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Zinc in PDB 5xog: Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1

Enzymatic activity of Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1

All present enzymatic activity of Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1, PDB code: 5xog was solved by H.Ehara, M.Shirouzu, S.Sekine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.55 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 155.250, 159.910, 268.930, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.5

Other elements in 5xog:

The structure of Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1 (pdb code 5xog). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1, PDB code: 5xog:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 5xog

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Zinc binding site 1 out of 9 in the Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1


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 Elongation Complex Bound with SPT5 KOW5 and ELF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:88.2
occ:1.00
 NE2 A:HIS80 2.0 58.5 1.0
SG A:CYS70 2.1 82.2 1.0
SG A:CYS67 2.3 84.7 1.0
SG A:CYS77 2.4 73.8 1.0
CD2 A:HIS80 2.9 64.3 1.0
CE1 A:HIS80 3.0 72.4 1.0
CB A:CYS67 3.1 89.0 1.0
CB A:CYS70 3.2 77.8 1.0
CB A:CYS77 3.5 74.7 1.0
N A:CYS70 3.8 83.7 1.0
CG A:HIS80 4.1 65.1 1.0
ND1 A:HIS80 4.1 64.2 1.0
CA A:CYS70 4.1 76.1 1.0
CA A:CYS77 4.1 71.7 1.0
CD A:PRO78 4.4 56.4 1.0
CA A:GLY59 4.4 68.6 1.0
CA A:CYS67 4.6 95.6 1.0
CB A:THR69 4.6 73.7 1.0
N A:GLY79 4.7 66.5 1.0
C A:CYS77 4.8 65.2 1.0
C A:THR69 4.8 81.3 1.0
N A:PRO78 4.8 55.0 1.0
C A:CYS70 4.9 76.5 1.0

Zinc binding site 2 out of 9 in 5xog

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Zinc binding site 2 out of 9 in the Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1


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 Elongation Complex Bound with SPT5 KOW5 and ELF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:99.9
occ:1.00
 SG A:CYS107 2.3 0.8 1.0
SG A:CYS110 2.4 96.8 1.0
SG A:CYS148 2.5 99.6 1.0
SG A:CYS168 2.8 0.3 1.0
CB A:CYS107 3.0 0.9 1.0
CB A:CYS148 3.2 98.3 1.0
CB A:CYS168 3.8 0.5 1.0
N A:CYS168 3.8 0.4 1.0
CB A:CYS110 3.9 0.4 1.0
N A:CYS110 4.1 0.1 1.0
CA A:CYS168 4.4 0.5 1.0
CA A:CYS107 4.5 0.7 1.0
CA A:CYS110 4.6 1.0 1.0
CA A:CYS148 4.7 1.0 1.0
CB A:ASN109 4.7 0.8 1.0
C A:GLY167 4.8 1.0 1.0
CA A:GLY167 4.8 0.7 1.0
NE2 A:GLN172 4.9 0.4 1.0
C A:CYS168 5.0 0.7 1.0
N A:GLY111 5.0 0.4 1.0

Zinc binding site 3 out of 9 in 5xog

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Zinc binding site 3 out of 9 in the Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1


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 Elongation Complex Bound with SPT5 KOW5 and ELF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:91.6
occ:1.00
 SG B:CYS1182 2.1 68.1 1.0
SG B:CYS1166 2.1 80.8 1.0
SG B:CYS1163 2.3 71.7 1.0
SG B:CYS1185 2.3 97.0 1.0
CB B:CYS1166 3.0 77.0 1.0
CB B:CYS1163 3.1 78.8 1.0
CB B:CYS1185 3.2 98.4 1.0
CB B:CYS1182 3.5 76.6 1.0
N B:CYS1166 3.7 77.0 1.0
CA B:CYS1166 3.9 82.2 1.0
N B:CYS1185 4.1 93.8 1.0
CA B:CYS1185 4.3 91.4 1.0
OG B:SER1170 4.3 75.9 1.0
CB B:ILE1165 4.6 83.5 1.0
CA B:CYS1163 4.6 68.0 1.0
C B:CYS1166 4.7 79.9 1.0
C B:ILE1165 4.8 78.9 1.0
CA B:CYS1182 4.8 75.5 1.0
N B:GLY1167 4.9 72.5 1.0
CB B:SER1184 4.9 88.3 1.0

Zinc binding site 4 out of 9 in 5xog

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Zinc binding site 4 out of 9 in the Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1


