Zinc in PDB 6j2p: Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3

Protein crystallography data

The structure of Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3, PDB code: 6j2p was solved by C.He, F.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.28 / 2.85
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 81.810, 106.170, 139.830, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 28.8

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3 (pdb code 6j2p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3, PDB code: 6j2p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 6j2p

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Zinc binding site 1 out of 12 in the Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:52.1
occ:1.00
 SG A:CYS69 2.4 50.1 1.0
SG A:CYS42 2.4 49.1 1.0
SG A:CYS39 2.4 43.0 1.0
SG A:CYS66 2.5 39.1 1.0
CB A:CYS39 3.2 46.5 1.0
N A:CYS42 3.5 55.1 1.0
CB A:CYS69 3.5 45.0 1.0
CB A:CYS66 3.6 43.7 1.0
CB A:CYS42 3.6 49.5 1.0
CA A:CYS42 4.0 51.8 1.0
N A:CYS66 4.1 46.9 1.0
CE2 A:PHE46 4.3 45.8 1.0
CZ A:PHE46 4.4 45.7 1.0
CA A:CYS66 4.4 52.5 1.0
N A:CYS69 4.4 51.0 1.0
O A:CYS42 4.5 61.2 1.0
C A:CYS42 4.5 56.2 1.0
C A:GLY41 4.5 58.5 1.0
CA A:CYS69 4.5 49.0 1.0
CG2 A:THR74 4.6 49.3 1.0
CA A:CYS39 4.6 49.4 1.0
N A:GLY41 4.6 45.9 1.0
CA A:GLY41 4.6 53.1 1.0

Zinc binding site 2 out of 12 in 6j2p

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Zinc binding site 2 out of 12 in the Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:49.5
occ:1.00
 SG A:CYS109 2.4 51.0 1.0
SG A:CYS98 2.5 71.3 1.0
SG A:CYS93 2.5 51.7 1.0
ND1 A:HIS113 2.6 53.8 1.0
CB A:CYS98 2.9 40.5 1.0
CB A:CYS93 3.2 52.9 1.0
CG A:HIS113 3.3 61.5 1.0
CE1 A:HIS113 3.3 58.3 1.0
CB A:CYS109 3.4 59.5 1.0
CB A:HIS113 3.6 58.6 1.0
N A:CYS109 3.9 57.6 1.0
CD2 A:HIS113 4.2 66.9 1.0
NE2 A:HIS113 4.2 64.1 1.0
CA A:CYS109 4.3 59.8 1.0
CA A:CYS98 4.4 56.7 1.0
CB A:ILE95 4.6 48.9 1.0
CG1 A:ILE95 4.7 50.1 1.0
CA A:CYS93 4.7 56.2 1.0
CB A:LYS100 4.8 59.0 1.0

Zinc binding site 3 out of 12 in 6j2p

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Zinc binding site 3 out of 12 in the Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:50.0
occ:1.00
 ND1 A:HIS47 2.1 51.2 1.0
SG A:CYS27 2.3 44.1 1.0
SG A:CYS50 2.4 42.1 1.0
SG A:CYS25 2.4 45.1 1.0
CB A:CYS25 3.0 43.7 1.0
CG A:HIS47 3.1 47.1 1.0
CE1 A:HIS47 3.1 46.3 1.0
CB A:CYS50 3.3 49.9 1.0
CB A:HIS47 3.3 43.0 1.0
CB A:CYS27 3.5 51.0 1.0
N A:HIS47 3.9 50.5 1.0
N A:CYS27 4.1 54.6 1.0
NE2 A:HIS47 4.2 40.1 1.0
CD2 A:HIS47 4.2 43.9 1.0
CA A:HIS47 4.2 46.7 1.0
CA A:CYS27 4.4 53.0 1.0
CA A:CYS25 4.4 49.1 1.0
CZ A:ARG29 4.6 56.8 1.0
NH2 A:ARG29 4.6 58.5 1.0
N A:ILE26 4.6 46.6 1.0
CA A:CYS50 4.7 50.0 1.0
NH1 A:ARG29 4.7 54.5 1.0
C A:CYS25 4.9 51.3 1.0
O A:TYR24 4.9 49.3 1.0
N A:CYS50 5.0 47.5 1.0
NE A:ARG29 5.0 62.7 1.0

