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Zinc in PDB 5e4h: Crystal Structure of Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A

Enzymatic activity of Crystal Structure of Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A

All present enzymatic activity of Crystal Structure of Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A:
2.7.11.7;

Protein crystallography data

The structure of Crystal Structure of Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A, PDB code: 5e4h was solved by Q.Ye, G.P.Cote, Z.Jia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.298, 103.469, 167.811, 90.00, 89.99, 90.00
R / Rfree (%) 24.1 / 26.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A (pdb code 5e4h). 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 Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A, PDB code: 5e4h:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5e4h

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Zinc binding site 1 out of 8 in the Crystal Structure of Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A


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 Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:76.2
occ:1.00
SG A:CYS796 2.0 62.9 1.0
SG A:CYS800 2.1 64.9 1.0
ND1 A:HIS742 2.2 69.0 1.0
NE2 A:HIS794 2.2 77.4 1.0
CE1 A:HIS742 2.9 68.1 1.0
CE1 A:HIS794 3.1 78.8 1.0
CG A:HIS742 3.1 67.2 1.0
CD2 A:HIS794 3.2 80.1 1.0
CB A:CYS800 3.3 76.5 1.0
CB A:CYS796 3.3 63.2 1.0
CA A:CYS796 3.5 66.3 1.0
CB A:HIS742 3.6 62.3 1.0
NE2 A:HIS742 3.9 70.0 1.0
CD2 A:HIS742 4.0 70.0 1.0
ND1 A:HIS794 4.2 77.3 1.0
N A:CYS796 4.2 66.3 1.0
CG A:HIS794 4.3 77.2 1.0
CA A:CYS800 4.6 78.5 1.0
N A:ASN797 4.7 70.3 1.0
C A:CYS796 4.7 69.2 1.0
C A:LYS795 4.9 67.7 1.0
CD1 A:LEU805 4.9 87.9 1.0
O A:LYS795 4.9 70.9 1.0

Zinc binding site 2 out of 8 in 5e4h

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Zinc binding site 2 out of 8 in the Crystal Structure of Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A


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 Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:81.7
occ:1.00
SG B:CYS800 2.0 59.9 1.0
ND1 B:HIS742 2.0 79.9 1.0
SG B:CYS796 2.2 67.6 1.0
NE2 B:HIS794 2.2 63.8 1.0
CE1 B:HIS742 2.9 78.5 1.0
CG B:HIS742 3.0 74.5 1.0
CE1 B:HIS794 3.1 65.8 1.0
CD2 B:HIS794 3.3 63.0 1.0
CB B:CYS800 3.3 66.4 1.0
CB B:HIS742 3.4 70.2 1.0
CB B:CYS796 3.5 66.5 1.0
CA B:CYS796 3.6 66.5 1.0
NE2 B:HIS742 3.9 74.3 1.0
CD2 B:HIS742 3.9 73.7 1.0
ND1 B:HIS794 4.2 65.9 1.0
CG B:HIS794 4.3 63.6 1.0
N B:CYS796 4.4 70.6 1.0
CA B:CYS800 4.5 68.9 1.0
CD1 B:LEU805 4.7 80.7 1.0
N B:ASN797 4.7 60.4 1.0
C B:CYS796 4.8 65.5 1.0
C B:LYS795 4.9 69.0 1.0
CA B:HIS742 4.9 68.5 1.0
O B:LYS795 5.0 67.3 1.0
CB B:LEU805 5.0 83.5 1.0

Zinc binding site 3 out of 8 in 5e4h

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Zinc binding site 3 out of 8 in the Crystal Structure of Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A


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 Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn901

b:64.0
occ:1.00
ND1 C:HIS742 2.0 78.5 1.0
SG C:CYS800 2.1 58.3 1.0
SG C:CYS796 2.1 61.4 1.0
NE2 C:HIS794 2.3 59.7 1.0
CE1 C:HIS742 2.8 77.5 1.0
CG C:HIS742 3.0 75.1 1.0
CE1 C:HIS794 3.2 62.2 1.0
CB C:CYS800 3.2 60.8 1.0
CD2 C:HIS794 3.3 57.9 1.0
CB C:CYS796 3.4 61.4 1.0
CB C:HIS742 3.5 70.8 1.0
CA C:CYS796 3.6 61.6 1.0
NE2 C:HIS742 3.8 76.3 1.0
CD2 C:HIS742 3.9 74.5 1.0
ND1 C:HIS794 4.3 61.9 1.0
N C:CYS796 4.3 65.4 1.0
CG C:HIS794 4.4 58.7 1.0
CA C:CYS800 4.4 64.6 1.0
CD1 C:LEU805 4.7 77.5 1.0
N C:ASN797 4.7 57.1 1.0
C C:CYS796 4.8 60.7 1.0
CB C:LEU805 4.9 84.3 1.0
C C:LYS795 4.9 66.4 1.0

Zinc binding site 4 out of 8 in 5e4h

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Zinc binding site 4 out of 8 in the Crystal Structure of Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A


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 Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn901

b:72.2
occ:1.00
SG D:CYS800 2.0 67.5 1.0
SG D:CYS796 2.1 69.8 1.0
CD2 D:HIS742 2.4 76.2 1.0
NE2 D:HIS794 2.4 66.8 1.0
CG D:HIS742 3.0 72.4 1.0
NE2 D:HIS742 3.0 75.6 1.0
CB D:CYS800 3.1 73.8 1.0
CE1 D:HIS794 3.2 67.4 1.0
CB D:CYS796 3.4 69.7 1.0
CD2 D:HIS794 3.4 70.6 1.0
CA D:CYS796 3.6 69.6 1.0
CB D:HIS742 3.6 65.6 1.0
ND1 D:HIS742 3.8 71.1 1.0
CE1 D:HIS742 3.8 73.3 1.0
ND1 D:HIS794 4.3 69.1 1.0
N D:CYS796 4.3 70.2 1.0
CA D:CYS800 4.4 75.4 1.0
CG D:HIS794 4.4 68.1 1.0
N D:ASN797 4.6 67.1 1.0
CD1 D:LEU805 4.7 86.4 1.0
C D:CYS796 4.7 68.0 1.0
CB D:LEU805 4.9 88.3 1.0
C D:LYS795 5.0 68.5 1.0
O D:LYS795 5.0 72.8 1.0

Zinc binding site 5 out of 8 in 5e4h

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Zinc binding site 5 out of 8 in the Crystal Structure of Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A


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 Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn901

b:77.7
occ:1.00
SG E:CYS800 2.0 58.2 1.0
ND1 E:HIS742 2.1 71.8 1.0
SG E:CYS796 2.1 65.1 1.0
NE2 E:HIS794 2.3 61.4 1.0
CE1 E:HIS742 2.8 70.6 1.0
CG E:HIS742 3.0 67.7 1.0
CE1 E:HIS794 3.1 61.5 1.0
CB E:CYS800 3.2 62.6 1.0
CD2 E:HIS794 3.3 61.3 1.0
CB E:CYS796 3.4 63.8 1.0
CB E:HIS742 3.5 66.1 1.0
CA E:CYS796 3.6 63.6 1.0
NE2 E:HIS742 3.9 65.6 1.0
CD2 E:HIS742 4.0 65.7 1.0
ND1 E:HIS794 4.3 63.0 1.0
N E:CYS796 4.3 67.2 1.0
CG E:HIS794 4.4 61.0 1.0
CA E:CYS800 4.5 65.0 1.0
CD1 E:LEU805 4.7 76.4 1.0
N E:ASN797 4.7 58.2 1.0
C E:CYS796 4.7 63.6 1.0
C E:LYS795 4.9 69.4 1.0
CB E:LEU805 5.0 84.7 1.0
O E:LYS795 5.0 71.5 1.0

Zinc binding site 6 out of 8 in 5e4h

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Zinc binding site 6 out of 8 in the Crystal Structure of Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A