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 Elongation Complex Bound with SPT5 KOW5 and ELF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:93.2
occ:1.00
 SG C:CYS91 2.3 0.1 1.0
SG C:CYS85 2.4 86.7 1.0
SG C:CYS94 2.6 95.3 1.0
SG C:CYS87 2.6 96.1 1.0
CB C:CYS94 3.2 79.1 1.0
CB C:CYS85 3.3 84.0 1.0
CB C:CYS91 3.3 1.0 1.0
N C:CYS94 3.8 1.0 1.0
CB C:CYS87 3.8 0.2 1.0
N C:CYS91 3.8 0.3 1.0
CA C:CYS91 4.1 0.4 1.0
CA C:CYS94 4.1 79.3 1.0
C C:CYS91 4.4 0.2 1.0
C C:GLU93 4.5 0.5 1.0
C C:TYR90 4.5 0.0 1.0
N C:GLU93 4.5 0.6 1.0
CB C:GLU93 4.6 1.0 1.0
O C:CYS91 4.7 0.4 1.0
CA C:CYS85 4.7 86.6 1.0
N C:CYS87 4.7 83.5 1.0
CA C:GLU93 4.8 0.0 1.0
CA C:CYS87 4.9 99.0 1.0
N C:ASP92 5.0 0.1 1.0
CA C:TYR90 5.0 0.8 1.0

Zinc binding site 5 out of 9 in 5xog

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Zinc binding site 5 out of 9 in the Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1


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 Elongation Complex Bound with SPT5 KOW5 and ELF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.7
occ:1.00
 SG I:CYS106 2.4 0.4 1.0
SG I:CYS75 2.4 0.9 1.0
SG I:CYS103 2.5 0.7 1.0
SG I:CYS78 2.5 0.5 1.0
CB I:CYS75 3.0 0.2 1.0
CB I:CYS103 3.2 0.1 1.0
CB I:CYS106 3.4 0.8 1.0
N I:CYS106 3.6 0.9 1.0
CB I:CYS78 3.7 0.8 1.0
N I:CYS78 3.8 0.5 1.0
CA I:CYS106 4.1 0.6 1.0
CA I:CYS78 4.3 0.7 1.0
CB I:ASN105 4.3 0.0 1.0
CA I:CYS75 4.5 0.7 1.0
CB I:GLU77 4.5 0.2 1.0
CB I:SER80 4.6 0.1 1.0
CA I:CYS103 4.7 0.0 1.0
OG I:SER80 4.7 0.7 1.0
C I:ASN105 4.7 0.7 1.0
N I:HIS79 4.7 0.6 1.0
N I:SER80 4.8 0.1 1.0
C I:CYS78 4.8 0.8 1.0
C I:CYS106 4.8 0.8 1.0
CA I:ASN105 4.9 0.9 1.0
N I:LYS107 4.9 0.6 1.0
N I:ASN105 4.9 0.1 1.0
C I:GLU77 4.9 0.8 1.0
OD1 I:ASN105 4.9 0.5 1.0
CB I:LYS108 5.0 0.3 1.0

Zinc binding site 6 out of 9 in 5xog

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Zinc binding site 6 out of 9 in the Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1


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 Elongation Complex Bound with SPT5 KOW5 and ELF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.1
occ:1.00
 CB I:CYS10 2.3 0.3 1.0
SG I:CYS7 2.6 0.3 1.0
SG I:CYS32 2.7 0.1 1.0
SG I:CYS29 2.9 0.3 1.0
CB I:CYS7 3.4 0.1 1.0
SG I:CYS10 3.4 0.1 1.0
CA I:CYS10 3.5 0.9 1.0
N I:CYS10 3.6 0.3 1.0
CB I:CYS32 3.7 0.6 1.0
CB I:CYS29 3.8 0.1 1.0
N I:CYS32 4.2 1.0 1.0
C I:CYS10 4.4 0.9 1.0
CA I:CYS32 4.5 0.7 1.0
C I:GLU9 4.6 0.0 1.0
CB I:TYR34 4.7 0.3 1.0
N I:ASN11 4.7 0.4 1.0
C I:ASN31 4.8 0.5 1.0
CA I:CYS7 4.8 0.5 1.0
CB I:ASN31 4.9 0.8 1.0
N I:ASN12 5.0 0.8 1.0
C I:CYS32 5.0 0.9 1.0

Zinc binding site 7 out of 9 in 5xog

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Zinc binding site 7 out of 9 in the Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1


