Atomistry » Cadmium » PDB 3oeo-3umh » 3sd6
Atomistry »
  Cadmium »
    PDB 3oeo-3umh »
      3sd6 »

Cadmium in PDB 3sd6: Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution.

Protein crystallography data

The structure of Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution., PDB code: 3sd6 was solved by X.L.Zhang, M.Paetzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.93 / 1.37
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 49.576, 49.576, 116.041, 90.00, 90.00, 120.00
R / Rfree (%) 13.3 / 14.8

Other elements in 3sd6:

The structure of Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution. also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution. (pdb code 3sd6). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution., PDB code: 3sd6:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 3sd6

Go back to Cadmium Binding Sites List in 3sd6
Cadmium binding site 1 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd101

b:19.1
occ:1.00
 OE2 A:GLU40 2.3 19.2 1.0
O A:PHE27 2.3 18.9 1.0
O A:HOH125 2.3 19.3 1.0
O A:HOH145 2.3 26.5 1.0
OE1 A:GLU40 2.4 18.4 1.0
CD A:GLU40 2.7 18.1 1.0
C A:PHE27 3.4 20.2 1.0
CG A:GLU40 4.2 17.8 1.0
CA A:PHE27 4.3 18.4 1.0
N A:VAL28 4.3 21.5 1.0
CA A:VAL28 4.3 22.2 1.0
O A:HOH99 4.3 22.2 1.0
CB A:PHE27 4.4 18.5 1.0
O A:HOH122 4.5 34.1 1.0
OXT A:ACT90 4.6 21.4 1.0
O A:ACT90 4.7 25.7 1.0
CA A:ILE36 4.7 16.6 1.0
CG2 A:ILE36 4.9 18.4 1.0
N A:SER37 4.9 18.3 1.0
O A:CYS35 4.9 16.8 1.0
CG1 A:VAL28 5.0 28.4 1.0
CB A:GLU40 5.0 19.2 1.0

Cadmium binding site 2 out of 7 in 3sd6

Go back to Cadmium Binding Sites List in 3sd6
Cadmium binding site 2 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd102

b:18.2
occ:1.00
 OD2 A:ASP87 2.2 19.2 1.0
OE1 A:GLU56 2.3 19.7 1.0
OE2 A:GLU56 2.3 23.1 1.0
SG A:CYS84 2.5 16.2 1.0
CD A:GLU56 2.7 20.7 1.0
CG A:ASP87 3.0 16.6 1.0
OD1 A:ASP87 3.1 19.7 1.0
CD A:CD103 3.5 16.0 1.0
CB A:CYS84 3.6 15.9 1.0
CA A:PRO52 3.7 19.0 1.0
CA A:CYS84 3.8 15.0 1.0
O A:HOH142 4.0 36.4 1.0
O A:HOH139 4.0 41.3 1.0
CB A:PRO52 4.1 19.5 1.0
CG A:GLU56 4.2 19.2 1.0
O A:CYS84 4.2 15.1 1.0
N A:PRO52 4.4 18.6 1.0
CB A:ASP87 4.4 16.4 1.0
C A:CYS84 4.5 14.4 1.0
O A:ASN51 4.8 19.2 1.0
C A:ASN51 4.8 18.7 1.0
N A:THR53 4.8 23.6 1.0
C A:PRO52 4.9 19.9 1.0
CB A:GLU56 4.9 19.5 1.0
N A:CYS84 5.0 14.4 1.0
CD A:PRO52 5.0 18.5 1.0

Cadmium binding site 3 out of 7 in 3sd6

Go back to Cadmium Binding Sites List in 3sd6
Cadmium binding site 3 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd103

b:16.0
occ:1.00
 O A:CYS84 2.3 15.1 1.0
OD1 A:ASP87 2.3 19.7 1.0
OE1 A:GLN50 2.4 18.5 1.0
SG A:CYS84 2.5 16.2 1.0
C A:CYS84 3.0 14.4 1.0
CG A:ASP87 3.3 16.6 1.0
CD A:GLN50 3.4 18.2 1.0
CD A:CD102 3.5 18.2 1.0
CB A:CYS84 3.5 15.9 1.0
CA A:CYS84 3.6 15.0 1.0
OD2 A:ASP87 3.7 19.2 1.0
N A:MET85 4.0 14.2 1.0
CB A:GLN50 4.2 19.6 1.0
NE2 A:GLN50 4.2 20.3 1.0
N A:ASN51 4.3 18.7 1.0
CG A:GLN50 4.3 18.8 1.0
CA A:MET85 4.3 14.3 1.0
CA A:GLN50 4.5 18.3 1.0
O A:HOH150 4.6 38.7 1.0
CB A:ASP87 4.6 16.4 1.0
N A:ASP87 4.6 15.4 1.0
C A:ASP87 4.6 17.2 1.0
N A:ASP88 4.7 17.3 1.0
C A:MET85 4.8 15.8 1.0
CA A:ASP87 4.8 16.1 1.0
C A:GLN50 4.9 19.2 1.0
O A:ASP87 5.0 19.1 1.0

