Zinc in PDB 5u7g: Crystal Structure of the Catalytic Core of Cbp

The structure of Crystal Structure of the Catalytic Core of Cbp, PDB code: 5u7g was solved by S.Park, R.L.Stanfield, M.M.Martinez-Yamout, H.J.Dyson, I.A.Wilson, P.E.Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.90 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	214.173, 87.170, 114.977, 90.00, 109.68, 90.00
R / Rfree (%)	25.4 / 28.3

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Core of Cbp (pdb code 5u7g). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Core of Cbp, PDB code: 5u7g:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the Catalytic Core of Cbp


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 Catalytic Core of Cbp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:33.8 occ:1.00 ND1 A:HIS1292 2.1 36.0 1.0 SG A:CYS1295 2.3 37.9 1.0 SG A:CYS1201 2.3 37.0 1.0 SG A:CYS1200 2.4 40.3 1.0 CG A:HIS1292 2.9 35.3 1.0 CB A:HIS1292 3.1 34.7 1.0 CE1 A:HIS1292 3.2 36.5 1.0 CB A:CYS1295 3.4 43.4 1.0 CB A:CYS1200 3.4 40.1 1.0 CB A:CYS1201 3.6 42.9 1.0 N A:CYS1201 3.7 43.9 1.0 C A:CYS1200 4.1 41.5 1.0 CA A:CYS1201 4.1 44.9 1.0 CD2 A:HIS1292 4.1 35.4 1.0 NE2 A:HIS1292 4.2 36.2 1.0 N A:HIS1292 4.3 35.7 1.0 CA A:HIS1292 4.3 34.8 1.0 CA A:CYS1200 4.3 42.9 1.0 O A:CYS1201 4.4 47.3 1.0 O A:HOH1911 4.4 29.9 1.0 C A:CYS1201 4.5 45.6 1.0 CE2 A:TYR1205 4.7 35.4 1.0 O A:CYS1200 4.7 39.6 1.0 NH2 A:ARG1683 4.8 41.3 1.0 CA A:CYS1295 4.8 43.1 1.0 CH2 A:TRP1152 4.9 49.2 1.0 N A:CYS1200 5.0 46.3 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the Catalytic Core of Cbp


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 Catalytic Core of Cbp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:48.5 occ:1.00 SG A:CYS1287 2.1 83.9 1.0 SG A:CYS1284 2.4 50.4 1.0 SG A:CYS1309 2.4 62.6 1.0 SG A:CYS1312 2.5 55.0 1.0 CB A:CYS1309 2.9 62.8 1.0 CB A:CYS1287 3.3 80.2 1.0 CB A:CYS1284 3.4 52.1 1.0 CB A:CYS1312 3.4 56.3 1.0 N A:CYS1287 3.7 84.1 1.0 CA A:CYS1309 3.9 61.5 1.0 N A:CYS1309 3.9 61.8 1.0 CA A:CYS1287 4.0 83.0 1.0 N A:CYS1312 4.1 54.8 1.0 CA A:CYS1312 4.4 56.3 1.0 CB A:GLU1286 4.5 70.5 1.0 C A:CYS1309 4.5 61.6 1.0 O A:CYS1309 4.6 62.4 1.0 C A:GLU1286 4.8 73.4 1.0 CA A:CYS1284 4.9 52.5 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the Catalytic Core of Cbp


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 Catalytic Core of Cbp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1803 b:45.7 occ:1.00 SG A:CYS1708 2.2 46.5 1.0 SG A:CYS1730 2.4 52.0 1.0 SG A:CYS1733 2.4 52.3 1.0 SG A:CYS1711 2.5 52.7 1.0 CB A:CYS1708 3.1 49.0 1.0 CB A:CYS1733 3.2 52.1 1.0 CB A:CYS1711 3.5 54.5 1.0 CB A:CYS1730 3.5 50.7 1.0 N A:CYS1711 3.8 54.4 1.0 N A:CYS1730 3.8 50.7 1.0 CA A:CYS1711 4.2 53.9 1.0 N A:CYS1733 4.2 57.4 1.0 CA A:CYS1730 4.2 49.6 1.0 CA A:CYS1733 4.3 55.7 1.0 CA A:CYS1708 4.5 49.5 1.0 CB A:GLU1710 4.5 71.6 1.0 C A:GLU1710 4.9 72.1 1.0 C A:CYS1730 4.9 51.5 1.0 C A:LEU1729 4.9 47.8 1.0 C A:CYS1711 4.9 54.4 1.0 O A:CYS1730 5.0 51.3 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the Catalytic Core of Cbp


