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Zinc in PDB 2rgx: Crystal Structure of Adenylate Kinase From Aquifex Aeolicus in Complex with AP5A

Enzymatic activity of Crystal Structure of Adenylate Kinase From Aquifex Aeolicus in Complex with AP5A

All present enzymatic activity of Crystal Structure of Adenylate Kinase From Aquifex Aeolicus in Complex with AP5A:
2.7.4.3;

Protein crystallography data

The structure of Crystal Structure of Adenylate Kinase From Aquifex Aeolicus in Complex with AP5A, PDB code: 2rgx was solved by V.Thai, M.Wolf-Watz, T.Fenn, E.Pozharski, M.A.Wilson, G.A.Petsko, D.Kern, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 68.611, 68.611, 85.479, 90.00, 90.00, 120.00
R / Rfree (%) 20.5 / 24.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Adenylate Kinase From Aquifex Aeolicus in Complex with AP5A (pdb code 2rgx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Adenylate Kinase From Aquifex Aeolicus in Complex with AP5A, PDB code: 2rgx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2rgx

Go back to Zinc Binding Sites List in 2rgx
Zinc binding site 1 out of 4 in the Crystal Structure of Adenylate Kinase From Aquifex Aeolicus in Complex with AP5A


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 Adenylate Kinase From Aquifex Aeolicus in Complex with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:21.2
occ:1.00
O A:HOH883 2.0 19.4 1.0
O A:HOH882 2.1 18.4 1.0
O2G A:AP5806 2.1 21.7 1.0
O A:HOH881 2.2 18.5 1.0
O A:HOH896 2.2 25.1 1.0
O2B A:AP5806 2.3 16.7 1.0
PG A:AP5806 3.2 23.3 1.0
PB A:AP5806 3.3 17.3 1.0
O3B A:AP5806 3.6 20.8 1.0
O1E A:AP5806 4.0 21.1 1.0
O2A A:AP5806 4.1 17.5 1.0
O A:HOH819 4.1 21.8 1.0
OD2 A:ASP81 4.2 16.6 1.0
N A:GLY14 4.2 16.1 1.0
O3G A:AP5806 4.2 27.6 1.0
OD1 A:ASP81 4.3 16.8 1.0
CA A:GLY14 4.3 17.3 1.0
O1G A:AP5806 4.4 22.1 1.0
O3A A:AP5806 4.4 15.8 1.0
O1B A:AP5806 4.4 15.2 1.0
O A:HOH824 4.4 21.8 1.0
NH1 A:ARG124 4.5 23.6 1.0
OG A:SER30 4.5 17.9 1.0
PA A:AP5806 4.6 16.4 1.0
PE A:AP5806 4.6 23.0 1.0
CG A:ASP81 4.7 17.1 1.0
O2E A:AP5806 4.7 22.5 1.0
O A:HOH830 4.7 22.1 1.0
O1D A:AP5806 4.7 29.5 1.0
OD2 A:ASP33 4.8 18.1 1.0
O3D A:AP5806 4.8 26.6 1.0
PD A:AP5806 4.8 28.5 1.0
O1A A:AP5806 4.9 15.9 1.0
NH1 A:ARG150 4.9 47.1 1.0

Zinc binding site 2 out of 4 in 2rgx

Go back to Zinc Binding Sites List in 2rgx
Zinc binding site 2 out of 4 in the Crystal Structure of Adenylate Kinase From Aquifex Aeolicus in Complex with AP5A


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 Adenylate Kinase From Aquifex Aeolicus in Complex with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:26.4
occ:1.00
OE2 A:GLU163 1.9 25.7 1.0
OE2 A:GLU167 2.1 28.5 1.0
OE1 A:GLU167 2.5 30.9 1.0
CD A:GLU167 2.6 28.1 1.0
CD A:GLU163 2.9 22.5 1.0
CG A:GLU163 3.3 23.5 1.0
OE1 A:GLU163 4.0 22.8 1.0
CG A:GLU167 4.1 27.9 1.0
O A:HOH900 4.3 33.3 1.0
CB A:GLU163 4.7 21.4 1.0
CB A:GLU167 5.0 26.9 1.0

Zinc binding site 3 out of 4 in 2rgx

Go back to Zinc Binding Sites List in 2rgx
Zinc binding site 3 out of 4 in the Crystal Structure of Adenylate Kinase From Aquifex Aeolicus in Complex with AP5A


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 Adenylate Kinase From Aquifex Aeolicus in Complex with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:36.6
occ:1.00
OE2 A:GLU98 2.1 38.0 1.0
O A:HOH893 2.2 31.0 1.0
OE1 A:GLU95 2.3 32.0 1.0
OE2 A:GLU95 2.6 25.9 1.0
CD A:GLU95 2.8 28.6 1.0
CD A:GLU98 3.0 39.9 1.0
OE1 A:GLU98 3.3 44.4 1.0
O A:HOH846 3.8 27.6 1.0
CE A:LYS99 4.3 37.9 1.0
CG A:GLU95 4.3 26.1 1.0
CG A:LYS99 4.3 35.0 1.0
CG A:GLU98 4.3 36.6 1.0
NZ A:LYS99 4.5 40.7 1.0
O A:GLU95 4.8 24.6 1.0
CB A:GLU98 4.9 33.1 1.0
CD A:LYS99 4.9 35.8 1.0

Zinc binding site 4 out of 4 in 2rgx

Go back to Zinc Binding Sites List in 2rgx
Zinc binding site 4 out of 4 in the Crystal Structure of Adenylate Kinase From Aquifex Aeolicus in Complex with AP5A


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 Adenylate Kinase From Aquifex Aeolicus in Complex with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:60.8
occ:1.00
NE2 A:HIS106 2.3 27.6 1.0
O A:HOH890 2.8 73.3 1.0
CD2 A:HIS106 3.2 27.0 1.0
CE1 A:HIS106 3.3 28.2 1.0
O A:ILE202 3.9 40.5 1.0
CG A:HIS106 4.4 26.9 1.0
ND1 A:HIS106 4.4 30.1 1.0
C A:ILE202 4.6 40.8 1.0
CA A:ILE202 4.9 39.7 1.0
CB A:ASP105 4.9 28.4 1.0

Reference:

K.A.Henzler-Wildman, V.Thai, M.Lei, M.Ott, M.Wolf-Watz, T.Fenn, E.Pozharski, M.A.Wilson, G.A.Petsko, M.Karplus, C.G.Hubner, D.Kern. Intrinsic Motions Along An Enzymatic Reaction Trajectory. Nature V. 450 838 2007.
ISSN: ISSN 0028-0836
PubMed: 18026086
DOI: 10.1038/NATURE06410
Page generated: Wed Dec 16 03:52:12 2020

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