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Nickel in PDB 4xds: Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel

Enzymatic activity of Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel

All present enzymatic activity of Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel:
3.1.5.1;

Protein crystallography data

The structure of Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel, PDB code: 4xds was solved by D.Singh, D.Gawel, M.Itsko, J.M.Krahn, R.E.London, R.M.Schaaper, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 3.35
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 189.800, 189.800, 296.800, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.9

Nickel Binding Sites:

The binding sites of Nickel atom in the Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel (pdb code 4xds). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel, PDB code: 4xds:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 4xds

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Nickel binding site 1 out of 6 in the Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni601

b:1.0
occ:1.00
 O A:HOH1001 1.9 85.5 1.0
O A:HOH1003 2.0 0.0 1.0
NE2 A:HIS117 2.1 93.2 1.0
O A:HOH1002 2.1 0.3 1.0
OD2 A:ASP268 2.1 0.6 1.0
NE2 A:HIS69 2.3 0.2 1.0
CG A:ASP268 2.9 0.9 1.0
OD1 A:ASP268 2.9 0.9 1.0
CD2 A:HIS117 3.0 97.9 1.0
CE1 A:HIS117 3.0 91.7 1.0
CD2 A:HIS69 3.2 0.8 1.0
CE1 A:HIS69 3.2 0.9 1.0
OD2 A:ASP118 4.1 0.9 1.0
ND1 A:HIS117 4.1 95.5 1.0
CG A:HIS117 4.2 1.0 1.0
ND1 A:HIS69 4.3 0.5 1.0
CG A:HIS69 4.3 0.4 1.0
CB A:ASP268 4.3 0.7 1.0
CG A:ASP118 4.7 0.4 1.0
CG2 A:VAL73 4.8 99.3 1.0
CA A:ASP268 4.9 0.5 1.0

Nickel binding site 2 out of 6 in 4xds

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Nickel binding site 2 out of 6 in the Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni601

b:0.1
occ:1.00
 O B:HOH1001 1.9 71.1 1.0
O B:HOH1003 2.0 0.0 1.0
O B:HOH1002 2.1 0.5 1.0
NE2 B:HIS117 2.1 94.4 1.0
OD2 B:ASP268 2.2 0.4 1.0
NE2 B:HIS69 2.3 0.7 1.0
CE1 B:HIS117 3.0 95.5 1.0
CD2 B:HIS117 3.0 95.7 1.0
CG B:ASP268 3.0 0.1 1.0
OD1 B:ASP268 3.1 0.0 1.0
CE1 B:HIS69 3.2 0.5 1.0
CD2 B:HIS69 3.2 99.1 1.0
OD2 B:ASP118 4.1 0.6 1.0
ND1 B:HIS117 4.1 98.3 1.0
CG B:HIS117 4.2 98.8 1.0
ND1 B:HIS69 4.3 0.6 1.0
CG B:HIS69 4.4 0.1 1.0
CB B:ASP268 4.5 0.7 1.0
CG B:ASP118 4.6 1.0 1.0
CG2 B:VAL73 4.8 87.7 1.0

Nickel binding site 3 out of 6 in 4xds

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Nickel binding site 3 out of 6 in the Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni601

b:91.6
occ:1.00
 O C:HOH1001 1.9 70.5 1.0
O C:HOH1003 2.0 95.7 1.0
NE2 C:HIS117 2.0 65.7 1.0
O C:HOH1002 2.1 47.6 1.0
OD2 C:ASP268 2.2 55.4 1.0
NE2 C:HIS69 2.3 71.0 1.0
CG C:ASP268 3.0 64.8 1.0
CE1 C:HIS117 3.0 67.3 1.0
CD2 C:HIS117 3.0 66.0 1.0
OD1 C:ASP268 3.0 68.9 1.0
CE1 C:HIS69 3.2 72.2 1.0
CD2 C:HIS69 3.2 68.6 1.0
OD2 C:ASP118 4.1 94.9 1.0
ND1 C:HIS117 4.1 68.3 1.0
CG C:HIS117 4.1 67.4 1.0
ND1 C:HIS69 4.3 66.2 1.0
CG C:HIS69 4.4 63.3 1.0
CB C:ASP268 4.4 69.3 1.0
CG C:ASP118 4.6 92.2 1.0
CG2 C:VAL73 4.8 46.8 1.0
OD1 C:ASP118 5.0 94.1 1.0

