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Zinc in PDB 6xre: Structure of the P53/Rna Polymerase II Assembly

Enzymatic activity of Structure of the P53/Rna Polymerase II Assembly

All present enzymatic activity of Structure of the P53/Rna Polymerase II Assembly:
2.7.7.6;

Other elements in 6xre:

The structure of Structure of the P53/Rna Polymerase II Assembly also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the P53/Rna Polymerase II Assembly (pdb code 6xre). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of the P53/Rna Polymerase II Assembly, PDB code: 6xre:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6xre

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Zinc binding site 1 out of 8 in the Structure of the P53/Rna Polymerase II Assembly


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the P53/Rna Polymerase II Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:17.0
occ:1.00
O A:GLY83 2.0 18.2 1.0
O A:PRO82 2.0 15.2 1.0
O B:MET1125 2.1 8.3 1.0
C A:PRO82 2.6 15.2 1.0
C A:GLY83 2.8 18.2 1.0
HB2 A:PRO82 2.9 18.2 1.0
HE2 B:MET1125 3.0 10.0 1.0
HA3 A:GLY83 3.0 21.9 1.0
N A:GLY83 3.1 18.2 1.0
CA A:GLY83 3.1 18.2 1.0
HG3 B:MET1125 3.2 10.0 1.0
C B:MET1125 3.4 8.3 1.0
HA B:ALA1126 3.4 8.5 1.0
HG2 A:PRO82 3.5 18.2 1.0
HE3 B:MET1125 3.6 10.0 1.0
HB2 B:MET1125 3.6 10.0 1.0
CB A:PRO82 3.6 15.2 1.0
CA A:PRO82 3.7 15.2 1.0
CE B:MET1125 3.7 8.3 1.0
H B:ILE1127 3.8 6.9 1.0
H A:GLY83 3.9 21.9 1.0
CG B:MET1125 4.0 8.3 1.0
HG11 B:VAL1116 4.0 5.7 1.0
N A:HIS84 4.1 21.6 1.0
CG A:PRO82 4.1 15.2 1.0
CB B:MET1125 4.1 8.3 1.0
HG13 B:VAL1116 4.1 5.7 1.0
HA2 A:GLY83 4.2 21.9 1.0
N B:ALA1126 4.2 7.1 1.0
CA B:ALA1126 4.2 7.1 1.0
HA A:HIS84 4.2 25.9 1.0
HA A:PRO82 4.3 18.2 1.0
CA B:MET1125 4.4 8.3 1.0
O B:ILE1127 4.5 5.7 1.0
N B:ILE1127 4.5 5.7 1.0
HB3 A:PRO82 4.6 18.2 1.0
CG1 B:VAL1116 4.6 4.8 1.0
HE1 B:MET1125 4.6 10.0 1.0
SD B:MET1125 4.7 8.3 1.0
C B:ALA1126 4.8 7.1 1.0
N A:PRO82 4.8 15.2 1.0
CA A:HIS84 4.8 21.6 1.0
HA B:MET1125 4.8 10.0 1.0
HG3 A:PRO82 4.8 18.2 1.0
H A:HIS84 4.8 25.9 1.0
HG2 B:MET1125 4.9 10.0 1.0
HG12 B:VAL1116 4.9 5.7 1.0

Zinc binding site 2 out of 8 in 6xre

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Zinc binding site 2 out of 8 in the Structure of the P53/Rna Polymerase II Assembly


