Zinc in PDB 5hda: Crystal Structure of the BS69 Coiled Coil-Mynd Domains Bound to An EBNA2 Pxlxp Motif

The structure of Crystal Structure of the BS69 Coiled Coil-Mynd Domains Bound to An EBNA2 Pxlxp Motif, PDB code: 5hda was solved by J.Song, M.Harter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.60 / 2.39
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.456, 38.190, 82.690, 90.00, 97.53, 90.00
R / Rfree (%)	22.2 / 26.2

The binding sites of Zinc atom in the Crystal Structure of the BS69 Coiled Coil-Mynd Domains Bound to An EBNA2 Pxlxp Motif (pdb code 5hda). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the BS69 Coiled Coil-Mynd Domains Bound to An EBNA2 Pxlxp Motif, PDB code: 5hda:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the BS69 Coiled Coil-Mynd Domains Bound to An EBNA2 Pxlxp Motif


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the BS69 Coiled Coil-Mynd Domains Bound to An EBNA2 Pxlxp Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:31.8 occ:1.00 NE2 A:HIS554 2.1 31.4 1.0 SG A:CYS534 2.3 28.4 1.0 SG A:CYS535 2.4 35.4 1.0 SG A:CYS558 2.4 34.3 1.0 CE1 A:HIS554 2.9 35.3 1.0 CD2 A:HIS554 3.2 31.5 1.0 CB A:CYS534 3.4 34.4 1.0 CB A:CYS558 3.4 33.7 1.0 CB A:CYS535 3.5 31.6 1.0 CA A:CYS558 3.7 33.0 1.0 N A:CYS535 3.8 38.4 1.0 C A:CYS534 4.0 33.1 1.0 ND1 A:HIS554 4.1 27.7 1.0 N A:ARG559 4.2 32.0 1.0 CA A:CYS535 4.3 25.6 1.0 CG A:HIS554 4.3 27.7 1.0 CA A:CYS534 4.3 39.0 1.0 C A:CYS558 4.4 42.6 1.0 CG2 A:THR538 4.4 25.2 1.0 CB A:ARG560 4.4 41.9 1.0 O A:CYS534 4.5 36.1 1.0 CB A:THR538 4.5 31.6 1.0 O A:HOH732 4.5 23.5 1.0 N A:ARG560 4.5 40.2 1.0 N A:CYS558 4.9 33.1 1.0 OG1 A:THR538 4.9 24.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the BS69 Coiled Coil-Mynd Domains Bound to An EBNA2 Pxlxp Motif


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the BS69 Coiled Coil-Mynd Domains Bound to An EBNA2 Pxlxp Motif within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:30.4 occ:1.00 SG A:CYS526 2.3 26.3 1.0 SG A:CYS545 2.4 37.6 1.0 SG A:CYS541 2.4 34.3 1.0 SG A:CYS523 2.4 33.1 1.0 CB A:CYS545 3.2 31.9 1.0 CB A:CYS523 3.2 29.2 1.0 CB A:CYS526 3.5 26.1 1.0 CB A:CYS541 3.5 35.0 1.0 N A:CYS526 3.8 31.7 1.0 N A:CYS541 3.9 30.8 1.0 CA A:CYS526 4.1 38.0 1.0 CA A:CYS541 4.3 32.1 1.0 OG A:SER542 4.4 28.0 1.0 C A:CYS526 4.4 47.2 1.0 O A:CYS526 4.6 61.9 1.0 N A:SER542 4.6 37.7 1.0 CA A:CYS545 4.7 31.0 1.0 CA A:CYS523 4.7 31.8 1.0 CB A:ASN525 4.8 29.2 1.0 CB A:GLU528 4.8 38.0 1.0 C A:CYS541 4.8 34.6 1.0 C A:ASN525 5.0 31.1 1.0 N A:GLU528 5.0 27.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the BS69 Coiled Coil-Mynd Domains Bound to An EBNA2 Pxlxp Motif


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the BS69 Coiled Coil-Mynd Domains Bound to An EBNA2 Pxlxp Motif within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:32.5 occ:1.00 SG C:CYS541 2.3 26.9 1.0 SG C:CYS523 2.4 32.1 1.0 SG C:CYS526 2.4 33.7 1.0 SG C:CYS545 2.4 38.6 1.0 CB C:CYS545 3.2 36.4 1.0 CB C:CYS523 3.2 36.6 1.0 CB C:CYS526 3.4 22.5 1.0 CB C:CYS541 3.5 29.6 1.0 N C:CYS526 3.6 36.6 1.0 N C:CYS541 3.9 27.8 1.0 CA C:CYS526 4.1 37.6 1.0 CA C:CYS541 4.2 27.3 1.0 CB C:ASN525 4.3 43.7 1.0 OG C:SER542 4.5 34.9 1.0 N C:SER542 4.6 36.3 1.0 C C:ASN525 4.7 35.8 1.0 CA C:CYS545 4.7 43.7 1.0 CA C:CYS523 4.7 34.3 1.0 ND2 C:ASN525 4.7 44.9 1.0 C C:CYS526 4.7 36.1 1.0 C C:CYS541 4.8 30.7 1.0 CA C:ASN525 4.9 39.2 1.0 N C:GLU527 4.9 39.7 1.0 N C:ASN525 5.0 37.4 1.0 C C:TYR540 5.0 25.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the BS69 Coiled Coil-Mynd Domains Bound to An EBNA2 Pxlxp Motif


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the BS69 Coiled Coil-Mynd Domains Bound to An EBNA2 Pxlxp Motif within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn602 b:32.7 occ:1.00 NE2 C:HIS554 2.1 33.1 1.0 SG C:CYS534 2.3 31.4 1.0 SG C:CYS558 2.4 37.9 1.0 SG C:CYS535 2.4 33.7 1.0 CE1 C:HIS554 3.1 29.3 1.0 CD2 C:HIS554 3.1 37.8 1.0 CB C:CYS558 3.3 39.0 1.0 CB C:CYS534 3.5 21.3 1.0 CB C:CYS535 3.5 30.1 1.0 CA C:CYS558 3.6 43.1 1.0 N C:CYS535 3.9 32.0 1.0 C C:CYS534 4.0 33.8 1.0 N C:ARG559 4.1 42.2 1.0 CB C:ARG560 4.1 30.7 1.0 ND1 C:HIS554 4.2 39.8 1.0 CG C:HIS554 4.2 40.1 1.0 C C:CYS558 4.3 41.4 1.0 CA C:CYS535 4.3 29.3 1.0 N C:ARG560 4.4 34.3 1.0 CA C:CYS534 4.4 27.6 1.0 O C:HOH730 4.4 26.7 1.0 CG2 C:THR538 4.5 37.9 1.0 O C:CYS534 4.5 31.2 1.0 CB C:THR538 4.6 36.6 1.0 N C:CYS558 4.8 37.2 1.0 CA C:ARG560 4.9 43.4 1.0 OG1 C:THR538 4.9 30.0 1.0

M.R.Harter, C.D.Liu, C.L.Shen, E.Gonzalez-Hurtado, Z.M.Zhang, M.Xu, E.Martinez, C.W.Peng, J.Song. BS69/ZMYND11 C-Terminal Domains Bind and Inhibit EBNA2. Plos Pathog. V. 12 05414 2016.
ISSN: ESSN 1553-7374
PubMed: 26845565
DOI: 10.1371/JOURNAL.PPAT.1005414