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 Elongation Complex Bound with SPT5 KOW5 and ELF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:63.8
occ:1.00
 SG J:CYS44 2.2 76.5 1.0
SG J:CYS45 2.3 76.0 1.0
SG J:CYS7 2.3 80.2 1.0
SG J:CYS10 2.4 74.4 1.0
N J:CYS45 3.1 66.3 1.0
CB J:CYS7 3.3 60.7 1.0
CB J:CYS44 3.4 61.1 1.0
CB J:CYS10 3.5 60.0 1.0
CB J:CYS45 3.5 61.1 1.0
CA J:CYS45 3.5 58.0 1.0
C J:CYS44 3.6 63.6 1.0
N J:CYS10 3.9 51.6 1.0
CA J:CYS44 4.0 64.1 1.0
NE J:ARG42 4.3 56.0 1.0
CA J:CYS10 4.3 58.8 1.0
O J:CYS44 4.4 58.5 1.0
CB J:ARG42 4.5 57.7 1.0
N J:CYS44 4.7 55.2 1.0
CB J:SER9 4.8 58.5 1.0
CA J:CYS7 4.8 50.7 1.0
C J:SER9 4.9 60.3 1.0
CD J:ARG42 4.9 64.1 1.0
CB J:LYS12 4.9 56.9 1.0
N J:GLY11 5.0 58.1 1.0
C J:CYS10 5.0 58.1 1.0

Zinc binding site 8 out of 9 in 5xog

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Zinc binding site 8 out of 9 in the Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:90.1
occ:1.00
 SG L:CYS53 2.2 95.8 1.0
SG L:CYS50 2.3 80.3 1.0
SG L:CYS36 2.4 98.0 1.0
SG L:CYS33 2.6 82.8 1.0
CB L:CYS50 3.1 83.3 1.0
CB L:CYS33 3.2 69.4 1.0
CB L:CYS36 3.3 83.0 1.0
CB L:CYS53 3.4 1.0 1.0
N L:CYS53 3.4 89.4 1.0
CA L:CYS53 3.9 96.1 1.0
N L:CYS36 4.1 80.6 1.0
CB L:GLU52 4.2 0.6 1.0
CA L:CYS36 4.3 82.8 1.0
CB L:HIS55 4.4 80.1 1.0
C L:GLU52 4.5 94.6 1.0
CA L:CYS50 4.5 90.0 1.0
C L:CYS53 4.6 93.2 1.0
N L:GLY54 4.6 85.2 1.0
N L:HIS55 4.6 87.0 1.0
CA L:GLU52 4.7 98.6 1.0
N L:GLU52 4.7 0.1 1.0
CA L:CYS33 4.7 71.3 1.0
CB L:HIS38 4.7 93.2 1.0
C L:CYS36 4.8 80.6 1.0
C L:CYS50 4.9 0.7 1.0

Zinc binding site 9 out of 9 in 5xog

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Zinc binding site 9 out of 9 in the Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:0.7
occ:1.00
 SG M:CYS52 2.2 0.4 1.0
SG M:CYS25 2.3 0.3 1.0
SG M:CYS49 2.3 0.6 1.0
SG M:CYS28 2.9 0.8 1.0
CB M:CYS49 2.9 0.7 1.0
CB M:CYS25 3.3 0.5 1.0
CB M:CYS28 3.7 1.0 1.0
CB M:CYS52 3.7 0.1 1.0
OE1 M:GLN54 4.0 0.6 1.0
N M:CYS28 4.1 0.5 1.0
N M:CYS52 4.1 1.0 1.0
CA M:CYS52 4.4 0.6 1.0
CA M:CYS49 4.4 0.4 1.0
CA M:CYS28 4.5 0.3 1.0
N M:GLY53 4.6 0.1 1.0
CB M:GLN54 4.7 0.3 1.0
CA M:CYS25 4.7 0.7 1.0
CD M:GLN54 4.7 0.9 1.0
N M:GLN54 4.7 0.6 1.0
C M:CYS52 4.7 0.3 1.0
CB M:PHE27 4.9 0.7 1.0

Reference:

H.Ehara, T.Yokoyama, H.Shigematsu, S.Yokoyama, M.Shirouzu, S.I.Sekine. Structure of the Complete Elongation Complex of Rna Polymerase II with Basal Factors Science V. 357 921 2017.
ISSN: ESSN 1095-9203
PubMed: 28775211
DOI: 10.1126/SCIENCE.AAN8552
Page generated: Mon Oct 28 15:11:24 2024

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