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Cadmium in PDB 1rwi: Extracellular Domain of Mycobacterium Tuberculosis Pknd

Enzymatic activity of Extracellular Domain of Mycobacterium Tuberculosis Pknd

All present enzymatic activity of Extracellular Domain of Mycobacterium Tuberculosis Pknd:
2.7.1.37;

Protein crystallography data

The structure of Extracellular Domain of Mycobacterium Tuberculosis Pknd, PDB code: 1rwi was solved by M.C.Good, A.E.Greenstein, T.A.Young, H.L.Ng, T.Alber, Tbstructural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.40 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.940, 94.580, 71.770, 90.00, 98.10, 90.00
R / Rfree (%) 19 / 22

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Extracellular Domain of Mycobacterium Tuberculosis Pknd (pdb code 1rwi). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 14 binding sites of Cadmium where determined in the Extracellular Domain of Mycobacterium Tuberculosis Pknd, PDB code: 1rwi:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14;

Cadmium binding site 1 out of 14 in 1rwi

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Cadmium binding site 1 out of 14 in the Extracellular Domain of Mycobacterium Tuberculosis Pknd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Extracellular Domain of Mycobacterium Tuberculosis Pknd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1004

b:25.0
occ:1.00
 OD2 A:ASP244 2.2 27.7 1.0
O A:HOH1229 2.2 17.7 1.0
OD1 B:ASP169 2.3 23.4 1.0
OD2 B:ASP169 2.4 22.9 1.0
OD1 A:ASP244 2.7 28.1 1.0
CG B:ASP169 2.7 20.0 1.0
CG A:ASP244 2.9 24.2 1.0
NE2 A:HIS269 3.9 41.6 1.0
CB B:ASP169 4.3 20.6 1.0
O A:HIS267 4.3 18.1 1.0
O B:HOH1317 4.4 21.5 1.0
CD B:CD1203 4.4 18.5 0.3
CB A:ASP244 4.4 21.5 1.0
CD2 A:HIS269 4.4 40.1 1.0
CB B:ASP151 4.7 20.3 1.0
OD2 B:ASP151 4.8 27.9 1.0
CG B:ASP151 4.9 22.6 1.0

Cadmium binding site 2 out of 14 in 1rwi

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Cadmium binding site 2 out of 14 in the Extracellular Domain of Mycobacterium Tuberculosis Pknd


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Extracellular Domain of Mycobacterium Tuberculosis Pknd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1101

b:31.7
occ:1.00
 O B:HOH1370 2.2 31.3 1.0
O B:HOH1354 2.3 17.2 1.0
OD1 B:ASP244 2.5 29.6 1.0
OD2 B:ASP244 2.7 34.0 1.0
CG B:ASP244 3.0 27.6 1.0
NE2 B:HIS269 3.3 40.7 1.0
CE1 B:HIS269 3.8 39.5 1.0
CD B:CD1303 4.3 24.6 0.3
O B:HIS267 4.4 22.9 1.0
CB B:ASP244 4.5 24.6 1.0
CD2 B:HIS269 4.5 38.9 1.0
CB B:HIS267 5.0 21.4 1.0

Cadmium binding site 3 out of 14 in 1rwi

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Cadmium binding site 3 out of 14 in the Extracellular Domain of Mycobacterium Tuberculosis Pknd


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Extracellular Domain of Mycobacterium Tuberculosis Pknd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1102

b:21.1
occ:1.00
 ND1 B:HIS267 2.3 22.9 1.0
O B:HOH1320 2.3 25.1 1.0
O B:HOH1312 2.3 21.3 1.0
OE1 B:GLU264 2.4 21.3 1.0
OE2 B:GLU264 2.6 22.6 1.0
CD B:GLU264 2.8 23.2 1.0
CE1 B:HIS267 3.2 23.1 1.0
CG B:HIS267 3.3 21.3 1.0
CB B:HIS267 3.6 21.4 1.0
CG B:GLU264 4.3 23.3 1.0
NE2 B:HIS267 4.4 22.5 1.0
CD B:CD1303 4.4 24.6 0.3
CD2 B:HIS267 4.4 22.0 1.0

Cadmium binding site 4 out of 14 in 1rwi

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Cadmium binding site 4 out of 14 in the Extracellular Domain of Mycobacterium Tuberculosis Pknd


