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Zinc in PDB 2pf4: Crystal Structure of the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit

Protein crystallography data

The structure of Crystal Structure of the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit, PDB code: 2pf4 was solved by U.Cho, S.Morrone, W.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 94.711, 105.501, 111.937, 115.64, 109.55, 94.11
R / Rfree (%) 24.4 / 30.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit (pdb code 2pf4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit, PDB code: 2pf4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2pf4

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Zinc binding site 1 out of 8 in the Crystal Structure of the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit


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 the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn601

b:0.7
occ:1.00
SG E:CYS103 2.3 0.9 1.0
SG E:CYS116 2.3 0.1 1.0
SG E:CYS113 2.3 0.8 1.0
SG E:CYS111 2.4 0.7 1.0
CB E:CYS116 3.4 0.3 1.0
CB E:CYS113 3.5 0.5 1.0
CB E:CYS103 3.5 0.7 1.0
CB E:CYS111 3.8 0.0 1.0
CB E:LYS98 3.9 1.0 1.0
N E:CYS113 4.0 0.0 1.0
CA E:CYS113 4.4 0.8 1.0
O E:CYS111 4.4 0.6 1.0
C E:CYS111 4.4 0.2 1.0
CA E:CYS103 4.5 0.4 1.0
CA E:CYS111 4.6 0.3 1.0
N E:CYS116 4.6 0.2 1.0
CA E:CYS116 4.6 0.6 1.0
N E:LYS98 4.6 0.0 1.0
O E:CYS113 4.7 0.3 1.0
N E:ILE112 4.8 0.4 1.0
CA E:LYS98 4.9 0.1 1.0
C E:CYS113 5.0 0.0 1.0

Zinc binding site 2 out of 8 in 2pf4

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Zinc binding site 2 out of 8 in the Crystal Structure of the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit


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 the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn602

b:99.7
occ:1.00
SG E:CYS138 2.3 0.4 1.0
SG E:CYS143 2.3 0.3 1.0
SG E:CYS140 2.4 0.1 1.0
CG E:HIS122 3.0 0.7 1.0
ND1 E:HIS122 3.0 0.9 1.0
CB E:CYS138 3.3 0.8 1.0
CB E:HIS122 3.3 0.4 1.0
CB E:CYS143 3.5 0.8 1.0
CD2 E:HIS122 3.5 0.4 1.0
CB E:CYS140 3.5 0.1 1.0
CE1 E:HIS122 3.6 0.6 1.0
NE2 E:HIS122 3.8 0.5 1.0
N E:CYS143 4.2 0.1 1.0
CA E:CYS143 4.4 0.9 1.0
N E:CYS140 4.5 0.1 1.0
CA E:CYS140 4.6 0.3 1.0
CA E:HIS122 4.7 0.1 1.0
CA E:CYS138 4.7 0.2 1.0
O E:CYS140 5.0 0.8 1.0

Zinc binding site 3 out of 8 in 2pf4

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Zinc binding site 3 out of 8 in the Crystal Structure of the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit


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 the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn701

b:0.0
occ:1.00
SG F:CYS116 2.3 0.8 1.0
SG F:CYS103 2.3 0.6 1.0
SG F:CYS113 2.3 0.6 1.0
SG F:CYS111 2.4 0.7 1.0
CB F:CYS111 3.4 0.3 1.0
CB F:CYS116 3.4 0.1 1.0
CB F:CYS113 3.5 0.8 1.0
CB F:CYS103 3.5 0.7 1.0
OG1 F:THR109 3.9 0.5 1.0
CD1 F:LEU115 4.2 0.3 1.0
N F:LYS98 4.4 0.0 1.0
CA F:CYS116 4.5 0.0 1.0
CA F:CYS103 4.5 0.5 1.0
N F:CYS116 4.6 0.5 1.0
CB F:LYS98 4.6 0.0 1.0
CA F:CYS113 4.7 0.9 1.0
O F:LYS98 4.7 0.8 1.0
CA F:CYS111 4.8 0.7 1.0
CB F:THR109 4.8 0.4 1.0
O F:CYS113 4.9 0.3 1.0
C F:CYS113 5.0 0.2 1.0

Zinc binding site 4 out of 8 in 2pf4

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Zinc binding site 4 out of 8 in the Crystal Structure of the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit


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 the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn702

b:0.7
occ:1.00
SG F:CYS140 2.3 0.3 1.0
SG F:CYS138 2.3 0.9 1.0
SG F:CYS143 2.3 0.3 1.0
ND1 F:HIS122 2.5 0.6 1.0
CG F:HIS122 3.0 0.6 1.0
CE1 F:HIS122 3.2 0.6 1.0
CB F:CYS140 3.3 0.3 1.0
CB F:HIS122 3.4 0.2 1.0
CB F:CYS143 3.4 0.6 1.0
CB F:CYS138 3.6 0.3 1.0
CD2 F:HIS122 3.9 0.5 1.0
NE2 F:HIS122 4.0 0.5 1.0
N F:CYS143 4.3 0.1 1.0
CA F:CYS143 4.4 0.8 1.0
N F:CYS140 4.4 0.9 1.0
CA F:CYS140 4.4 0.3 1.0
CA F:HIS122 4.5 0.9 1.0
CB F:LEU133 4.6 0.1 1.0
CA F:CYS138 4.8 0.8 1.0
O F:CYS140 4.9 0.4 1.0
C F:CYS140 4.9 0.0 1.0
C F:CYS138 5.0 0.8 1.0

Zinc binding site 5 out of 8 in 2pf4

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Zinc binding site 5 out of 8 in the Crystal Structure of the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit


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 the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn801

b:0.5
occ:1.00
SG G:CYS116 2.3 0.2 1.0
SG G:CYS111 2.3 0.9 1.0
SG G:CYS103 2.3 0.8 1.0
SG G:CYS113 2.3 0.2 1.0
CB G:CYS113 3.3 0.0 1.0
CB G:CYS111 3.3 0.5 1.0
CB G:CYS116 3.5 0.8 1.0
CB G:CYS103 3.6 1.0 1.0
O G:LYS98 3.9 0.9 1.0
CB G:SER108 4.2 1.0 1.0
CA G:CYS113 4.4 0.9 1.0
CA G:CYS103 4.4 0.4 1.0
N G:CYS116 4.6 0.4 1.0
CA G:CYS116 4.6 0.8 1.0
CD1 G:LEU115 4.7 0.0 1.0
O G:SER108 4.7 0.6 1.0
CA G:CYS111 4.8 0.7 1.0
OG G:SER108 4.8 0.8 1.0
N G:CYS113 4.9 0.4 1.0
C G:LYS98 4.9 0.8 1.0

Zinc binding site 6 out of 8 in 2pf4

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Zinc binding site 6 out of 8 in the Crystal Structure of the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit


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 the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn802

b:98.2
occ:1.00
ND1 G:HIS122 2.2 0.5 1.0
SG G:CYS143 2.3 0.5 1.0
SG G:CYS138 2.3 0.8 1.0
SG G:CYS140 2.3 0.8 1.0
CE1 G:HIS122 2.9 0.7 1.0
CG G:HIS122 3.1 0.1 1.0
CB G:CYS138 3.2 0.5 1.0
CB G:CYS143 3.3 0.0 1.0
CB G:CYS140 3.5 0.8 1.0
CB G:HIS122 3.5 0.8 1.0
NE2 G:HIS122 3.9 0.6 1.0
CD2 G:HIS122 4.0 0.8 1.0
N G:CYS143 4.1 1.0 1.0
CA G:CYS143 4.3 1.0 1.0
N G:CYS140 4.4 0.4 1.0
CA G:CYS140 4.5 0.2 1.0
CA G:CYS138 4.6 0.5 1.0
CA G:HIS122 4.7 0.2 1.0
CB G:LEU133 4.8 0.0 1.0
C G:CYS138 4.9 0.2 1.0
C G:CYS140 4.9 0.3 1.0
CG G:LEU133 5.0 99.4 1.0

Zinc binding site 7 out of 8 in 2pf4

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Zinc binding site 7 out of 8 in the Crystal Structure of the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn901

b:0.6
occ:1.00
SG H:CYS103 2.3 0.7 1.0
SG H:CYS111 2.3 0.5 1.0
SG H:CYS116 2.3 0.9 1.0
SG H:CYS113 2.3 0.2 1.0
CB H:CYS113 3.4 0.2 1.0
CB H:CYS116 3.4 0.1 1.0
CB H:CYS103 3.5 0.2 1.0
CB H:CYS111 3.5 0.4 1.0
OG1 H:THR109 3.9 0.8 1.0
N H:CYS113 4.2 0.6 1.0
N H:LYS98 4.4 0.6 1.0
CA H:CYS113 4.4 0.4 1.0
CB H:LYS98 4.4 0.3 1.0
N H:CYS116 4.5 0.7 1.0
CA H:CYS116 4.5 0.1 1.0
CA H:CYS103 4.6 0.8 1.0
CA H:CYS111 4.7 0.7 1.0
C H:CYS111 4.8 0.7 1.0
CB H:THR109 4.8 1.0 1.0
CA H:LYS98 4.9 0.3 1.0
O H:CYS113 5.0 0.3 1.0
O H:CYS111 5.0 0.2 1.0
CG2 H:THR109 5.0 0.8 1.0

Zinc binding site 8 out of 8 in 2pf4

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Zinc binding site 8 out of 8 in the Crystal Structure of the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit


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 the Full-Length Simian Virus 40 Small T Antigen Complexed with the Protein Phosphatase 2A Aalpha Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn902

b:98.6
occ:1.00
ND1 H:HIS122 2.0 94.2 1.0
SG H:CYS138 2.3 0.2 1.0
SG H:CYS143 2.3 0.2 1.0
SG H:CYS140 2.3 0.4 1.0
CE1 H:HIS122 3.0 93.6 1.0
CG H:HIS122 3.1 95.5 1.0
CB H:CYS138 3.1 0.8 1.0
CB H:CYS143 3.4 0.7 1.0
CB H:HIS122 3.4 97.1 1.0
CB H:CYS140 3.5 0.3 1.0
NE2 H:HIS122 4.1 92.6 1.0
CD2 H:HIS122 4.2 93.8 1.0
N H:CYS143 4.4 0.3 1.0
CB H:LEU133 4.5 99.4 1.0
CA H:CYS138 4.5 0.0 1.0
N H:CYS140 4.5 0.5 1.0
CA H:CYS143 4.5 0.9 1.0
CA H:CYS140 4.5 0.4 1.0
CA H:HIS122 4.7 97.5 1.0
C H:CYS138 4.7 0.7 1.0
O H:CYS138 4.7 0.2 1.0
CG H:LEU133 4.7 99.0 1.0
O H:CYS140 4.9 0.4 1.0
C H:CYS140 5.0 0.3 1.0

Reference:

U.S.Cho, S.Morrone, A.A.Sablina, J.D.Arroyo, W.C.Hahn, W.Xu. Structural Basis of PP2A Inhibition By Small T Antigen. Plos Biol. V. 5 E202 2007.
ISSN: ISSN 1544-9173
PubMed: 17608567
DOI: 10.1371/JOURNAL.PBIO.0050202
Page generated: Wed Dec 16 03:48:03 2020

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