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Cadmium in PDB 5fxm: Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff Goniometer

Enzymatic activity of Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff Goniometer

All present enzymatic activity of Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff Goniometer:
3.1.1.73;

Protein crystallography data

The structure of Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff Goniometer, PDB code: 5fxm was solved by M.W.Bowler, D.Nurizzo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.18 / 1.99
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 111.974, 111.974, 66.031, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 19.7

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff Goniometer (pdb code 5fxm). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff Goniometer, PDB code: 5fxm:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 5fxm

Go back to Cadmium Binding Sites List in 5fxm
Cadmium binding site 1 out of 5 in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff Goniometer


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3086

b:37.0
occ:1.00
 ND1 A:HIS886 2.4 31.2 1.0
O A:HOH2027 2.4 29.2 1.0
SG A:CYS823 2.6 35.7 1.0
SE A:MSE889 2.8 40.8 1.0
CE1 A:HIS886 3.0 32.4 1.0
CG A:HIS886 3.4 30.0 1.0
CB A:CYS823 3.6 33.9 1.0
CA A:HIS886 3.8 29.2 1.0
CE A:MSE889 3.9 41.2 1.0
CB A:HIS886 3.9 29.2 1.0
CG A:MSE889 4.0 38.0 1.0
NE2 A:HIS886 4.1 32.5 1.0
CB A:MSE889 4.1 35.9 1.0
CD2 A:HIS886 4.3 30.8 1.0
CA A:CYS823 4.3 35.5 1.0
CD A:PRO824 4.3 37.7 1.0
N A:HIS886 4.6 27.6 1.0
O A:HIS886 4.7 31.7 1.0
C A:HIS886 4.8 29.3 1.0
O A:ASP885 4.8 27.0 1.0
N A:PRO824 5.0 37.4 1.0

Cadmium binding site 2 out of 5 in 5fxm

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Cadmium binding site 2 out of 5 in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff Goniometer


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3087

b:35.0
occ:1.00
 OE1 A:GLU1079 2.2 40.2 1.0
OE2 A:GLU894 2.3 38.6 1.0
NE2 A:HIS1085 2.4 38.3 1.0
ND1 A:HIS1083 2.5 43.1 1.0
ND1 A:HIS1076 2.5 32.8 1.0
OE2 A:GLU1079 2.6 41.2 1.0
CD A:GLU1079 2.8 40.7 1.0
OE1 A:GLU894 2.9 35.4 1.0
CD A:GLU894 2.9 34.3 1.0
CE1 A:HIS1076 3.2 33.2 1.0
CD2 A:HIS1085 3.3 36.8 1.0
CE1 A:HIS1085 3.3 36.9 1.0
CE1 A:HIS1083 3.4 43.9 1.0
CG A:HIS1083 3.4 41.6 1.0
CG A:HIS1076 3.6 32.2 1.0
CB A:HIS1083 3.7 38.6 1.0
CB A:HIS1076 4.0 34.0 1.0
CG A:GLU1079 4.3 41.5 1.0
CA A:HIS1076 4.4 34.7 1.0
NE2 A:HIS1076 4.4 34.0 1.0
CG A:GLU894 4.4 33.2 1.0
ND1 A:HIS1085 4.4 37.3 1.0
CG A:HIS1085 4.4 38.2 1.0
NE2 A:HIS1083 4.5 46.8 1.0
CD2 A:HIS1083 4.5 44.9 1.0
CD2 A:HIS1076 4.6 32.2 1.0
CB A:GLU1079 5.0 40.4 1.0

Cadmium binding site 3 out of 5 in 5fxm

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Cadmium binding site 3 out of 5 in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff Goniometer


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3088

b:45.2
occ:1.00
 OE2 A:GLU1007 2.2 42.1 1.0
OE1 A:GLU1007 2.5 38.9 1.0
CD A:GLU1007 2.7 38.4 1.0
CG A:GLU1007 4.2 36.4 1.0
N A:SER1004 4.7 39.6 1.0
CD2 A:LEU1003 4.8 37.4 1.0
O A:GLY1002 4.8 43.9 1.0
CA A:LEU1003 4.9 39.9 1.0

Cadmium binding site 4 out of 5 in 5fxm

Go back to Cadmium Binding Sites List in 5fxm
Cadmium binding site 4 out of 5 in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff Goniometer


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3089

b:44.9
occ:1.00
 O A:HOH2038 1.8 32.8 1.0
O A:HOH2036 2.2 53.7 1.0
NE2 A:HIS1080 2.3 55.7 1.0
NE2 A:HIS947 2.4 36.9 1.0
O A:HOH2035 2.7 46.5 1.0
CE1 A:HIS1080 3.1 60.2 1.0
CD2 A:HIS947 3.2 35.9 1.0
CD2 A:HIS1080 3.4 54.9 1.0
CE1 A:HIS947 3.4 36.2 1.0
ND1 A:HIS1080 4.2 63.0 1.0
CG A:HIS1080 4.4 55.7 1.0
CG A:HIS947 4.4 34.2 1.0
ND1 A:HIS947 4.5 35.2 1.0
O A:LEU1078 4.6 52.8 1.0
CD2 A:TYR932 4.7 41.5 1.0

Cadmium binding site 5 out of 5 in 5fxm

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Cadmium binding site 5 out of 5 in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff Goniometer


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Esrf Robodiff Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd3090

b:57.4
occ:0.30
 ND1 A:HIS1081 1.8 65.3 1.0
CE1 A:HIS1081 2.5 71.0 1.0
CG A:HIS1081 2.8 63.1 1.0
CB A:HIS1081 3.4 57.6 1.0
NE2 A:HIS1081 3.5 68.0 1.0
CD2 A:HIS1081 3.6 63.0 1.0
CA A:HIS1081 3.7 53.8 1.0
N A:HIS1081 4.6 51.8 1.0
N A:HIS1082 4.7 47.8 1.0
O A:HIS1080 4.8 57.2 1.0
C A:HIS1081 4.8 50.5 1.0

Reference:

D.Nurizzo, M.W.Bowler, H.Caserotto, F.Dobias, T.Giraud, J.Surr, N.Guichard, G.Papp, M.Guijarro, C.Mueller-Dieckmann, D.Flot, S.Mcsweeney, F.Cipriani, P.Theveneau, G.A.Leonard. Robodiff: Combining A Sample Changer and Goniometer For Highly Automated Macromolecular Crystallography Experiments. Acta Crystallogr.,Sect.D V. 72 966 2016.
ISSN: ISSN 0907-4449
PubMed: 27487827
DOI: 10.1107/S205979831601158X
Page generated: Fri Jul 19 18:24:15 2024

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