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Zinc in PDB 5erc: X-Ray Crystal Structure of BRPF1 Pzp Domain

Protein crystallography data

The structure of X-Ray Crystal Structure of BRPF1 Pzp Domain, PDB code: 5erc was solved by B.J.Klein, F.H.Andrews, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.97 / 2.05
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 73.870, 73.870, 147.130, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 19.3

Other elements in 5erc:

The structure of X-Ray Crystal Structure of BRPF1 Pzp Domain also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Crystal Structure of BRPF1 Pzp Domain (pdb code 5erc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the X-Ray Crystal Structure of BRPF1 Pzp Domain, PDB code: 5erc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5erc

Go back to Zinc Binding Sites List in 5erc
Zinc binding site 1 out of 5 in the X-Ray Crystal Structure of BRPF1 Pzp Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of BRPF1 Pzp Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:22.3
occ:0.77
SG A:CYS320 2.2 20.8 1.0
SG A:CYS293 2.3 22.5 1.0
SG A:CYS296 2.4 25.1 1.0
SG A:CYS317 2.4 20.3 1.0
CB A:CYS293 3.2 22.8 1.0
CB A:CYS296 3.2 25.4 1.0
CB A:CYS320 3.3 22.1 1.0
CB A:CYS317 3.5 24.6 1.0
N A:CYS296 3.7 29.6 1.0
N A:CYS317 4.0 20.1 1.0
CA A:CYS296 4.0 30.7 1.0
N A:CYS320 4.1 17.1 1.0
CA A:CYS320 4.3 18.5 1.0
NH2 A:ARG319 4.3 60.2 1.0
CA A:CYS317 4.3 18.6 1.0
NE A:ARG319 4.4 51.2 1.0
CB A:LEU298 4.5 22.1 1.0
CA A:CYS293 4.6 24.7 1.0
C A:CYS296 4.7 29.9 1.0
CB A:MET295 4.8 40.3 1.0
C A:MET295 4.8 39.5 1.0
O A:CYS317 4.8 17.8 1.0
C A:CYS317 4.8 20.1 1.0
CZ A:ARG319 4.9 57.5 1.0
N A:ASN297 5.0 29.3 1.0
O A:HOH694 5.0 19.3 1.0

Zinc binding site 2 out of 5 in 5erc

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Zinc binding site 2 out of 5 in the X-Ray Crystal Structure of BRPF1 Pzp Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure of BRPF1 Pzp Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:32.9
occ:0.75
SG A:CYS276 2.2 27.8 1.0
SG A:CYS304 2.2 37.4 1.0
ND1 A:HIS301 2.2 20.0 1.0
SG A:CYS279 2.4 34.4 1.0
CG A:HIS301 3.0 20.0 1.0
CB A:HIS301 3.1 20.0 1.0
CB A:CYS276 3.1 33.5 1.0
CB A:CYS304 3.2 24.5 1.0
CB A:CYS279 3.3 39.1 1.0
CE1 A:HIS301 3.3 20.0 1.0
N A:CYS279 3.8 41.7 1.0
N A:HIS301 4.0 28.7 1.0
CA A:CYS279 4.1 41.0 1.0
CA A:HIS301 4.2 27.5 1.0
CD2 A:HIS301 4.2 20.0 1.0
NE2 A:HIS301 4.4 20.0 1.0
CA A:CYS276 4.6 39.4 1.0
CA A:CYS304 4.6 22.1 1.0
CB A:ILE278 4.7 24.7 1.0
C A:ILE278 4.8 38.0 1.0
C A:CYS279 4.9 38.5 1.0
N A:CYS304 4.9 24.2 1.0
C A:CYS276 5.0 35.2 1.0

Zinc binding site 3 out of 5 in 5erc

Go back to Zinc Binding Sites List in 5erc
Zinc binding site 3 out of 5 in the X-Ray Crystal Structure of BRPF1 Pzp Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structure of BRPF1 Pzp Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:12.7
occ:0.82
ND1 A:HIS350 2.1 9.8 1.0
SG A:CYS333 2.3 10.9 1.0
SG A:CYS330 2.3 9.3 1.0
SG A:CYS353 2.3 10.1 1.0
CB A:CYS330 3.0 9.2 1.0
CE1 A:HIS350 3.1 13.7 1.0
CG A:HIS350 3.1 10.2 1.0
CB A:CYS333 3.2 8.6 1.0
CB A:HIS350 3.4 10.7 1.0
CB A:CYS353 3.5 9.7 1.0
N A:CYS333 3.9 12.1 1.0
CG2 A:THR412 4.0 13.1 1.0
N A:HIS350 4.1 9.5 1.0
CA A:CYS333 4.1 10.7 1.0
NE2 A:HIS350 4.2 13.6 1.0
CD2 A:HIS350 4.2 13.3 1.0
OG1 A:THR412 4.3 9.9 1.0
C A:LEU332 4.3 13.2 1.0
CA A:HIS350 4.4 9.9 1.0
CB A:LEU332 4.5 7.5 1.0
CA A:CYS330 4.5 8.8 1.0
N A:LEU332 4.7 7.6 1.0
C A:CYS333 4.7 13.3 1.0
CA A:LEU332 4.7 7.5 1.0
CA A:CYS353 4.8 12.9 1.0
O A:CYS333 4.8 11.2 1.0
CB A:THR412 4.8 12.6 1.0
O A:LEU332 4.9 11.7 1.0
O A:ASN335 5.0 17.2 1.0

Zinc binding site 4 out of 5 in 5erc

Go back to Zinc Binding Sites List in 5erc
Zinc binding site 4 out of 5 in the X-Ray Crystal Structure of BRPF1 Pzp Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Crystal Structure of BRPF1 Pzp Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:16.3
occ:0.82
ND1 A:HIS410 2.2 9.2 1.0
SG A:CYS413 2.2 15.2 1.0
SG A:CYS386 2.3 12.0 1.0
SG A:CYS389 2.4 16.6 1.0
CB A:CYS386 3.1 9.7 1.0
CE1 A:HIS410 3.1 13.9 1.0
CG A:HIS410 3.2 10.3 1.0
CB A:CYS389 3.2 19.4 1.0
CB A:CYS413 3.3 14.5 1.0
CB A:HIS410 3.5 10.8 1.0
N A:CYS389 3.7 17.9 1.0
CA A:CYS389 4.1 20.3 1.0
N A:HIS410 4.1 14.7 1.0
NE2 A:HIS410 4.2 15.3 1.0
CD2 A:HIS410 4.3 10.3 1.0
CA A:HIS410 4.4 12.3 1.0
CG A:PRO334 4.5 19.0 1.0
CA A:CYS386 4.5 15.2 1.0
CD A:PRO334 4.7 17.8 1.0
CA A:CYS413 4.7 14.2 1.0
C A:ILE388 4.8 24.4 1.0
CB A:ILE388 4.8 15.7 1.0
C A:CYS389 4.9 18.7 1.0
O A:HOH718 4.9 34.1 1.0

Zinc binding site 5 out of 5 in 5erc

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Zinc binding site 5 out of 5 in the X-Ray Crystal Structure of BRPF1 Pzp Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Crystal Structure of BRPF1 Pzp Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:13.7
occ:0.81
ND1 A:HIS447 2.0 15.8 1.0
SG A:CYS400 2.3 12.7 1.0
SG A:CYS444 2.3 13.1 1.0
SG A:CYS405 2.3 12.9 1.0
CE1 A:HIS447 2.9 17.8 1.0
CB A:CYS400 3.1 11.8 1.0
CG A:HIS447 3.1 14.8 1.0
CB A:CYS405 3.2 13.2 1.0
CB A:CYS444 3.5 14.2 1.0
CB A:HIS447 3.6 14.6 1.0
N A:CYS444 4.0 12.3 1.0
NE2 A:HIS447 4.1 14.9 1.0
CD2 A:HIS447 4.2 15.2 1.0
CA A:CYS444 4.3 12.4 1.0
CB A:LYS402 4.3 16.6 1.0
O A:HOH627 4.4 16.4 1.0
N A:HIS447 4.5 14.8 1.0
CA A:CYS400 4.6 15.1 1.0
CA A:CYS405 4.6 22.9 1.0
CB A:THR407 4.6 18.1 1.0
CA A:HIS447 4.7 22.2 1.0
OG1 A:THR407 4.8 17.8 1.0
O A:HOH728 4.8 28.8 1.0
C A:CYS444 4.8 13.1 1.0
O A:CYS444 4.8 13.7 1.0

Reference:

B.J.Klein, U.M.Muthurajan, M.E.Lalonde, M.D.Gibson, F.H.Andrews, M.Hepler, S.Machida, K.Yan, H.Kurumizaka, M.G.Poirier, J.Cote, K.Luger, T.G.Kutateladze. Bivalent Interaction of the Pzp Domain of BRPF1 with the Nucleosome Impacts Chromatin Dynamics and Acetylation. Nucleic Acids Res. V. 44 472 2016.
ISSN: ESSN 1362-4962
PubMed: 26626149
DOI: 10.1093/NAR/GKV1321
Page generated: Wed Dec 16 06:10:19 2020

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