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the P53/Rna Polymerase II Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:21.2
occ:1.00
OE1 A:GLU211 2.0 25.1 1.0
O A:PHE112 2.1 30.6 1.0
OH A:TYR187 2.5 32.3 1.0
HB2 A:PHE113 2.9 50.3 1.0
HH A:TYR187 3.0 38.7 1.0
HD1 A:PHE113 3.1 50.3 1.0
CD A:GLU211 3.2 25.1 1.0
C A:PHE112 3.3 30.6 1.0
HE2 A:TYR187 3.4 38.7 1.0
HB2 A:PHE112 3.6 36.7 1.0
HE2 A:LYS212 3.6 22.4 1.0
CZ A:TYR187 3.7 32.3 1.0
HG3 A:LYS212 3.7 22.4 1.0
HG2 A:LYS212 3.7 22.4 1.0
OE2 A:GLU211 3.7 25.1 1.0
SG A:CYS114 3.8 31.4 1.0
HE3 A:LYS212 3.8 22.4 1.0
CB A:PHE113 3.9 41.9 1.0
CE2 A:TYR187 4.0 32.3 1.0
H A:PHE112 4.0 36.7 1.0
CD1 A:PHE113 4.1 41.9 1.0
CA A:PHE112 4.1 30.6 1.0
HB3 A:CYS111 4.1 29.0 1.0
N A:PHE112 4.2 30.6 1.0
CG A:LYS212 4.2 18.7 1.0
CE A:LYS212 4.2 18.7 1.0
HG2 A:GLU211 4.2 30.1 1.0
N A:PHE113 4.2 41.9 1.0
H A:CYS114 4.3 37.7 1.0
CB A:PHE112 4.3 30.6 1.0
CG A:GLU211 4.3 25.1 1.0
HG A:CYS114 4.4 37.7 1.0
HB3 A:PHE112 4.5 36.7 1.0
CA A:PHE113 4.5 41.9 1.0
CG A:PHE113 4.5 41.9 1.0
N A:CYS114 4.5 31.4 1.0
HB3 A:GLU211 4.6 30.1 1.0
HB3 A:PHE113 4.6 50.3 1.0
C A:PHE113 4.6 41.9 1.0
HB2 A:CYS111 4.9 29.0 1.0
CD A:LYS212 4.9 18.7 1.0
CE1 A:TYR187 4.9 32.3 1.0

Zinc binding site 3 out of 8 in 6xre

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Zinc binding site 3 out of 8 in the Structure of the P53/Rna Polymerase II Assembly


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the P53/Rna Polymerase II Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2004

b:16.6
occ:1.00
OE2 A:GLU30 2.0 19.6 1.0
OE1 A:GLU30 2.2 19.6 1.0
CD A:GLU30 2.3 19.6 1.0
SG B:CYS1122 3.4 6.0 1.0
CG A:GLU30 3.7 19.6 1.0
HG2 A:GLU30 3.9 23.5 1.0
HA B:CYS1122 4.0 7.2 1.0
HB3 B:CYS1122 4.2 7.2 1.0
HB3 A:GLU30 4.3 23.5 1.0
CB B:CYS1122 4.3 6.0 1.0
HG B:CYS1122 4.4 7.2 1.0
HG3 A:GLU30 4.4 23.5 1.0
CB A:GLU30 4.5 19.6 1.0
O B:LEU1121 4.6 4.3 1.0
CA B:CYS1122 4.7 6.0 1.0
HB2 A:GLU30 4.7 23.5 1.0

Zinc binding site 4 out of 8 in 6xre

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Zinc binding site 4 out of 8 in the Structure of the P53/Rna Polymerase II Assembly


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the P53/Rna Polymerase II Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:11.4
occ:1.00
OE2 B:GLU959 1.9 14.4 1.0
O C:ALA180 2.0 7.1 1.0
CD B:GLU959 2.4 14.4 1.0
O B:GLU959 2.4 14.4 1.0
OE1 B:GLU959 2.6 14.4 1.0
HG J:CYS10 2.8 10.4 1.0
HA3 B:GLY960 3.1 16.5 1.0
HA J:CYS10 3.2 10.4 1.0
C C:ALA180 3.2 7.1 1.0
O J:CYS10 3.2 8.7 1.0
C B:GLU959 3.2 14.4 1.0
HB1 C:ALA180 3.6 8.5 1.0
CA B:GLY960 3.6 13.8 1.0
HA C:ALA180 3.7 8.5 1.0
N B:GLY960 3.7 13.8 1.0
CG B:GLU959 3.7 14.4 1.0
SG J:CYS10 3.7 8.7 1.0
C B:GLY960 3.7 13.8 1.0
HA3 C:GLY181 3.8 4.4 1.0
HG23 B:ILE961 3.9 14.8 1.0
C J:CYS10 3.9 8.7 1.0
CA C:ALA180 3.9 7.1 1.0
N B:ILE961 3.9 12.3 1.0
CA J:CYS10 3.9 8.7 1.0
HG2 B:GLU959 4.0 17.2 1.0
H B:ILE961 4.0 14.8 1.0
HB3 B:GLU959 4.1 17.2 1.0
N C:GLY181 4.2 3.7 1.0
HG22 B:ILE961 4.2 14.8 1.0
CB B:GLU959 4.2 14.4 1.0
O B:GLY960 4.3 13.8 1.0
CA B:GLU959 4.3 14.4 1.0
CB C:ALA180 4.3 7.1 1.0
HA B:ILE961 4.4 14.8 1.0
CB J:CYS10 4.4 8.7 1.0
CA C:GLY181 4.5 3.7 1.0
HG3 B:GLU959 4.5 17.2 1.0
H B:GLY960 4.6 16.5 1.0
CG2 B:ILE961 4.6 12.3 1.0
HA B:GLU959 4.6 17.2 1.0
HA2 B:GLY960 4.7 16.5 1.0
CA B:ILE961 4.7 12.3 1.0
HA2 C:GLY181 4.8 4.4 1.0
HB2 J:CYS10 4.9 10.4 1.0
O J:THR9 4.9 11.7 1.0
HB3 C:ALA180 4.9 8.5 1.0
HG J:CYS44 4.9 19.4 1.0

