Zinc in PDB 6u04: Crystal Structure of Human BRPF1 Pzp Bound to Histone H3 Tail

Protein crystallography data

The structure of Crystal Structure of Human BRPF1 Pzp Bound to Histone H3 Tail, PDB code: 6u04 was solved by B.J.Klein, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.68 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 72.461, 72.461, 155.297, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 20.9

Other elements in 6u04:

The structure of Crystal Structure of Human BRPF1 Pzp Bound to Histone H3 Tail also contains other interesting chemical elements:

Praseodymium (Pr) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human BRPF1 Pzp Bound to Histone H3 Tail (pdb code 6u04). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Human BRPF1 Pzp Bound to Histone H3 Tail, PDB code: 6u04:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 6u04

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Zinc binding site 1 out of 5 in the Crystal Structure of Human BRPF1 Pzp Bound to Histone H3 Tail


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 Human BRPF1 Pzp Bound to Histone H3 Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:23.4
occ:1.00
ND1 A:HIS350 2.0 23.0 1.0
SG A:CYS353 2.2 23.9 1.0
SG A:CYS333 2.3 21.3 1.0
SG A:CYS330 2.3 21.5 1.0
CE1 A:HIS350 3.0 19.1 1.0
CG A:HIS350 3.0 23.3 1.0
CB A:CYS330 3.0 17.7 1.0
CB A:CYS333 3.2 23.0 1.0
CB A:HIS350 3.3 21.1 1.0
CB A:CYS353 3.4 25.7 1.0
N A:CYS333 3.9 18.5 1.0
CG2 A:THR412 4.0 20.7 1.0
N A:HIS350 4.1 23.0 1.0
CA A:CYS333 4.1 22.4 1.0
NE2 A:HIS350 4.1 18.6 1.0
CD2 A:HIS350 4.1 24.6 1.0
OG1 A:THR412 4.2 26.0 1.0
CA A:HIS350 4.3 20.0 1.0
C A:LEU332 4.4 26.9 1.0
CA A:CYS330 4.5 22.3 1.0
CB A:LEU332 4.6 17.4 1.0
C A:CYS333 4.7 29.3 1.0
CA A:CYS353 4.7 24.3 1.0
N A:LEU332 4.8 17.6 1.0
O A:CYS333 4.8 23.4 1.0
CB A:THR412 4.8 24.1 1.0
CA A:LEU332 4.8 17.5 1.0
O A:LEU332 4.9 22.7 1.0
O A:ASN335 5.0 26.4 1.0

Zinc binding site 2 out of 5 in 6u04

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Zinc binding site 2 out of 5 in the Crystal Structure of Human BRPF1 Pzp Bound to Histone H3 Tail


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 Human BRPF1 Pzp Bound to Histone H3 Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:27.8
occ:1.00
ND1 A:HIS410 2.1 28.7 1.0
SG A:CYS389 2.2 24.0 1.0
SG A:CYS386 2.3 25.6 1.0
SG A:CYS413 2.3 25.8 1.0
CE1 A:HIS410 2.9 22.2 1.0
CB A:CYS386 3.1 25.5 1.0
CG A:HIS410 3.2 22.5 1.0
CB A:CYS389 3.2 20.0 1.0
CB A:CYS413 3.3 19.3 1.0
N A:CYS389 3.6 30.0 1.0
CB A:HIS410 3.6 17.6 1.0
CA A:CYS389 4.0 30.3 1.0
NE2 A:HIS410 4.1 29.1 1.0
N A:HIS410 4.1 19.4 1.0
CD2 A:HIS410 4.2 29.7 1.0
CG A:PRO334 4.4 27.7 1.0
CA A:HIS410 4.5 27.5 1.0
CA A:CYS386 4.6 24.5 1.0
CA A:CYS413 4.7 27.6 1.0
CD A:PRO334 4.7 31.3 1.0
C A:ILE388 4.7 27.8 1.0
C A:CYS389 4.8 25.8 1.0
CB A:ILE388 4.9 24.4 1.0

Zinc binding site 3 out of 5 in 6u04

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Zinc binding site 3 out of 5 in the Crystal Structure of Human BRPF1 Pzp Bound to Histone H3 Tail


