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Cadmium in PDB 6fj4: Structure of Fae Solved By Sad From Data Collected at the Peak of the Selenium Absorption Edge on ID30B

Enzymatic activity of Structure of Fae Solved By Sad From Data Collected at the Peak of the Selenium Absorption Edge on ID30B

All present enzymatic activity of Structure of Fae Solved By Sad From Data Collected at the Peak of the Selenium Absorption Edge on ID30B:
3.2.1.8;

Protein crystallography data

The structure of Structure of Fae Solved By Sad From Data Collected at the Peak of the Selenium Absorption Edge on ID30B, PDB code: 6fj4 was solved by A.A.Mccarthy, C.Mueller-Dieckmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.21 / 1.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 112.023, 112.023, 65.865, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 17.8

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Fae Solved By Sad From Data Collected at the Peak of the Selenium Absorption Edge on ID30B (pdb code 6fj4). 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 at the Peak of the Selenium Absorption Edge on ID30B, PDB code: 6fj4:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 6fj4

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Cadmium binding site 1 out of 5 in the Structure of Fae Solved By Sad From Data Collected at the Peak of the Selenium Absorption Edge on ID30B


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 at the Peak of the Selenium Absorption Edge on ID30B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1101

b:33.7
occ:1.00
 ND1 A:HIS886 2.4 21.5 1.0
SG A:CYS823 2.6 24.4 1.0
SE A:MSE889 2.8 27.3 1.0
CE1 A:HIS886 3.0 20.1 1.0
CG A:HIS886 3.5 18.2 1.0
CB A:CYS823 3.7 20.1 1.0
CA A:HIS886 3.9 15.8 1.0
CG A:MSE889 4.0 21.9 1.0
CE A:MSE889 4.1 25.4 1.0
CB A:HIS886 4.1 17.1 1.0
CB A:MSE889 4.1 19.1 1.0
NE2 A:HIS886 4.2 19.3 1.0
CD2 A:HIS886 4.4 18.4 1.0
CA A:CYS823 4.5 19.3 1.0
O A:HIS886 4.7 14.7 1.0
N A:HIS886 4.7 14.4 1.0
CD A:PRO824 4.7 17.2 1.0
O A:ASP885 4.8 15.2 1.0
C A:HIS886 4.8 14.8 1.0
OD1 A:ASN890 4.9 26.2 0.8

Cadmium binding site 2 out of 5 in 6fj4

Go back to Cadmium Binding Sites List in 6fj4
Cadmium binding site 2 out of 5 in the Structure of Fae Solved By Sad From Data Collected at the Peak of the Selenium Absorption Edge on ID30B


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 at the Peak of the Selenium Absorption Edge on ID30B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1102

b:27.9
occ:1.00
 OE1 A:GLU1079 2.2 25.9 1.0
OE2 A:GLU894 2.3 26.0 1.0
NE2 A:HIS1085 2.3 25.0 1.0
OE2 A:GLU1079 2.3 25.3 1.0
ND1 A:HIS1083 2.4 21.7 1.0
ND1 A:HIS1076 2.4 19.6 1.0
OE1 A:GLU894 2.4 28.9 1.0
CD A:GLU1079 2.6 24.9 1.0
CD A:GLU894 2.8 22.5 1.0
CE1 A:HIS1076 3.2 20.5 1.0
CD2 A:HIS1085 3.2 23.4 1.0
CE1 A:HIS1085 3.3 24.2 1.0
CE1 A:HIS1083 3.3 21.2 1.0
CG A:HIS1083 3.4 20.4 1.0
CG A:HIS1076 3.4 18.3 1.0
CB A:HIS1083 3.7 20.0 1.0
CB A:HIS1076 3.9 18.3 1.0
O A:HOH1282 4.0 45.5 1.0
CG A:GLU1079 4.2 25.0 1.0
NE2 A:HIS1076 4.4 19.4 1.0
CA A:HIS1076 4.4 18.2 1.0
ND1 A:HIS1085 4.4 23.1 1.0
CG A:HIS1085 4.4 23.6 1.0
CG A:GLU894 4.4 21.8 1.0
NE2 A:HIS1083 4.4 21.3 1.0
O A:HOH1203 4.5 43.9 1.0
CD2 A:HIS1076 4.5 18.8 1.0
CD2 A:HIS1083 4.5 19.8 1.0
O A:HOH1274 4.8 40.8 1.0
CB A:GLU1079 5.0 24.9 1.0

