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Cadmium in PDB 3zi7: Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer

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

All present enzymatic activity of Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer:
3.2.1.8;

Protein crystallography data

The structure of Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer, PDB code: 3zi7 was solved by M.W.Bowler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.609, 108.639, 113.317, 90.00, 90.00, 90.00
R / Rfree (%) 12.253 / 15.951

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

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 Grob Robot Goniometer (pdb code 3zi7). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 12 binding sites of Cadmium where determined in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer, PDB code: 3zi7:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 12 in 3zi7

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Cadmium binding site 1 out of 12 in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot 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 Grob Robot Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2086

b:8.5
occ:1.00
 O A:HOH3178 2.2 6.1 1.0
ND1 A:HIS886 2.3 6.5 1.0
SG A:CYS823 2.5 8.0 1.0
SE A:MSE889 2.8 9.8 1.0
CE1 A:HIS886 3.0 6.5 1.0
CG A:HIS886 3.4 6.3 1.0
CB A:CYS823 3.6 8.5 1.0
CA A:HIS886 3.7 6.0 1.0
CE A:MSE889 3.9 9.8 1.0
CB A:HIS886 3.9 6.0 1.0
CG A:MSE889 4.0 9.4 1.0
CB A:MSE889 4.1 9.3 1.0
NE2 A:HIS886 4.2 6.5 1.0
CA A:CYS823 4.3 8.7 1.0
CD A:PRO824 4.4 9.0 1.0
CD2 A:HIS886 4.4 6.3 1.0
N A:HIS886 4.6 6.1 1.0
O A:HIS886 4.6 5.9 1.0
C A:HIS886 4.7 6.1 1.0
O A:ASP885 4.9 5.1 1.0
ND2 A:ASN890 5.0 8.4 0.5

Cadmium binding site 2 out of 12 in 3zi7

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Cadmium binding site 2 out of 12 in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot 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 Grob Robot Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2087

b:7.3
occ:1.00
 OE2 A:GLU894 2.2 8.2 1.0
OE1 A:GLU1079 2.3 8.4 1.0
NE2 A:HIS1085 2.3 8.5 1.0
ND1 A:HIS1083 2.3 9.9 1.0
OE2 A:GLU1079 2.4 9.4 1.0
ND1 A:HIS1076 2.5 8.0 1.0
CD A:GLU1079 2.7 9.9 1.0
CD A:GLU894 3.0 8.8 1.0
OE1 A:GLU894 3.1 9.3 1.0
CE1 A:HIS1076 3.1 8.3 1.0
CD2 A:HIS1085 3.2 8.9 1.0
CE1 A:HIS1083 3.2 10.9 1.0
CE1 A:HIS1085 3.3 9.2 1.0
CG A:HIS1083 3.3 10.3 1.0
CG A:HIS1076 3.6 8.5 1.0
CB A:HIS1083 3.7 9.6 1.0
CB A:HIS1076 4.0 8.5 1.0
O A:HOH3190 4.2 25.6 1.0
CG A:GLU1079 4.2 10.9 1.0
O A:HOH3129 4.2 16.7 1.0
NE2 A:HIS1076 4.4 8.6 1.0
CG A:HIS1085 4.4 9.5 1.0
NE2 A:HIS1083 4.4 11.4 1.0
ND1 A:HIS1085 4.4 9.8 1.0
CG A:GLU894 4.4 8.3 1.0
CD2 A:HIS1083 4.5 10.6 1.0
CA A:HIS1076 4.5 8.9 1.0
CD2 A:HIS1076 4.6 8.7 1.0
O A:HOH3346 4.9 11.9 1.0
CB A:GLU1079 5.0 12.6 1.0

Cadmium binding site 3 out of 12 in 3zi7

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Cadmium binding site 3 out of 12 in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot 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 Grob Robot Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2088

b:11.4
occ:1.00
 OE2 A:GLU1007 2.1 10.8 1.0
O A:HOH3380 2.4 8.6 1.0
O A:HOH3290 2.5 14.7 1.0
OE1 A:GLU1007 2.5 9.0 1.0
CD A:GLU1007 2.7 9.0 1.0
CG A:GLU1007 4.2 8.9 1.0
N A:SER1004 4.6 8.1 1.0
CD2 A:LEU1003 4.7 7.9 1.0
CA A:LEU1003 4.8 8.8 1.0
O A:HOH3284 4.9 21.7 1.0
OG A:SER1004 5.0 8.2 1.0