Zinc binding site 5 out of 8 in 6xre

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Zinc binding site 5 out of 8 in the Structure of the P53/Rna Polymerase II Assembly


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the P53/Rna Polymerase II Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:9.9
occ:1.00
OG1 C:THR89 2.4 14.9 1.0
HG21 C:THR89 2.9 17.9 1.0
HG23 C:THR89 3.0 17.9 1.0
HG1 C:THR89 3.0 17.9 1.0
CG2 C:THR89 3.3 14.9 1.0
CB C:THR89 3.4 14.9 1.0
H C:THR89 3.5 17.9 1.0
HB C:THR89 4.0 17.9 1.0
N C:THR89 4.3 14.9 1.0
HG22 C:THR89 4.3 17.9 1.0
CA C:THR89 4.4 14.9 1.0

Zinc binding site 6 out of 8 in 6xre

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Zinc binding site 6 out of 8 in the Structure of the P53/Rna Polymerase II Assembly


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the P53/Rna Polymerase II Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:15.1
occ:1.00
O I:ARG40 2.0 11.9 1.0
HA I:ASN41 2.3 20.0 1.0
OD1 I:ASN41 2.3 16.7 1.0
C I:ARG40 3.0 11.9 1.0
CA I:ASN41 3.2 16.7 1.0
CG I:ASN41 3.4 16.7 1.0
N I:ASN41 3.5 16.7 1.0
HB3 I:ARG40 3.6 14.3 1.0
CB I:ASN41 3.8 16.7 1.0
CA I:ARG40 4.2 11.9 1.0
HB3 I:ASN41 4.2 20.0 1.0
CB I:ARG40 4.3 11.9 1.0
C I:ASN41 4.4 16.7 1.0
HA I:ARG40 4.4 14.3 1.0
H I:ASN41 4.5 20.0 1.0
ND2 I:ASN41 4.5 16.7 1.0
O I:ASN41 4.6 16.7 1.0
HB2 I:ARG40 4.6 14.3 1.0
HD21 I:ASN41 4.7 20.0 1.0
HE22 B:GLN312 4.8 10.5 1.0
HB2 I:ASN41 4.8 20.0 1.0

Zinc binding site 7 out of 8 in 6xre

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Zinc binding site 7 out of 8 in the Structure of the P53/Rna Polymerase II Assembly