Nickel binding site 4 out of 6 in 4xds

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Nickel binding site 4 out of 6 in the Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni602

b:88.3
occ:1.00
 O D:HOH1001 1.8 43.2 1.0
O D:HOH1003 1.9 94.5 1.0
O D:HOH1002 1.9 53.4 1.0
NE2 D:HIS117 2.0 53.6 1.0
NE2 D:HIS69 2.2 64.1 1.0
OD2 D:ASP268 2.2 67.9 1.0
CE1 D:HIS117 3.0 60.9 1.0
CG D:ASP268 3.0 75.8 1.0
CD2 D:HIS117 3.0 52.9 1.0
OD1 D:ASP268 3.1 79.3 1.0
CE1 D:HIS69 3.2 65.0 1.0
CD2 D:HIS69 3.2 60.1 1.0
ND1 D:HIS117 4.1 63.8 1.0
CG D:HIS117 4.2 54.9 1.0
OD2 D:ASP118 4.2 98.3 1.0
ND1 D:HIS69 4.3 64.3 1.0
CG D:HIS69 4.3 60.1 1.0
CB D:ASP268 4.5 51.5 1.0
CG2 D:VAL73 4.7 40.3 1.0
CG D:ASP118 4.7 87.6 1.0

Nickel binding site 5 out of 6 in 4xds

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Nickel binding site 5 out of 6 in the Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni601

b:73.8
occ:1.00
 O E:HOH1001 1.9 63.5 1.0
O E:HOH1003 2.0 67.8 1.0
NE2 E:HIS117 2.0 46.6 1.0
O E:HOH1002 2.1 44.9 1.0
OD2 E:ASP268 2.2 60.8 1.0
NE2 E:HIS69 2.2 70.8 1.0
CG E:ASP268 2.9 67.2 1.0
CE1 E:HIS117 3.0 49.2 1.0
OD1 E:ASP268 3.0 72.8 1.0
CD2 E:HIS117 3.0 48.2 1.0
CE1 E:HIS69 3.2 70.2 1.0
CD2 E:HIS69 3.2 70.4 1.0
ND1 E:HIS117 4.1 51.1 1.0
CG E:HIS117 4.1 52.6 1.0
OD2 E:ASP118 4.2 0.7 1.0
ND1 E:HIS69 4.3 67.1 1.0
CG E:HIS69 4.3 68.5 1.0
CB E:ASP268 4.4 58.9 1.0
CG2 E:VAL73 4.7 49.9 1.0
CG E:ASP118 4.7 99.7 1.0
CA E:ASP268 5.0 56.7 1.0

Nickel binding site 6 out of 6 in 4xds

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Nickel binding site 6 out of 6 in the Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Deoxyguanosinetriphosphate Triphosphohydrolase From Escherichia Coli with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni602

b:85.2
occ:1.00
 O F:HOH1001 1.8 38.3 1.0
O F:HOH1002 1.8 54.0 1.0
O F:HOH1003 1.9 76.7 1.0
NE2 F:HIS117 2.1 46.9 1.0
NE2 F:HIS69 2.2 57.8 1.0
OD2 F:ASP268 2.2 55.1 1.0
CE1 F:HIS117 3.0 47.8 1.0
CG F:ASP268 3.0 64.5 1.0
CD2 F:HIS117 3.0 49.7 1.0
CE1 F:HIS69 3.1 59.7 1.0
CD2 F:HIS69 3.1 57.9 1.0
OD1 F:ASP268 3.2 73.7 1.0
ND1 F:HIS117 4.1 54.5 1.0
CG F:HIS117 4.2 53.0 1.0
OD2 F:ASP118 4.2 99.5 1.0
ND1 F:HIS69 4.2 60.8 1.0
CG F:HIS69 4.3 58.9 1.0
CB F:ASP268 4.5 60.0 1.0
CG2 F:VAL73 4.7 47.5 1.0
CG F:ASP118 4.7 93.8 1.0
CB F:TYR272 4.8 98.0 1.0

Reference:

D.Singh, D.Gawel, M.Itsko, A.Hochkoeppler, J.M.Krahn, R.E.London, R.M.Schaaper. Structure of Escherichia Coli Dgtp Triphosphohydrolase: A Hexameric Enzyme with Dna Effector Molecules. J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
PubMed: 25694425
DOI: 10.1074/JBC.M115.636936
Page generated: Wed Dec 16 01:38:19 2020

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