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Cobalt in PDB 2j4j: Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution

Enzymatic activity of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution

All present enzymatic activity of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution:
2.7.4.22;

Protein crystallography data

The structure of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution, PDB code: 2j4j 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) 25.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.174, 126.438, 134.991, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 24.2

Other elements in 2j4j:

The structure of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution (pdb code 2j4j). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution, PDB code: 2j4j:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in 2j4j

Go back to Cobalt Binding Sites List in 2j4j
Cobalt binding site 1 out of 6 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co229

b:50.3
occ:1.00
 O1P A:U5P227 2.1 20.6 1.0
OE1 A:GLU182 2.2 47.0 1.0
O A:HOH2070 2.3 27.3 1.0
O2B A:ACP228 2.3 32.9 1.0
O2G A:ACP228 2.4 36.6 1.0
O A:HOH2069 2.4 37.4 1.0
CD A:GLU182 3.0 46.3 1.0
P A:U5P227 3.3 24.2 1.0
PG A:ACP228 3.3 38.0 1.0
PB A:ACP228 3.4 34.4 1.0
C3B A:ACP228 3.5 34.7 1.0
OE2 A:GLU182 3.6 47.5 1.0
O3G A:ACP228 3.7 29.8 1.0
O3P A:U5P227 3.8 23.2 1.0
O A:HOH2066 3.8 30.6 1.0
O2P A:U5P227 3.8 26.2 1.0
CG A:GLU182 3.9 44.5 1.0
O3' A:U5P227 4.1 21.0 1.0
O3A A:ACP228 4.3 35.9 1.0
CB A:GLU182 4.5 43.1 1.0
O1B A:ACP228 4.5 34.1 1.0
NH2 A:ARG48 4.5 40.2 1.0
O5' A:U5P227 4.5 22.7 1.0
O A:HOH2001 4.6 25.8 1.0
O1G A:ACP228 4.6 32.8 1.0
C3' A:U5P227 4.8 17.7 1.0
C5' A:U5P227 4.9 20.1 1.0

Cobalt binding site 2 out of 6 in 2j4j

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Cobalt binding site 2 out of 6 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co230

b:27.5
occ:1.00
 NE2 C:HIS104 2.1 18.7 1.0
NE2 A:HIS104 2.1 19.8 1.0
NE2 E:HIS104 2.1 19.5 1.0
CD2 E:HIS104 3.0 21.0 1.0
CD2 A:HIS104 3.0 20.9 1.0
CD2 C:HIS104 3.1 21.1 1.0
CE1 C:HIS104 3.1 19.2 1.0
CE1 A:HIS104 3.2 19.2 1.0
CE1 E:HIS104 3.2 19.2 1.0
OH A:TYR88 3.5 24.9 1.0
OH E:TYR88 3.5 24.3 1.0
OH C:TYR88 3.6 24.5 1.0
CZ A:TYR88 4.1 23.6 1.0
CE1 A:TYR88 4.1 24.3 1.0
CZ E:TYR88 4.1 23.5 1.0
CE1 E:TYR88 4.2 24.3 1.0
CG A:HIS104 4.2 21.9 1.0
ND1 C:HIS104 4.2 20.3 1.0
CG E:HIS104 4.2 22.1 1.0
ND1 A:HIS104 4.2 20.3 1.0
CG C:HIS104 4.2 21.8 1.0
CZ C:TYR88 4.2 23.5 1.0
ND1 E:HIS104 4.2 20.1 1.0
O A:HOH2032 4.3 31.1 1.0
CE1 C:TYR88 4.4 24.5 1.0
O E:HOH2028 4.5 30.7 1.0

Cobalt binding site 3 out of 6 in 2j4j

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Cobalt binding site 3 out of 6 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co229

b:53.6
occ:1.00
 O2B B:ACP228 2.2 33.7 1.0
O1P B:U5P227 2.3 25.7 1.0
O2G B:ACP228 2.5 38.4 1.0
PB B:ACP228 3.2 36.5 1.0
PG B:ACP228 3.3 38.7 1.0
P B:U5P227 3.3 27.7 1.0
C3B B:ACP228 3.4 37.1 1.0
O3G B:ACP228 3.7 32.8 1.0
O3P B:U5P227 3.7 25.1 1.0
O2P B:U5P227 3.9 26.4 1.0
O3' B:U5P227 4.0 19.4 1.0
O3A B:ACP228 4.1 35.9 1.0
O B:HOH2002 4.2 51.6 1.0
O B:HOH2068 4.3 26.9 1.0
O1B B:ACP228 4.5 34.9 1.0
O5' B:U5P227 4.6 22.5 1.0
O1G B:ACP228 4.7 38.9 1.0
C3' B:U5P227 4.8 17.7 1.0

Cobalt binding site 4 out of 6 in 2j4j

Go back to Cobalt Binding Sites List in 2j4j
Cobalt binding site 4 out of 6 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co230

b:26.8
occ:1.00
 NE2 F:HIS104 2.1 18.9 1.0
NE2 D:HIS104 2.1 19.2 1.0
NE2 B:HIS104 2.1 19.1 1.0
CD2 F:HIS104 3.0 20.8 1.0
CD2 D:HIS104 3.0 20.7 1.0
CD2 B:HIS104 3.1 20.4 1.0
CE1 F:HIS104 3.1 19.1 1.0
CE1 D:HIS104 3.1 18.9 1.0
CE1 B:HIS104 3.2 18.8 1.0
OH D:TYR88 3.5 24.4 1.0
OH B:TYR88 3.5 24.2 1.0
OH F:TYR88 3.6 24.5 1.0
CZ D:TYR88 4.1 23.7 1.0
CZ B:TYR88 4.2 23.6 1.0
CG F:HIS104 4.2 22.0 1.0
ND1 F:HIS104 4.2 20.3 1.0
CG D:HIS104 4.2 21.8 1.0
ND1 D:HIS104 4.2 20.2 1.0
CE1 B:TYR88 4.2 24.2 1.0
CE1 D:TYR88 4.2 24.3 1.0
CG B:HIS104 4.2 22.0 1.0
CZ F:TYR88 4.2 23.7 1.0
ND1 B:HIS104 4.2 20.3 1.0
CE1 F:TYR88 4.3 24.5 1.0
O D:HOH2022 4.7 29.6 1.0
O B:HOH2033 4.7 36.5 1.0
O F:HOH2024 4.7 35.3 1.0

Cobalt binding site 5 out of 6 in 2j4j

Go back to Cobalt Binding Sites List in 2j4j
Cobalt binding site 5 out of 6 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co229

b:43.5
occ:1.00
 O1P C:U5P227 2.1 26.3 1.0
O2B C:ACP228 2.2 30.3 1.0
O2G C:ACP228 2.2 30.9 1.0
O C:HOH2042 2.5 39.0 1.0
P C:U5P227 3.2 28.1 1.0
PG C:ACP228 3.3 34.4 1.0
PB C:ACP228 3.3 33.2 1.0
C3B C:ACP228 3.5 31.7 1.0
O2P C:U5P227 3.7 24.9 1.0
O3P C:U5P227 3.8 24.3 1.0
O3G C:ACP228 4.0 30.0 1.0
O C:HOH2041 4.1 34.4 1.0
O3A C:ACP228 4.1 36.0 1.0
O3' C:U5P227 4.3 25.5 1.0
O C:HOH2039 4.3 26.4 1.0
O1B C:ACP228 4.5 34.3 1.0
O5' C:U5P227 4.5 28.0 1.0
O C:HOH2036 4.5 41.1 1.0
O1G C:ACP228 4.6 29.8 1.0
C3' C:U5P227 4.9 24.4 1.0
C5' C:U5P227 4.9 25.1 1.0
NH2 C:ARG48 5.0 39.3 1.0
O C:HOH2038 5.0 34.7 1.0

Cobalt binding site 6 out of 6 in 2j4j

Go back to Cobalt Binding Sites List in 2j4j
Cobalt binding site 6 out of 6 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Ump and Amppcp to 2.1 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Co229

b:70.1
occ:1.00
 O2B E:ACP228 2.2 46.8 1.0
O1P E:U5P227 2.3 34.3 1.0
O2G E:ACP228 2.4 47.4 1.0
OE1 E:GLU182 2.9 52.1 1.0
P E:U5P227 3.2 32.8 1.0
PB E:ACP228 3.3 46.9 1.0
PG E:ACP228 3.4 48.8 1.0
C3B E:ACP228 3.4 46.2 1.0
O2P E:U5P227 3.6 34.3 1.0
CD E:GLU182 3.8 51.4 1.0
O3G E:ACP228 3.9 44.0 1.0
O E:HOH2046 3.9 39.9 1.0
O3P E:U5P227 3.9 34.6 1.0
O E:HOH2047 4.0 28.9 1.0
OE2 E:GLU182 4.0 55.5 1.0
O3A E:ACP228 4.1 46.8 1.0
O3' E:U5P227 4.2 29.0 1.0
O E:HOH2002 4.4 32.2 1.0
O1B E:ACP228 4.5 45.3 1.0
O5' E:U5P227 4.6 31.7 1.0
O1G E:ACP228 4.6 45.0 1.0
C3' E:U5P227 4.8 25.7 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: Sun Dec 13 10:38:16 2020

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