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Zinc in PDB 8se1: Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation

Enzymatic activity of Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation

All present enzymatic activity of Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation:
2.7.11.13;

Protein crystallography data

The structure of Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation, PDB code: 8se1 was solved by A.T.Q.Cong, T.L.Witter, E.S.Bruinsma, S.Jayaraman, M.B.Dugan, 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) 48.75 / 3.32
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 130.556, 89.098, 160.714, 90, 107.05, 90
R / Rfree (%) 19.9 / 25.6

Other elements in 8se1:

The structure of Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation (pdb code 8se1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation, PDB code: 8se1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 8se1

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Zinc binding site 1 out of 10 in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the 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 2 (Pkcbii) in the Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:60.6
occ:1.00
 ND1 A:HIS102 2.0 116.7 1.0
SG A:CYS132 2.2 78.2 1.0
SG A:CYS135 2.3 81.8 1.0
SG A:CYS151 2.4 103.1 1.0
CG A:HIS102 2.9 112.2 1.0
CE1 A:HIS102 3.1 114.0 1.0
CB A:HIS102 3.2 105.8 1.0
CA A:HIS102 3.2 104.2 1.0
CB A:CYS132 3.3 75.0 1.0
CB A:CYS151 3.3 101.7 1.0
CB A:CYS135 3.6 84.4 1.0
N A:CYS135 4.0 89.6 1.0
CD2 A:HIS102 4.0 114.4 1.0
NE2 A:HIS102 4.1 112.6 1.0
CA A:CYS151 4.1 98.6 1.0
O A:HIS102 4.1 83.0 1.0
N A:HIS102 4.1 103.3 1.0
C A:HIS102 4.1 98.3 1.0
CA A:CYS135 4.4 85.7 1.0
CB A:THR134 4.5 97.2 1.0
CA A:CYS132 4.7 86.4 1.0
N A:GLY152 4.9 95.0 1.0
C A:THR134 5.0 95.0 1.0

Zinc binding site 2 out of 10 in 8se1

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Zinc binding site 2 out of 10 in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the 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 2 (Pkcbii) in the Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:50.9
occ:1.00
 ND1 A:HIS140 2.0 88.1 1.0
SG A:CYS118 2.3 49.9 1.0
SG A:CYS115 2.4 61.4 1.0
SG A:CYS143 2.4 61.1 1.0
CG A:HIS140 2.8 84.2 1.0
CB A:HIS140 2.9 79.9 1.0
CE1 A:HIS140 3.2 84.9 1.0
CB A:CYS115 3.2 57.0 1.0
CB A:CYS118 3.4 52.2 1.0
CB A:CYS143 3.5 64.4 1.0
N A:HIS140 3.6 76.0 1.0
CA A:HIS140 3.9 77.9 1.0
N A:CYS118 3.9 63.4 1.0
CD2 A:HIS140 4.0 85.9 1.0
NE2 A:HIS140 4.2 83.5 1.0
CA A:CYS118 4.3 56.5 1.0
CB A:HIS117 4.7 68.8 1.0
CA A:CYS115 4.7 56.3 1.0
NE A:ARG142 4.8 65.0 1.0
C A:VAL139 4.8 73.0 1.0
CA A:CYS143 4.8 70.6 1.0
NH1 A:ARG142 4.9 58.2 1.0
CD2 A:HIS117 4.9 71.8 1.0
C A:HIS140 4.9 73.6 1.0

Zinc binding site 3 out of 10 in 8se1

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Zinc binding site 3 out of 10 in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the 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 2 (Pkcbii) in the Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:51.9
occ:1.00
 ND1 A:HIS37 2.1 86.6 1.0
SG A:CYS70 2.3 64.2 1.0
SG A:CYS67 2.3 50.6 1.0
SG A:CYS86 2.3 79.4 1.0
CE1 A:HIS37 2.6 86.8 1.0
CB A:CYS86 3.2 76.5 1.0
CB A:CYS67 3.2 50.3 1.0
CG A:HIS37 3.2 79.8 1.0
CB A:CYS70 3.4 70.0 1.0
NE2 A:HIS37 3.7 85.2 1.0
N A:CYS70 3.8 70.4 1.0
CA A:CYS86 3.9 74.7 1.0
CB A:HIS37 3.9 71.7 1.0
CA A:HIS37 4.0 64.2 1.0
CD2 A:HIS37 4.1 83.4 1.0
CA A:CYS70 4.1 73.5 1.0
CD A:PRO87 4.6 75.8 1.0
CB A:PHE72 4.6 58.7 1.0
CA A:CYS67 4.7 50.9 1.0
CB A:VAL69 4.7 53.4 1.0
C A:CYS86 4.8 71.6 1.0
C A:CYS70 4.8 77.5 1.0
N A:HIS37 4.8 61.7 1.0
N A:LYS38 4.9 50.8 1.0
C A:VAL69 4.9 71.9 1.0
N A:PRO87 4.9 70.9 1.0
N A:CYS86 5.0 75.6 1.0

