Zinc in PDB 8cef: Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna

The structure of Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna, PDB code: 8cef was solved by A.K.M.Patel, T.B.Shaik, A.G.Mcewen, D.Moras, B.P.Klaholz, I.M.L.Billas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	94.72 / 2.49
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	167.846, 70.747, 94.719, 90, 90, 90
R / Rfree (%)	21.5 / 23.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna (pdb code 8cef). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna, PDB code: 8cef:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:33.0 occ:1.00 SG C:CYS82 2.2 26.1 1.0 SG C:CYS99 2.2 29.4 1.0 SG C:CYS79 2.4 33.9 1.0 SG C:CYS96 2.4 33.0 1.0 CB C:CYS99 3.2 28.4 1.0 CB C:CYS79 3.3 35.4 1.0 CB C:CYS82 3.5 27.0 1.0 CB C:CYS96 3.7 32.3 1.0 N C:CYS82 3.8 27.2 1.0 N C:CYS99 4.1 28.8 1.0 N C:CYS96 4.2 32.9 1.0 NH1 C:ARG128 4.2 26.8 1.0 CA C:CYS82 4.2 27.7 1.0 CA C:CYS99 4.3 28.2 1.0 CB C:VAL81 4.4 28.9 1.0 CA C:CYS96 4.5 32.2 1.0 CB C:ASP84 4.5 38.0 1.0 C C:VAL81 4.6 27.4 1.0 CA C:CYS79 4.8 36.6 1.0 N C:ASP84 4.8 34.4 1.0 C C:CYS82 4.9 29.4 1.0 CA C:VAL81 4.9 28.3 1.0 OG C:SER95 4.9 39.1 1.0 N C:GLY83 4.9 30.5 1.0 N C:VAL81 5.0 29.6 1.0 O C:CYS96 5.0 32.3 1.0 C C:CYS96 5.0 32.4 1.0

Zinc binding site 2 out of 12 in the Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:32.0 occ:1.00 SG C:CYS121 2.2 40.3 1.0 SG C:CYS115 2.2 34.1 1.0 SG C:CYS134 2.2 31.3 1.0 SG C:CYS131 2.4 33.9 1.0 CB C:CYS121 3.3 35.2 1.0 CB C:CYS131 3.3 32.4 1.0 CB C:CYS134 3.4 26.6 1.0 CB C:CYS115 3.4 34.9 1.0 N C:CYS121 4.1 34.3 1.0 N C:CYS134 4.2 25.6 1.0 CA C:CYS115 4.2 35.6 1.0 CA C:CYS121 4.3 34.1 1.0 CA C:CYS134 4.4 25.4 1.0 CD C:PRO116 4.4 34.3 1.0 CA C:ASN119 4.5 35.7 1.0 N C:GLU120 4.6 34.1 1.0 O C:HOH304 4.7 25.9 1.0 N C:ASN119 4.7 35.8 1.0 CA C:CYS131 4.8 32.2 1.0 C C:ASN119 4.9 35.1 1.0 C C:CYS115 4.9 35.6 1.0 N C:PRO116 4.9 35.2 1.0

Zinc binding site 3 out of 12 in the Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:51.7 occ:1.00 SG D:CYS82 2.2 53.1 1.0 SG D:CYS99 2.3 54.1 1.0 SG D:CYS79 2.4 67.0 1.0 SG D:CYS96 2.5 55.9 1.0 CB D:CYS82 3.3 53.5 1.0 CB D:CYS99 3.4 51.3 1.0 CB D:CYS79 3.4 67.0 1.0 N D:CYS82 3.6 54.1 1.0 CB D:CYS96 3.7 53.7 1.0 CA D:CYS82 3.9 53.9 1.0 N D:CYS99 4.1 50.4 1.0 N D:CYS96 4.2 54.4 1.0 CA D:CYS99 4.4 50.7 1.0 CB D:ASP84 4.4 63.2 1.0 CB D:VAL81 4.5 56.7 1.0 CA D:CYS96 4.5 53.5 1.0 C D:VAL81 4.6 54.8 1.0 C D:CYS82 4.6 54.8 1.0 N D:ASP84 4.8 59.9 1.0 N D:GLY83 4.8 55.6 1.0 CA D:CYS79 4.8 67.2 1.0 CA D:VAL81 4.9 56.2 1.0

Zinc binding site 4 out of 12 in the Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:34.5 occ:1.00 SG D:CYS121 2.2 43.2 1.0 SG D:CYS115 2.2 43.6 1.0 SG D:CYS134 2.3 42.8 1.0 SG D:CYS131 2.3 43.1 1.0 CB D:CYS121 3.2 41.8 1.0 CB D:CYS131 3.2 39.1 1.0 CB D:CYS134 3.4 39.9 1.0 CB D:CYS115 3.5 43.1 1.0 N D:CYS121 4.1 42.7 1.0 N D:CYS134 4.2 39.4 1.0 CA D:CYS115 4.2 43.4 1.0 CA D:CYS121 4.3 42.2 1.0 CA D:CYS134 4.3 39.5 1.0 CD D:PRO116 4.5 43.4 1.0 CA D:ASN119 4.6 44.7 1.0 N D:GLU120 4.7 44.2 1.0 CA D:CYS131 4.7 38.7 1.0 N D:ASN119 4.8 44.5 1.0 C D:ASN119 4.9 44.6 1.0 C D:CYS115 4.9 44.0 1.0 N D:PRO116 5.0 44.1 1.0

Zinc binding site 5 out of 12 in the Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn201 b:51.6 occ:1.00 SG G:CYS99 2.2 56.1 1.0 SG G:CYS82 2.3 58.9 1.0 SG G:CYS79 2.3 74.3 1.0 SG G:CYS96 2.4 67.8 1.0 CB G:CYS99 3.2 59.6 1.0 CB G:CYS82 3.3 60.1 1.0 CB G:CYS79 3.4 72.7 1.0 N G:CYS82 3.6 61.7 1.0 CB G:CYS96 3.7 66.8 1.0 N G:CYS99 4.0 61.2 1.0 CA G:CYS82 4.0 60.9 1.0 N G:CYS96 4.2 67.8 1.0 CA G:CYS99 4.2 60.9 1.0 CB G:VAL81 4.5 63.8 1.0 CA G:CYS96 4.5 67.0 1.0 C G:VAL81 4.6 63.0 1.0 CB G:ASP84 4.6 67.4 1.0 N G:GLY83 4.8 61.6 1.0 C G:CYS82 4.8 61.4 1.0 CA G:CYS79 4.8 72.8 1.0 N G:ASP84 4.9 64.9 1.0 CA G:VAL81 4.9 63.9 1.0 OG G:SER95 4.9 73.0 1.0 O G:CYS96 4.9 66.5 1.0 C G:CYS96 5.0 66.2 1.0 N G:VAL81 5.0 65.2 1.0

Zinc binding site 6 out of 12 in the Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn202 b:48.3 occ:1.00 SG G:CYS134 2.2 55.8 1.0 SG G:CYS115 2.2 58.2 1.0 SG G:CYS121 2.3 54.7 1.0 SG G:CYS131 2.3 59.3 1.0 CB G:CYS131 3.2 53.9 1.0 CB G:CYS121 3.3 54.0 1.0 CB G:CYS134 3.4 52.2 1.0 CB G:CYS115 3.4 59.3 1.0 N G:CYS134 4.1 52.4 1.0 N G:CYS121 4.2 55.8 1.0 CA G:CYS115 4.2 60.4 1.0 CA G:CYS134 4.3 52.1 1.0 CA G:CYS121 4.4 54.4 1.0 CD G:PRO116 4.4 59.2 1.0 CA G:ASN119 4.6 62.2 1.0 CA G:CYS131 4.7 53.0 1.0 N G:GLU120 4.7 59.9 1.0 N G:ASN119 4.7 62.4 1.0 C G:CYS115 4.9 60.3 1.0 C G:ASN119 4.9 61.3 1.0 N G:PRO116 4.9 59.9 1.0

Zinc binding site 7 out of 12 in the Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn201 b:43.4 occ:1.00 SG H:CYS79 2.2 64.3 1.0 SG H:CYS99 2.2 35.5 1.0 SG H:CYS82 2.4 44.5 1.0 SG H:CYS96 2.5 45.1 1.0 CB H:CYS99 3.2 34.4 1.0 CB H:CYS79 3.3 60.2 1.0 CB H:CYS82 3.5 45.2 1.0 N H:CYS82 3.6 46.0 1.0 CB H:CYS96 3.7 43.7 1.0 N H:CYS96 4.1 44.3 1.0 CA H:CYS82 4.1 45.4 1.0 N H:CYS99 4.1 36.5 1.0 CB H:VAL81 4.2 47.6 1.0 CA H:CYS99 4.3 35.3 1.0 NH1 H:ARG128 4.3 46.4 1.0 CA H:CYS96 4.4 43.6 1.0 C H:VAL81 4.5 47.3 1.0 CA H:VAL81 4.7 47.8 1.0 CA H:CYS79 4.7 59.4 1.0 CB H:ASP84 4.7 53.4 1.0 N H:VAL81 4.8 49.2 1.0 OG H:SER95 4.8 51.0 1.0 N H:GLY83 4.8 46.0 1.0 C H:CYS82 4.8 45.4 1.0 O H:CYS96 4.9 42.7 1.0 CG1 H:VAL81 4.9 47.7 1.0 N H:ASP84 4.9 50.6 1.0 C H:CYS96 4.9 43.0 1.0