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Extracellular Domain of Mycobacterium Tuberculosis Pknd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1103

b:39.9
occ:1.00
 NE2 B:HIS266 2.3 22.0 1.0
NE2 B:HIS265 2.3 26.9 1.0
CE1 B:HIS266 3.1 26.0 1.0
CD2 B:HIS265 3.2 30.9 1.0
CD2 B:HIS266 3.3 26.7 1.0
CE1 B:HIS265 3.4 32.2 1.0
ND1 B:HIS266 4.2 26.4 1.0
CG B:HIS266 4.3 22.9 1.0
CG B:HIS265 4.4 28.4 1.0
ND1 B:HIS265 4.5 30.3 1.0
O B:HOH1359 4.8 32.3 1.0

Cadmium binding site 5 out of 14 in 1rwi

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Cadmium binding site 5 out of 14 in the Extracellular Domain of Mycobacterium Tuberculosis Pknd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Extracellular Domain of Mycobacterium Tuberculosis Pknd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1104

b:24.6
occ:1.00
 O B:HOH1351 2.2 27.9 1.0
NE2 B:HIS268 2.3 22.2 1.0
O B:HOH1314 2.4 19.7 1.0
NE2 B:HIS270 2.4 34.3 1.0
CD2 B:HIS268 3.2 26.3 1.0
CE1 B:HIS268 3.2 26.9 1.0
CD2 B:HIS270 3.3 34.9 1.0
CE1 B:HIS270 3.4 33.5 1.0
ND1 B:HIS268 4.3 24.1 1.0
CG B:HIS268 4.4 27.0 1.0
CG B:HIS270 4.5 35.7 1.0
ND1 B:HIS270 4.5 33.9 1.0

Cadmium binding site 6 out of 14 in 1rwi

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Cadmium binding site 6 out of 14 in the Extracellular Domain of Mycobacterium Tuberculosis Pknd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Extracellular Domain of Mycobacterium Tuberculosis Pknd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1201

b:29.0
occ:1.00
 O A:HIS270 2.2 33.9 1.0
OD2 B:ASP153 2.3 30.5 1.0
OD1 B:ASP153 2.4 27.0 1.0
OE1 B:GLU111 2.4 26.0 1.0
CG B:ASP153 2.7 25.7 1.0
C A:HIS270 2.9 34.1 1.0
CD B:GLU111 3.5 24.1 1.0
O B:HOH1357 4.0 35.2 1.0
CB B:GLU111 4.1 18.9 1.0
CB B:ASP153 4.2 21.7 1.0
OE2 B:GLU111 4.3 23.0 1.0
CG B:GLU111 4.3 20.9 1.0
OE1 B:GLN70 4.4 23.3 1.0
CA A:HIS270 4.4 34.2 1.0
CE1 A:HIS268 4.4 22.6 1.0
CD1 B:TRP195 4.7 34.2 1.0
ND1 A:HIS268 4.8 21.1 1.0
O B:HOH1306 4.8 22.9 1.0
CA B:ASP153 4.9 20.9 1.0
NE1 B:TRP195 5.0 36.1 1.0

Cadmium binding site 7 out of 14 in 1rwi

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Cadmium binding site 7 out of 14 in the Extracellular Domain of Mycobacterium Tuberculosis Pknd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Extracellular Domain of Mycobacterium Tuberculosis Pknd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1203

b:18.5
occ:0.30
 OD2 B:ASP169 2.3 22.9 1.0
OD1 B:ASN150 2.3 25.1 1.0
OD2 B:ASP151 2.4 27.9 1.0
O B:HOH1356 2.4 32.3 1.0
CG B:ASP169 3.2 20.0 1.0
CG B:ASN150 3.3 24.2 1.0
CG B:ASP151 3.4 22.6 1.0
O B:HOH1374 3.4 40.6 1.0
CB B:ASP169 3.6 20.6 1.0
ND2 B:ASN150 3.7 28.1 1.0
CB B:ASP151 3.9 20.3 1.0
OD2 A:ASP244 4.0 27.7 1.0
O B:HOH1322 4.1 19.1 1.0
CD B:CD1004 4.4 25.0 1.0
OD1 B:ASP169 4.4 23.4 1.0
CD A:CD1001 4.4 18.5 1.0
OD1 B:ASP151 4.5 19.8 1.0
N B:ASP151 4.5 19.7 1.0
C B:ASN150 4.5 20.5 1.0
O A:HOH1285 4.6 32.9 1.0
CB B:ASN150 4.7 21.9 1.0
O B:ASN150 4.7 19.8 1.0
ND1 A:HIS267 4.7 18.2 1.0
O A:HOH1229 4.8 17.7 1.0
CA B:ASP151 4.8 19.9 1.0
CA B:ASN150 5.0 21.7 1.0

