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Zinc in PDB 8qeq: Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation

Enzymatic activity of Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation

All present enzymatic activity of Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation:
2.7.7.6;

Other elements in 8qeq:

The structure of Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation (pdb code 8qeq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation, PDB code: 8qeq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 8qeq

Go back to Zinc Binding Sites List in 8qeq
Zinc binding site 1 out of 7 in the Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:96.7
occ:1.00
 NE2 A:HIS84 2.1 46.0 1.0
SG A:CYS74 2.3 67.6 1.0
SG A:CYS71 2.3 71.9 1.0
SG A:CYS81 2.3 67.8 1.0
CD2 A:HIS84 3.0 49.0 1.0
CE1 A:HIS84 3.2 46.8 1.0
OG1 A:THR73 3.3 66.2 1.0
CB A:CYS81 3.6 56.7 1.0
CB A:CYS74 3.8 71.0 1.0
N A:CYS74 3.8 72.7 1.0
CB A:CYS71 3.9 65.7 1.0
O A:CYS74 4.1 72.1 1.0
CG A:HIS84 4.2 43.2 1.0
CA A:CYS74 4.2 72.4 1.0
ND1 A:HIS84 4.2 47.6 1.0
CA A:CYS81 4.4 58.9 1.0
C A:CYS74 4.5 71.9 1.0
CB A:THR73 4.5 61.5 1.0
C A:THR73 4.6 64.7 1.0
CA A:GLY76 4.7 74.2 1.0
CD A:PRO82 4.9 49.8 1.0
CA A:THR73 4.9 62.4 1.0
N A:THR73 5.0 66.3 1.0

Zinc binding site 2 out of 7 in 8qeq

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Zinc binding site 2 out of 7 in the Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:143.5
occ:1.00
 SG A:CYS111 2.3 102.4 1.0
SG A:CYS114 2.3 98.0 1.0
SG A:CYS184 2.3 97.2 1.0
SG A:CYS154 2.3 103.5 1.0
O A:GLY183 2.8 102.1 1.0
CB A:CYS154 3.3 103.2 1.0
CB A:CYS111 3.4 93.3 1.0
CB A:CYS114 3.4 91.3 1.0
O A:CYS184 3.6 99.5 1.0
C A:GLY183 3.9 99.4 1.0
N A:CYS114 3.9 91.5 1.0
CB A:CYS184 4.0 97.6 1.0
CA A:CYS114 4.2 91.0 1.0
NE2 A:GLN188 4.5 101.6 1.0
C A:CYS184 4.5 98.0 1.0
CA A:CYS184 4.6 98.3 1.0
N A:CYS184 4.7 98.2 1.0
CA A:CYS154 4.7 102.5 1.0
CA A:CYS111 4.8 94.2 1.0
N A:GLY183 4.8 99.8 1.0
C A:CYS114 4.9 93.4 1.0
CA A:GLY183 5.0 98.5 1.0

Zinc binding site 3 out of 7 in 8qeq

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Zinc binding site 3 out of 7 in the Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:111.1
occ:1.00
 SG B:CYS1137 2.3 79.9 1.0
SG B:CYS1122 2.3 71.7 1.0
SG B:CYS1140 2.3 85.2 1.0
SG B:CYS1119 2.3 71.2 1.0
CB B:CYS1119 3.2 65.7 1.0
CB B:CYS1140 3.4 81.6 1.0
CB B:CYS1137 3.5 76.8 1.0
CB B:CYS1122 3.6 65.2 1.0
N B:CYS1122 3.7 67.1 1.0
O B:CYS1122 4.0 66.0 1.0
CA B:CYS1122 4.1 66.5 1.0
C B:CYS1122 4.4 65.5 1.0
C B:LEU1121 4.5 64.3 1.0
N B:CYS1140 4.6 81.9 1.0
CA B:CYS1140 4.6 81.2 1.0
CA B:CYS1119 4.7 62.4 1.0
CB B:LEU1121 4.7 63.5 1.0
CA B:CYS1137 4.9 75.7 1.0
N B:LEU1121 5.0 64.9 1.0
CA B:LEU1121 5.0 62.7 1.0

Zinc binding site 4 out of 7 in 8qeq

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Zinc binding site 4 out of 7 in the Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:105.0
occ:1.00
 SG I:CYS42 2.3 73.2 1.0
SG I:CYS17 2.3 66.0 1.0
SG I:CYS20 2.3 77.1 1.0
SG I:CYS39 2.3 81.3 1.0
CB I:CYS17 3.0 56.2 1.0
CB I:CYS39 3.1 66.0 1.0
CB I:CYS20 3.7 61.7 1.0
CB I:CYS42 3.7 67.7 1.0
N I:CYS20 4.0 60.2 1.0
N I:CYS42 4.3 67.6 1.0
CA I:CYS20 4.4 59.6 1.0
CA I:CYS42 4.5 65.1 1.0
CA I:CYS17 4.5 54.5 1.0
CA I:CYS39 4.6 63.9 1.0
CB I:GLU19 4.6 60.4 1.0
CB I:TYR44 4.6 57.5 1.0
CB I:ASN22 4.7 44.5 1.0
OE1 I:GLU19 4.8 69.4 1.0
ND2 I:ASN22 4.8 58.9 1.0
C I:CYS20 4.8 61.6 1.0
C I:ASN41 4.8 69.6 1.0
N I:ASN22 4.8 49.8 1.0
C I:CYS42 4.9 67.6 1.0
N I:ASN21 5.0 60.8 1.0

