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Zinc in PDB 5yug: ATVAL1 Phd-Like Domain in the P31 Space Group

Protein crystallography data

The structure of ATVAL1 Phd-Like Domain in the P31 Space Group, PDB code: 5yug was solved by M.M.Zhang, B.X.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.11 / 1.57
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 52.228, 52.228, 121.674, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 25.4

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the ATVAL1 Phd-Like Domain in the P31 Space Group (pdb code 5yug). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the ATVAL1 Phd-Like Domain in the P31 Space Group, PDB code: 5yug:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 5yug

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Zinc binding site 1 out of 12 in the ATVAL1 Phd-Like Domain in the P31 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of ATVAL1 Phd-Like Domain in the P31 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:9.5
occ:1.00
ND1 A:HIS56 2.1 9.2 1.0
ND1 A:HIS73 2.1 9.8 1.0
SG A:CYS76 2.3 8.9 1.0
SG A:CYS52 2.3 9.5 1.0
CE1 A:HIS56 3.0 11.4 1.0
CE1 A:HIS73 3.0 8.8 1.0
CG A:HIS56 3.2 8.6 1.0
CG A:HIS73 3.2 8.1 1.0
CB A:CYS76 3.2 9.8 1.0
CB A:CYS52 3.3 8.4 1.0
CB A:HIS56 3.6 10.9 1.0
CB A:HIS73 3.6 8.3 1.0
NE2 A:HIS56 4.1 11.9 1.0
NE2 A:HIS73 4.1 8.0 1.0
CA A:CYS52 4.1 8.1 1.0
CD2 A:HIS56 4.2 8.6 1.0
CD2 A:HIS73 4.3 8.7 1.0
CB A:ALA78 4.5 8.8 1.0
CA A:CYS76 4.6 9.6 1.0
OG A:SER79 4.7 11.3 1.0
O A:HIS73 4.8 9.5 1.0
OE1 A:GLN59 4.9 14.4 1.0
N A:CYS52 5.0 8.9 1.0
CA A:HIS73 5.0 7.8 1.0
N A:SER79 5.0 8.2 1.0

Zinc binding site 2 out of 12 in 5yug

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Zinc binding site 2 out of 12 in the ATVAL1 Phd-Like Domain in the P31 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of ATVAL1 Phd-Like Domain in the P31 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:11.6
occ:1.00
SG A:CYS96 2.3 12.3 1.0
SG A:CYS68 2.3 11.1 1.0
SG A:CYS65 2.3 9.6 1.0
SG A:CYS93 2.4 12.5 1.0
CB A:CYS93 3.2 11.0 1.0
CB A:CYS65 3.2 10.5 1.0
CB A:CYS96 3.3 12.0 1.0
CB A:CYS68 3.4 10.0 1.0
N A:CYS68 3.8 10.9 1.0
N A:CYS93 3.8 10.3 1.0
CA A:CYS68 4.1 10.4 1.0
CA A:CYS93 4.1 11.5 1.0
O A:HOH302 4.4 18.8 1.0
CB A:LYS70 4.6 11.1 1.0
CA A:CYS65 4.6 10.4 1.0
CA A:CYS96 4.6 16.2 1.0
C A:CYS68 4.7 10.1 1.0
N A:SER69 4.7 11.2 1.0
CB A:LEU67 4.8 11.2 1.0
N A:LYS70 4.9 10.6 1.0
C A:LEU67 4.9 14.5 1.0
N A:CYS96 4.9 14.8 1.0

Zinc binding site 3 out of 12 in 5yug

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Zinc binding site 3 out of 12 in the ATVAL1 Phd-Like Domain in the P31 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of ATVAL1 Phd-Like Domain in the P31 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:13.4
occ:1.00
SG A:CYS16 2.3 15.7 1.0
SG A:CYS11 2.3 11.8 1.0
SG A:CYS39 2.3 13.0 1.0
SG A:CYS42 2.4 13.0 1.0
CB A:CYS16 3.1 14.5 1.0
CB A:CYS11 3.1 11.5 1.0
CB A:CYS42 3.3 10.9 1.0
CB A:CYS39 3.5 13.0 1.0
N A:CYS39 4.0 9.2 1.0
CG2 A:THR18 4.2 17.5 1.0
N A:CYS42 4.2 13.2 1.0
CA A:CYS39 4.3 10.9 1.0
NH2 A:ARG41 4.4 24.6 1.0
CA A:CYS42 4.4 14.7 1.0
CB A:ASN13 4.5 9.9 1.0
CA A:CYS16 4.5 11.6 1.0
CA A:CYS11 4.6 13.1 1.0
ND2 A:ASN13 4.7 12.1 1.0
CZ A:ARG41 4.9 22.2 1.0
NE A:ARG41 4.9 25.9 1.0
N A:GLY17 4.9 16.0 1.0
C A:CYS39 5.0 12.0 1.0
N A:THR18 5.0 17.1 1.0

