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Manganese in PDB 3aca: Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dadp and Manganese

Enzymatic activity of Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dadp and Manganese

All present enzymatic activity of Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dadp and Manganese:
3.6.1.13;

Protein crystallography data

The structure of Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dadp and Manganese, PDB code: 3aca was solved by T.Arimori, Y.Yamagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.89 / 2.05
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.636, 40.701, 99.791, 90.00, 121.64, 90.00
R / Rfree (%) 19.9 / 24.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dadp and Manganese (pdb code 3aca). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dadp and Manganese, PDB code: 3aca:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 3aca

Go back to Manganese Binding Sites List in 3aca
Manganese binding site 1 out of 5 in the Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dadp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dadp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn3

b:38.2
occ:0.36
 MN A:MN4 2.4 57.0 0.4
O A:ALA96 2.4 29.2 1.0
O2A A:8DD2 2.4 47.9 1.0
O A:HOH387 2.5 26.4 1.0
O A:HOH388 2.5 41.9 1.0
OE2 A:GLU116 2.5 36.1 1.0
O3B A:8DD2 2.8 58.9 1.0
CD A:GLU116 3.4 27.6 1.0
C A:ALA96 3.6 31.1 1.0
PA A:8DD2 3.7 92.3 1.0
OE2 A:GLU112 3.7 36.5 1.0
PB A:8DD2 3.8 90.5 1.0
O A:HOH340 3.9 70.4 1.0
O1B A:8DD2 3.9 81.5 1.0
OE1 A:GLU116 4.0 31.3 1.0
O3A A:8DD2 4.0 78.9 1.0
N A:ALA96 4.4 19.7 1.0
OE1 A:GLN82 4.4 34.2 1.0
CG A:GLU116 4.5 28.6 1.0
NH2 A:ARG84 4.5 27.0 1.0
N A:GLY97 4.5 26.1 1.0
CA A:GLY97 4.5 35.6 1.0
CA A:ALA96 4.5 28.9 1.0
CD A:GLU112 4.5 35.1 1.0
O A:HOH303 4.6 20.6 1.0
O5' A:8DD2 4.7 75.8 1.0
NE2 A:GLN82 4.7 31.6 1.0
O1A A:8DD2 4.8 78.4 1.0
CG A:GLU112 5.0 39.6 1.0

Manganese binding site 2 out of 5 in 3aca

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Manganese binding site 2 out of 5 in the Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dadp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dadp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn4

b:57.0
occ:0.43
 OE2 A:GLU112 2.4 36.5 1.0
MN A:MN3 2.4 38.2 0.4
O A:HOH340 2.4 70.4 1.0
O3B A:8DD2 2.6 58.9 1.0
O A:HOH326 2.7 47.7 1.0
OE2 A:GLU116 2.8 36.1 1.0
O A:HOH388 3.2 41.9 1.0
CD A:GLU116 3.5 27.6 1.0
CD A:GLU112 3.5 35.1 1.0
PB A:8DD2 3.7 90.5 1.0
O1B A:8DD2 3.7 81.5 1.0
O A:ALA96 3.7 29.2 1.0
CG A:GLU116 3.7 28.6 1.0
OE1 A:GLU166 3.9 86.8 1.0
CD A:GLU166 4.0 91.5 1.0
OE2 A:GLU166 4.1 93.9 1.0
OE1 A:GLU112 4.2 40.1 1.0
O2A A:8DD2 4.3 47.9 1.0
MN A:MN5 4.4 80.7 0.8
O A:HOH387 4.5 26.4 1.0
O2B A:8DD2 4.5 57.4 1.0
CG A:GLU112 4.5 39.6 1.0
OE1 A:GLU116 4.6 31.3 1.0
O3A A:8DD2 4.7 78.9 1.0
C A:ALA96 4.9 31.1 1.0
CG A:GLU166 4.9 85.2 1.0
CA A:GLY97 5.0 35.6 1.0

Manganese binding site 3 out of 5 in 3aca

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Manganese binding site 3 out of 5 in the Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dadp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dadp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn5

b:80.7
occ:0.81
 O A:HOH307 2.8 50.7 1.0
O2B A:8DD2 3.0 57.4 1.0
OE1 A:GLU112 3.1 40.1 1.0
O A:HOH407 3.3 51.0 1.0
O3B A:8DD2 3.5 58.9 1.0
NH1 A:ARG111 3.7 37.2 1.0
PB A:8DD2 3.8 90.5 1.0
CD A:GLU112 3.9 35.1 1.0
OE2 A:GLU112 4.0 36.5 1.0
O A:HOH326 4.2 47.7 1.0
OE2 A:GLU115 4.3 38.7 1.0
N A:LEU98 4.3 37.3 1.0
MN A:MN4 4.4 57.0 0.4
O A:HOH340 4.6 70.4 1.0
CA A:GLY97 4.6 35.6 1.0
O1B A:8DD2 4.7 81.5 1.0
O A:LEU98 4.7 34.9 1.0
CZ A:ARG111 4.7 39.2 1.0
NH2 A:ARG111 4.7 38.4 1.0
C A:GLY97 4.9 37.8 1.0