Zinc binding site 5 out of 7 in 8qeq

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Zinc binding site 5 out of 7 in the Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:103.7
occ:1.00
 SG I:CYS119 2.3 51.2 1.0
SG I:CYS86 2.3 57.0 1.0
SG I:CYS114 2.3 50.2 1.0
SG I:CYS89 2.3 65.5 1.0
CB I:CYS114 2.9 32.2 1.0
CB I:CYS86 3.0 56.0 1.0
CB I:CYS119 3.3 48.9 1.0
CB I:CYS89 3.9 61.1 1.0
CB I:HIS91 4.2 56.9 1.0
N I:CYS89 4.2 64.1 1.0
CA I:CYS114 4.4 29.7 1.0
CA I:CYS86 4.4 52.1 1.0
CB I:HIS121 4.5 42.6 1.0
CA I:CYS89 4.6 65.7 1.0
CB I:LYS88 4.7 60.2 1.0
N I:HIS91 4.7 53.8 1.0
CA I:CYS119 4.7 52.9 1.0
C I:CYS86 4.9 59.0 1.0

Zinc binding site 6 out of 7 in 8qeq

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Zinc binding site 6 out of 7 in the Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:73.0
occ:1.00
 SG J:CYS10 2.3 36.9 1.0
SG J:CYS45 2.3 42.8 1.0
SG J:CYS44 2.3 41.2 1.0
SG J:CYS7 2.3 33.3 1.0
CB J:CYS7 3.3 18.6 1.0
N J:CYS45 3.4 32.6 1.0
CB J:CYS10 3.5 20.5 1.0
C J:CYS44 3.6 25.2 1.0
CB J:CYS45 3.6 27.8 1.0
CA J:CYS45 3.7 27.1 1.0
CB J:CYS44 3.8 23.5 1.0
O J:CYS44 3.8 24.7 1.0
N J:CYS10 4.0 24.0 1.0
CA J:CYS10 4.3 19.6 1.0
CA J:CYS44 4.3 19.1 1.0
NE J:ARG42 4.4 32.5 1.0
CB J:THR9 4.5 22.5 1.0
CB J:LYS12 4.6 13.5 1.0
CA J:CYS7 4.7 17.8 1.0
NH2 J:ARG42 4.9 30.6 1.0
C J:THR9 4.9 24.5 1.0
C J:CYS10 4.9 24.1 1.0
CB J:ARG42 4.9 24.6 1.0
N J:LYS12 5.0 21.4 1.0
N J:GLY11 5.0 18.7 1.0

Zinc binding site 7 out of 7 in 8qeq

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Zinc binding site 7 out of 7 in the Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase II Bound to Minimal Alu Rna Right Arm in the Alternative Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:83.4
occ:1.00
 SG L:CYS36 2.3 42.8 1.0
SG L:CYS39 2.3 58.0 1.0
SG L:CYS19 2.3 41.8 1.0
SG L:CYS22 2.3 31.5 1.0
CB L:CYS19 3.0 22.4 1.0
CB L:CYS36 3.3 36.1 1.0
CB L:CYS22 3.5 28.8 1.0
CB L:CYS39 3.7 51.2 1.0
N L:CYS22 3.8 30.9 1.0
O L:ARG37 4.1 49.9 1.0
CA L:CYS22 4.2 30.0 1.0
OG1 L:THR24 4.2 35.2 1.0
CB L:TYR41 4.3 27.5 1.0
CA L:CYS19 4.5 23.7 1.0
CB L:GLU21 4.6 40.7 1.0
N L:CYS39 4.6 42.7 1.0
CA L:CYS39 4.6 42.5 1.0
CA L:CYS36 4.7 38.7 1.0
C L:GLU21 4.7 32.4 1.0
N L:TYR41 4.8 38.7 1.0
N L:GLU21 4.8 26.9 1.0
C L:CYS22 4.8 30.1 1.0
CA L:GLU21 4.9 28.2 1.0
C L:CYS36 5.0 41.6 1.0

Reference:

K.Tluckova, A.T.Salmazo, C.Bernecky. Mechanism of Mammalian Transcriptional Repression By Noncoding Rna To Be Published.
Page generated: Sun Dec 15 12:13:00 2024

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