Cadmium binding site 4 out of 7 in 3sd6

Go back to Cadmium Binding Sites List in 3sd6
Cadmium binding site 4 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd104

b:18.5
occ:1.00
 OD1 A:ASP33 2.3 19.2 1.0
OXT A:ACT90 2.3 21.4 1.0
O A:HOH97 2.4 23.4 1.0
O A:CYS35 2.5 16.8 1.0
OD2 A:ASP33 2.5 20.2 1.0
SG A:CYS35 2.5 17.1 1.0
CG A:ASP33 2.7 17.3 1.0
C A:ACT90 3.2 24.6 1.0
C A:CYS35 3.3 15.9 1.0
CH3 A:ACT90 3.4 28.0 1.0
CA A:CYS35 3.6 17.1 1.0
CB A:CYS35 3.7 17.6 1.0
N A:CYS35 3.7 15.5 1.0
O A:HOH125 3.7 19.3 1.0
CB A:ASP33 4.2 19.7 1.0
O A:ACT90 4.3 25.7 1.0
N A:ILE36 4.3 16.6 1.0
CA A:ILE36 4.8 16.6 1.0
N A:GLY34 4.9 16.9 1.0
C A:ILE36 4.9 18.5 1.0
C A:GLY34 5.0 16.7 1.0
CA A:ASP33 5.0 19.6 1.0

Cadmium binding site 5 out of 7 in 3sd6

Go back to Cadmium Binding Sites List in 3sd6
Cadmium binding site 5 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd105

b:18.4
occ:1.00
 OD2 A:ASP73 2.3 19.8 1.0
OD2 A:ASP75 2.3 19.9 1.0
OE2 A:GLU66 2.4 31.9 1.0
OD1 A:ASP75 2.4 19.4 1.0
OD1 A:ASP73 2.6 17.8 1.0
CG A:ASP75 2.7 16.9 1.0
OE1 A:GLU66 2.8 35.3 1.0
CG A:ASP73 2.8 17.0 1.0
CD A:GLU66 3.0 27.5 0.5
CB A:ASP75 4.2 16.4 1.0
CB A:ASP73 4.3 18.3 1.0
CG A:GLU76 4.3 16.0 1.0
CG A:GLU66 4.4 28.1 0.5
N A:GLU76 4.6 16.0 1.0
CD A:GLU76 4.6 17.2 1.0
OE2 A:GLU76 4.7 27.9 1.0
N A:ASP75 4.8 16.3 1.0
CE1 A:TYR5 4.9 33.4 1.0
CA A:ASP75 4.9 15.6 1.0

Cadmium binding site 6 out of 7 in 3sd6

Go back to Cadmium Binding Sites List in 3sd6
Cadmium binding site 6 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd106

b:26.6
occ:0.60
 OE2 A:GLU59 2.3 30.5 1.0
O A:HOH133 2.4 37.9 1.0
O A:HOH131 2.4 34.7 1.0
O A:HOH132 2.4 38.2 1.0
OE1 A:GLU59 2.5 32.7 1.0
O A:HOH146 2.7 19.5 1.0
CD A:GLU59 2.7 25.1 1.0
CG A:GLU59 4.2 27.1 1.0
O A:HOH134 4.2 50.2 1.0
OD2 A:ASP62 4.8 36.7 1.0

Cadmium binding site 7 out of 7 in 3sd6

Go back to Cadmium Binding Sites List in 3sd6
Cadmium binding site 7 out of 7 in the Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of the Amino-Terminal Domain of Human Cardiac Troponin C in Complex with Cadmium at 1.4 Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd107

b:21.6
occ:0.50
 O A:HOH148 2.0 29.8 1.0
O A:HOH147 2.1 31.8 1.0
OD2 A:ASP65 2.2 30.7 0.5
OE1 A:GLU76 2.3 20.6 1.0
O A:THR71 2.5 23.2 1.0
OE2 A:GLU76 2.6 27.9 1.0
O A:HOH151 2.6 44.4 1.0
CD A:GLU76 2.8 17.2 1.0
CG A:ASP65 3.4 39.2 0.5
C A:THR71 3.6 19.9 1.0
OG1 A:THR71 3.8 30.8 1.0
CA A:VAL72 4.0 16.2 1.0
N A:VAL72 4.1 17.8 1.0
OD1 A:ASP65 4.1 41.5 0.5
N A:GLU66 4.2 38.8 1.0
CG A:GLU76 4.3 16.0 1.0
N A:ASP73 4.3 14.9 1.0
CB A:ASP65 4.4 37.7 1.0
OE1 A:GLU66 4.5 35.3 1.0
CA A:ASP65 4.6 38.2 1.0
C A:VAL72 4.6 14.9 1.0
CA A:THR71 4.7 23.2 1.0
CB A:THR71 4.7 24.1 1.0
CB A:GLU66 4.9 35.2 0.5
C A:ASP65 4.9 39.8 1.0
CB A:GLU76 4.9 16.0 1.0

Reference:

X.L.Zhang, G.F.Tibbits, M.Paetzel. The Structure of Cardiac Troponin C Regulatory Domain with Bound Cd(2+) Reveals A Closed Conformation and Unique Ion Coordination. Acta Crystallogr.,Sect.D V. 69 722 2013.
ISSN: ISSN 0907-4449
PubMed: 23633581
DOI: 10.1107/S0907444913001182
Page generated: Fri Jul 19 16:27:34 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy