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Zinc in PDB 8se4: Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation

Enzymatic activity of Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation

All present enzymatic activity of Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation:
2.7.11.13;

Protein crystallography data

The structure of Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation, PDB code: 8se4 was solved by A.T.Q.Cong, T.L.Witter, E.S.Bruinsma, S.Jayaraman, J.R.Hawse, M.P.Goetz, M.J.Schellenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.88 / 2.68
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 163.029, 158.572, 86.615, 90, 112.44, 90
R / Rfree (%) 20.3 / 25.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation (pdb code 8se4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation, PDB code: 8se4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8se4

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Zinc binding site 1 out of 8 in the Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:111.2
occ:1.00
 ND1 A:HIS37 2.0 145.9 1.0
SG A:CYS67 2.3 122.2 1.0
SG A:CYS70 2.3 117.3 1.0
SG A:CYS86 2.3 132.9 1.0
CE1 A:HIS37 2.6 131.4 1.0
CB A:CYS67 3.2 95.5 1.0
CB A:CYS86 3.2 144.0 1.0
CG A:HIS37 3.3 123.6 1.0
CB A:CYS70 3.6 134.6 1.0
N A:CYS70 3.7 144.1 1.0
NE2 A:HIS37 3.8 123.8 1.0
CB A:HIS37 4.0 119.7 1.0
CA A:CYS86 4.0 152.1 1.0
CD2 A:HIS37 4.1 128.4 1.0
CA A:CYS70 4.2 140.1 1.0
CA A:HIS37 4.2 110.2 1.0
CB A:VAL69 4.4 97.9 1.0
CA A:CYS67 4.6 98.6 1.0
C A:VAL69 4.8 135.7 1.0
CB A:PHE72 4.8 86.5 1.0
C A:CYS70 4.8 137.1 1.0
C A:CYS86 5.0 142.5 1.0
N A:LYS38 5.0 120.8 1.0
CA A:VAL69 5.0 108.4 1.0
CG1 A:VAL69 5.0 97.1 1.0

Zinc binding site 2 out of 8 in 8se4

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Zinc binding site 2 out of 8 in the Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:111.6
occ:1.00
 ND1 A:HIS75 2.0 107.4 1.0
SG A:CYS78 2.1 120.1 1.0
SG A:CYS53 2.2 124.6 1.0
SG A:CYS50 2.4 122.6 1.0
CE1 A:HIS75 3.0 91.2 1.0
CB A:CYS50 3.0 97.6 1.0
CB A:CYS53 3.0 105.6 1.0
CG A:HIS75 3.1 95.9 1.0
CB A:CYS78 3.3 87.2 1.0
CB A:HIS75 3.4 102.5 1.0
N A:CYS53 3.9 118.2 1.0
N A:HIS75 4.0 102.3 1.0
CA A:CYS53 4.1 108.2 1.0
NE2 A:HIS75 4.1 95.2 1.0
CD2 A:HIS75 4.2 93.3 1.0
CA A:HIS75 4.3 86.8 1.0
CA A:CYS50 4.5 80.3 1.0
NE A:ARG77 4.7 99.2 1.0
CA A:CYS78 4.7 82.0 1.0
CB A:HIS52 4.7 107.1 1.0
NH2 A:ARG77 4.8 106.8 1.0
C A:HIS52 4.9 107.0 1.0
CD2 A:HIS52 4.9 116.6 1.0
C A:CYS53 4.9 114.0 1.0
N A:CYS78 4.9 81.8 1.0
C A:CYS50 5.0 86.0 1.0

Zinc binding site 3 out of 8 in 8se4

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Zinc binding site 3 out of 8 in the Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:135.6
occ:1.00
 ND1 A:HIS102 2.0 156.5 1.0
SG A:CYS135 2.3 139.1 1.0
SG A:CYS151 2.5 182.4 1.0
SG A:CYS132 2.5 113.8 1.0
CE1 A:HIS102 2.7 147.6 1.0
CG A:HIS102 3.0 146.5 1.0
CB A:CYS135 3.6 137.2 1.0
CB A:CYS151 3.6 172.1 1.0
CB A:HIS102 3.6 141.3 1.0
CB A:CYS132 3.7 118.8 1.0
CA A:CYS151 3.7 158.6 1.0
NE2 A:HIS102 3.7 144.9 1.0
N A:GLY152 3.9 159.8 1.0
CA A:HIS102 3.9 129.5 1.0
CD2 A:HIS102 3.9 145.6 1.0
N A:CYS135 3.9 156.5 1.0
C A:CYS151 4.3 165.9 1.0
CA A:CYS135 4.4 146.8 1.0
CB A:THR134 4.5 149.9 1.0
N A:LYS103 4.8 136.4 1.0
N A:HIS102 4.8 133.9 1.0
CA A:GLY152 4.9 147.8 1.0
N A:CYS151 5.0 150.1 1.0
C A:HIS102 5.0 125.7 1.0