Zinc binding site 4 out of 12 in 6j2p

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Zinc binding site 4 out of 12 in the Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:60.8
occ:1.00
 ND1 B:HIS47 2.3 75.5 1.0
SG B:CYS27 2.3 73.8 1.0
SG B:CYS25 2.5 49.0 1.0
SG B:CYS50 2.5 68.0 1.0
CB B:CYS50 3.1 61.7 1.0
CG B:HIS47 3.1 67.8 1.0
CB B:CYS27 3.2 60.4 1.0
CB B:CYS25 3.3 58.2 1.0
CE1 B:HIS47 3.3 75.0 1.0
CB B:HIS47 3.4 65.4 1.0
N B:CYS27 3.8 73.4 1.0
N B:HIS47 3.9 60.1 1.0
CA B:CYS27 4.1 70.8 1.0
CD2 B:HIS47 4.3 69.0 1.0
CA B:HIS47 4.3 63.7 1.0
NE2 B:HIS47 4.3 71.3 1.0
N B:ILE26 4.5 55.6 1.0
CA B:CYS50 4.6 64.1 1.0
NH2 B:ARG29 4.6 72.9 1.0
CA B:CYS25 4.7 63.4 1.0
C B:CYS25 4.9 66.0 1.0
N B:CYS50 4.9 63.5 1.0
CG1 B:ILE26 4.9 60.0 1.0
C B:CYS27 5.0 72.0 1.0
C B:ILE26 5.0 68.0 1.0

Zinc binding site 5 out of 12 in 6j2p

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Zinc binding site 5 out of 12 in the Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3


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 Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:55.7
occ:1.00
 SG B:CYS42 2.3 54.7 1.0
SG B:CYS69 2.3 48.0 1.0
SG B:CYS66 2.4 46.4 1.0
SG B:CYS39 2.4 53.1 1.0
CB B:CYS42 3.3 61.5 1.0
N B:CYS42 3.3 60.1 1.0
CB B:CYS69 3.3 55.2 1.0
CB B:CYS39 3.4 51.8 1.0
CB B:CYS66 3.7 48.5 1.0
CA B:CYS42 3.8 63.7 1.0
N B:CYS66 4.0 58.5 1.0
O B:CYS42 4.1 67.9 1.0
OG1 B:THR74 4.1 62.5 1.0
C B:CYS42 4.2 67.0 1.0
C B:GLY41 4.4 59.2 1.0
N B:CYS69 4.4 57.4 1.0
CA B:CYS66 4.4 55.7 1.0
CA B:CYS69 4.4 58.2 1.0
CE1 B:PHE46 4.5 48.8 1.0
CA B:GLY41 4.6 59.5 1.0
N B:GLY41 4.7 61.5 1.0
CZ B:PHE46 4.7 49.1 1.0
CB B:THR74 4.7 63.4 1.0
CA B:CYS39 4.8 51.6 1.0
O B:CYS66 4.9 53.6 1.0

Zinc binding site 6 out of 12 in 6j2p

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Zinc binding site 6 out of 12 in the Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3


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 Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:51.5
occ:1.00
 ND1 B:HIS113 2.1 59.7 1.0
SG B:CYS109 2.3 46.2 1.0
SG B:CYS98 2.5 54.5 1.0
SG B:CYS93 2.6 56.7 1.0
CE1 B:HIS113 3.0 61.6 1.0
CB B:CYS93 3.1 54.9 1.0
CG B:HIS113 3.2 58.6 1.0
CB B:CYS98 3.3 59.7 1.0
CB B:CYS109 3.4 56.7 1.0
CB B:HIS113 3.5 52.7 1.0
N B:CYS109 4.0 47.3 1.0
NE2 B:HIS113 4.1 74.0 1.0
CD2 B:HIS113 4.2 69.5 1.0
CA B:CYS109 4.3 55.8 1.0
CB B:ILE95 4.4 58.7 1.0
CB B:LYS100 4.5 44.7 1.0
CG1 B:ILE95 4.6 54.3 1.0
CA B:CYS93 4.6 57.0 1.0
CA B:CYS98 4.7 59.3 1.0
OG B:SER110 5.0 63.5 1.0

Zinc binding site 7 out of 12 in 6j2p

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Zinc binding site 7 out of 12 in the Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:68.3
occ:1.00
 ND1 C:HIS47 2.2 82.0 1.0
SG C:CYS50 2.4 60.6 1.0
CB C:CYS27 2.4 76.8 1.0
SG C:CYS27 2.5 0.5 1.0
SG C:CYS25 2.5 64.8 1.0
CG C:HIS47 3.1 75.8 1.0
CE1 C:HIS47 3.2 78.4 1.0
CB C:CYS25 3.3 73.0 1.0
CB C:HIS47 3.3 72.4 1.0
CB C:CYS50 3.4 70.8 1.0
N C:CYS27 3.6 67.5 1.0
CA C:CYS27 3.6 72.9 1.0
N C:HIS47 4.0 75.7 1.0
CD2 C:HIS47 4.2 82.1 1.0
NE2 C:HIS47 4.2 83.1 1.0
CA C:HIS47 4.3 76.2 1.0
NH2 C:ARG29 4.5 83.5 1.0
NE C:ARG29 4.5 91.6 1.0
CA C:CYS25 4.6 72.5 1.0
C C:CYS27 4.7 73.6 1.0
CZ C:ARG29 4.7 92.5 1.0
N C:ILE26 4.7 69.1 1.0
CA C:CYS50 4.8 72.7 1.0
C C:ILE26 4.8 66.6 1.0
C C:CYS25 4.9 69.2 1.0
CG C:ARG29 4.9 88.3 1.0
N C:LYS28 4.9 77.3 1.0

