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Calcium in PDB 8fny: Nucleotide-Bound Structure of A Functional Construct of Eukaryotic Elongation Factor 2 Kinase.

Enzymatic activity of Nucleotide-Bound Structure of A Functional Construct of Eukaryotic Elongation Factor 2 Kinase.

All present enzymatic activity of Nucleotide-Bound Structure of A Functional Construct of Eukaryotic Elongation Factor 2 Kinase.:
2.7.11.20;

Protein crystallography data

The structure of Nucleotide-Bound Structure of A Functional Construct of Eukaryotic Elongation Factor 2 Kinase., PDB code: 8fny was solved by A.Piserchio, E.A.Isiorho, K.N.Dalby, R.Ghose, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.79 / 2.22
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.16, 83.352, 88.978, 65.35, 90.03, 86.47
R / Rfree (%) 20.8 / 22.9

Other elements in 8fny:

The structure of Nucleotide-Bound Structure of A Functional Construct of Eukaryotic Elongation Factor 2 Kinase. also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Nucleotide-Bound Structure of A Functional Construct of Eukaryotic Elongation Factor 2 Kinase. (pdb code 8fny). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Nucleotide-Bound Structure of A Functional Construct of Eukaryotic Elongation Factor 2 Kinase., PDB code: 8fny:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 8fny

Go back to Calcium Binding Sites List in 8fny
Calcium binding site 1 out of 4 in the Nucleotide-Bound Structure of A Functional Construct of Eukaryotic Elongation Factor 2 Kinase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Nucleotide-Bound Structure of A Functional Construct of Eukaryotic Elongation Factor 2 Kinase. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:25.0
occ:1.00
 OD1 B:ASP95 2.2 27.1 1.0
O B:TYR99 2.3 23.4 1.0
OE2 B:GLU104 2.3 19.2 1.0
OD1 B:ASN97 2.4 20.3 1.0
OE1 B:GLU104 2.4 24.4 1.0
OD1 B:ASP93 2.5 25.9 1.0
CD B:GLU104 2.7 27.9 1.0
CG B:ASP95 3.3 30.6 1.0
CG B:ASN97 3.4 21.3 1.0
C B:TYR99 3.5 23.2 1.0
CG B:ASP93 3.7 24.8 1.0
OD2 B:ASP95 3.8 27.5 1.0
N B:TYR99 4.1 26.6 1.0
ND2 B:ASN97 4.2 21.9 1.0
CG B:GLU104 4.2 29.6 1.0
N B:ASP95 4.3 25.9 1.0
N B:ASN97 4.3 24.6 1.0
CA B:TYR99 4.3 26.8 1.0
CA B:ASP93 4.4 19.8 1.0
CB B:ASP95 4.4 28.0 1.0
OD2 A:ASP208 4.4 26.5 1.0
CB B:ASN97 4.4 21.9 1.0
N B:ILE100 4.5 18.0 1.0
OD2 B:ASP93 4.5 25.1 1.0
N B:LYS94 4.5 28.5 1.0
N B:GLY96 4.5 25.1 1.0
C B:ASP93 4.5 26.0 1.0
CB B:ASP93 4.6 24.9 1.0
CA B:ILE100 4.6 21.6 1.0
N B:SER101 4.6 26.6 1.0
CB B:TYR99 4.7 24.9 1.0
CA B:ASP95 4.7 24.0 1.0
NZ A:LYS192 4.8 30.1 1.0
CA B:ASN97 4.8 27.5 1.0
C B:ASP95 4.9 26.1 1.0
N B:GLY98 4.9 24.6 1.0

Calcium binding site 2 out of 4 in 8fny

Go back to Calcium Binding Sites List in 8fny
Calcium binding site 2 out of 4 in the Nucleotide-Bound Structure of A Functional Construct of Eukaryotic Elongation Factor 2 Kinase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Nucleotide-Bound Structure of A Functional Construct of Eukaryotic Elongation Factor 2 Kinase. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:36.1
occ:1.00
 OD2 B:ASP131 2.0 41.8 1.0
OD1 B:ASP133 2.4 33.2 1.0
O B:GLN135 2.5 35.0 1.0
OE1 B:GLU140 2.6 35.1 1.0
OD1 B:ASP129 2.9 28.6 1.0
OE2 B:GLU140 2.9 35.8 1.0
CD B:GLU140 3.1 37.5 1.0
ND2 B:ASN137 3.1 35.5 1.0
CG B:ASP133 3.1 35.6 1.0
CG B:ASP131 3.2 41.6 1.0
OD2 B:ASP133 3.3 36.0 1.0
C B:GLN135 3.4 29.5 1.0
OD1 B:ASP131 3.8 43.9 1.0
N B:ASN137 3.8 31.7 1.0
CG B:ASP129 3.9 33.3 1.0
CG B:ASN137 4.0 35.5 1.0
CA B:VAL136 4.1 28.5 1.0
N B:VAL136 4.1 28.4 1.0
CB B:ASP131 4.3 42.9 1.0
C B:VAL136 4.4 29.3 1.0
CB B:ASP133 4.4 31.8 1.0
CA B:GLN135 4.5 28.9 1.0
N B:GLN135 4.5 30.3 1.0
OD2 B:ASP129 4.5 36.5 1.0
CG B:GLU140 4.5 35.5 1.0
CB B:ASN137 4.5 34.3 1.0
N B:ASP133 4.6 32.8 1.0
CA B:ASP129 4.8 36.0 1.0
OD1 B:ASN137 4.8 38.4 1.0
N B:ASP131 4.8 37.5 1.0
CA B:ASN137 4.8 33.5 1.0
CB B:ASP129 4.8 32.2 1.0
CB B:GLN135 4.9 28.6 1.0
N B:GLY132 5.0 36.7 1.0