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the P53/Rna Polymerase II Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:13.9
occ:1.00
O I:LYS92 2.0 5.7 1.0
ND1 I:HIS91 2.3 7.2 1.0
O I:HIS91 2.4 7.2 1.0
C I:HIS91 2.8 7.2 1.0
HB3 I:HIS91 2.8 8.7 1.0
SG I:CYS114 3.0 9.2 1.0
C I:LYS92 3.0 5.7 1.0
CG I:HIS91 3.2 7.2 1.0
N I:LYS92 3.3 5.7 1.0
CB I:HIS91 3.3 7.2 1.0
HH2 I:TRP123 3.4 5.8 1.0
CE1 I:HIS91 3.4 7.2 1.0
HG I:CYS114 3.5 11.0 1.0
CA I:LYS92 3.6 5.7 1.0
CA I:HIS91 3.6 7.2 1.0
HE1 I:HIS91 3.7 8.7 1.0
HA I:LYS92 3.7 6.8 1.0
HB2 I:GLU93 3.8 5.2 1.0
H I:LYS92 4.0 6.8 1.0
SG I:CYS89 4.0 7.7 1.0
HB2 I:CYS114 4.0 11.0 1.0
HA I:CYS114 4.1 11.0 1.0
CB I:CYS114 4.1 9.2 1.0
N I:GLU93 4.1 4.3 1.0
HB2 I:ALA116 4.2 13.7 1.0
H I:THR115 4.2 9.7 1.0
O I:GLU93 4.3 4.3 1.0
C I:GLU93 4.3 4.3 1.0
H I:ALA116 4.3 13.7 1.0
HB2 I:HIS91 4.3 8.7 1.0
HA I:HIS91 4.4 8.7 1.0
CD2 I:HIS91 4.4 7.2 1.0
H I:HIS91 4.4 8.7 1.0
CH2 I:TRP123 4.5 4.8 1.0
NE2 I:HIS91 4.5 7.2 1.0
N I:HIS91 4.5 7.2 1.0
HA I:ALA94 4.6 4.4 1.0
CA I:GLU93 4.6 4.3 1.0
CA I:CYS114 4.6 9.2 1.0
N I:ALA94 4.7 3.7 1.0
HB2 I:ALA94 4.7 4.4 1.0
CB I:GLU93 4.7 4.3 1.0
HB3 I:ALA116 4.7 13.7 1.0
HG22 I:THR115 4.8 9.7 1.0
HG I:CYS89 4.8 9.3 1.0
HZ2 I:TRP123 4.8 5.8 1.0
H I:GLU93 5.0 5.2 1.0
CB I:ALA116 5.0 11.4 1.0

Zinc binding site 8 out of 8 in 6xre

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Zinc binding site 8 out of 8 in the Structure of the P53/Rna Polymerase II Assembly


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of the P53/Rna Polymerase II Assembly within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:25.4
occ:1.00
O L:CYS39 2.0 22.5 1.0
O L:CYS36 2.4 27.8 1.0
HB2 L:CYS36 2.5 33.3 1.0
C L:CYS39 3.2 22.5 1.0
C L:CYS36 3.4 27.8 1.0
H L:CYS36 3.4 33.3 1.0
CB L:CYS36 3.4 27.8 1.0
H L:CYS39 3.5 27.0 1.0
HA2 L:GLY40 3.6 26.5 1.0
CA L:CYS36 3.7 27.8 1.0
N L:CYS36 3.8 27.8 1.0
HG2 L:ARG42 3.8 43.2 1.0
HB3 L:CYS39 3.8 27.0 1.0
HB3 L:CYS36 3.9 33.3 1.0
O L:TYR41 4.1 33.0 1.0
N L:GLY40 4.1 22.1 1.0
N L:CYS39 4.1 22.5 1.0
CA L:CYS39 4.1 22.5 1.0
CA L:GLY40 4.1 22.1 1.0
HG3 L:ARG42 4.1 43.2 1.0
C L:GLY40 4.2 22.1 1.0
O L:GLY40 4.4 22.1 1.0
CB L:CYS39 4.5 22.5 1.0
CG L:ARG42 4.5 36.0 1.0
CZ L:ARG42 4.5 36.0 1.0
N L:ARG37 4.6 25.8 1.0
NH2 L:ARG42 4.7 36.0 1.0
N L:TYR41 4.7 33.0 1.0
NH1 L:ARG42 4.7 36.0 1.0
C L:TYR41 4.7 33.0 1.0
SG L:CYS36 4.8 27.8 1.0
HA L:CYS36 4.8 33.3 1.0
HA L:ARG35 4.8 37.7 1.0
NE L:ARG42 4.8 36.0 1.0
C L:ARG35 4.8 31.4 1.0
HA L:ARG37 4.8 31.0 1.0
HB2 L:CYS19 4.8 22.4 1.0
HB3 L:ARG35 4.9 37.7 1.0
HH22 L:ARG42 4.9 43.2 1.0
HH21 L:ARG42 4.9 43.2 1.0
HH12 L:ARG42 4.9 43.2 1.0
HA L:ARG42 5.0 43.2 1.0
H L:TYR41 5.0 39.6 1.0

Reference:

S.-H.Liou, S.Singh, R.H.Singer, R.A.Coleman, W.Liu. Structure of the P53/Rna Polymerase II Assembly To Be Published 2021.
DOI: 10.1038/S42003-021-01934-4
Page generated: Tue Oct 29 11:05:03 2024

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