Zinc binding site 4 out of 8 in 8se4

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Zinc binding site 4 out of 8 in the Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:163.5
occ:1.00
 ND1 A:HIS140 2.0 99.8 1.0
SG A:CYS118 2.1 105.5 1.0
SG A:CYS143 2.2 115.3 1.0
SG A:CYS115 2.2 115.1 1.0
CE1 A:HIS140 2.9 82.0 1.0
CG A:HIS140 3.1 93.3 1.0
CB A:CYS115 3.1 114.3 1.0
CB A:CYS118 3.4 105.0 1.0
CB A:CYS143 3.5 103.1 1.0
CB A:HIS140 3.5 99.4 1.0
N A:CYS118 3.9 108.5 1.0
N A:HIS140 3.9 114.0 1.0
NE2 A:HIS140 4.1 95.5 1.0
CD2 A:HIS140 4.2 84.9 1.0
CA A:CYS118 4.2 104.1 1.0
CA A:HIS140 4.3 84.7 1.0
NH1 A:ARG142 4.5 127.1 1.0
CB A:HIS117 4.6 82.7 1.0
CA A:CYS115 4.6 103.4 1.0
CZ A:ARG142 4.7 142.7 1.0
CA A:CYS143 4.8 97.1 1.0
CD2 A:HIS117 4.9 100.6 1.0
C A:HIS117 4.9 102.6 1.0
C A:CYS118 5.0 100.3 1.0

Zinc binding site 5 out of 8 in 8se4

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Zinc binding site 5 out of 8 in the Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:146.3
occ:1.00
 ND1 B:HIS37 2.1 188.8 1.0
SG B:CYS86 2.2 191.3 1.0
SG B:CYS70 2.3 119.7 1.0
SG B:CYS67 2.3 174.8 1.0
CB B:CYS86 2.7 184.9 1.0
CE1 B:HIS37 2.7 177.5 1.0
CG B:HIS37 3.2 167.6 1.0
CB B:CYS67 3.3 156.5 1.0
CB B:CYS70 3.7 137.5 1.0
CB B:HIS37 3.8 144.9 1.0
CA B:CYS86 3.9 177.4 1.0
NE2 B:HIS37 3.9 167.4 1.0
CA B:HIS37 3.9 138.0 1.0
N B:CYS70 3.9 133.7 1.0
CD2 B:HIS37 4.1 169.9 1.0
CA B:CYS70 4.3 122.3 1.0
CB B:VAL69 4.5 131.5 1.0
CA B:CYS67 4.7 150.0 1.0
CB B:PHE72 4.8 142.8 1.0
N B:LYS38 4.8 174.8 1.0
O B:ASN36 4.8 173.9 1.0
N B:CYS86 4.8 173.0 1.0
N B:HIS37 4.8 136.7 1.0
C B:CYS70 4.9 129.1 1.0
C B:CYS86 4.9 170.9 1.0
C B:HIS37 4.9 159.6 1.0

Zinc binding site 6 out of 8 in 8se4

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Zinc binding site 6 out of 8 in the Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:99.3
occ:1.00
 ND1 B:HIS75 2.0 99.5 1.0
SG B:CYS50 2.3 112.2 1.0
SG B:CYS78 2.3 122.0 1.0
SG B:CYS53 2.4 89.1 1.0
CB B:CYS50 2.9 106.6 1.0
CG B:HIS75 3.0 100.4 1.0
CE1 B:HIS75 3.0 90.2 1.0
CB B:CYS53 3.2 85.8 1.0
CB B:HIS75 3.3 109.7 1.0
CB B:CYS78 3.4 123.0 1.0
N B:HIS75 3.9 99.7 1.0
N B:CYS53 3.9 98.8 1.0
NE2 B:HIS75 4.1 98.3 1.0
CD2 B:HIS75 4.1 103.8 1.0
CA B:CYS53 4.2 82.9 1.0
CA B:HIS75 4.2 98.6 1.0
CA B:CYS50 4.4 93.4 1.0
CA B:CYS78 4.8 123.9 1.0
CB B:HIS52 4.8 110.6 1.0
NE B:ARG77 4.8 146.7 1.0
NH2 B:ARG77 4.9 134.4 1.0
C B:HIS52 4.9 106.8 1.0
C B:CYS53 5.0 101.9 1.0

