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Cadmium in PDB 4nqw: Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska

Protein crystallography data

The structure of Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska, PDB code: 4nqw was solved by J.K.Shukla, B.Gopal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.69 / 2.40
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.390, 57.390, 150.870, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 26

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska (pdb code 4nqw). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 10 binding sites of Cadmium where determined in the Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska, PDB code: 4nqw:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 4nqw

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Cadmium binding site 1 out of 10 in the Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:46.9
occ:1.00
 OD1 A:ASP90 2.4 35.5 1.0
O A:HOH313 2.7 23.7 1.0
O A:HOH305 2.9 37.8 1.0
SG A:CYS94 2.9 25.6 1.0
CB A:CYS94 3.1 29.6 1.0
OD2 A:ASP90 3.1 32.4 1.0
CG A:ASP90 3.1 32.2 1.0
CD A:CD202 3.9 42.9 0.6
O A:ASP90 4.3 29.0 1.0
O A:HOH325 4.3 37.5 1.0
CB A:ASP90 4.6 29.7 1.0
C A:ASP90 4.6 29.4 1.0
CA A:CYS94 4.7 32.1 1.0

Cadmium binding site 2 out of 10 in 4nqw

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Cadmium binding site 2 out of 10 in the Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:42.9
occ:0.60
 SG A:CYS94 2.2 25.6 1.0
CB A:CYS94 3.0 29.6 1.0
CA A:CYS94 3.8 32.1 1.0
CD A:CD201 3.9 46.9 1.0
O A:HOH349 4.6 42.1 1.0
O A:CYS94 4.7 36.8 1.0
C A:CYS94 4.7 34.9 1.0
N A:CYS94 4.9 32.2 1.0
OD2 A:ASP90 5.0 32.4 1.0

Cadmium binding site 3 out of 10 in 4nqw

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Cadmium binding site 3 out of 10 in the Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:29.3
occ:1.00
 CD A:CD208 2.4 19.7 0.2
OE2 A:GLU52 2.4 32.2 1.0
NE2 B:HIS69 2.5 19.1 1.0
O A:HOH331 2.5 38.8 1.0
O A:HOH348 2.7 29.1 1.0
OE1 A:GLU52 2.8 29.5 1.0
CD A:GLU52 3.0 29.7 1.0
CD2 B:HIS69 3.3 20.3 1.0
CE1 B:HIS69 3.5 21.3 1.0
CG B:PRO67 4.2 19.9 1.0
CG A:GLU52 4.4 26.6 1.0
CG B:HIS69 4.5 23.0 1.0
CB B:PRO67 4.6 22.1 1.0
ND1 B:HIS69 4.6 21.9 1.0

Cadmium binding site 4 out of 10 in 4nqw

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Cadmium binding site 4 out of 10 in the Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:46.4
occ:1.00
 CD A:CD207 2.4 23.4 0.2
OE1 A:GLU61 2.6 34.3 1.0
O A:HOH328 2.7 21.7 1.0
OE2 A:GLU61 2.8 35.4 1.0
O A:HOH309 2.9 28.1 1.0
CD A:GLU61 3.0 34.5 1.0
NH2 A:ARG87 4.0 23.9 1.0
NE A:ARG86 4.3 26.2 1.0
CD A:ARG86 4.4 22.0 1.0
O A:HOH335 4.5 20.6 1.0
CG A:GLU61 4.5 32.9 1.0
CZ A:ARG87 4.9 22.8 1.0
O A:HOH318 5.0 36.7 1.0
CB A:MET83 5.0 26.8 1.0

Cadmium binding site 5 out of 10 in 4nqw

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Cadmium binding site 5 out of 10 in the Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:42.1
occ:0.20
 OE2 A:GLU28 3.3 48.7 1.0
CD A:GLU28 3.4 51.0 1.0
O A:HOH343 3.4 40.0 1.0
OE1 A:GLU28 3.8 55.9 1.0
CG A:GLU28 3.9 46.6 1.0
O A:HOH358 4.4 46.0 1.0
ND1 A:HIS32 4.7 67.6 1.0
CE1 A:HIS32 5.0 70.0 1.0