Manganese binding site 4 out of 5 in 3aca

Go back to Manganese Binding Sites List in 3aca
Manganese binding site 4 out of 5 in the Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dadp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dadp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1

b:34.7
occ:0.51
 O B:ALA96 2.5 25.2 1.0
O B:HOH519 2.5 27.1 1.0
OE1 B:GLU116 2.5 39.7 1.0
O2B B:8DD209 2.5 51.8 1.0
O B:HOH518 2.5 30.5 1.0
O2A B:8DD209 2.6 37.2 1.0
MN B:MN2 3.2 38.7 0.4
O B:HOH452 3.3 47.3 1.0
C B:ALA96 3.6 24.3 1.0
CD B:GLU116 3.6 28.7 1.0
O3A B:8DD209 3.6 88.4 1.0
PA B:8DD209 3.7 93.8 1.0
PB B:8DD209 3.7 84.7 1.0
NH2 B:ARG84 4.2 22.6 1.0
OE2 B:GLU116 4.2 31.2 1.0
OE1 B:GLU112 4.2 31.5 1.0
O B:HOH426 4.3 21.2 1.0
OE1 B:GLN82 4.3 29.3 1.0
N B:ALA96 4.4 18.6 1.0
CA B:ALA96 4.5 24.1 1.0
N B:GLY97 4.5 28.6 1.0
O3B B:8DD209 4.5 75.2 1.0
CA B:GLY97 4.5 32.2 1.0
O1A B:8DD209 4.6 70.4 1.0
NE2 B:GLN82 4.6 24.3 1.0
CG B:GLU116 4.8 23.3 1.0
O5' B:8DD209 4.8 76.0 1.0
CB B:ALA96 4.9 25.2 1.0
O1B B:8DD209 4.9 40.7 1.0
CD B:GLU112 4.9 38.7 1.0
CD B:GLN82 4.9 31.9 1.0
NH1 B:ARG84 5.0 20.5 1.0

Manganese binding site 5 out of 5 in 3aca

Go back to Manganese Binding Sites List in 3aca
Manganese binding site 5 out of 5 in the Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dadp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Human NUDT5 Complexed with 8-Oxo-Dadp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2

b:38.7
occ:0.40
 OE1 B:GLU112 2.3 31.5 1.0
O2B B:8DD209 2.4 51.8 1.0
O B:HOH452 2.5 47.3 1.0
O B:HOH491 2.6 43.6 1.0
OE1 B:GLU116 2.8 39.7 1.0
MN B:MN1 3.2 34.7 0.5
OE2 B:GLU166 3.2 67.5 1.0
CD B:GLU112 3.3 38.7 1.0
OE2 B:GLU112 3.6 38.0 1.0
PB B:8DD209 3.6 84.7 1.0
O B:ALA96 3.7 25.2 1.0
CD B:GLU116 3.8 28.7 1.0
CD B:GLU166 3.8 72.3 1.0
OE1 B:GLU166 3.9 74.2 1.0
CG B:GLU116 3.9 23.3 1.0
O3B B:8DD209 3.9 75.2 1.0
O B:HOH518 4.2 30.5 1.0
O1B B:8DD209 4.4 40.7 1.0
CG B:GLU112 4.5 38.5 1.0
CA B:GLY97 4.6 32.2 1.0
OE2 B:GLU115 4.7 40.6 1.0
O B:HOH476 4.7 38.7 1.0
O3A B:8DD209 4.7 88.4 1.0
C B:ALA96 4.8 24.3 1.0
OE2 B:GLU116 5.0 31.2 1.0
CG B:GLU166 5.0 65.7 1.0

Reference:

T.Arimori, H.Tamaoki, T.Nakamura, H.Kamiya, S.Ikemizu, Y.Takagi, T.Ishibashi, H.Harashima, M.Sekiguchi, Y.Yamagata. Diverse Substrate Recognition and Hydrolysis Mechanisms of Human NUDT5 Nucleic Acids Res. V. 39 8972 2011.
ISSN: ISSN 0305-1048
PubMed: 21768126
DOI: 10.1093/NAR/GKR575
Page generated: Sat Oct 5 15:45:26 2024

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