Atomistry » Calcium » PDB 8fd7-8fvo » 8fny
Atomistry »
  Calcium »
    PDB 8fd7-8fvo »
      8fny »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy