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Zinc in PDB 2fsa: Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME2 Bound State

Protein crystallography data

The structure of Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME2 Bound State, PDB code: 2fsa was solved by H.Li, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.451, 85.169, 109.567, 90.00, 99.03, 90.00
R / Rfree (%) 20 / 22

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME2 Bound State (pdb code 2fsa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME2 Bound State, PDB code: 2fsa:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2fsa

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Zinc binding site 1 out of 6 in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME2 Bound State


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 Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME2 Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:19.1
occ:1.00
ND1 A:HIS34 2.1 19.0 1.0
SG A:CYS37 2.3 23.3 1.0
SG A:CYS13 2.3 21.3 1.0
SG A:CYS11 2.3 15.5 1.0
CE1 A:HIS34 3.1 22.1 1.0
CG A:HIS34 3.1 17.4 1.0
CB A:CYS11 3.2 17.5 1.0
CB A:CYS37 3.3 17.6 1.0
CB A:HIS34 3.4 16.3 1.0
CB A:CYS13 3.5 23.4 1.0
N A:CYS13 4.1 23.4 1.0
NE2 A:HIS34 4.2 19.9 1.0
N A:HIS34 4.2 14.3 1.0
CD2 A:HIS34 4.3 19.1 1.0
O A:HOH575 4.4 35.2 1.0
CA A:CYS13 4.4 23.9 1.0
CA A:HIS34 4.5 14.7 1.0
N A:ILE12 4.6 22.0 1.0
CA A:CYS11 4.6 19.1 1.0
CA A:CYS37 4.7 20.4 1.0
CG1 A:ILE12 4.8 28.9 1.0
O A:HOH665 4.9 51.0 1.0
C A:CYS11 4.9 21.3 1.0
OG1 A:THR15 4.9 25.8 1.0

Zinc binding site 2 out of 6 in 2fsa

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Zinc binding site 2 out of 6 in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME2 Bound State


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 Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME2 Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:16.5
occ:1.00
SG A:CYS26 2.3 16.1 1.0
SG A:CYS29 2.3 15.3 1.0
SG A:CYS56 2.4 15.9 1.0
SG A:CYS53 2.4 15.8 1.0
CB A:CYS26 3.2 15.6 1.0
CB A:CYS56 3.3 15.1 1.0
CB A:CYS29 3.3 15.5 1.0
CB A:CYS53 3.5 16.1 1.0
N A:CYS29 3.6 15.6 1.0
OH A:TYR33 4.0 16.3 1.0
N A:CYS53 4.0 16.2 1.0
CA A:CYS29 4.1 14.5 1.0
O A:HOH530 4.2 24.7 1.0
CA A:CYS53 4.3 15.9 1.0
CE1 A:TYR33 4.3 12.9 1.0
CB A:ARG28 4.4 20.9 1.0
N A:CYS56 4.4 15.7 1.0
CA A:CYS56 4.4 16.0 1.0
CZ A:TYR33 4.5 14.4 1.0
O A:HOH599 4.6 41.1 1.0
CA A:CYS26 4.6 15.7 1.0
C A:ARG28 4.7 17.5 1.0
O A:CYS53 4.9 14.2 1.0
CA A:ARG28 4.9 18.4 1.0
C A:CYS53 4.9 16.1 1.0
N A:ARG28 4.9 18.4 1.0
C A:CYS29 5.0 13.6 1.0

Zinc binding site 3 out of 6 in 2fsa

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Zinc binding site 3 out of 6 in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME2 Bound State


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 Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME2 Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:22.0
occ:1.00
ND1 B:HIS34 2.2 23.2 1.0
SG B:CYS13 2.2 25.1 1.0
SG B:CYS37 2.3 22.7 1.0
SG B:CYS11 2.3 21.7 1.0
CG B:HIS34 3.1 21.2 1.0
CE1 B:HIS34 3.2 23.4 1.0
CB B:CYS11 3.2 22.6 1.0
CB B:CYS37 3.2 24.1 1.0
CB B:HIS34 3.4 21.9 1.0
CB B:CYS13 3.5 26.1 1.0
N B:CYS13 4.0 26.9 1.0
N B:HIS34 4.2 21.2 1.0
NE2 B:HIS34 4.3 23.1 1.0
O B:HOH227 4.3 30.6 1.0
CD2 B:HIS34 4.3 22.6 1.0
CA B:CYS13 4.3 27.2 1.0
CA B:HIS34 4.5 21.6 1.0
N B:ILE12 4.5 28.4 1.0
CA B:CYS11 4.6 26.0 1.0
CA B:CYS37 4.7 27.0 1.0
C B:CYS11 4.8 27.5 1.0
OG1 B:THR15 4.8 27.7 1.0

Zinc binding site 4 out of 6 in 2fsa

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Zinc binding site 4 out of 6 in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME2 Bound State