Zinc binding site 4 out of 12 in 5yug

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Zinc binding site 4 out of 12 in the ATVAL1 Phd-Like Domain in the P31 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of ATVAL1 Phd-Like Domain in the P31 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:9.6
occ:1.00
ND1 B:HIS73 2.1 9.9 1.0
ND1 B:HIS56 2.1 8.6 1.0
SG B:CYS52 2.2 9.0 1.0
SG B:CYS76 2.3 8.3 1.0
CE1 B:HIS73 2.9 9.9 1.0
CE1 B:HIS56 3.0 11.6 1.0
CG B:HIS56 3.2 9.5 1.0
CG B:HIS73 3.2 7.6 1.0
CB B:CYS76 3.2 10.4 1.0
CB B:CYS52 3.3 9.0 1.0
CB B:HIS56 3.6 9.6 1.0
CB B:HIS73 3.6 8.0 1.0
O E:HOH326 4.1 11.3 1.0
NE2 B:HIS73 4.1 8.8 1.0
NE2 B:HIS56 4.1 10.5 1.0
CA B:CYS52 4.1 8.4 1.0
CD2 B:HIS73 4.2 8.1 1.0
CD2 B:HIS56 4.2 9.6 1.0
CB B:ALA78 4.6 9.4 1.0
CA B:CYS76 4.6 11.0 1.0
OG B:SER79 4.7 11.9 1.0
O B:HIS73 4.8 8.9 1.0
OE1 B:GLN59 4.9 16.3 1.0
N B:CYS52 5.0 7.9 1.0
CA B:HIS73 5.0 8.9 1.0

Zinc binding site 5 out of 12 in 5yug

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Zinc binding site 5 out of 12 in the ATVAL1 Phd-Like Domain in the P31 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of ATVAL1 Phd-Like Domain in the P31 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:11.6
occ:1.00
SG B:CYS68 2.3 10.9 1.0
SG B:CYS96 2.3 13.2 1.0
SG B:CYS65 2.3 9.4 1.0
SG B:CYS93 2.4 12.4 1.0
CB B:CYS93 3.2 12.5 1.0
CB B:CYS65 3.2 11.4 1.0
CB B:CYS96 3.3 12.5 1.0
CB B:CYS68 3.3 10.7 1.0
N B:CYS68 3.8 9.7 1.0
N B:CYS93 3.8 10.8 1.0
O G:HOH331 3.8 17.4 1.0
CA B:CYS68 4.1 11.0 1.0
CA B:CYS93 4.1 11.4 1.0
O B:HOH307 4.2 17.9 1.0
CB B:LYS70 4.6 11.2 1.0
CA B:CYS65 4.6 11.0 1.0
CA B:CYS96 4.7 15.8 1.0
C B:CYS68 4.7 9.0 1.0
N B:SER69 4.8 12.0 1.0
CB B:LEU67 4.8 10.1 1.0
N B:LYS70 4.9 9.4 1.0
C B:LEU67 4.9 13.5 1.0
N B:CYS96 4.9 13.4 1.0

Zinc binding site 6 out of 12 in 5yug

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Zinc binding site 6 out of 12 in the ATVAL1 Phd-Like Domain in the P31 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of ATVAL1 Phd-Like Domain in the P31 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:13.2
occ:1.00
SG B:CYS16 2.3 15.1 1.0
SG B:CYS11 2.3 11.3 1.0
SG B:CYS39 2.4 12.9 1.0
SG B:CYS42 2.4 13.2 1.0
CB B:CYS16 3.1 13.9 1.0
CB B:CYS11 3.1 9.9 1.0
CB B:CYS42 3.3 9.9 1.0
CB B:CYS39 3.5 13.4 1.0
N B:CYS39 4.0 9.4 1.0
CG2 B:THR18 4.1 16.6 1.0
N B:CYS42 4.2 13.0 1.0
CA B:CYS39 4.3 11.0 1.0
CA B:CYS42 4.4 13.1 1.0
NH2 B:ARG41 4.4 24.6 1.0
CB B:ASN13 4.5 9.0 1.0
CA B:CYS16 4.5 10.9 1.0
CA B:CYS11 4.6 11.5 1.0
ND2 B:ASN13 4.7 11.0 1.0
NE B:ARG41 4.9 26.1 1.0
CZ B:ARG41 4.9 25.4 1.0
N B:GLY17 4.9 15.9 1.0
N B:THR18 5.0 17.8 1.0
C B:CYS39 5.0 11.3 1.0

Zinc binding site 7 out of 12 in 5yug

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Zinc binding site 7 out of 12 in the ATVAL1 Phd-Like Domain in the P31 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of ATVAL1 Phd-Like Domain in the P31 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:8.9
occ:1.00
ND1 E:HIS73 2.0 8.5 1.0
ND1 E:HIS56 2.1 10.0 1.0
SG E:CYS76 2.2 9.4 1.0
SG E:CYS52 2.3 10.7 1.0
CE1 E:HIS73 2.9 8.1 1.0
CE1 E:HIS56 3.0 12.6 1.0
CB E:CYS76 3.2 10.6 1.0
CG E:HIS56 3.2 12.1 1.0
CG E:HIS73 3.2 8.8 1.0
CB E:CYS52 3.2 11.8 1.0
CB E:HIS56 3.5 10.4 1.0
CB E:HIS73 3.7 8.8 1.0
NE2 E:HIS73 4.0 8.6 1.0
CA E:CYS52 4.0 8.9 1.0
NE2 E:HIS56 4.1 14.5 1.0
CD2 E:HIS73 4.2 10.5 1.0
O E:HOH315 4.2 10.5 1.0
CD2 E:HIS56 4.2 10.4 1.0
CB E:ALA78 4.4 9.2 1.0
CA E:CYS76 4.6 8.4 1.0
OG E:SER79 4.6 13.0 1.0
O E:HIS73 4.9 9.9 1.0
N E:CYS52 4.9 9.2 1.0
OE1 E:GLN59 4.9 11.8 1.0

