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Zinc in PDB 4wb7: Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit)

Enzymatic activity of Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit)

All present enzymatic activity of Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit):
2.7.11.11;

Protein crystallography data

The structure of Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit), PDB code: 4wb7 was solved by J.Cheung, C.Ginter, M.Cassidy, M.C.Franklin, M.J.Rudolph, W.A.Hendrickson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.15 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.233, 121.155, 173.672, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 18.8

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit) (pdb code 4wb7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 15 binding sites of Zinc where determined in the Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit), PDB code: 4wb7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 15 in 4wb7

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Zinc binding site 1 out of 15 in the Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha 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 A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:22.8
occ:1.00
 O2A A:ATP501 2.0 20.1 1.0
OD1 A:ASN226 2.0 18.0 1.0
O2G A:ATP501 2.0 18.0 1.0
OD2 A:ASP239 2.1 20.9 1.0
O A:HOH706 2.3 22.6 1.0
O3B A:ATP501 2.8 22.2 1.0
CG A:ASN226 3.0 18.8 1.0
PG A:ATP501 3.0 21.5 1.0
CG A:ASP239 3.1 21.2 1.0
ND2 A:ASN226 3.3 19.3 1.0
PA A:ATP501 3.3 22.1 1.0
CB A:ASP239 3.6 19.4 1.0
O3G A:ATP501 3.8 20.4 1.0
PB A:ATP501 3.8 21.1 1.0
O3A A:ATP501 3.9 20.8 1.0
CE A:LYS223 3.9 19.8 1.0
ZN A:ZN503 3.9 27.1 1.0
O2B A:ATP501 4.1 19.5 1.0
NZ A:LYS223 4.1 17.5 1.0
OD1 A:ASP239 4.2 20.4 1.0
O1G A:ATP501 4.2 20.4 1.0
O1A A:ATP501 4.2 20.3 1.0
O3' A:ATP501 4.3 19.3 1.0
OD2 A:ASP221 4.3 22.3 1.0
CB A:ASN226 4.4 18.5 1.0
O5' A:ATP501 4.4 22.6 1.0
O I:HOH208 4.5 25.6 0.8
C5' A:ATP501 4.6 19.3 1.0
CA A:ASN226 4.8 19.4 1.0
C3' A:ATP501 4.8 19.9 1.0
O A:HOH735 4.8 17.6 1.0
O A:GLU225 4.9 22.0 1.0

Zinc binding site 2 out of 15 in 4wb7

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Zinc binding site 2 out of 15 in the Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha 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 A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:27.1
occ:1.00
 O3G A:ATP501 2.0 20.4 1.0
O2B A:ATP501 2.1 19.5 1.0
O A:HOH734 2.2 19.0 1.0
O A:HOH735 2.2 17.6 1.0
OD1 A:ASP239 2.2 20.4 1.0
OD2 A:ASP239 2.3 20.9 1.0
CG A:ASP239 2.6 21.2 1.0
PG A:ATP501 3.1 21.5 1.0
PB A:ATP501 3.2 21.1 1.0
O3B A:ATP501 3.3 22.2 1.0
O2G A:ATP501 3.6 18.0 1.0
ZN A:ZN502 3.9 22.8 1.0
OD2 A:ASP221 4.0 22.3 1.0
CD2 A:PHE109 4.1 25.3 1.0
CB A:ASP239 4.1 19.4 1.0
NZ A:LYS127 4.2 19.9 1.0
O A:HOH748 4.2 22.1 1.0
O1B A:ATP501 4.3 23.9 1.0
O3A A:ATP501 4.3 20.8 1.0
CA A:GLY241 4.3 19.9 1.0
O1G A:ATP501 4.4 20.4 1.0
CE2 A:PHE109 4.4 21.9 1.0
O2A A:ATP501 4.5 20.1 1.0
N A:GLY241 4.5 18.2 1.0
O1A A:ATP501 4.6 20.3 1.0
PA A:ATP501 4.6 22.1 1.0
O A:HOH790 4.9 25.4 1.0
CA A:ASP239 4.9 21.1 1.0
CB I:ALA21 5.0 22.0 1.0

Zinc binding site 3 out of 15 in 4wb7

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Zinc binding site 3 out of 15 in the Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha 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 A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:33.4
occ:1.00
 O A:HOH606 1.7 24.5 1.0
OE1 A:GLU79 2.1 35.8 1.0
CD A:GLU79 2.9 44.8 1.0
OE2 A:GLU79 3.0 48.1 1.0
OD2 A:ASP80 3.6 36.1 1.0
O A:HOH630 3.7 53.3 1.0
CA A:ASP80 3.9 27.3 1.0
CB A:ASP80 4.2 32.6 1.0
CG A:ASP80 4.3 34.3 1.0
N A:ASP80 4.4 27.6 1.0
CG A:GLU79 4.4 32.9 1.0
O A:GLU79 4.7 33.3 1.0
CG A:LYS83 4.7 36.2 1.0
C A:GLU79 4.7 33.7 1.0
CB A:LYS83 5.0 28.8 1.0

