Calcium in PDB 5ue1: Crystal Structure of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase in Complex with Adenine From Vibrio Fischeri ES114

Enzymatic activity of Crystal Structure of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase in Complex with Adenine From Vibrio Fischeri ES114

All present enzymatic activity of Crystal Structure of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase in Complex with Adenine From Vibrio Fischeri ES114:
3.2.2.9;

Protein crystallography data

The structure of Crystal Structure of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase in Complex with Adenine From Vibrio Fischeri ES114, PDB code: 5ue1 was solved by E.V.Filippova, G.Minasov, L.Shuvalova, O.Kiryukhina, I.Dubrovska, S.Grimshaw, W.F.Anderson, Center For Structural Genomics Of Infectiousdiseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.14
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.642, 72.915, 57.563, 90.00, 109.60, 90.00
R / Rfree (%) 12.9 / 15.8

Other elements in 5ue1:

The structure of Crystal Structure of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase in Complex with Adenine From Vibrio Fischeri ES114 also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase in Complex with Adenine From Vibrio Fischeri ES114 (pdb code 5ue1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase in Complex with Adenine From Vibrio Fischeri ES114, PDB code: 5ue1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5ue1

Go back to Calcium Binding Sites List in 5ue1
Calcium binding site 1 out of 4 in the Crystal Structure of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase in Complex with Adenine From Vibrio Fischeri ES114


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase in Complex with Adenine From Vibrio Fischeri ES114 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:13.1
occ:0.80
 O A:ASN-1 2.3 20.8 1.0
O A:HOH597 2.4 20.6 1.0
C A:ASN-1 3.5 23.1 1.0
N A:ALA0 4.4 19.1 1.0
N A:ASN-1 4.4 41.4 1.0
CA A:ALA0 4.4 16.7 1.0
CA A:ASN-1 4.5 30.1 1.0
CB A:ALA0 4.8 18.8 1.0
O A:HOH573 4.8 19.6 1.0

Calcium binding site 2 out of 4 in 5ue1

Go back to Calcium Binding Sites List in 5ue1
Calcium binding site 2 out of 4 in the Crystal Structure of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase in Complex with Adenine From Vibrio Fischeri ES114


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase in Complex with Adenine From Vibrio Fischeri ES114 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:13.9
occ:0.50
 CA A:CA304 0.0 13.9 0.5
CA A:CA304 1.2 21.3 0.5
O A:ASP18 2.3 15.6 1.0
O A:HOH559 2.4 24.9 1.0
O A:HOH457 3.2 29.6 1.0
C A:ASP18 3.4 12.7 1.0
O A:HOH647 3.5 35.5 1.0
CA A:ASP18 4.0 13.3 1.0
N A:LYS19 4.4 12.0 0.5
N A:LYS19 4.4 12.5 0.5
CB A:ASP18 4.4 16.6 1.0
O A:ILE20 4.5 14.9 1.0
CA A:LYS19 4.6 12.3 0.5
CA A:LYS19 4.6 13.1 0.5
O A:HOH492 4.6 36.4 1.0
C A:LYS19 4.9 12.1 0.5
O A:HOH542 4.9 21.9 0.5
OD1 A:ASP18 4.9 25.0 1.0
C A:LYS19 5.0 12.9 0.5
OE2 A:GLU21 5.0 31.1 0.5

Calcium binding site 3 out of 4 in 5ue1

Go back to Calcium Binding Sites List in 5ue1
Calcium binding site 3 out of 4 in the Crystal Structure of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase in Complex with Adenine From Vibrio Fischeri ES114


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase in Complex with Adenine From Vibrio Fischeri ES114 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:21.3
occ:0.50
 CA A:CA304 0.0 21.3 0.5
CA A:CA304 1.2 13.9 0.5
O A:HOH559 2.3 24.9 1.0
O A:ASP18 2.4 15.6 1.0
O A:HOH647 2.4 35.5 1.0
C A:ASP18 3.6 12.7 1.0
O A:HOH542 4.1 21.9 0.5
O A:HOH457 4.1 29.6 1.0
CA A:LYS19 4.4 12.3 0.5
CA A:LYS19 4.4 13.1 0.5
N A:LYS19 4.4 12.0 0.5
N A:LYS19 4.4 12.5 0.5
O A:HOH688 4.5 38.4 1.0
OE2 A:GLU21 4.5 31.1 0.5
CA A:ASP18 4.6 13.3 1.0
C A:LYS19 4.7 12.1 0.5
C A:LYS19 4.8 12.9 0.5
CB A:ASP18 4.9 16.6 1.0
O A:ILE20 4.9 14.9 1.0
O A:LYS19 5.0 13.0 0.5
O A:HOH542 5.0 20.1 0.5

Calcium binding site 4 out of 4 in 5ue1

Go back to Calcium Binding Sites List in 5ue1
Calcium binding site 4 out of 4 in the Crystal Structure of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase in Complex with Adenine From Vibrio Fischeri ES114


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase in Complex with Adenine From Vibrio Fischeri ES114 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:13.2
occ:0.80
 O A:MET206 2.3 16.1 1.0
O A:HOH598 2.4 19.2 1.0
O A:HOH609 2.4 20.8 1.0
OD1 A:ASP209 2.4 20.4 1.0
OE1 A:GLU210 2.4 17.5 1.0
OE2 A:GLU210 2.5 20.0 1.0
OD2 A:ASP209 2.6 24.2 1.0
CD A:GLU210 2.8 15.1 1.0
CG A:ASP209 2.9 17.5 1.0
C A:MET206 3.5 13.0 1.0
O A:HOH645 4.2 33.2 1.0
CG A:GLU210 4.3 15.9 1.0
O A:HOH649 4.4 24.9 1.0
CA A:MET206 4.4 15.4 1.0
CB A:ASP209 4.4 15.0 1.0
N A:SER207 4.4 12.7 1.0
CA A:SER207 4.5 12.8 1.0
O A:HOH419 4.6 28.8 1.0
O A:HOH418 4.7 25.2 1.0
N A:GLU210 4.8 11.2 1.0
O A:HOH575 4.8 29.9 1.0
CB A:MET206 4.8 23.2 1.0
N A:ASP209 5.0 12.4 1.0
C A:SER207 5.0 12.2 1.0
O A:HOH687 5.0 30.6 1.0
CG A:MET206 5.0 50.5 1.0

Reference:

E.V.Filippova, G.Minasov, L.Shuvalova, O.Kiryukhina, I.Dubrovska, S.Grimshaw, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase From Vibrio Fischeri ES114 To Be Published.
Page generated: Sat Dec 12 05:45:56 2020

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