Zinc binding site 8 out of 12 in 6j2p

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Zinc binding site 8 out of 12 in the Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3


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 Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:72.7
occ:1.00
 SG C:CYS69 2.3 61.1 1.0
SG C:CYS42 2.4 91.0 1.0
SG C:CYS39 2.5 72.3 1.0
SG C:CYS66 2.5 70.1 1.0
CB C:CYS42 3.4 83.3 1.0
CB C:CYS69 3.4 70.4 1.0
CB C:CYS66 3.4 66.9 1.0
N C:CYS42 3.5 88.7 1.0
CB C:CYS39 3.5 72.0 1.0
OG1 C:THR74 3.7 81.4 1.0
CA C:CYS42 4.0 83.2 1.0
N C:CYS66 4.2 71.8 1.0
CZ C:PHE46 4.2 77.3 1.0
N C:CYS69 4.2 68.4 1.0
CE1 C:PHE46 4.3 79.5 1.0
CA C:CYS66 4.4 69.4 1.0
CA C:CYS69 4.4 70.9 1.0
C C:CYS42 4.5 86.3 1.0
C C:GLY41 4.6 85.9 1.0
O C:THR74 4.6 0.9 1.0
CA C:GLY41 4.8 80.3 1.0
O C:CYS42 4.8 92.5 1.0
N C:GLY41 4.9 80.7 1.0
CB C:THR74 4.9 81.2 1.0
CA C:CYS39 4.9 76.0 1.0
C C:CYS66 5.0 62.0 1.0

Zinc binding site 9 out of 12 in 6j2p

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Zinc binding site 9 out of 12 in the Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn203

b:0.1
occ:1.00
 SG C:CYS93 2.4 0.7 1.0
SG C:CYS98 2.4 0.8 1.0
SG C:CYS109 2.5 0.7 1.0
ND1 C:HIS113 2.5 0.4 1.0
CB C:CYS109 3.0 0.8 1.0
CB C:CYS98 3.0 0.1 1.0
CE1 C:HIS113 3.1 0.2 1.0
CG C:HIS113 3.3 0.3 1.0
CB C:CYS93 3.5 0.3 1.0
N C:CYS109 3.7 0.2 1.0
CB C:HIS113 3.8 0.3 1.0
CA C:CYS109 3.9 1.0 1.0
CG2 C:ILE95 3.9 0.3 1.0
NE2 C:HIS113 4.0 0.8 1.0
CD2 C:HIS113 4.1 0.8 1.0
CA C:CYS98 4.5 0.4 1.0
C C:CYS109 4.7 0.7 1.0
N C:SER110 4.8 0.5 1.0
C C:TYR108 4.9 0.9 1.0
CB C:TYR108 4.9 0.3 1.0
CA C:CYS93 5.0 0.1 1.0

Zinc binding site 10 out of 12 in 6j2p

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Zinc binding site 10 out of 12 in the Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Saccharomyces Cerevisiae SPP1 in Complex with H3K4ME3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:50.5
occ:1.00
 ND1 D:HIS47 2.1 59.9 1.0
SG D:CYS50 2.3 57.9 1.0
SG D:CYS27 2.4 54.0 1.0
SG D:CYS25 2.4 42.5 1.0
CG D:HIS47 3.0 54.6 1.0
CE1 D:HIS47 3.0 57.2 1.0
CB D:CYS25 3.0 59.4 1.0
CB D:CYS27 3.2 64.0 1.0
CB D:HIS47 3.3 52.4 1.0
CB D:CYS50 3.4 59.9 1.0
N D:CYS27 3.8 57.6 1.0
N D:HIS47 4.0 58.2 1.0
NE2 D:HIS47 4.0 63.4 1.0
CD2 D:HIS47 4.0 53.9 1.0
CA D:CYS27 4.1 57.5 1.0
CA D:HIS47 4.3 55.6 1.0
NH2 D:ARG29 4.4 60.9 1.0
N D:ILE26 4.4 56.2 1.0
CA D:CYS25 4.4 56.4 1.0
CA D:CYS50 4.8 56.3 1.0
C D:CYS25 4.8 60.3 1.0
CZ D:ARG29 4.8 71.6 1.0
C D:CYS27 4.9 55.3 1.0
C D:ILE26 5.0 54.7 1.0
CG1 D:ILE26 5.0 60.8 1.0

Reference:

C.He, N.Liu, D.Xie, Y.Liu, Y.Xiao, F.Li. Structural Basis For Histone H3K4ME3 Recognition By the N-Terminal Domain of the Phd Finger Protein SPP1. Biochem.J. V. 476 1957 2019.
ISSN: ESSN 1470-8728
PubMed: 31253666
DOI: 10.1042/BCJ20190091
Page generated: Wed Dec 16 12:02:34 2020

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