Cadmium binding site 3 out of 5 in 6fj4

Go back to Cadmium Binding Sites List in 6fj4
Cadmium binding site 3 out of 5 in the Structure of Fae Solved By Sad From Data Collected at the Peak of the Selenium Absorption Edge on ID30B


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 at the Peak of the Selenium Absorption Edge on ID30B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1103

b:32.9
occ:1.00
 O A:HOH1374 2.2 36.6 1.0
OE2 A:GLU1007 2.3 22.4 1.0
OE1 A:GLU1007 2.3 18.7 1.0
CD A:GLU1007 2.7 17.5 1.0
CG A:GLU1007 4.2 18.1 1.0
N A:SER1004 4.6 16.5 1.0
CD2 A:LEU1003 4.7 18.0 1.0
CA A:LEU1003 4.9 17.4 1.0

Cadmium binding site 4 out of 5 in 6fj4

Go back to Cadmium Binding Sites List in 6fj4
Cadmium binding site 4 out of 5 in the Structure of Fae Solved By Sad From Data Collected at the Peak of the Selenium Absorption Edge on ID30B


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 at the Peak of the Selenium Absorption Edge on ID30B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1104

b:36.5
occ:1.00
 O A:HOH1375 2.1 41.4 1.0
O A:HOH1214 2.2 38.2 1.0
O A:HOH1372 2.2 46.2 1.0
NE2 A:HIS1080 2.2 35.5 1.0
NE2 A:HIS947 2.3 18.9 1.0
O A:HOH1377 2.5 36.4 1.0
CE1 A:HIS1080 3.1 37.5 1.0
CD2 A:HIS947 3.2 19.9 1.0
CD2 A:HIS1080 3.3 36.0 1.0
CE1 A:HIS947 3.3 22.1 1.0
O A:HOH1350 4.1 35.7 1.0
ND1 A:HIS1080 4.2 37.3 1.0
CG A:HIS1080 4.4 34.2 1.0
CG A:HIS947 4.4 19.2 1.0
ND1 A:HIS947 4.4 19.5 1.0
O A:LEU1078 4.5 30.5 1.0
CD2 A:TYR932 4.8 20.1 1.0

Cadmium binding site 5 out of 5 in 6fj4

Go back to Cadmium Binding Sites List in 6fj4
Cadmium binding site 5 out of 5 in the Structure of Fae Solved By Sad From Data Collected at the Peak of the Selenium Absorption Edge on ID30B


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 at the Peak of the Selenium Absorption Edge on ID30B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1105

b:57.9
occ:0.30
 ND1 A:HIS1081 2.3 48.7 1.0
O1 A:SO41108 2.8 75.2 1.0
O A:HOH1279 2.8 56.0 1.0
CG A:HIS1081 3.0 43.7 1.0
CB A:HIS1081 3.1 37.6 1.0
CE1 A:HIS1081 3.4 49.0 1.0
CA A:HIS1081 3.6 31.8 1.0
O2 A:SO41108 3.7 74.5 1.0
S A:SO41108 3.9 63.9 1.0
CD2 A:HIS1081 4.3 47.1 1.0
NE2 A:HIS1081 4.4 51.3 1.0
N A:HIS1081 4.6 30.5 1.0
C A:HIS1081 4.7 27.7 1.0
N A:HIS1082 4.7 23.2 1.0
O3 A:SO41108 4.8 77.3 1.0
O4 A:SO41108 4.9 80.3 1.0
NE2 A:HIS1083 5.0 21.3 1.0
O A:HIS1080 5.0 32.5 1.0

Reference:

A.A.Mccarthy, R.Barrett, A.Beteva, H.Caserotto, F.Dobias, F.Felisaz, T.Giraud, M.Guijarro, R.Janocha, A.Khadrouche, M.Lentini, G.A.Leonard, M.Lopez Marrero, S.Malbet-Monaco, S.Mcsweeney, D.Nurizzo, G.Papp, C.Rossi, J.Sinoir, C.Sorez, J.Surr, O.Svensson, U.Zander, F.Cipriani, P.Theveneau, C.Mueller-Dieckmann. ID30B - A Versatile Beamline For Macromolecular Crystallography Experiments at the Esrf. J Synchrotron Radiat V. 25 1249 2018.
ISSN: ESSN 1600-5775
PubMed: 29979188
DOI: 10.1107/S1600577518007166
Page generated: Fri Jul 19 19:14:58 2024

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