Zinc binding site 8 out of 12 in the Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn202 b:36.1 occ:1.00 SG H:CYS134 2.2 28.1 1.0 SG H:CYS121 2.2 44.0 1.0 SG H:CYS115 2.3 29.7 1.0 SG H:CYS131 2.4 46.3 1.0 CB H:CYS121 3.2 40.6 1.0 CB H:CYS134 3.2 30.6 1.0 CB H:CYS131 3.3 40.1 1.0 CB H:CYS115 3.5 31.0 1.0 N H:CYS121 4.0 39.3 1.0 N H:CYS134 4.1 32.0 1.0 CA H:CYS134 4.2 31.1 1.0 CA H:CYS121 4.2 40.4 1.0 CA H:CYS115 4.3 32.0 1.0 CD H:PRO116 4.5 32.8 1.0 O H:HOH304 4.6 19.0 1.0 CA H:ASN119 4.6 35.7 1.0 N H:GLU120 4.6 36.1 1.0 N H:ASN119 4.7 36.8 1.0 CA H:CYS131 4.8 38.8 1.0 C H:ASN119 4.9 35.7 1.0 C H:CYS115 5.0 33.0 1.0 N H:PRO116 5.0 33.5 1.0

Zinc binding site 9 out of 12 in the Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn201 b:45.8 occ:1.00 SG J:CYS99 2.1 44.8 1.0 SG J:CYS82 2.1 43.9 1.0 SG J:CYS79 2.4 52.0 1.0 SG J:CYS96 2.4 42.3 1.0 CB J:CYS99 3.2 40.7 1.0 CB J:CYS79 3.4 49.9 1.0 CB J:CYS82 3.5 42.0 1.0 CB J:CYS96 3.7 39.4 1.0 N J:CYS82 3.7 41.9 1.0 N J:CYS99 4.0 38.8 1.0 N J:CYS96 4.2 39.0 1.0 CA J:CYS99 4.2 39.3 1.0 CA J:CYS82 4.2 41.4 1.0 NH1 J:ARG128 4.3 47.3 1.0 CB J:VAL81 4.4 42.3 1.0 CA J:CYS96 4.5 38.9 1.0 CB J:ASP84 4.6 45.5 1.0 C J:VAL81 4.6 42.7 1.0 CA J:CYS79 4.8 50.3 1.0 CA J:VAL81 4.9 43.0 1.0 N J:ASP84 4.9 42.9 1.0 C J:CYS82 4.9 41.3 1.0 O J:CYS96 4.9 39.1 1.0 N J:GLY83 4.9 41.5 1.0 N J:VAL81 5.0 44.6 1.0 C J:CYS96 5.0 39.1 1.0 NH2 J:ARG135 5.0 45.6 1.0

Zinc binding site 10 out of 12 in the Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn202 b:65.3 occ:1.00 SG J:CYS131 2.2 63.7 1.0 SG J:CYS121 2.2 66.2 1.0 SG J:CYS115 2.2 75.3 1.0 SG J:CYS134 2.3 54.1 1.0 CB J:CYS131 3.1 57.8 1.0 CB J:CYS121 3.3 64.8 1.0 CB J:CYS115 3.4 72.6 1.0 CB J:CYS134 3.4 52.7 1.0 N J:CYS121 4.1 66.2 1.0 CA J:CYS115 4.2 72.2 1.0 N J:CYS134 4.2 52.5 1.0 CA J:CYS121 4.3 64.6 1.0 CD J:PRO116 4.3 72.3 1.0 CA J:CYS134 4.4 52.1 1.0 CA J:CYS131 4.6 56.1 1.0 O J:HOH301 4.6 47.1 1.0 N J:ASN119 4.6 73.2 1.0 CA J:ASN119 4.7 72.5 1.0 N J:GLU120 4.7 70.0 1.0 N J:PRO116 4.8 73.0 1.0 C J:CYS115 4.9 72.8 1.0 N J:ALA117 4.9 74.1 1.0

A.K.M.Patel, P.Vilela, T.B.Shaik, A.G.Mcewen, I.Hazemann, K.Brillet, E.Ennifar, A.Hamiche, G.V.Markov, V.Laudet, D.Moras, B.P.Klaholz, I.M.L.Billas. Asymmetric Dimerization in A Transcription Factor Superfamily Is Promoted By Allosteric Interactions with Dna. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 37503845
DOI: 10.1093/NAR/GKAD632