Zinc binding site 4 out of 10 in 8se1

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Zinc binding site 4 out of 10 in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the 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 2 (Pkcbii) in the Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:38.1
occ:1.00
 ND1 A:HIS75 2.1 67.8 1.0
SG A:CYS50 2.3 49.1 1.0
SG A:CYS53 2.3 49.6 1.0
SG A:CYS78 2.3 59.1 1.0
CG A:HIS75 2.8 62.9 1.0
CB A:HIS75 3.0 59.1 1.0
CB A:CYS53 3.1 49.5 1.0
CE1 A:HIS75 3.2 65.6 1.0
CB A:CYS50 3.3 68.8 1.0
CB A:CYS78 3.3 53.8 1.0
N A:HIS75 3.6 50.8 1.0
N A:CYS53 3.7 62.5 1.0
CA A:HIS75 3.9 54.9 1.0
CA A:CYS53 4.0 61.0 1.0
CD2 A:HIS75 4.0 63.5 1.0
NE2 A:HIS75 4.2 64.3 1.0
CA A:CYS50 4.7 68.4 1.0
CA A:CYS78 4.7 49.3 1.0
C A:CYS53 4.7 59.5 1.0
O A:CYS50 4.8 68.8 1.0
C A:VAL74 4.8 46.0 1.0
N A:CYS78 4.9 47.6 1.0
C A:HIS52 4.9 64.4 1.0
CB A:HIS52 4.9 61.5 1.0
C A:HIS75 4.9 55.7 1.0
C A:CYS50 5.0 68.0 1.0

Zinc binding site 5 out of 10 in 8se1

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Zinc binding site 5 out of 10 in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the 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 2 (Pkcbii) in the Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn705

b:32.2
occ:1.00
 OE2 B:GLU657 2.0 80.5 1.0
ND1 A:HIS32 2.0 63.6 1.0
NE2 A:HIS79 2.0 62.3 1.0
OE1 B:GLU657 2.0 78.9 1.0
O A:HOH813 2.1 22.4 1.0
CD B:GLU657 2.2 74.1 1.0
CE1 A:HIS32 2.9 62.0 1.0
CE1 A:HIS79 3.0 60.9 1.0
CD2 A:HIS79 3.1 61.2 1.0
CG A:HIS32 3.1 59.1 1.0
CB A:HIS32 3.6 52.3 1.0
CG B:GLU657 3.7 64.4 1.0
NE2 A:HIS32 4.1 60.5 1.0
ND1 A:HIS79 4.1 61.7 1.0
CG A:HIS79 4.2 59.3 1.0
CD2 A:HIS32 4.2 62.1 1.0
CG A:GLU80 4.5 49.3 1.0
CA A:HIS32 4.7 49.5 1.0
CB B:GLU657 4.7 59.2 1.0
CE2 A:PHE65 4.8 54.8 1.0
CD A:GLU80 4.9 53.4 1.0

Zinc binding site 6 out of 10 in 8se1

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Zinc binding site 6 out of 10 in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the 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 2 (Pkcbii) in the Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:35.6
occ:1.00
 ND1 B:HIS102 2.0 57.3 1.0
SG B:CYS151 2.3 63.2 1.0
SG B:CYS135 2.3 38.0 1.0
SG B:CYS132 2.4 43.8 1.0
CE1 B:HIS102 2.9 54.0 1.0
CG B:HIS102 3.1 53.2 1.0
CB B:CYS151 3.2 55.7 1.0
CB B:CYS132 3.3 46.9 1.0
CB B:HIS102 3.5 49.7 1.0
CA B:HIS102 3.6 49.9 1.0
CB B:CYS135 3.6 46.9 1.0
CA B:CYS151 3.8 48.7 1.0
NE2 B:HIS102 4.1 53.0 1.0
CD2 B:HIS102 4.1 55.0 1.0
N B:CYS135 4.2 55.0 1.0
CA B:CYS135 4.5 51.6 1.0
N B:LYS103 4.5 50.4 1.0
N B:HIS102 4.5 52.2 1.0
N B:GLY152 4.5 47.5 1.0
C B:HIS102 4.6 49.8 1.0
CB B:THR134 4.6 52.9 1.0
C B:CYS151 4.7 47.8 1.0
CA B:CYS132 4.8 52.4 1.0
CB B:MET137 4.8 37.1 1.0
N B:CYS151 4.9 48.2 1.0

Zinc binding site 7 out of 10 in 8se1

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Zinc binding site 7 out of 10 in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the 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 2 (Pkcbii) in the Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:30.3
occ:1.00
 ND1 B:HIS140 2.1 58.7 1.0
SG B:CYS118 2.3 36.0 1.0
SG B:CYS115 2.3 36.0 1.0
SG B:CYS143 2.5 39.9 1.0
CG B:HIS140 2.9 56.3 1.0
CB B:HIS140 3.1 52.1 1.0
CE1 B:HIS140 3.1 57.2 1.0
CB B:CYS115 3.2 42.7 1.0
CB B:CYS118 3.4 38.1 1.0
CB B:CYS143 3.5 43.3 1.0
N B:HIS140 3.7 44.7 1.0
N B:CYS118 3.9 43.1 1.0
CA B:HIS140 4.0 48.1 1.0
CD2 B:HIS140 4.1 57.9 1.0
NE2 B:HIS140 4.2 56.8 1.0
CA B:CYS118 4.2 40.5 1.0
NH2 B:ARG142 4.5 55.1 1.0
CA B:CYS115 4.6 40.5 1.0
CB B:HIS117 4.7 38.8 1.0
C B:VAL139 4.8 46.8 1.0
NH1 B:ARG142 4.9 54.2 1.0
CZ B:ARG142 4.9 57.2 1.0
CA B:CYS143 4.9 49.2 1.0
CD2 B:HIS117 5.0 38.4 1.0