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 Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn901

b:72.0
occ:1.00
SG F:CYS800 2.0 63.2 1.0
SG F:CYS796 2.0 66.7 1.0
NE2 F:HIS794 2.2 68.4 1.0
ND1 F:HIS742 2.3 69.3 1.0
CE1 F:HIS742 3.0 68.8 1.0
CE1 F:HIS794 3.1 68.4 1.0
CG F:HIS742 3.2 67.9 1.0
CD2 F:HIS794 3.2 71.7 1.0
CB F:CYS800 3.2 68.4 1.0
CB F:CYS796 3.3 69.4 1.0
CA F:CYS796 3.4 68.8 1.0
CB F:HIS742 3.7 61.4 1.0
NE2 F:HIS742 4.0 70.4 1.0
CD2 F:HIS742 4.1 70.2 1.0
N F:CYS796 4.1 68.1 1.0
ND1 F:HIS794 4.2 68.3 1.0
CG F:HIS794 4.3 68.1 1.0
CA F:CYS800 4.5 70.6 1.0
N F:ASN797 4.6 67.4 1.0
C F:CYS796 4.6 68.3 1.0
C F:LYS795 4.7 71.4 1.0
O F:LYS795 4.8 77.3 1.0
CD1 F:LEU805 4.9 77.7 1.0

Zinc binding site 7 out of 8 in 5e4h

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Zinc binding site 7 out of 8 in the Crystal Structure of Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A


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 Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn901

b:77.9
occ:1.00
SG G:CYS796 2.0 69.8 1.0
SG G:CYS800 2.1 62.7 1.0
ND1 G:HIS742 2.2 71.1 1.0
NE2 G:HIS794 2.2 73.5 1.0
CE1 G:HIS742 2.9 71.8 1.0
CE1 G:HIS794 3.1 74.6 1.0
CG G:HIS742 3.1 69.8 1.0
CD2 G:HIS794 3.2 76.1 1.0
CB G:CYS800 3.2 74.0 1.0
CB G:CYS796 3.3 69.7 1.0
CA G:CYS796 3.5 71.6 1.0
CB G:HIS742 3.6 63.3 1.0
NE2 G:HIS742 3.9 74.1 1.0
CD2 G:HIS742 4.1 73.4 1.0
N G:CYS796 4.2 74.0 1.0
ND1 G:HIS794 4.2 74.6 1.0
CG G:HIS794 4.3 73.1 1.0
CA G:CYS800 4.5 74.0 1.0
N G:ASN797 4.6 71.9 1.0
C G:CYS796 4.7 71.4 1.0
C G:LYS795 4.8 70.5 1.0
CD1 G:LEU805 4.8 83.6 1.0
O G:LYS795 4.9 72.4 1.0

Zinc binding site 8 out of 8 in 5e4h

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Zinc binding site 8 out of 8 in the Crystal Structure of Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A


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 Apoenzyme Alpha-Kinase Domain of Myosin-II Heavy Chain Kinase A within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn901

b:69.1
occ:1.00
SG H:CYS800 2.0 63.9 1.0
ND1 H:HIS742 2.0 77.0 1.0
SG H:CYS796 2.1 66.7 1.0
NE2 H:HIS794 2.3 59.7 1.0
CE1 H:HIS742 2.8 76.9 1.0
CG H:HIS742 3.0 72.4 1.0
CE1 H:HIS794 3.2 63.4 1.0
CB H:CYS800 3.2 67.2 1.0
CD2 H:HIS794 3.3 60.4 1.0
CB H:CYS796 3.4 65.7 1.0
CB H:HIS742 3.5 68.5 1.0
CA H:CYS796 3.6 65.8 1.0
NE2 H:HIS742 3.8 75.5 1.0
CD2 H:HIS742 4.0 72.4 1.0
ND1 H:HIS794 4.3 66.4 1.0
N H:CYS796 4.3 68.3 1.0
CG H:HIS794 4.4 63.3 1.0
CA H:CYS800 4.4 70.2 1.0
CD1 H:LEU805 4.7 79.9 1.0
N H:ASN797 4.7 60.9 1.0
C H:CYS796 4.8 65.6 1.0
CB H:LEU805 4.9 87.3 1.0
C H:LYS795 4.9 68.5 1.0

Reference:

Q.Ye, Y.Yang, L.Van Staalduinen, S.W.Crawley, L.Liu, S.Brennan, G.P.Cote, Z.Jia. Structure of the Dictyostelium Myosin-II Heavy Chain Kinase A (Mhck-A) Alpha-Kinase Domain Apoenzyme Reveals A Novel Autoinhibited Conformation. Sci Rep V. 6 26634 2016.
ISSN: ESSN 2045-2322
PubMed: 27211275
DOI: 10.1038/SREP26634
Page generated: Wed Dec 16 06:09:07 2020

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