Zinc binding site 8 out of 12 in 5yug

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Zinc binding site 8 out of 12 in the ATVAL1 Phd-Like Domain in the P31 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of ATVAL1 Phd-Like Domain in the P31 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn202

b:12.4
occ:1.00
SG E:CYS93 2.3 13.5 1.0
SG E:CYS96 2.3 12.0 1.0
SG E:CYS68 2.3 11.2 1.0
SG E:CYS65 2.4 10.0 1.0
CB E:CYS96 3.1 14.8 1.0
CB E:CYS68 3.3 10.9 1.0
CB E:CYS65 3.3 11.1 1.0
CB E:CYS93 3.5 11.0 1.0
N E:CYS68 3.7 12.7 1.0
OG1 E:THR95 3.9 29.0 1.0
N E:CYS93 4.0 11.6 1.0
CA E:CYS68 4.1 10.5 1.0
N E:CYS96 4.1 17.9 1.0
CA E:CYS96 4.2 16.4 1.0
CA E:CYS93 4.3 13.1 1.0
C E:CYS68 4.7 12.4 1.0
CB E:LYS70 4.7 11.9 1.0
CA E:CYS65 4.7 11.7 1.0
CB E:LEU67 4.8 13.1 1.0
C E:LEU67 4.8 13.3 1.0
N E:SER69 4.9 11.3 1.0
C E:CYS93 4.9 14.4 1.0
N E:LEU67 5.0 11.2 1.0

Zinc binding site 9 out of 12 in 5yug

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Zinc binding site 9 out of 12 in the ATVAL1 Phd-Like Domain in the P31 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of ATVAL1 Phd-Like Domain in the P31 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn203

b:15.8
occ:1.00
SG E:CYS11 2.3 16.2 1.0
SG E:CYS42 2.3 15.9 1.0
SG E:CYS16 2.4 19.8 1.0
SG E:CYS39 2.4 18.1 1.0
CB E:CYS16 3.1 18.7 1.0
CB E:CYS11 3.2 14.6 1.0
CB E:CYS42 3.3 13.5 1.0
CB E:CYS39 3.5 18.1 1.0
N E:CYS39 4.0 14.1 1.0
CG2 E:THR18 4.1 16.5 1.0
N E:CYS42 4.3 17.5 1.0
CA E:CYS39 4.3 16.7 1.0
CB E:ASN13 4.4 12.8 1.0
CA E:CYS42 4.4 15.7 1.0
CA E:CYS16 4.6 15.6 1.0
CA E:CYS11 4.7 15.2 1.0
N E:GLY17 4.8 16.9 1.0
ND2 E:ASN13 4.9 13.6 1.0
N E:THR18 5.0 18.4 1.0

Zinc binding site 10 out of 12 in 5yug

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Zinc binding site 10 out of 12 in the ATVAL1 Phd-Like Domain in the P31 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of ATVAL1 Phd-Like Domain in the P31 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn201

b:8.9
occ:1.00
ND1 G:HIS73 2.1 8.6 1.0
ND1 G:HIS56 2.1 11.2 1.0
SG G:CYS76 2.2 9.8 1.0
SG G:CYS52 2.3 10.9 1.0
CE1 G:HIS73 2.9 6.9 1.0
CE1 G:HIS56 2.9 10.4 1.0
CB G:CYS76 3.1 10.2 1.0
CG G:HIS56 3.2 13.7 1.0
CG G:HIS73 3.2 9.9 1.0
CB G:CYS52 3.2 10.8 1.0
CB G:HIS56 3.6 13.3 1.0
CB G:HIS73 3.7 9.3 1.0
NE2 G:HIS73 4.0 8.6 1.0
CA G:CYS52 4.1 9.4 1.0
NE2 G:HIS56 4.1 13.4 1.0
CD2 G:HIS73 4.2 10.5 1.0
CD2 G:HIS56 4.2 11.7 1.0
O G:HOH314 4.3 10.7 1.0
CB G:ALA78 4.4 9.4 1.0
CA G:CYS76 4.6 8.0 1.0
OG G:SER79 4.7 13.8 1.0
O G:HIS73 4.9 10.2 1.0
OE1 G:GLN59 4.9 11.9 1.0
N G:CYS52 4.9 8.8 1.0

Reference:

M.M.Zhang, B.X.Wu. ATVAL1 Phd-Like Domain in the P31 Space Group To Be Published.
Page generated: Wed Dec 16 11:24:36 2020

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