Zinc binding site 4 out of 15 in 4wb7

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Zinc binding site 4 out of 15 in the Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha 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 A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:42.0
occ:0.76
 O A:HOH1065 1.8 42.2 1.0
O1P A:SEP194 1.8 67.4 0.5
ND1 A:HIS197 2.4 49.4 1.0
O A:HOH602 3.2 54.5 1.0
O A:HOH681 3.3 61.5 1.0
CG A:HIS197 3.3 45.5 1.0
P A:SEP194 3.3 42.8 0.5
CE1 A:HIS197 3.4 46.2 1.0
CB A:HIS197 3.5 31.4 1.0
N A:SEP194 3.8 31.9 1.0
OG A:SEP194 3.9 46.7 1.0
O3P A:SEP194 4.1 38.3 0.5
CA A:PHE193 4.3 27.1 1.0
CB A:SEP194 4.4 34.7 1.0
O2P A:SEP194 4.4 62.2 0.5
CD2 A:HIS197 4.5 42.4 1.0
NE2 A:HIS197 4.5 44.1 1.0
C A:PHE193 4.5 29.4 1.0
CD1 A:PHE193 4.7 38.0 1.0
CB A:PHE193 4.7 25.9 1.0
CA A:SEP194 4.7 32.2 1.0

Zinc binding site 5 out of 15 in 4wb7

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Zinc binding site 5 out of 15 in the Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha 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 A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:39.5
occ:0.39
 OE2 A:GLU176 2.2 46.3 1.0
O A:HOH905 2.2 40.2 1.0
OE1 A:GLN236 2.3 45.0 1.0
O A:HOH912 2.4 60.7 1.0
CD A:GLU176 2.8 63.3 1.0
OE1 A:GLU176 2.9 67.3 1.0
CD A:GLN236 3.1 36.8 1.0
NE2 A:GLN236 3.4 29.9 1.0
O A:HOH750 3.6 40.6 1.0
O A:HOH869 4.1 37.6 0.7
CE A:LYS160 4.2 70.7 1.0
O A:LEU158 4.2 26.4 1.0
CG A:GLU176 4.2 55.6 1.0
CG A:GLN236 4.4 27.3 1.0
CD A:LYS160 4.4 64.0 1.0
CG A:LYS160 4.5 53.3 1.0
O A:PRO156 4.6 28.2 1.0
CA A:VAL159 4.7 22.8 1.0
N A:LYS160 4.7 23.2 1.0
O A:HOH859 4.9 48.8 1.0
C A:LEU158 5.0 27.0 1.0

Zinc binding site 6 out of 15 in 4wb7

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Zinc binding site 6 out of 15 in the Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha 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 A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:70.9
occ:0.59
 O A:HOH1010 2.2 55.8 1.0
ND1 A:HIS123 2.3 52.7 1.0
O A:HOH916 2.9 61.2 1.0
CG A:HIS123 3.2 39.1 1.0
CE1 A:HIS123 3.3 49.8 1.0
CB A:HIS123 3.4 35.3 1.0
N A:HIS123 3.6 38.8 1.0
O A:PRO376 3.7 1.0 1.0
CB A:PRO376 4.0 0.6 1.0
CA A:HIS123 4.1 35.4 1.0
O A:HOH1026 4.4 61.4 1.0
CD2 A:HIS123 4.4 37.6 1.0
NE2 A:HIS123 4.4 43.2 1.0
C A:PRO376 4.5 0.3 1.0
O A:GLY121 4.5 48.1 1.0
C A:ASN122 4.5 34.7 1.0
CA A:PRO376 4.6 0.2 1.0
CA A:ASN122 4.7 37.5 1.0

Zinc binding site 7 out of 15 in 4wb7

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Zinc binding site 7 out of 15 in the Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha 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 A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:26.8
occ:1.00
 O2A B:ATP501 2.0 22.0 1.0
OD1 B:ASN226 2.0 21.8 1.0
O2G B:ATP501 2.1 20.5 1.0
OD2 B:ASP239 2.1 22.4 1.0
O B:HOH906 2.2 21.1 1.0
O3B B:ATP501 2.8 22.8 1.0
CG B:ASN226 3.0 20.4 1.0
PG B:ATP501 3.0 23.2 1.0
CG B:ASP239 3.1 24.8 1.0
ND2 B:ASN226 3.3 19.1 1.0
PA B:ATP501 3.4 20.9 1.0
CB B:ASP239 3.6 20.6 1.0
PB B:ATP501 3.8 22.3 1.0
O3G B:ATP501 3.8 22.1 1.0
O3A B:ATP501 3.8 19.2 1.0
CE B:LYS223 3.9 24.4 1.0
ZN B:ZN503 3.9 28.9 1.0
O2B B:ATP501 4.1 18.6 1.0
NZ B:LYS223 4.2 20.0 1.0
OD1 B:ASP239 4.2 19.3 1.0
O1A B:ATP501 4.2 21.5 1.0
O1G B:ATP501 4.3 23.6 1.0
O J:HOH226 4.3 34.4 1.0
OD2 B:ASP221 4.3 22.2 1.0
O3' B:ATP501 4.3 21.3 1.0
CB B:ASN226 4.4 17.9 1.0
O5' B:ATP501 4.4 24.7 1.0
C5' B:ATP501 4.6 21.0 1.0
CA B:ASN226 4.8 22.7 1.0
C3' B:ATP501 4.8 21.3 1.0
O B:HOH774 4.8 21.9 1.0
O B:GLU225 4.9 20.7 1.0