Calcium binding site 3 out of 4 in 8fny

Go back to Calcium Binding Sites List in 8fny
Calcium binding site 3 out of 4 in the Nucleotide-Bound Structure of A Functional Construct of Eukaryotic Elongation Factor 2 Kinase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Nucleotide-Bound Structure of A Functional Construct of Eukaryotic Elongation Factor 2 Kinase. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:22.4
occ:1.00
 OD1 D:ASP95 2.2 28.2 1.0
OE2 D:GLU104 2.3 24.8 1.0
O D:TYR99 2.4 27.5 1.0
OD1 D:ASN97 2.4 24.9 1.0
OE1 D:GLU104 2.5 27.6 1.0
OD1 D:ASP93 2.5 20.4 1.0
CD D:GLU104 2.7 27.1 1.0
CG D:ASP95 3.2 28.7 1.0
CG D:ASN97 3.4 24.8 1.0
C D:TYR99 3.6 26.5 1.0
CG D:ASP93 3.7 28.5 1.0
OD2 D:ASP95 3.8 24.9 1.0
ND2 D:ASN97 4.1 23.4 1.0
OD2 C:ASP208 4.2 21.7 1.0
CG D:GLU104 4.2 25.7 1.0
N D:TYR99 4.2 19.9 1.0
N D:ASP95 4.3 24.7 1.0
N D:ASN97 4.4 23.3 1.0
CB D:ASP95 4.4 23.7 1.0
CA D:TYR99 4.4 26.9 1.0
CB D:ASN97 4.4 25.5 1.0
CA D:ASP93 4.5 26.4 1.0
OD2 D:ASP93 4.5 28.9 1.0
N D:ILE100 4.6 23.3 1.0
N D:GLY96 4.6 23.3 1.0
NZ C:LYS192 4.6 29.3 1.0
N D:LYS94 4.6 34.2 1.0
CB D:ASP93 4.7 29.6 1.0
C D:ASP93 4.7 29.7 1.0
CA D:ILE100 4.7 23.9 1.0
CA D:ASP95 4.8 24.4 1.0
N D:SER101 4.8 24.6 1.0
CB D:TYR99 4.8 27.1 1.0
CA D:ASN97 4.9 27.9 1.0
C D:ASP95 4.9 26.9 1.0
N D:GLY98 4.9 28.8 1.0

Calcium binding site 4 out of 4 in 8fny

Go back to Calcium Binding Sites List in 8fny
Calcium binding site 4 out of 4 in the Nucleotide-Bound Structure of A Functional Construct of Eukaryotic Elongation Factor 2 Kinase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Nucleotide-Bound Structure of A Functional Construct of Eukaryotic Elongation Factor 2 Kinase. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:35.8
occ:1.00
 OD1 D:ASP131 2.2 45.3 1.0
OD1 D:ASP133 2.3 35.7 1.0
O D:GLN135 2.4 34.0 1.0
OD1 D:ASP129 2.5 35.1 1.0
OE1 D:GLU140 2.5 41.3 1.0
OE2 D:GLU140 3.0 38.8 1.0
CD D:GLU140 3.1 44.0 1.0
CG D:ASP133 3.2 39.9 1.0
ND2 D:ASN137 3.3 38.1 1.0
CG D:ASP131 3.4 44.3 1.0
C D:GLN135 3.4 28.2 1.0
OD2 D:ASP133 3.5 39.5 1.0
CG D:ASP129 3.6 35.5 1.0
OD2 D:ASP131 3.9 41.9 1.0
N D:ASN137 4.1 26.5 1.0
CA D:VAL136 4.1 28.2 1.0
N D:VAL136 4.1 28.3 1.0
OD2 D:ASP129 4.2 31.4 1.0
CG D:ASN137 4.2 35.3 1.0
N D:GLN135 4.4 32.2 1.0
CA D:GLN135 4.4 30.5 1.0
CA D:ASP129 4.4 38.3 1.0
CB D:ASP133 4.5 36.3 1.0
N D:ASP133 4.5 36.4 1.0
CB D:ASP129 4.5 35.4 1.0
C D:VAL136 4.5 28.1 1.0
CB D:ASP131 4.6 41.5 1.0
CG D:GLU140 4.6 37.0 1.0
N D:ASP131 4.6 45.2 1.0
N D:GLY132 4.7 42.4 1.0
N D:ILE130 4.8 45.0 1.0
CB D:GLN135 4.8 33.0 1.0
CB D:ASN137 4.9 30.2 1.0
C D:ASP129 4.9 44.3 1.0
OD1 D:ASN137 5.0 36.1 1.0
CA D:ASP133 5.0 37.5 1.0

Reference:

A.Piserchio, K.J.Long, L.S.Browning, A.L.Bohanon, E.A.Isiorho, K.N.Dalby, R.Ghose. Adp Enhances the Allosteric Activation of Eukaryotic Elongation Factor 2 Kinase By Calmodulin. Proc.Natl.Acad.Sci.Usa V. 120 02120 2023.
ISSN: ESSN 1091-6490
PubMed: 37068230
DOI: 10.1073/PNAS.2300902120
Page generated: Fri Jul 19 09:02:21 2024

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