475.1 1.0
N Y:SER20 4.9 435.7 1.0
CA Y:LEU18 5.0 463.2 1.0
N Y:LEU18 5.0 463.2 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 2023.
ISSN: ISSN 1097-2765
PubMed: 37369200
DOI: 10.1016/J.MOLCEL.2023.06.002
Page generated: Thu Oct 31 09:06:30 2024

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