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 Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME2 Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:19.9
occ:1.00
SG B:CYS29 2.3 19.4 1.0
SG B:CYS26 2.3 17.1 1.0
SG B:CYS53 2.3 20.1 1.0
SG B:CYS56 2.4 18.5 1.0
CB B:CYS26 3.2 19.5 1.0
CB B:CYS56 3.2 20.2 1.0
CB B:CYS29 3.3 19.8 1.0
CB B:CYS53 3.5 19.9 1.0
N B:CYS29 3.7 17.9 1.0
N B:CYS53 4.0 20.5 1.0
OH B:TYR33 4.0 20.8 1.0
CA B:CYS29 4.1 18.1 1.0
O B:HOH206 4.2 23.4 1.0
CA B:CYS53 4.3 21.0 1.0
N B:CYS56 4.3 20.5 1.0
CA B:CYS56 4.4 19.8 1.0
CB B:ARG28 4.5 17.0 1.0
CE1 B:TYR33 4.6 18.1 1.0
CA B:CYS26 4.6 19.8 1.0
CZ B:TYR33 4.7 21.4 1.0
C B:ARG28 4.7 17.1 1.0
C B:CYS53 4.9 21.7 1.0
O B:CYS53 4.9 22.9 1.0
C B:CYS29 4.9 19.9 1.0
N B:ARG28 5.0 17.8 1.0
CA B:ARG28 5.0 17.6 1.0

Zinc binding site 5 out of 6 in 2fsa

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Zinc binding site 5 out of 6 in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME2 Bound State


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 Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME2 Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn505

b:31.1
occ:1.00
SG C:CYS37 2.2 36.3 1.0
SG C:CYS13 2.2 34.2 1.0
ND1 C:HIS34 2.3 29.1 1.0
SG C:CYS11 2.3 26.1 1.0
CB C:CYS11 3.1 27.2 1.0
CB C:CYS37 3.2 39.4 1.0
CG C:HIS34 3.2 30.1 1.0
CE1 C:HIS34 3.3 31.5 1.0
CB C:HIS34 3.4 29.1 1.0
CB C:CYS13 3.5 39.9 1.0
N C:CYS13 4.1 39.8 1.0
N C:HIS34 4.2 26.4 1.0
CD2 C:HIS34 4.4 29.2 1.0
NE2 C:HIS34 4.4 30.8 1.0
CA C:CYS13 4.4 39.9 1.0
CA C:HIS34 4.4 27.2 1.0
CA C:CYS11 4.5 32.0 1.0
N C:ILE12 4.6 35.2 1.0
CA C:CYS37 4.6 39.6 1.0
CG1 C:ILE12 4.7 38.7 1.0
C C:CYS11 4.9 32.7 1.0
N C:CYS37 5.0 40.1 1.0
OG1 C:THR15 5.0 36.8 1.0

Zinc binding site 6 out of 6 in 2fsa

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Zinc binding site 6 out of 6 in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME2 Bound State


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 Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME2 Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn506

b:25.1
occ:1.00
SG C:CYS26 2.3 25.4 1.0
SG C:CYS53 2.4 26.7 1.0
SG C:CYS29 2.4 25.1 1.0
SG C:CYS56 2.4 22.6 1.0
CB C:CYS26 3.1 24.8 1.0
CB C:CYS56 3.2 27.5 1.0
CB C:CYS29 3.3 24.2 1.0
CB C:CYS53 3.6 27.7 1.0
N C:CYS29 3.7 23.2 1.0
OH C:TYR33 3.9 30.6 1.0
N C:CYS53 4.0 28.5 1.0
CA C:CYS29 4.1 23.6 1.0
N C:CYS56 4.3 30.7 1.0
CA C:CYS53 4.3 28.8 1.0
O C:HOH361 4.3 32.6 1.0
CA C:CYS56 4.3 28.8 1.0
CB C:ARG28 4.4 24.2 1.0
CE1 C:TYR33 4.5 27.6 1.0
CZ C:TYR33 4.6 27.2 1.0
CA C:CYS26 4.6 26.0 1.0
C C:ARG28 4.7 23.9 1.0
O C:CYS53 4.9 28.8 1.0
C C:CYS53 4.9 29.5 1.0
C C:CYS29 5.0 24.1 1.0
CA C:ARG28 5.0 24.9 1.0

Reference:

H.Li, S.Ilin, W.Wang, E.M.Duncan, J.Wysocka, C.D.Allis, D.J.Patel. Molecular Basis For Site-Specific Read-Out of Histone H3K4ME3 By the Bptf Phd Finger of Nurf. Nature V. 442 91 2006.
ISSN: ISSN 0028-0836
PubMed: 16728978
DOI: 10.1038/NATURE04802
Page generated: Wed Dec 16 03:28:37 2020

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