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Cadmium in PDB 2j4k: Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution

Enzymatic activity of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution

All present enzymatic activity of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution:
2.7.4.22;

Protein crystallography data

The structure of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution, PDB code: 2j4k was solved by K.S.Jensen, E.Johansson, K.F.Jensen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.67 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.802, 136.043, 77.938, 90.00, 113.17, 90.00
R / Rfree (%) 21.9 / 25.1

Other elements in 2j4k:

The structure of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution (pdb code 2j4k). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 18 binding sites of Cadmium where determined in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution, PDB code: 2j4k:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 18 in 2j4k

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Cadmium binding site 1 out of 18 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom 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 Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd228

b:27.7
occ:1.00
 NE2 C:HIS104 2.1 16.9 1.0
NE2 F:HIS104 2.4 24.6 1.0
NE2 A:HIS104 2.5 20.5 1.0
CE1 C:HIS104 3.0 21.9 1.0
OH F:TYR88 3.2 26.5 1.0
CD2 F:HIS104 3.3 23.4 1.0
CD2 A:HIS104 3.3 20.2 1.0
CD2 C:HIS104 3.3 22.2 1.0
CE1 F:HIS104 3.4 22.7 1.0
OH C:TYR88 3.5 23.3 1.0
OH A:TYR88 3.5 25.8 1.0
CE1 A:HIS104 3.5 21.2 1.0
CZ F:TYR88 4.0 22.2 1.0
ND1 C:HIS104 4.1 21.2 1.0
CE1 F:TYR88 4.2 24.7 1.0
CZ C:TYR88 4.2 23.7 1.0
CZ A:TYR88 4.2 24.4 1.0
CE1 A:TYR88 4.3 25.7 1.0
CG C:HIS104 4.3 19.1 1.0
CE1 C:TYR88 4.4 21.9 1.0
O A:HOH2028 4.4 21.8 1.0
CG F:HIS104 4.5 24.3 1.0
ND1 F:HIS104 4.5 25.4 1.0
CG A:HIS104 4.5 21.7 1.0
O C:HOH2015 4.6 28.5 1.0
ND1 A:HIS104 4.6 20.3 1.0

Cadmium binding site 2 out of 18 in 2j4k

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Cadmium binding site 2 out of 18 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom 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 Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd229

b:43.8
occ:1.00
 NE2 A:HIS90 2.6 20.6 1.0
O A:HOH2020 2.7 26.4 1.0
CD2 A:HIS90 3.3 20.5 1.0
CE1 A:HIS90 3.7 20.4 1.0
OE1 A:GLU97 4.4 30.2 1.0
CG A:HIS90 4.5 22.0 1.0
O A:HOH2016 4.6 17.2 1.0
ND1 A:HIS90 4.7 23.0 1.0
OE2 A:GLU97 4.7 32.7 1.0
O A:VAL91 4.9 17.4 1.0
CD A:GLU97 4.9 30.4 1.0

Cadmium binding site 3 out of 18 in 2j4k

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Cadmium binding site 3 out of 18 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom 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 Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd230

b:0.6
occ:1.00
 NE2 A:HIS160 2.5 47.4 1.0
CE1 A:HIS160 3.5 45.5 1.0
CD2 A:HIS160 3.5 45.1 1.0
ND1 A:HIS160 4.6 46.0 1.0
CG A:HIS160 4.6 44.0 1.0

Cadmium binding site 4 out of 18 in 2j4k

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Cadmium binding site 4 out of 18 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom 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 Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd228

b:23.8
occ:1.00
 NE2 E:HIS104 2.3 20.6 1.0
NE2 D:HIS104 2.3 20.6 1.0
NE2 B:HIS104 2.4 22.9 1.0
O D:HOH2021 2.6 21.6 1.0
OH E:TYR88 3.0 24.6 1.0
CD2 E:HIS104 3.2 20.7 1.0
CD2 B:HIS104 3.2 24.3 1.0
CE1 D:HIS104 3.3 22.8 1.0
OH B:TYR88 3.3 27.4 1.0
CD2 D:HIS104 3.3 20.2 1.0
CE1 E:HIS104 3.3 18.2 1.0
CE1 B:HIS104 3.4 22.9 1.0
OH D:TYR88 3.5 29.7 1.0
CZ E:TYR88 3.9 24.5 1.0
CZ B:TYR88 4.0 24.5 1.0
CE1 B:TYR88 4.2 24.2 1.0
CE1 E:TYR88 4.3 25.1 1.0
CZ D:TYR88 4.3 26.3 1.0
O E:HOH2023 4.4 31.7 1.0
CE1 D:TYR88 4.4 26.5 1.0
CG E:HIS104 4.4 19.7 1.0
O D:HOH2031 4.4 32.0 1.0
ND1 D:HIS104 4.4 21.8 1.0
ND1 E:HIS104 4.4 19.9 1.0
CG B:HIS104 4.4 21.9 1.0
CG D:HIS104 4.5 20.9 1.0
ND1 B:HIS104 4.5 23.9 1.0
NE2 D:GLN100 4.9 21.3 1.0
CE2 E:TYR88 4.9 24.4 1.0

Cadmium binding site 5 out of 18 in 2j4k

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Cadmium binding site 5 out of 18 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom 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 Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd229

b:46.6
occ:1.00
 O B:HOH2020 2.3 32.6 1.0
NE2 B:HIS90 2.4 21.9 1.0
O B:HOH2008 2.7 33.2 1.0
CD2 B:HIS90 3.4 21.4 1.0
CE1 B:HIS90 3.4 19.0 1.0
OE1 B:GLU97 4.3 26.9 1.0
O B:HOH2016 4.5 23.6 1.0
ND1 B:HIS90 4.5 21.6 1.0
CG B:HIS90 4.5 21.1 1.0
O B:VAL91 4.7 18.1 1.0
CD B:GLU97 4.9 29.3 1.0
OE2 B:GLU97 5.0 33.6 1.0

Cadmium binding site 6 out of 18 in 2j4k

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Cadmium binding site 6 out of 18 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom 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 Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd230

b:78.3
occ:1.00
 NE2 B:HIS160 2.6 43.6 1.0
CD2 B:HIS160 3.2 41.0 1.0
CE1 B:HIS160 3.8 42.8 1.0
CG B:HIS160 4.5 42.0 1.0
ND1 B:HIS160 4.8 42.5 1.0
O B:HOH2045 4.9 38.6 1.0

Cadmium binding site 7 out of 18 in 2j4k

Go back to Cadmium Binding Sites List in 2j4k
Cadmium binding site 7 out of 18 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom 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 Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd231

b:80.1
occ:1.00
 O B:HOH2036 2.4 27.8 1.0
OE1 B:GLU146 3.2 56.0 1.0
OE2 B:GLU146 3.3 56.3 1.0
CD B:GLU146 3.7 55.2 1.0
O B:ASP154 4.5 51.9 1.0

Cadmium binding site 8 out of 18 in 2j4k

Go back to Cadmium Binding Sites List in 2j4k
Cadmium binding site 8 out of 18 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd232

b:0.4
occ:1.00
 OE2 B:GLU224 2.7 56.1 1.0
CD B:GLU224 3.3 54.9 1.0
CG B:GLU224 3.7 52.9 1.0
O B:HOH2046 3.8 36.4 1.0
OE1 B:GLU224 4.2 57.7 1.0
CB B:GLU224 4.4 47.6 1.0

Cadmium binding site 9 out of 18 in 2j4k

Go back to Cadmium Binding Sites List in 2j4k
Cadmium binding site 9 out of 18 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd233

b:45.2
occ:1.00
 OD1 C:ASP18 2.5 40.2 1.0
OD2 C:ASP18 2.7 38.8 1.0
CG C:ASP18 2.9 38.8 1.0
O C:HOH2001 4.2 46.4 1.0
CB C:ASP18 4.4 37.4 1.0
CG2 C:VAL17 4.5 45.1 1.0
CD C:CD231 4.8 56.9 0.5
CD B:CD234 4.9 61.1 0.5

Cadmium binding site 10 out of 18 in 2j4k

Go back to Cadmium Binding Sites List in 2j4k
Cadmium binding site 10 out of 18 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump to 2.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd234

b:61.1
occ:0.50
 O C:HOH2001 2.6 46.4 1.0
CD C:CD231 3.3 56.9 0.5
OD2 C:ASP18 4.2 38.8 1.0
CD B:CD233 4.9 45.2 1.0

Reference:

K.S.Jensen, E.Johansson, K.F.Jensen. Structural and Enzymatic Investigation of the Sulfolobus Solfataricus Uridylate Kinase Shows Competitive Utp Inhibition and the Lack of Gtp Stimulation Biochemistry V. 46 2745 2007.
ISSN: ISSN 0006-2960
PubMed: 17297917
DOI: 10.1021/BI0618159
Page generated: Fri Jul 19 14:59:56 2024

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