Zinc in PDB 8xmd: Pre-Translocated Pol IV Transcription Elongation Complex

Enzymatic activity of Pre-Translocated Pol IV Transcription Elongation Complex

All present enzymatic activity of Pre-Translocated Pol IV Transcription Elongation Complex:
2.7.7.48; 2.7.7.6;

Other elements in 8xmd:

The structure of Pre-Translocated Pol IV Transcription Elongation Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Pre-Translocated Pol IV Transcription Elongation Complex (pdb code 8xmd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Pre-Translocated Pol IV Transcription Elongation Complex, PDB code: 8xmd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 8xmd

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Zinc binding site 1 out of 9 in the Pre-Translocated Pol IV Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pre-Translocated Pol IV Transcription Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1501

b:325.6
occ:1.00
 NE2 A:HIS70 2.1 211.9 1.0
SG A:CYS67 2.3 245.4 1.0
SG A:CYS59 2.3 214.3 1.0
SG A:CYS56 2.3 229.4 1.0
CB A:CYS59 2.9 211.3 1.0
CD2 A:HIS70 3.0 210.3 1.0
CE1 A:HIS70 3.1 209.2 1.0
N A:CYS59 3.7 210.0 1.0
CB A:CYS56 3.7 226.3 1.0
CB A:CYS67 3.8 245.1 1.0
CA A:CYS59 3.9 209.2 1.0
O A:GLU68 4.0 230.9 1.0
ND1 A:HIS70 4.2 206.8 1.0
CG A:HIS70 4.2 207.7 1.0
CA A:CYS67 4.5 244.8 1.0
CB A:THR58 4.6 191.9 1.0
C A:THR58 4.6 191.5 1.0
N A:GLU68 4.7 229.6 1.0
C A:CYS59 4.8 208.8 1.0
C A:CYS67 4.9 244.4 1.0
CA A:THR58 5.0 191.6 1.0

Zinc binding site 2 out of 9 in 8xmd

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Zinc binding site 2 out of 9 in the Pre-Translocated Pol IV Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pre-Translocated Pol IV Transcription Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1503

b:240.8
occ:1.00
 ND1 A:HIS983 2.0 168.5 1.0
NE2 A:HIS985 2.0 168.2 1.0
SG A:CYS1031 2.3 216.1 1.0
SG A:CYS1044 2.3 179.3 1.0
CE1 A:HIS983 2.6 169.0 1.0
CE1 A:HIS985 2.9 165.5 1.0
CB A:CYS1031 3.1 212.0 1.0
CD2 A:HIS985 3.1 166.0 1.0
CB A:CYS1044 3.3 173.3 1.0
CG A:HIS983 3.3 165.7 1.0
NE2 A:HIS983 3.8 167.8 1.0
ND1 A:HIS985 4.0 162.4 1.0
CB A:HIS983 4.0 165.9 1.0
CG A:HIS985 4.1 164.5 1.0
CD2 A:HIS983 4.2 165.1 1.0
CE A:MET964 4.3 175.0 1.0
CB A:SER1033 4.5 214.3 1.0
CA A:CYS1031 4.6 212.2 1.0
CA A:CYS1044 4.6 172.6 1.0

Zinc binding site 3 out of 9 in 8xmd

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Zinc binding site 3 out of 9 in the Pre-Translocated Pol IV Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pre-Translocated Pol IV Transcription Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1504

b:417.7
occ:1.00
 SG A:CYS97 2.3 289.2 1.0
CB A:CYS97 3.3 287.7 1.0
CB A:CYS121 3.4 336.5 1.0
CB A:CYS100 3.5 246.7 1.0
SG A:CYS100 3.6 245.1 1.0
SG A:CYS121 3.8 335.4 1.0
SG A:CYS118 4.0 291.8 1.0
CB A:CYS118 4.4 291.2 1.0
CA A:CYS121 4.5 336.8 1.0
CA A:CYS97 4.7 287.0 1.0
CB A:TYR102 4.7 256.0 1.0
N A:CYS121 4.8 336.6 1.0
O A:TYR102 4.9 256.8 1.0
CA A:CYS100 4.9 245.5 1.0
N A:CYS97 5.0 287.2 1.0

Zinc binding site 4 out of 9 in 8xmd

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Zinc binding site 4 out of 9 in the Pre-Translocated Pol IV Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pre-Translocated Pol IV Transcription Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:331.4
occ:1.00
 SG B:CYS1108 2.3 183.2 1.0
SG B:CYS1133 2.3 242.1 1.0
SG B:CYS1111 2.3 179.0 1.0
CB B:CYS1136 3.2 223.0 1.0
CB B:CYS1108 3.3 179.1 1.0
CB B:CYS1133 3.4 237.5 1.0
CB B:CYS1111 3.9 169.5 1.0
SG B:CYS1136 4.1 223.3 1.0
N B:CYS1111 4.3 170.6 1.0
CA B:CYS1136 4.4 223.1 1.0
N B:CYS1136 4.5 223.5 1.0
CG1 B:VAL1135 4.5 224.7 1.0
CA B:CYS1111 4.6 167.7 1.0
CA B:CYS1108 4.7 177.8 1.0
OG1 B:THR1113 4.7 182.1 1.0
O B:CYS1111 4.7 169.5 1.0
CA B:CYS1133 4.8 235.7 1.0
O B:VAL1137 4.8 212.1 1.0

Zinc binding site 5 out of 9 in 8xmd

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Zinc binding site 5 out of 9 in the Pre-Translocated Pol IV Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Pre-Translocated Pol IV Transcription Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:292.6
occ:1.00
 SG C:CYS99 2.3 176.6 1.0
SG C:CYS102 2.3 196.6 1.0
SG C:CYS93 2.3 201.5 1.0
SG C:CYS90 2.3 180.4 1.0
CB C:CYS99 3.2 175.1 1.0
CB C:CYS102 3.3 184.5 1.0
CB C:CYS90 3.6 181.2 1.0
CB C:CYS93 3.9 196.6 1.0
N C:CYS102 4.1 183.6 1.0
CA C:CYS102 4.3 183.2 1.0
N C:CYS93 4.6 200.0 1.0
O C:CYS93 4.6 200.3 1.0
CA C:CYS99 4.7 174.1 1.0
CA C:CYS93 4.7 198.2 1.0
N C:SER103 4.7 165.1 1.0
C C:CYS93 4.9 199.5 1.0
CA C:CYS90 4.9 179.7 1.0
C C:CYS102 5.0 181.2 1.0

Zinc binding site 6 out of 9 in 8xmd

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Zinc binding site 6 out of 9 in the Pre-Translocated Pol IV Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Pre-Translocated Pol IV Transcription Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:222.3
occ:1.00
 SG I:CYS108 2.3 165.8 1.0
SG I:CYS79 2.3 168.8 1.0
SG I:CYS76 2.3 173.0 1.0
SG I:CYS103 2.3 178.1 1.0
CB I:CYS108 3.1 161.2 1.0
CB I:CYS76 3.2 170.9 1.0
CB I:CYS103 3.3 169.0 1.0
CB I:CYS79 3.7 168.1 1.0
N I:CYS79 4.0 168.2 1.0
CA I:CYS79 4.3 167.9 1.0
CB I:ASN105 4.3 172.4 1.0
O I:CYS79 4.3 169.4 1.0
CA I:CYS108 4.6 161.2 1.0
C I:CYS79 4.6 168.6 1.0
CA I:CYS76 4.6 169.2 1.0
CB I:HIS110 4.7 146.6 1.0
CA I:CYS103 4.7 165.2 1.0
CB I:HIS81 4.8 164.9 1.0
ND2 I:ASN105 5.0 173.6 1.0

Zinc binding site 7 out of 9 in 8xmd

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Zinc binding site 7 out of 9 in the Pre-Translocated Pol IV Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Pre-Translocated Pol IV Transcription Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:275.3
occ:1.00
 SG I:CYS10 2.3 195.8 1.0
SG I:CYS29 2.3 206.7 1.0
SG I:CYS32 2.3 209.5 1.0
SG I:CYS7 2.3 196.1 1.0
CB I:CYS10 3.7 191.4 1.0
CB I:CYS32 3.7 205.2 1.0
CB I:CYS7 3.9 194.4 1.0
N I:CYS10 3.9 193.7 1.0
CB I:CYS29 4.0 201.3 1.0
N I:CYS32 4.1 205.8 1.0
CA I:CYS10 4.3 192.4 1.0
CA I:CYS32 4.4 205.1 1.0
O I:CYS32 4.4 206.0 1.0
CB I:GLU9 4.5 194.3 1.0
CB I:HIS34 4.7 195.4 1.0
CB I:ASN12 4.7 171.0 1.0
C I:CYS32 4.8 205.1 1.0
CB I:ASN31 4.8 198.4 1.0
C I:CYS10 4.8 191.7 1.0
N I:ASN11 4.9 179.2 1.0
C I:GLU9 5.0 193.9 1.0
N I:ASN12 5.0 174.1 1.0

Zinc binding site 8 out of 9 in 8xmd

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Zinc binding site 8 out of 9 in the Pre-Translocated Pol IV Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Pre-Translocated Pol IV Transcription Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn200

b:219.2
occ:1.00
 SG J:CYS10 2.3 149.2 1.0
SG J:CYS44 2.3 144.6 1.0
SG J:CYS45 2.3 158.4 1.0
O J:THR9 3.0 133.7 1.0
SG J:CYS7 3.1 164.9 1.0
N J:CYS45 3.5 141.6 1.0
CB J:CYS10 3.7 142.9 1.0
CB J:LYS12 3.7 137.4 1.0
CB J:CYS45 3.7 147.1 1.0
CB J:CYS44 3.7 135.0 1.0
CA J:CYS45 3.9 145.2 1.0
C J:CYS44 4.1 135.5 1.0
NE J:ARG42 4.1 134.0 1.0
C J:THR9 4.2 132.0 1.0
CB J:CYS7 4.4 153.0 1.0
CA J:CYS44 4.5 135.0 1.0
NH2 J:ARG42 4.5 138.3 1.0
N J:LYS12 4.5 135.7 1.0
O J:CYS7 4.5 151.0 1.0
CA J:CYS10 4.6 139.4 1.0
CG J:LYS12 4.6 132.4 1.0
C J:CYS10 4.7 138.8 1.0
CA J:LYS12 4.8 134.7 1.0
N J:CYS10 4.8 137.5 1.0
CZ J:ARG42 4.8 138.5 1.0
O J:CYS44 4.9 139.4 1.0
N J:GLY11 4.9 121.5 1.0
CB J:ARG42 5.0 129.1 1.0

Zinc binding site 9 out of 9 in 8xmd

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Zinc binding site 9 out of 9 in the Pre-Translocated Pol IV Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Pre-Translocated Pol IV Transcription Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:338.6
occ:1.00
 SG L:CYS32 2.3 213.1 1.0
SG L:CYS12 2.3 200.9 1.0
SG L:CYS15 2.3 184.6 1.0
SG L:CYS29 2.3 200.3 1.0
CB L:CYS32 2.5 207.7 1.0
CB L:CYS15 2.8 183.0 1.0
CB L:CYS12 3.2 191.2 1.0
CB L:CYS29 3.3 197.4 1.0
CA L:CYS15 4.0 180.7 1.0
CA L:CYS32 4.0 205.3 1.0
O L:CYS15 4.1 177.2 1.0
C L:CYS15 4.3 177.9 1.0
N L:CYS15 4.4 182.9 1.0
CA L:CYS12 4.7 189.0 1.0
CA L:CYS29 4.7 196.4 1.0
N L:CYS32 4.8 205.2 1.0
C L:CYS32 4.9 204.1 1.0
N L:GLY13 4.9 183.0 1.0
O L:ARG30 4.9 169.9 1.0

Reference:

K.Huang, C.L.Fang, Y.Zhang. Transcription of the Plant Rna Polymerase IV Is Prone to Backtracking To Be Published.
Page generated: Thu Oct 31 13:55:17 2024

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