Cadmium binding site 4 out of 12 in 3zi7

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Cadmium binding site 4 out of 12 in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot 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 Grob Robot Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2089

b:16.6
occ:1.00
 O A:HOH3237 1.6 3.4 1.0
NE2 A:HIS1080 2.1 21.9 1.0
O A:HOH3238 2.4 11.4 1.0
O A:HOH3233 2.4 19.7 1.0
NE2 A:HIS947 2.4 11.9 1.0
O A:HOH3353 2.7 17.4 1.0
CE1 A:HIS1080 2.8 28.7 1.0
CD2 A:HIS1080 3.3 26.4 1.0
CE1 A:HIS947 3.3 12.6 1.0
CD2 A:HIS947 3.4 11.2 1.0
O A:HOH3232 3.6 10.5 1.0
ND1 A:HIS1080 4.0 27.9 1.0
CG A:HIS1080 4.3 21.9 1.0
ND1 A:HIS947 4.5 13.0 1.0
O A:LEU1078 4.5 21.9 1.0
CG A:HIS947 4.5 11.1 1.0
O A:ALA943 4.7 11.4 1.0
CD2 A:TYR932 4.9 7.1 1.0

Cadmium binding site 5 out of 12 in 3zi7

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Cadmium binding site 5 out of 12 in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot 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 Grob Robot Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2090

b:18.8
occ:0.30
 O A:HOH3382 2.4 37.4 1.0
CE1 A:HIS1081 3.2 26.2 1.0
O A:HOH3356 3.5 16.8 1.0
ND1 A:HIS1081 3.6 29.6 1.0
NE2 A:HIS1081 4.3 27.4 1.0
O A:HOH3355 4.5 31.4 1.0
CD A:LYS855 4.5 26.5 1.0
O A:HOH3366 4.7 37.4 1.0
CE A:LYS855 4.7 33.8 1.0
CG A:HIS1081 5.0 25.1 1.0
O A:HOH3118 5.0 27.3 1.0

Cadmium binding site 6 out of 12 in 3zi7

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Cadmium binding site 6 out of 12 in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2091

b:81.3
occ:1.00
 O A:ALA933 2.5 10.8 1.0
O A:HOH3217 2.5 2.0 1.0
O A:HOH3221 2.6 12.7 1.0
O A:HOH3225 2.7 20.6 1.0
C A:ALA933 3.7 12.0 1.0
O A:THR931 3.8 7.8 1.0
O A:GLU926 4.1 7.1 1.0
N A:THR931 4.2 6.8 1.0
N A:GLU934 4.5 15.7 1.0
CA A:GLU934 4.5 21.1 1.0
C A:THR931 4.6 7.0 1.0
CA A:ALA933 4.6 10.2 1.0
N A:ALA933 4.6 8.5 1.0
CA A:SER930 4.6 7.8 1.0
O A:GLU934 4.6 19.5 1.0
C A:GLU934 4.7 19.1 1.0
OG1 A:THR931 4.7 6.0 1.0
O A:TYR929 4.8 7.6 1.0
OG A:SER930 4.8 9.6 0.5
CB A:ALA933 4.8 10.2 1.0
OG A:SER930 4.9 8.9 0.5
C A:SER930 4.9 7.3 1.0
CA A:THR931 4.9 6.6 1.0

Cadmium binding site 7 out of 12 in 3zi7

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Cadmium binding site 7 out of 12 in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2086

b:7.7
occ:1.00
 O B:HOH3185 2.2 4.8 1.0
ND1 B:HIS886 2.3 6.0 1.0
SG B:CYS823 2.5 7.1 1.0
SE B:MSE889 2.8 9.5 1.0
CE1 B:HIS886 3.1 5.9 1.0
CG B:HIS886 3.4 5.7 1.0
CB B:CYS823 3.5 7.7 1.0
CA B:HIS886 3.8 5.4 1.0
CE B:MSE889 3.9 10.3 1.0
CB B:HIS886 3.9 5.5 1.0
CG B:MSE889 4.0 8.0 1.0
CB B:MSE889 4.0 7.7 1.0
NE2 B:HIS886 4.2 6.0 1.0
CA B:CYS823 4.3 7.9 1.0
CD B:PRO824 4.3 8.3 1.0
CD2 B:HIS886 4.4 5.9 1.0
N B:HIS886 4.6 5.2 1.0
O B:HIS886 4.6 5.2 1.0
O B:HOH3050 4.7 31.9 1.0
C B:HIS886 4.7 5.4 1.0
O B:ASP885 4.8 5.0 1.0
C B:ASP885 4.9 5.2 1.0
ND2 B:ASN890 5.0 7.3 0.5
N B:PRO824 5.0 7.8 1.0