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 Human BRPF1 Pzp Bound to Histone H3 Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:32.6
occ:1.00
SG A:CYS320 2.3 30.4 1.0
SG A:CYS293 2.4 31.6 1.0
SG A:CYS317 2.4 25.9 1.0
SG A:CYS296 2.4 33.6 1.0
CB A:CYS293 3.2 34.1 1.0
CB A:CYS296 3.3 36.0 1.0
CB A:CYS320 3.3 27.0 1.0
CB A:CYS317 3.6 25.0 1.0
N A:CYS296 3.7 40.8 1.0
O A:HOH667 3.9 39.0 1.0
N A:CYS317 4.0 27.0 1.0
CA A:CYS296 4.1 34.9 1.0
N A:CYS320 4.1 27.1 1.0
CA A:CYS320 4.3 32.1 1.0
CA A:CYS317 4.3 25.7 1.0
CB A:LEU298 4.6 34.5 1.0
CA A:CYS293 4.6 35.0 1.0
CB A:MET295 4.7 45.1 1.0
C A:MET295 4.7 45.3 1.0
C A:CYS296 4.8 37.7 1.0
NH2 A:ARG319 4.8 50.6 1.0
C A:CYS317 4.8 27.3 1.0
O A:CYS317 4.8 29.3 1.0
N A:ASN297 5.0 30.7 1.0

Zinc binding site 4 out of 5 in 6u04

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Zinc binding site 4 out of 5 in the Crystal Structure of Human BRPF1 Pzp Bound to Histone H3 Tail


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 Human BRPF1 Pzp Bound to Histone H3 Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:26.2
occ:1.00
ND1 A:HIS447 2.0 26.6 1.0
SG A:CYS405 2.3 23.9 1.0
SG A:CYS444 2.4 22.9 1.0
SG A:CYS400 2.4 23.0 1.0
CE1 A:HIS447 2.9 27.7 1.0
CG A:HIS447 3.1 25.4 1.0
CB A:CYS400 3.1 22.0 1.0
CB A:CYS405 3.1 24.3 1.0
CB A:CYS444 3.5 21.7 1.0
CB A:HIS447 3.5 25.1 1.0
N A:CYS444 4.0 24.2 1.0
NE2 A:HIS447 4.1 28.7 1.0
CB A:LYS402 4.1 38.1 1.0
CD2 A:HIS447 4.2 28.1 1.0
CA A:CYS444 4.3 21.8 1.0
O A:HOH629 4.5 22.6 1.0
N A:HIS447 4.6 25.1 1.0
CA A:CYS405 4.6 33.7 1.0
CA A:CYS400 4.6 22.5 1.0
OG1 A:THR407 4.6 29.8 1.0
CB A:THR407 4.7 31.6 1.0
O A:HOH701 4.7 42.9 1.0
CA A:HIS447 4.7 26.6 1.0
C A:CYS444 4.8 22.6 1.0
CG A:LYS402 4.8 41.2 1.0
O A:CYS444 4.8 29.0 1.0

Zinc binding site 5 out of 5 in 6u04

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Zinc binding site 5 out of 5 in the Crystal Structure of Human BRPF1 Pzp Bound to Histone H3 Tail


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 Human BRPF1 Pzp Bound to Histone H3 Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:37.1
occ:1.00
ND1 A:HIS301 2.1 41.2 1.0
SG A:CYS304 2.2 31.8 1.0
SG A:CYS276 2.2 32.7 1.0
SG A:CYS279 2.4 43.0 1.0
CB A:CYS276 3.0 42.3 1.0
CE1 A:HIS301 3.0 33.6 1.0
CG A:HIS301 3.1 34.5 1.0
CB A:CYS304 3.2 27.2 1.0
CB A:CYS279 3.3 31.6 1.0
CB A:HIS301 3.4 30.1 1.0
N A:CYS279 3.7 38.5 1.0
N A:HIS301 4.0 39.1 1.0
CA A:CYS279 4.1 32.6 1.0
NE2 A:HIS301 4.1 37.9 1.0
CD2 A:HIS301 4.2 37.5 1.0
O A:HOH653 4.4 40.8 1.0
CA A:HIS301 4.4 32.7 1.0
CA A:CYS276 4.4 30.1 1.0
CA A:CYS304 4.6 27.4 1.0
CB A:ILE278 4.7 37.2 1.0
C A:ILE278 4.8 43.0 1.0
C A:CYS276 4.8 40.9 1.0
C A:CYS279 4.9 39.1 1.0
O A:CYS276 4.9 39.2 1.0
N A:CYS304 4.9 35.4 1.0
O A:ASP281 5.0 48.0 1.0
N A:ILE278 5.0 29.0 1.0

Reference:

B.J.Klein, K.L.Cox, S.M.Jang, J.Cote, M.G.Poirier, T.G.Kutateladze. Molecular Basis For the Pzp Domain of BRPF1 Association with Chromatin. Structure 2019.
ISSN: ISSN 0969-2126
PubMed: 31711755
DOI: 10.1016/J.STR.2019.10.014
Page generated: Wed Dec 16 12:56:40 2020

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