Zinc binding site 7 out of 8 in 8se4

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Zinc binding site 7 out of 8 in the Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:109.8
occ:1.00
 ND1 B:HIS102 2.0 123.4 1.0
SG B:CYS135 2.3 133.6 1.0
SG B:CYS151 2.4 103.7 1.0
SG B:CYS132 2.4 131.2 1.0
CE1 B:HIS102 2.5 114.4 1.0
CG B:HIS102 2.9 130.8 1.0
CB B:CYS132 3.4 111.4 1.0
NE2 B:HIS102 3.4 106.8 1.0
CB B:CYS135 3.5 119.8 1.0
CB B:CYS151 3.5 118.0 1.0
CD2 B:HIS102 3.6 126.7 1.0
CB B:HIS102 3.7 93.5 1.0
N B:CYS135 3.7 119.0 1.0
CA B:HIS102 3.9 110.8 1.0
CA B:CYS151 3.9 125.9 1.0
CA B:CYS135 4.2 112.0 1.0
N B:GLY152 4.4 121.2 1.0
CB B:THR134 4.4 148.9 1.0
C B:CYS151 4.7 123.3 1.0
N B:LYS103 4.7 131.0 1.0
CA B:CYS132 4.8 121.0 1.0
C B:THR134 4.8 142.3 1.0
N B:HIS102 4.8 107.8 1.0
CB B:MET137 4.9 98.7 1.0
C B:CYS135 4.9 108.2 1.0
C B:HIS102 4.9 123.9 1.0
N B:THR134 5.0 158.0 1.0
CA B:THR134 5.0 154.6 1.0

Zinc binding site 8 out of 8 in 8se4

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Zinc binding site 8 out of 8 in the Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Full-Length Human Protein Kinase C Beta 1 (Pkcbi) in the Active and Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn705

b:117.1
occ:1.00
 ND1 B:HIS140 2.0 133.3 1.0
SG B:CYS143 2.3 130.5 1.0
SG B:CYS115 2.4 116.8 1.0
SG B:CYS118 2.4 91.1 1.0
CG B:HIS140 2.9 126.3 1.0
CE1 B:HIS140 3.1 125.3 1.0
CB B:HIS140 3.1 125.7 1.0
CB B:CYS115 3.2 106.7 1.0
CB B:CYS143 3.3 115.9 1.0
N B:HIS140 3.6 123.2 1.0
CB B:CYS118 3.7 86.3 1.0
CA B:HIS140 4.0 117.7 1.0
N B:CYS118 4.0 116.3 1.0
CD2 B:HIS140 4.1 131.6 1.0
NE2 B:HIS140 4.1 127.9 1.0
NH1 B:ARG142 4.3 117.4 1.0
CA B:CYS118 4.4 110.7 1.0
CZ B:ARG142 4.5 127.1 1.0
CA B:CYS143 4.6 120.8 1.0
CA B:CYS115 4.6 105.7 1.0
NH2 B:ARG142 4.7 116.1 1.0
C B:VAL139 4.8 119.8 1.0
N B:CYS143 4.9 141.6 1.0
C B:HIS140 4.9 120.6 1.0
CB B:HIS117 4.9 99.7 1.0

Reference:

A.T.Q.Cong, T.L.Witter, E.S.Bruinsma, S.S.Bhattacharya, S.Jayaraman, M.B.Dugan, J.Paluncic, M.J.Kuffel, J.Farmakes, J.Alvey, X.Wu, A.P.Fields, A.Pandey, J.R.Hawse, M.P.Goetz, M.J.Schellenberg. Molecular Basis of Allosteric Regulation and Pharmaceutical Targeting of Protein Kinase C B To Be Published.
Page generated: Tue Aug 26 21:59:02 2025

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