Cadmium binding site 8 out of 12 in 3zi7

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Cadmium binding site 8 out of 12 in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2087

b:7.2
occ:1.00
 OE1 B:GLU1079 2.2 8.4 1.0
NE2 B:HIS1085 2.3 10.7 1.0
OE2 B:GLU894 2.3 7.3 1.0
ND1 B:HIS1083 2.4 11.6 1.0
OE2 B:GLU1079 2.4 9.7 1.0
ND1 B:HIS1076 2.5 7.4 1.0
CD B:GLU1079 2.6 9.7 1.0
OE1 B:GLU894 2.9 7.7 1.0
CD B:GLU894 3.0 7.0 1.0
CE1 B:HIS1076 3.2 7.4 1.0
CD2 B:HIS1085 3.2 10.7 1.0
CE1 B:HIS1083 3.3 12.7 1.0
CE1 B:HIS1085 3.4 10.7 1.0
CG B:HIS1083 3.4 11.4 1.0
CG B:HIS1076 3.5 7.5 1.0
CB B:HIS1083 3.7 10.7 1.0
CB B:HIS1076 4.0 7.4 1.0
O B:HOH3141 4.1 13.5 1.0
CG B:GLU1079 4.2 10.7 1.0
NE2 B:HIS1076 4.3 7.9 1.0
O B:HOH3194 4.4 22.8 1.0
CG B:HIS1085 4.4 10.4 1.0
NE2 B:HIS1083 4.4 13.5 1.0
CA B:HIS1076 4.4 7.4 1.0
ND1 B:HIS1085 4.4 10.7 1.0
CG B:GLU894 4.5 6.7 1.0
CD2 B:HIS1083 4.5 12.0 1.0
CD2 B:HIS1076 4.5 7.6 1.0
O B:HOH3345 4.7 35.9 1.0
O B:HOH3341 4.9 2.0 0.5
CB B:GLU1079 5.0 12.5 1.0

Cadmium binding site 9 out of 12 in 3zi7

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Cadmium binding site 9 out of 12 in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2088

b:11.4
occ:1.00
 OE2 B:GLU1007 2.2 7.3 1.0
O B:HOH3279 2.4 11.2 1.0
O B:HOH3278 2.5 21.3 1.0
OE1 B:GLU1007 2.5 8.1 1.0
CD B:GLU1007 2.7 7.2 1.0
CG B:GLU1007 4.2 7.1 1.0
N B:SER1004 4.5 8.2 1.0
CD2 B:LEU1003 4.8 8.0 1.0
CA B:LEU1003 4.9 8.1 1.0
O B:HOH3270 4.9 15.6 1.0
OG B:SER1004 4.9 8.9 1.0

Cadmium binding site 10 out of 12 in 3zi7

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Cadmium binding site 10 out of 12 in the Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structure of Fae Solved By Sad From Data Collected By Direct Data Collection (Ddc) Using the Grob Robot Goniometer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2089

b:16.3
occ:1.00
 O B:HOH3232 1.6 4.2 1.0
NE2 B:HIS1080 2.1 21.0 1.0
O B:HOH3233 2.2 16.4 1.0
O B:HOH3228 2.4 17.5 1.0
NE2 B:HIS947 2.4 13.0 1.0
O B:HOH3347 2.6 15.7 1.0
CE1 B:HIS1080 2.7 26.4 1.0
CD2 B:HIS1080 3.2 24.7 1.0
CD2 B:HIS947 3.3 11.3 1.0
CE1 B:HIS947 3.4 13.5 1.0
ND1 B:HIS1080 3.9 27.3 1.0
O B:HOH3229 3.9 11.8 1.0
CG B:HIS1080 4.2 21.8 1.0
O B:HOH3114 4.5 40.7 1.0
CG B:HIS947 4.5 11.3 1.0
O B:LEU1078 4.5 17.5 1.0
ND1 B:HIS947 4.5 13.7 1.0
O B:HOH3227 4.5 31.6 1.0
CD2 B:TYR932 4.8 7.5 1.0
O B:ALA943 4.9 10.8 1.0

Reference:

J.L.Ferrer, N.A.Larive, M.W.Bowler, D.Nurizzo. Recent Progress in Robot-Based Systems For Crystallography and Their Contribution to Drug Discovery. Expert Opin.Drug Discov. V. 8 835 2013.
ISSN: ISSN 1746-0441
PubMed: 23656378
DOI: 10.1517/17460441.2013.793666
Page generated: Fri Jul 19 16:49:36 2024

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