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 Catalytic Core of Cbp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1804 b:71.8 occ:1.00 NE2 A:HIS1739 1.9 49.0 1.0 ND1 A:HIS1741 2.2 79.5 1.0 SG A:CYS1724 2.2 58.6 1.0 SG A:CYS1721 2.4 48.3 1.0 CE1 A:HIS1739 2.8 45.9 1.0 CE1 A:HIS1741 2.9 77.0 1.0 CD2 A:HIS1739 3.1 46.5 1.0 CG A:HIS1741 3.2 73.7 1.0 CB A:CYS1724 3.4 54.7 1.0 CB A:CYS1721 3.6 45.6 1.0 CB A:HIS1741 3.7 68.6 1.0 N A:CYS1724 3.8 57.7 1.0 ND1 A:HIS1739 3.9 48.4 1.0 NE2 A:HIS1741 4.0 76.0 1.0 CG A:HIS1739 4.1 46.7 1.0 CD2 A:HIS1741 4.1 74.5 1.0 CA A:CYS1724 4.2 54.6 1.0 CB A:VAL1723 4.6 56.7 1.0 CD2 A:TYR1727 4.8 50.4 1.0 C A:VAL1723 4.8 56.5 1.0 CB A:TYR1727 4.8 48.9 1.0 CG A:TYR1727 4.9 49.8 1.0 CA A:CYS1721 4.9 44.4 1.0 CA A:HIS1741 4.9 69.1 1.0 N A:VAL1723 5.0 54.8 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the Catalytic Core of Cbp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Catalytic Core of Cbp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1801 b:55.6 occ:1.00 ND1 B:HIS1292 2.0 61.0 1.0 SG B:CYS1201 2.3 62.1 1.0 SG B:CYS1295 2.4 59.4 1.0 SG B:CYS1200 2.5 63.5 1.0 CG B:HIS1292 2.8 60.1 1.0 CE1 B:HIS1292 3.1 61.4 1.0 CB B:HIS1292 3.1 59.5 1.0 CB B:CYS1295 3.6 62.1 1.0 CB B:CYS1200 3.7 63.5 1.0 CB B:CYS1201 3.7 64.2 1.0 N B:CYS1201 3.8 67.5 1.0 CD2 B:HIS1292 4.0 60.1 1.0 NE2 B:HIS1292 4.1 60.9 1.0 CA B:CYS1201 4.2 67.8 1.0 N B:HIS1292 4.3 62.9 1.0 CA B:HIS1292 4.3 60.6 1.0 C B:CYS1200 4.3 64.8 1.0 O B:CYS1201 4.4 69.0 1.0 C B:CYS1201 4.5 67.6 1.0 CE2 B:TYR1205 4.6 56.0 1.0 CA B:CYS1200 4.6 65.4 1.0 CH2 B:TRP1152 4.8 81.9 1.0 NH2 B:ARG1683 4.8 50.7 1.0 CD2 B:TYR1205 4.9 56.1 1.0 CA B:CYS1295 5.0 60.8 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the Catalytic Core of Cbp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Catalytic Core of Cbp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1802 b:71.4 occ:1.00 SG B:CYS1287 2.2 0.6 1.0 SG B:CYS1284 2.5 80.0 1.0 SG B:CYS1312 2.6 90.5 1.0 SG B:CYS1309 2.6 0.2 1.0 CB B:CYS1309 2.7 0.1 1.0 CB B:CYS1287 3.3 0.2 1.0 CB B:CYS1284 3.6 79.5 1.0 N B:CYS1309 3.6 97.5 1.0 CA B:CYS1309 3.7 97.3 1.0 CB B:CYS1312 3.7 90.3 1.0 N B:CYS1287 3.8 0.6 1.0 CA B:CYS1287 4.2 0.7 1.0 C B:CYS1309 4.5 97.9 1.0 N B:CYS1312 4.5 87.9 1.0 CB B:GLU1286 4.6 1.0 1.0 O B:CYS1309 4.6 99.2 1.0 C B:VAL1308 4.8 82.6 1.0 CA B:CYS1312 4.8 90.5 1.0 CA B:CYS1284 5.0 79.5 1.0 C B:GLU1286 5.0 0.5 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the Catalytic Core of Cbp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Catalytic Core of Cbp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1803 b:46.2 occ:1.00 SG B:CYS1730 2.3 44.7 1.0 SG B:CYS1708 2.3 42.7 1.0 SG B:CYS1733 2.4 49.4 1.0 SG B:CYS1711 2.5 46.3 1.0 CB B:CYS1708 3.2 45.2 1.0 CB B:CYS1733 3.2 48.3 1.0 CB B:CYS1711 3.4 50.4 1.0 CB B:CYS1730 3.4 43.2 1.0 N B:CYS1711 3.7 50.5 1.0 N B:CYS1730 3.9 42.0 1.0 CA B:CYS1711 4.2 50.8 1.0 CA B:CYS1730 4.2 42.5 1.0 N B:CYS1733 4.3 49.1 1.0 CA B:CYS1733 4.4 47.9 1.0 CA B:CYS1708 4.6 45.9 1.0 CB B:GLU1710 4.6 69.4 1.0 C B:GLU1710 4.8 69.5 1.0 C B:CYS1730 4.9 43.4 1.0 C B:CYS1711 4.9 51.4 1.0 O B:CYS1730 4.9 43.6 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the Catalytic Core of Cbp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Catalytic Core of Cbp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1804 b:58.5 occ:1.00 NE2 B:HIS1739 2.1 44.8 1.0 ND1 B:HIS1741 2.1 60.5 1.0 SG B:CYS1724 2.2 49.2 1.0 SG B:CYS1721 2.5 42.8 1.0 CE1 B:HIS1741 3.0 60.3 1.0 CE1 B:HIS1739 3.1 45.4 1.0 CD2 B:HIS1739 3.1 45.0 1.0 CG B:HIS1741 3.2 54.9 1.0 CB B:CYS1724 3.3 46.5 1.0 CB B:CYS1721 3.5 42.6 1.0 CB B:HIS1741 3.5 51.4 1.0 N B:CYS1724 3.7 47.6 1.0 CA B:CYS1724 4.0 46.5 1.0 NE2 B:HIS1741 4.2 57.4 1.0 ND1 B:HIS1739 4.2 46.0 1.0 CG B:HIS1739 4.2 45.8 1.0 CD2 B:HIS1741 4.3 57.4 1.0 CB B:VAL1723 4.6 47.7 1.0 CD2 B:TYR1727 4.6 43.2 1.0 C B:VAL1723 4.7 46.2 1.0 CA B:HIS1741 4.8 52.3 1.0 CA B:CYS1721 4.8 43.7 1.0 CB B:TYR1727 4.9 43.6 1.0 CG B:TYR1727 4.9 42.1 1.0 N B:HIS1741 4.9 54.1 1.0 N B:VAL1723 5.0 47.5 1.0 CA B:VAL1723 5.0 48.7 1.0

S.Park, R.L.Stanfield, M.A.Martinez-Yamout, H.J.Dyson, I.A.Wilson, P.E.Wright. Role of the Cbp Catalytic Core in Intramolecular Sumoylation and Control of Histone H3 Acetylation. Proc. Natl. Acad. Sci. V. 114 E5335 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28630323
DOI: 10.1073/PNAS.1703105114