Zinc binding site 8 out of 15 in 4wb7

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Zinc binding site 8 out of 15 in the Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha 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 A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:28.9
occ:1.00
 O B:HOH775 2.1 21.6 1.0
O3G B:ATP501 2.1 22.1 1.0
O2B B:ATP501 2.1 18.6 1.0
O B:HOH774 2.2 21.9 1.0
OD1 B:ASP239 2.2 19.3 1.0
OD2 B:ASP239 2.3 22.4 1.0
CG B:ASP239 2.6 24.8 1.0
PG B:ATP501 3.1 23.2 1.0
PB B:ATP501 3.2 22.3 1.0
O3B B:ATP501 3.3 22.8 1.0
O2G B:ATP501 3.7 20.5 1.0
ZN B:ZN502 3.9 26.8 1.0
CD2 B:PHE109 3.9 27.1 1.0
OD2 B:ASP221 4.0 22.2 1.0
O B:HOH765 4.1 23.5 1.0
CB B:ASP239 4.1 20.6 1.0
NZ B:LYS127 4.2 22.4 1.0
CE2 B:PHE109 4.3 23.4 1.0
O3A B:ATP501 4.3 19.2 1.0
O1B B:ATP501 4.3 21.6 1.0
CA B:GLY241 4.3 24.3 1.0
O1G B:ATP501 4.4 23.6 1.0
O2A B:ATP501 4.5 22.0 1.0
N B:GLY241 4.5 23.4 1.0
PA B:ATP501 4.7 20.9 1.0
O1A B:ATP501 4.7 21.5 1.0
O B:HOH783 4.8 28.1 1.0
CA B:ASP239 4.9 20.4 1.0
CB J:ALA21 5.0 23.1 1.0
O B:ASP239 5.0 21.9 1.0

Zinc binding site 9 out of 15 in 4wb7

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Zinc binding site 9 out of 15 in the Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:37.3
occ:1.00
 O B:HOH603 1.7 27.0 1.0
OE1 B:GLU79 2.2 45.5 1.0
CD B:GLU79 3.1 64.5 1.0
OD1 B:ASP80 3.1 42.5 1.0
OE2 B:GLU79 3.1 64.2 1.0
CA B:ASP80 3.9 39.5 1.0
O B:HOH607 4.0 39.3 1.0
CG B:ASP80 4.1 37.5 1.0
CB B:ASP80 4.2 38.4 1.0
N B:ASP80 4.4 38.2 1.0
CG B:GLU79 4.6 47.1 1.0
CG B:LYS83 4.8 41.2 1.0
C B:GLU79 4.8 39.0 1.0
O B:GLU79 4.8 42.9 1.0
CB B:LYS83 4.9 35.5 1.0

Zinc binding site 10 out of 15 in 4wb7

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Zinc binding site 10 out of 15 in the Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of A Chimeric Fusion of Human Dnaj (HSP40) and Camp- Dependent Protein Kinase A (Catalytic Alpha Subunit) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn505

b:53.8
occ:0.56
 O B:HOH633 2.1 41.8 1.0
ND1 B:HIS197 2.1 55.7 1.0
O1P B:SEP194 2.5 41.3 0.5
O B:HOH848 2.7 56.1 1.0
CE1 B:HIS197 3.1 47.9 1.0
CG B:HIS197 3.1 51.7 1.0
CB B:HIS197 3.4 37.4 1.0
P B:SEP194 3.4 53.3 0.5
O B:HOH666 3.4 45.9 1.0
O2P B:SEP194 3.5 65.5 0.5
OG B:SEP194 4.0 37.9 1.0
NE2 B:HIS197 4.2 50.2 1.0
CD2 B:HIS197 4.2 48.8 1.0
CB B:PRO368 4.3 50.6 1.0
O B:HOH602 4.4 60.6 1.0
N B:SEP194 4.5 27.8 1.0
CA B:HIS197 4.8 27.9 1.0
O3P B:SEP194 4.9 46.3 0.5
CB B:SEP194 4.9 27.9 1.0

Reference:

J.Cheung, C.Ginter, M.Cassidy, M.C.Franklin, M.J.Rudolph, N.Robine, R.B.Darnell, W.A.Hendrickson. Structural Insights Into Mis-Regulation of Protein Kinase A in Human Tumors. Proc.Natl.Acad.Sci.Usa V. 112 1374 2015.
ISSN: ESSN 1091-6490
PubMed: 25605907
DOI: 10.1073/PNAS.1424206112
Page generated: Sun Oct 27 09:46:09 2024

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