Cadmium binding site 6 out of 10 in 4nqw

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Cadmium binding site 6 out of 10 in the Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:35.3
occ:0.20
 O A:HOH332 2.5 33.8 1.0
OD1 A:ASP70 2.5 45.0 1.0
CG A:ASP70 3.4 45.7 1.0
OD2 A:ASP70 3.8 43.9 1.0
O A:HOH347 4.0 43.6 1.0
CB A:ALA72 4.5 63.9 1.0
CB A:ASP70 4.6 44.3 1.0
CA A:ASP70 4.8 43.8 1.0
N A:ALA72 4.8 61.7 1.0
N A:SER71 4.9 48.9 1.0

Cadmium binding site 7 out of 10 in 4nqw

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Cadmium binding site 7 out of 10 in the Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:23.4
occ:0.20
 CD A:CD204 2.4 46.4 1.0
CD A:ARG86 3.3 22.0 1.0
NE A:ARG86 3.5 26.2 1.0
CG A:ARG86 3.7 20.0 1.0
OE2 A:GLU61 3.9 35.4 1.0
O A:HOH309 4.0 28.1 1.0
O A:MET83 4.1 19.7 1.0
N A:ARG87 4.1 14.2 1.0
NH2 A:ARG87 4.1 23.9 1.0
CB A:ARG86 4.2 18.2 1.0
NE A:ARG87 4.2 22.0 1.0
CB A:ARG87 4.2 15.8 1.0
CA A:ARG87 4.3 14.3 1.0
O A:HOH328 4.3 21.7 1.0
CZ A:ARG87 4.4 22.8 1.0
O A:HOH335 4.4 20.6 1.0
C A:ARG86 4.5 16.8 1.0
CG A:ARG87 4.7 17.6 1.0
OE1 A:GLU61 4.7 34.3 1.0
CZ A:ARG86 4.7 32.0 1.0
CD A:GLU61 4.8 34.5 1.0
O A:ARG86 4.9 18.6 1.0
CA A:ARG86 5.0 17.3 1.0

Cadmium binding site 8 out of 10 in 4nqw

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Cadmium binding site 8 out of 10 in the Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:19.7
occ:0.20
 CD A:CD203 2.4 29.3 1.0
OE1 A:GLU52 3.7 29.5 1.0
NE2 B:HIS69 3.8 19.1 1.0
O A:HOH331 3.9 38.8 1.0
O A:HOH348 4.3 29.1 1.0
CE1 B:HIS69 4.3 21.3 1.0
OE2 A:GLU52 4.4 32.2 1.0
CD A:GLU52 4.5 29.7 1.0
CD2 B:HIS69 4.5 20.3 1.0

Cadmium binding site 9 out of 10 in 4nqw

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Cadmium binding site 9 out of 10 in the Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd101

b:30.9
occ:1.00
 OD2 B:ASP76 2.4 32.8 1.0
O B:HOH212 2.4 20.9 1.0
OD1 B:ASP76 2.6 32.9 1.0
CG B:ASP76 2.8 31.3 1.0
CB B:ASP76 4.4 29.8 1.0
O B:ASP76 4.8 34.5 1.0
CD B:LYS79 4.9 51.3 1.0

Cadmium binding site 10 out of 10 in 4nqw

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Cadmium binding site 10 out of 10 in the Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structure of Mycobacterium Tuberculosis Extracytoplasmic Function Sigma Factor Sigk in Complex with the Cytosolic Domain of Its Cognate Anti-Sigma Factor Rska within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd102

b:47.6
occ:0.60
 OD2 B:ASP23 2.3 27.4 1.0
OD2 A:ASP90 2.4 32.4 1.0
CG B:ASP23 3.1 26.7 1.0
OD1 B:ASP23 3.3 27.4 1.0
CG A:ASP90 3.4 32.2 1.0
CB A:ASP90 3.8 29.7 1.0
O A:HOH359 3.8 41.1 1.0
SG A:CYS94 3.9 25.6 1.0
CA A:ASP90 4.3 27.8 1.0
CB B:ASP23 4.6 23.8 1.0
OD1 A:ASP90 4.6 35.5 1.0

Reference:

J.Shukla, R.Gupta, K.G.Thakur, R.Gokhale, B.Gopal. Structural Basis For the Redox Sensitivity of the Mycobacterium Tuberculosis Sigk-Rska Sigma-Anti-Sigma Complex Acta Crystallogr.,Sect.D V. 70 1026 2014.
ISSN: ISSN 0907-4449
PubMed: 24699647
DOI: 10.1107/S1399004714000121
Page generated: Fri Jul 19 17:43:08 2024

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