Zinc binding site 8 out of 10 in 8se1

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Zinc binding site 8 out of 10 in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the 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 2 (Pkcbii) in the Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:41.3
occ:1.00
 ND1 B:HIS37 2.0 77.8 1.0
SG B:CYS70 2.3 59.3 1.0
SG B:CYS86 2.3 53.1 1.0
SG B:CYS67 2.3 36.8 1.0
CE1 B:HIS37 2.6 82.4 1.0
CG B:HIS37 3.2 37.6 1.0
CB B:CYS86 3.2 51.2 1.0
CB B:CYS67 3.3 35.5 1.0
CB B:CYS70 3.4 53.2 1.0
NE2 B:HIS37 3.7 37.2 1.0
N B:CYS70 3.8 46.0 1.0
CB B:HIS37 3.8 38.2 1.0
CA B:HIS37 3.8 39.2 1.0
CA B:CYS86 3.9 49.6 1.0
CD2 B:HIS37 4.0 37.8 1.0
CA B:CYS70 4.1 47.7 1.0
CD B:PRO87 4.4 38.0 1.0
CB B:VAL69 4.7 38.9 1.0
CB B:PHE72 4.7 42.0 1.0
N B:LYS38 4.7 39.0 1.0
N B:HIS37 4.7 40.4 1.0
CA B:CYS67 4.7 35.3 1.0
C B:CYS86 4.8 53.3 1.0
C B:CYS70 4.8 48.0 1.0
N B:PRO87 4.9 53.3 1.0
C B:HIS37 4.9 39.5 1.0
C B:VAL69 4.9 48.7 1.0
O B:ASN36 4.9 42.9 1.0

Zinc binding site 9 out of 10 in 8se1

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Zinc binding site 9 out of 10 in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:37.0
occ:1.00
 ND1 B:HIS75 2.1 60.5 1.0
SG B:CYS53 2.3 40.5 1.0
SG B:CYS78 2.3 52.5 1.0
SG B:CYS50 2.4 41.4 1.0
CG B:HIS75 2.9 56.8 1.0
CB B:CYS53 3.0 41.2 1.0
CB B:HIS75 3.0 52.7 1.0
CE1 B:HIS75 3.2 59.0 1.0
CB B:CYS50 3.3 40.1 1.0
CB B:CYS78 3.4 49.0 1.0
N B:CYS53 3.7 41.7 1.0
N B:HIS75 3.8 41.4 1.0
CA B:CYS53 3.9 41.7 1.0
CA B:HIS75 4.0 45.1 1.0
CD2 B:HIS75 4.1 57.6 1.0
NE2 B:HIS75 4.2 58.3 1.0
C B:CYS53 4.7 45.0 1.0
CA B:CYS50 4.7 41.4 1.0
CA B:CYS78 4.7 45.5 1.0
ND1 B:HIS52 4.8 53.4 1.0
CB B:HIS52 4.8 46.4 1.0
C B:HIS52 4.9 45.4 1.0
O B:CYS50 4.9 37.0 1.0
N B:CYS78 4.9 42.4 1.0
NH2 B:ARG77 4.9 59.1 1.0
CZ B:ARG77 5.0 62.0 1.0

Zinc binding site 10 out of 10 in 8se1

Go back to Zinc Binding Sites List in 8se1
Zinc binding site 10 out of 10 in the Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Full-Length Human Protein Kinase C Beta 2 (Pkcbii) in the Inactive Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn705

b:22.6
occ:1.00
 ND1 B:HIS32 2.0 73.5 1.0
NE2 B:HIS79 2.1 62.2 1.0
O B:HOH836 2.4 3.8 1.0
CD2 B:HIS79 3.0 60.3 1.0
CG B:HIS32 3.0 76.1 1.0
CE1 B:HIS32 3.1 40.5 1.0
CE1 B:HIS79 3.1 61.5 1.0
CB B:HIS32 3.3 40.0 1.0
CG B:HIS79 4.1 57.5 1.0
ND1 B:HIS79 4.1 59.1 1.0
CD2 B:HIS32 4.1 39.7 1.0
NE2 B:HIS32 4.1 40.0 1.0
CA B:HIS32 4.4 50.4 1.0
CG B:GLU80 4.5 71.2 1.0
CG2 B:VAL34 4.8 43.9 1.0
CE2 B:PHE65 4.9 64.6 1.0
CD B:GLU80 4.9 76.3 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 21:59:00 2025

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