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Zinc in PDB 4nn2: Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6

Protein crystallography data

The structure of Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6, PDB code: 4nn2 was solved by Z.Liu, F.Li, J.Zhang, Y.Mei, J.Wu, Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.29 / 1.47
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.780, 102.780, 51.250, 90.00, 90.00, 120.00
R / Rfree (%) 15.9 / 17.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6 (pdb code 4nn2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6, PDB code: 4nn2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4nn2

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Zinc binding site 1 out of 6 in the Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:7.1
occ:1.00
ND1 A:HIS239 2.2 7.5 1.0
SG A:CYS242 2.3 8.6 1.0
SG A:CYS215 2.3 8.0 1.0
SG A:CYS212 2.4 7.3 1.0
CE1 A:HIS239 3.1 7.5 1.0
CB A:CYS212 3.1 7.7 1.0
CG A:HIS239 3.2 7.4 1.0
CB A:CYS242 3.3 8.6 1.0
CB A:CYS215 3.4 7.6 1.0
CB A:HIS239 3.5 7.3 1.0
N A:CYS215 3.9 7.2 1.0
N A:HIS239 4.1 7.5 1.0
CA A:CYS215 4.2 7.5 1.0
NE2 A:HIS239 4.2 7.5 1.0
CD2 A:HIS239 4.3 7.3 1.0
O A:HOH525 4.4 12.0 1.0
CA A:HIS239 4.4 7.5 1.0
CD A:ARG225 4.5 10.2 1.0
CA A:CYS212 4.6 8.1 1.0
O A:HOH505 4.6 8.5 1.0
CB A:PHE214 4.7 6.8 1.0
CA A:CYS242 4.7 8.8 1.0
CB A:ARG225 4.8 10.3 1.0
C A:CYS215 4.9 7.7 1.0
O A:VAL217 4.9 8.5 1.0
C A:PHE214 5.0 7.1 1.0

Zinc binding site 2 out of 6 in 4nn2

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Zinc binding site 2 out of 6 in the Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:6.9
occ:1.00
ND1 A:HIS302 2.2 6.6 1.0
SG A:CYS305 2.3 7.9 1.0
SG A:CYS280 2.3 7.2 1.0
SG A:CYS283 2.3 7.5 1.0
CB A:CYS280 3.0 7.7 1.0
CE1 A:HIS302 3.1 6.6 1.0
CB A:CYS305 3.2 8.4 1.0
CG A:HIS302 3.2 6.6 1.0
CB A:CYS283 3.3 7.9 1.0
CB A:HIS302 3.6 6.7 1.0
N A:CYS283 3.9 8.0 1.0
N A:HIS302 4.1 6.8 1.0
CA A:CYS283 4.2 8.0 1.0
NE2 A:HIS302 4.2 6.5 1.0
CD2 A:HIS302 4.3 6.5 1.0
O A:HOH627 4.4 24.0 1.0
CA A:HIS302 4.5 6.8 1.0
CA A:CYS280 4.5 7.7 1.0
CA A:CYS305 4.6 8.3 1.0
O B:HOH533 4.7 11.1 1.0
CB A:LEU282 4.8 8.1 1.0
CE1 A:HIS304 4.9 9.8 1.0
C A:CYS283 4.9 8.4 1.0
C A:LEU282 5.0 8.0 1.0

Zinc binding site 3 out of 6 in 4nn2

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Zinc binding site 3 out of 6 in the Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:7.4
occ:1.00
ND1 A:HIS329 2.1 8.6 1.0
SG A:CYS326 2.3 8.6 1.0
SG A:CYS292 2.3 8.0 1.0
SG A:CYS297 2.3 8.1 1.0
CE1 A:HIS329 3.0 8.8 1.0
CB A:CYS292 3.1 8.2 1.0
CG A:HIS329 3.2 9.1 1.0
CB A:CYS297 3.2 8.3 1.0
CB A:CYS326 3.4 8.9 1.0
CB A:HIS329 3.6 10.0 1.0
N A:CYS326 3.9 9.3 1.0
O A:HOH531 3.9 19.2 1.0
NE2 A:HIS329 4.2 8.7 1.0
CA A:CYS326 4.2 9.3 1.0
CD2 A:HIS329 4.3 9.0 1.0
N A:HIS329 4.5 10.9 1.0
CA A:CYS292 4.6 8.4 1.0
CB A:ILE294 4.6 11.1 1.0
CA A:CYS297 4.7 8.7 1.0
CA A:HIS329 4.7 10.9 1.0
C A:CYS326 4.8 9.9 1.0
CB A:LYS299 4.8 9.7 1.0
CG1 A:ILE294 4.8 10.9 1.0
O A:CYS326 4.9 9.1 1.0
CB A:ASN328 5.0 13.9 1.0

Zinc binding site 4 out of 6 in 4nn2

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Zinc binding site 4 out of 6 in the Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:7.7
occ:1.00
ND1 B:HIS239 2.1 8.4 1.0
SG B:CYS242 2.3 8.7 1.0
SG B:CYS215 2.3 8.9 1.0
SG B:CYS212 2.4 8.3 1.0
CB B:CYS212 3.0 9.3 1.0
CE1 B:HIS239 3.1 8.5 1.0
CG B:HIS239 3.2 8.4 1.0
CB B:CYS242 3.3 9.1 1.0
CB B:CYS215 3.4 8.8 1.0
CB B:HIS239 3.5 8.4 1.0
N B:CYS215 3.9 8.4 1.0
N B:HIS239 4.0 8.6 1.0
CA B:CYS215 4.2 8.7 1.0
NE2 B:HIS239 4.2 8.5 1.0
CD2 B:HIS239 4.3 8.4 1.0
CA B:HIS239 4.4 8.6 1.0
O B:HOH558 4.4 13.8 1.0
CD B:ARG225 4.4 11.4 1.0
CA B:CYS212 4.5 9.5 1.0
O B:HOH501 4.6 9.7 1.0
CB B:ARG225 4.7 11.9 1.0
CA B:CYS242 4.7 9.3 1.0
CB B:PHE214 4.8 8.0 1.0
C B:CYS215 4.9 9.0 1.0
O B:VAL217 4.9 9.5 1.0
C B:PHE214 5.0 8.4 1.0

Zinc binding site 5 out of 6 in 4nn2

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Zinc binding site 5 out of 6 in the Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:7.5
occ:1.00
ND1 B:HIS302 2.2 7.6 1.0
SG B:CYS305 2.3 8.1 1.0
SG B:CYS283 2.3 8.5 1.0
SG B:CYS280 2.4 8.1 1.0
CB B:CYS280 3.0 8.4 1.0
CE1 B:HIS302 3.1 7.5 1.0
CG B:HIS302 3.2 7.7 1.0
CB B:CYS305 3.2 8.5 1.0
CB B:CYS283 3.3 8.5 1.0
CB B:HIS302 3.6 7.7 1.0
N B:CYS283 3.9 8.6 1.0
N B:HIS302 4.1 7.8 1.0
CA B:CYS283 4.2 8.6 1.0
NE2 B:HIS302 4.2 7.5 1.0
CD2 B:HIS302 4.3 7.6 1.0
O B:HOH600 4.3 25.8 1.0
CA B:HIS302 4.5 7.9 1.0
CA B:CYS280 4.5 8.7 1.0
CA B:CYS305 4.7 8.8 1.0
O A:HOH547 4.7 9.6 1.0
C B:CYS283 4.9 9.1 1.0
CE1 B:HIS304 4.9 11.1 1.0
CB B:LEU282 4.9 8.2 1.0
C B:LEU282 5.0 8.6 1.0

Zinc binding site 6 out of 6 in 4nn2

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Zinc binding site 6 out of 6 in the Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Protein Crystal Structure of Human Borjeson-Forssman-Lehmann Syndrome Associated Protein PHF6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:11.5
occ:1.00
ND1 B:HIS329 2.1 14.2 1.0
SG B:CYS297 2.3 11.4 1.0
SG B:CYS292 2.3 10.9 1.0
SG B:CYS326 2.3 11.9 1.0
CE1 B:HIS329 2.9 15.3 1.0
CB B:CYS297 3.2 12.8 1.0
CB B:CYS292 3.2 10.2 1.0
CG B:HIS329 3.2 14.9 1.0
CB B:CYS326 3.3 11.4 1.0
CB B:HIS329 3.7 14.8 1.0
N B:CYS326 4.0 11.0 1.0
O B:HOH568 4.0 25.2 1.0
NE2 B:HIS329 4.1 15.5 1.0
CA B:CYS326 4.2 11.4 1.0
CD2 B:HIS329 4.3 15.3 1.0
CA B:CYS297 4.6 13.6 1.0
CB B:ILE294 4.6 13.1 1.0
N B:HIS329 4.6 15.1 1.0
CA B:CYS292 4.6 10.0 1.0
C B:CYS326 4.8 12.3 1.0
CA B:HIS329 4.8 14.9 1.0
CG1 B:ILE294 4.8 13.6 1.0
CB B:LYS299 4.9 12.7 1.0
O B:CYS326 4.9 12.3 1.0
CD B:LYS299 5.0 14.4 1.0

Reference:

Z.Liu, F.Li, J.Zhang, Y.Mei, J.Wu, Y.Shi. Crystal Structure of the Second Extended Phd Domain of Human PHF6 Protein J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
Page generated: Wed Dec 16 05:37:21 2020

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