Cadmium binding site 8 out of 14 in 1rwi

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Cadmium binding site 8 out of 14 in the Extracellular Domain of Mycobacterium Tuberculosis Pknd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Extracellular Domain of Mycobacterium Tuberculosis Pknd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1301

b:25.8
occ:0.30
 CE1 B:HIS268 4.6 26.9 1.0
O B:HOH1314 4.9 19.7 1.0

Cadmium binding site 9 out of 14 in 1rwi

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Cadmium binding site 9 out of 14 in the Extracellular Domain of Mycobacterium Tuberculosis Pknd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Extracellular Domain of Mycobacterium Tuberculosis Pknd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1302

b:25.8
occ:0.30
 ND1 B:HIS269 2.1 39.4 1.0
O B:HIS269 2.3 34.3 1.0
CE1 B:HIS269 2.7 39.5 1.0
C B:HIS269 3.2 33.9 1.0
CG B:HIS269 3.3 36.1 1.0
CB B:HIS269 3.9 34.6 1.0
NE2 B:HIS269 3.9 40.7 1.0
CA B:HIS269 4.0 33.4 1.0
N B:HIS270 4.1 35.2 1.0
CA B:HIS270 4.2 35.5 1.0
CD2 B:HIS269 4.2 38.9 1.0
N B:HIS269 4.5 31.7 1.0
OG B:SER243 4.7 30.5 1.0
CB B:HIS270 4.8 36.3 1.0

Cadmium binding site 10 out of 14 in 1rwi

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Cadmium binding site 10 out of 14 in the Extracellular Domain of Mycobacterium Tuberculosis Pknd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Extracellular Domain of Mycobacterium Tuberculosis Pknd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1303

b:24.6
occ:0.30
 OD2 B:ASP244 3.7 34.0 1.0
O B:HOH1320 4.0 25.1 1.0
CD B:CD1101 4.3 31.7 1.0
CD B:CD1102 4.4 21.1 1.0
O B:HOH1361 4.7 43.1 1.0
ND1 B:HIS267 4.8 22.9 1.0
CG B:ASP244 4.9 27.6 1.0
O B:HOH1354 4.9 17.2 1.0

Cadmium binding site 11 out of 14 in 1rwi

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Cadmium binding site 11 out of 14 in the Extracellular Domain of Mycobacterium Tuberculosis Pknd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of Extracellular Domain of Mycobacterium Tuberculosis Pknd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1001

b:18.5
occ:1.00
 OD1 B:ASP151 2.3 19.8 1.0
ND1 A:HIS267 2.3 18.2 1.0
OE2 A:GLU264 2.3 21.2 1.0
O B:HOH1304 2.3 18.1 1.0
O B:HOH1322 2.4 19.1 1.0
OD2 B:ASP151 2.5 27.9 1.0
OE1 A:GLU264 2.6 21.7 1.0
CG B:ASP151 2.7 22.6 1.0
CD A:GLU264 2.8 21.5 1.0
CE1 A:HIS267 3.2 18.1 1.0
CG A:HIS267 3.4 17.6 1.0
CB A:HIS267 3.7 18.0 1.0
O B:HOH1374 3.9 40.6 1.0
CB B:ASP151 4.3 20.3 1.0
CG A:GLU264 4.3 18.4 1.0
NE2 A:HIS267 4.3 19.2 1.0
CD B:CD1203 4.4 18.5 0.3
CD2 A:HIS267 4.4 17.5 1.0
O B:ARG126 4.5 18.4 1.0
NE B:ARG126 4.6 18.3 1.0
OD1 B:ASN129 4.8 23.3 1.0
NH2 B:ARG126 4.8 19.1 1.0
CA B:GLY127 4.8 19.2 1.0
CA B:ASP151 4.9 19.9 1.0

Cadmium binding site 12 out of 14 in 1rwi

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Cadmium binding site 12 out of 14 in the Extracellular Domain of Mycobacterium Tuberculosis Pknd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of Extracellular Domain of Mycobacterium Tuberculosis Pknd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1002

b:27.3
occ:1.00
 NE2 A:HIS266 2.2 20.2 1.0
NE2 A:HIS265 2.3 19.1 1.0
O A:HOH1267 2.5 27.9 1.0
CE1 A:HIS266 3.1 21.3 1.0
CD2 A:HIS266 3.2 20.8 1.0
CE1 A:HIS265 3.3 22.5 1.0
CD2 A:HIS265 3.3 21.6 1.0
ND1 A:HIS266 4.2 20.2 1.0
CG A:HIS266 4.3 21.2 1.0
ND1 A:HIS265 4.4 19.4 1.0
CG A:HIS265 4.4 19.2 1.0

Cadmium binding site 13 out of 14 in 1rwi

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Cadmium binding site 13 out of 14 in the Extracellular Domain of Mycobacterium Tuberculosis Pknd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 13 of Extracellular Domain of Mycobacterium Tuberculosis Pknd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1003

b:23.9
occ:1.00
 OE2 B:GLU42 2.3 28.1 1.0
O B:HOH1365 2.3 24.8 1.0
NE2 A:HIS268 2.3 19.1 1.0
ND1 A:HIS270 2.3 34.3 1.0
OE1 B:GLU42 2.5 23.1 1.0
O B:HOH1306 2.5 22.9 1.0
CD B:GLU42 2.7 27.2 1.0
CE1 A:HIS270 3.1 34.8 1.0
CD2 A:HIS268 3.3 23.1 1.0
CE1 A:HIS268 3.3 22.6 1.0
CG A:HIS270 3.5 35.5 1.0
O A:HIS269 3.5 34.8 1.0
CA A:HIS270 3.7 34.2 1.0
O B:HOH1375 3.8 39.1 1.0
CB A:HIS270 4.0 34.8 1.0
CG B:GLU42 4.2 29.5 1.0
NE2 A:HIS270 4.3 36.4 1.0
NE2 B:GLN70 4.3 22.3 1.0
C A:HIS269 4.4 33.3 1.0
NH1 B:ARG252 4.4 24.3 1.0
OE1 B:GLN70 4.4 23.3 1.0
ND1 A:HIS268 4.4 21.1 1.0
CG A:HIS268 4.4 22.8 1.0
CD2 A:HIS270 4.5 36.6 1.0
N A:HIS270 4.5 33.6 1.0
NH2 B:ARG252 4.5 26.0 1.0
C A:HIS270 4.7 34.1 1.0
O A:HIS270 4.8 33.9 1.0
CD B:GLN70 4.8 22.2 1.0
CZ B:ARG252 4.9 27.5 1.0

Cadmium binding site 14 out of 14 in 1rwi

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Cadmium binding site 14 out of 14 in the Extracellular Domain of Mycobacterium Tuberculosis Pknd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 14 of Extracellular Domain of Mycobacterium Tuberculosis Pknd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1202

b:20.8
occ:0.30
 ND1 A:HIS269 2.5 41.5 1.0
NE2 B:HIS210 2.6 44.1 1.0
CG A:HIS269 3.2 38.0 1.0
CB A:HIS269 3.3 32.9 1.0
CD2 B:HIS210 3.3 43.0 1.0
O A:HOH1253 3.4 24.5 1.0
CE1 A:HIS269 3.6 42.5 1.0
CE1 B:HIS210 3.6 44.5 1.0
OE2 A:GLU201 4.1 42.7 1.0
CA A:HIS269 4.4 32.7 1.0
OE1 A:GLU201 4.4 40.9 1.0
CD2 A:HIS269 4.5 40.1 1.0
CG B:HIS210 4.5 40.5 1.0
NE2 A:HIS269 4.6 41.6 1.0
ND1 B:HIS210 4.6 42.7 1.0
CD A:GLU201 4.7 38.0 1.0

Reference:

M.C.Good, A.E.Greenstein, T.A.Young, H.L.Ng, T.Alber. Sensor Domain of the Mycobacterium Tuberculosis Receptor Ser/Thr Protein Kinase, Pknd, Forms A Highly Symmetric Beta Propeller. J.Mol.Biol. V. 339 459 2004.
ISSN: ISSN 0022-2836
PubMed: 15136047
DOI: 10.1016/J.JMB.2004.03.063
Page generated: Fri Aug 28 12:25:06 2020
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