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Magnesium in PDB 2dqb: Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase

Enzymatic activity of Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase

All present enzymatic activity of Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase:
3.1.5.1;

Protein crystallography data

The structure of Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase, PDB code: 2dqb was solved by N.Kondo, N.Nakagawa, A.Ebihara, L.Chen, Z.-J.Liu, B.-C.Wang, S.Yokoyama, S.Kuramitsu, R.Masui, Riken Structural Genomics/Proteomics Initiative(Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 74.100, 84.200, 108.000, 110.20, 109.70, 94.40
R / Rfree (%) 22.3 / 28.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase (pdb code 2dqb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase, PDB code: 2dqb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2dqb

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Magnesium binding site 1 out of 6 in the Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:40.3
occ:1.00
 OD1 A:ASP196 2.2 23.3 1.0
OD2 A:ASP109 2.3 34.2 1.0
NE2 A:HIS79 2.4 31.5 1.0
CD2 A:HIS79 2.9 29.1 1.0
CG A:ASP196 3.0 21.9 1.0
OD2 A:ASP196 3.1 27.7 1.0
CE1 A:TYR200 3.2 50.1 1.0
CG A:ASP109 3.4 32.8 1.0
CE1 A:HIS108 3.4 35.1 1.0
CE1 A:HIS79 3.6 29.8 1.0
OD1 A:ASP109 3.8 32.3 1.0
CZ A:TYR200 3.9 51.6 1.0
OH A:TYR200 3.9 56.2 1.0
CD1 A:TYR200 4.0 46.3 1.0
NE2 A:GLN63 4.0 40.9 1.0
O A:HOH561 4.0 32.2 1.0
NE2 A:HIS108 4.2 35.7 1.0
CG A:HIS79 4.2 25.0 1.0
CB A:ASP196 4.4 18.8 1.0
ND1 A:HIS108 4.4 35.4 1.0
ND1 A:HIS79 4.5 28.2 1.0
CG2 A:VAL83 4.6 20.7 1.0
CB A:ASP109 4.7 29.5 1.0
CD A:GLN63 4.9 43.7 1.0
CA A:ASP196 5.0 24.1 1.0

Magnesium binding site 2 out of 6 in 2dqb

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Magnesium binding site 2 out of 6 in the Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:27.4
occ:1.00
 O B:HOH537 2.1 22.2 1.0
NE2 B:HIS169 2.4 29.8 1.0
ND1 B:HIS108 2.5 23.0 1.0
OE2 B:GLU170 2.6 31.7 1.0
CE1 B:HIS169 3.2 30.4 1.0
CE1 B:HIS108 3.3 22.6 1.0
CD2 B:HIS169 3.5 33.9 1.0
CG B:HIS108 3.6 22.9 1.0
ND2 B:ASN136 3.7 18.8 1.0
CD B:GLU170 3.8 42.8 1.0
NE2 B:HIS135 3.9 42.4 1.0
CB B:HIS108 4.0 25.4 1.0
OD2 B:ASP196 4.0 28.0 1.0
OD1 B:ASP109 4.1 24.7 1.0
CG B:GLU170 4.3 45.3 1.0
ND1 B:HIS169 4.4 33.4 1.0
NE2 B:HIS108 4.5 27.7 1.0
CG B:HIS169 4.5 35.0 1.0
O B:HOH538 4.6 33.6 1.0
CD2 B:HIS108 4.7 20.3 1.0
N B:ASP109 4.7 29.8 1.0
OE1 B:GLU170 4.8 44.3 1.0
CD2 B:HIS135 4.8 35.5 1.0
OD1 B:ASP193 4.8 26.9 1.0
CG B:ASN136 4.8 26.1 1.0
CE1 B:HIS135 4.8 41.4 1.0
CG B:ASP109 5.0 32.6 1.0
CA B:HIS108 5.0 28.7 1.0
OD1 B:ASN136 5.0 28.9 1.0

Magnesium binding site 3 out of 6 in 2dqb

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Magnesium binding site 3 out of 6 in the Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:36.2
occ:1.00
 OD2 C:ASP109 2.5 28.6 1.0
OD1 C:ASP196 2.5 28.8 1.0
NE2 C:HIS79 2.7 22.6 1.0
CD2 C:HIS79 3.1 21.6 1.0
OE1 C:GLN63 3.2 43.7 1.0
CG C:ASP196 3.3 32.6 1.0
OD2 C:ASP196 3.4 29.8 1.0
CE2 C:TYR200 3.4 43.0 1.0
CG C:ASP109 3.5 28.6 1.0
OD1 C:ASP109 3.7 34.8 1.0
CE1 C:HIS79 3.8 23.2 1.0
CD2 C:TYR200 4.0 38.7 1.0
CE1 C:HIS108 4.1 21.0 1.0
CG C:HIS79 4.3 23.0 1.0
CZ C:TYR200 4.3 44.3 1.0
CD C:GLN63 4.3 37.7 1.0
OH C:TYR200 4.5 48.1 1.0
ND1 C:HIS79 4.6 26.6 1.0
NE2 C:HIS108 4.6 22.1 1.0
CB C:ASP196 4.7 28.9 1.0
CB C:ASP109 4.8 26.7 1.0
NE2 C:GLN63 4.9 33.5 1.0

Magnesium binding site 4 out of 6 in 2dqb

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Magnesium binding site 4 out of 6 in the Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg504

b:39.4
occ:1.00
 OD2 D:ASP109 2.4 28.7 1.0
OD1 D:ASP196 2.5 29.2 1.0
NE2 D:HIS79 2.7 35.7 1.0
O D:HOH534 3.0 40.6 1.0
OD2 D:ASP196 3.0 31.3 1.0
CG D:ASP196 3.0 28.8 1.0
CG D:ASP109 3.1 28.6 1.0
OD1 D:ASP109 3.2 28.1 1.0
NE2 D:HIS108 3.3 30.7 1.0
CD2 D:HIS79 3.4 31.9 1.0
CE1 D:HIS79 3.7 31.5 1.0
CE1 D:TYR200 3.8 51.8 1.0
OE1 D:GLN63 4.0 49.3 1.0
CD2 D:HIS108 4.0 29.5 1.0
CD1 D:TYR200 4.1 51.5 1.0
CE1 D:HIS108 4.3 25.1 1.0
CB D:ASP196 4.4 25.2 1.0
CB D:ASP109 4.5 26.7 1.0
CG D:HIS79 4.6 31.7 1.0
ND1 D:HIS79 4.7 30.8 1.0
CZ D:TYR200 4.7 54.4 1.0
CE1 D:HIS112 4.9 37.1 1.0
O D:HOH544 4.9 40.7 1.0
CG2 D:VAL83 5.0 20.5 1.0

Magnesium binding site 5 out of 6 in 2dqb

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Magnesium binding site 5 out of 6 in the Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg501

b:34.8
occ:1.00
 ND1 E:HIS108 2.4 26.6 1.0
NE2 E:HIS169 2.4 32.0 1.0
OE1 E:GLU170 2.6 35.5 1.0
CG E:HIS108 3.3 28.4 1.0
CD2 E:HIS169 3.4 34.6 1.0
CE1 E:HIS108 3.4 28.4 1.0
CE1 E:HIS169 3.4 29.8 1.0
CB E:HIS108 3.5 23.5 1.0
OD2 E:ASP196 3.8 26.9 1.0
CD E:GLU170 3.9 40.0 1.0
ND2 E:ASN136 3.9 32.4 1.0
OD1 E:ASP109 4.1 33.4 1.0
NE2 E:HIS135 4.3 26.6 1.0
O E:HIS108 4.4 32.0 1.0
CD2 E:HIS108 4.5 24.2 1.0
NE2 E:HIS108 4.5 26.6 1.0
C E:HIS108 4.5 25.8 1.0
ND1 E:HIS169 4.6 37.8 1.0
CG E:HIS169 4.6 35.1 1.0
CA E:HIS108 4.6 26.8 1.0
OE2 E:GLU170 4.7 37.7 1.0
CG E:GLU170 4.8 41.0 1.0
CG E:ASP196 4.8 30.3 1.0
CB E:GLU170 4.8 41.5 1.0
OD2 E:ASP193 4.9 23.5 1.0
CG E:ASP109 4.9 30.5 1.0
CD2 E:HIS135 4.9 24.7 1.0

Magnesium binding site 6 out of 6 in 2dqb

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Magnesium binding site 6 out of 6 in the Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Dntp Triphosphohydrolase From Thermus Thermophilus HB8, Which Is Homologous to Dgtp Triphosphohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg505

b:42.5
occ:1.00
 OE2 F:GLU170 2.1 48.9 1.0
O F:HOH526 2.3 23.4 1.0
NE2 F:HIS169 2.4 38.2 1.0
ND1 F:HIS108 2.7 28.7 1.0
CD F:GLU170 3.2 51.0 1.0
CE1 F:HIS169 3.2 36.7 1.0
OD1 F:ASN136 3.3 27.6 1.0
OD1 F:ASP109 3.5 34.4 1.0
CD2 F:HIS169 3.5 38.5 1.0
CG F:HIS108 3.6 29.3 1.0
CE1 F:HIS108 3.6 24.9 1.0
O F:HIS108 3.7 35.6 1.0
CB F:HIS108 3.7 29.8 1.0
CG F:GLU170 3.8 49.3 1.0
NE2 F:HIS135 3.9 35.8 1.0
C F:HIS108 4.2 33.9 1.0
OE1 F:GLU170 4.2 51.3 1.0
OD1 F:ASP196 4.2 26.7 1.0
CG F:ASN136 4.3 26.3 1.0
CD2 F:HIS135 4.4 32.5 1.0
ND1 F:HIS169 4.4 37.6 1.0
CG F:ASP109 4.5 28.7 1.0
CA F:HIS108 4.5 32.3 1.0
CG F:HIS169 4.6 39.4 1.0
ND2 F:ASN136 4.7 23.9 1.0
NE2 F:HIS108 4.7 25.4 1.0
CD2 F:HIS108 4.7 23.4 1.0
N F:ASP109 4.9 32.1 1.0

Reference:

N.Kondo, N.Nakagawa, A.Ebihara, L.Chen, Z.-J.Liu, B.-C.Wang, S.Yokoyama, S.Kuramitsu, R.Masui. Structure of Dntp-Inducible Dntp Triphosphohydrolase: Insight Into Broad Specificity For Dntps and Triphosphohydrolase-Type Hydrolysis Acta Crystallogr.,Sect.D V. 63 230 2007.
ISSN: ISSN 0907-4449
PubMed: 17242516
DOI: 10.1107/S0907444906049262
Page generated: Tue Aug 13 22:34:31 2024

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