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Manganese in PDB 2dfj: Crystal Structure of the Diadenosine Tetraphosphate Hydrolase From Shigella Flexneri 2A

Enzymatic activity of Crystal Structure of the Diadenosine Tetraphosphate Hydrolase From Shigella Flexneri 2A

All present enzymatic activity of Crystal Structure of the Diadenosine Tetraphosphate Hydrolase From Shigella Flexneri 2A:
3.6.1.41;

Protein crystallography data

The structure of Crystal Structure of the Diadenosine Tetraphosphate Hydrolase From Shigella Flexneri 2A, PDB code: 2dfj was solved by Q.H.Wang, W.X.Hu, R.C.Bi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.95 / 2.72
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.498, 54.965, 119.203, 90.00, 129.14, 90.00
R / Rfree (%) 22.9 / 26.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Diadenosine Tetraphosphate Hydrolase From Shigella Flexneri 2A (pdb code 2dfj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Diadenosine Tetraphosphate Hydrolase From Shigella Flexneri 2A, PDB code: 2dfj:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2dfj

Go back to Manganese Binding Sites List in 2dfj
Manganese binding site 1 out of 4 in the Crystal Structure of the Diadenosine Tetraphosphate Hydrolase From Shigella Flexneri 2A


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 the Diadenosine Tetraphosphate Hydrolase From Shigella Flexneri 2A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1001

b:64.6
occ:1.00
 OD1 A:ASN65 2.1 32.7 1.0
ND1 A:HIS227 2.2 41.1 1.0
NE2 A:HIS120 2.2 29.0 1.0
O A:HOH1021 2.3 57.7 1.0
OD2 A:ASP37 2.4 31.9 1.0
O A:HOH1029 2.4 54.1 1.0
CE1 A:HIS120 3.1 28.2 1.0
CE1 A:HIS227 3.1 41.2 1.0
CG A:ASN65 3.1 30.0 1.0
CG A:HIS227 3.2 41.2 1.0
CD2 A:HIS120 3.3 28.1 1.0
CG A:ASP37 3.4 28.8 1.0
MN A:MN1002 3.4 64.7 1.0
ND2 A:ASN65 3.5 32.2 1.0
CB A:HIS227 3.5 40.2 1.0
CA A:HIS227 3.8 40.1 1.0
OD1 A:ASP37 3.9 28.7 1.0
OD2 A:ASP8 3.9 32.1 1.0
O A:HOH1016 4.1 38.9 1.0
NE2 A:HIS227 4.2 41.4 1.0
ND1 A:HIS120 4.2 28.3 1.0
CD2 A:HIS227 4.3 40.9 1.0
O A:HOH1022 4.3 49.0 1.0
N A:ASN65 4.4 26.6 1.0
CG A:HIS120 4.4 27.0 1.0
O A:THR181 4.4 30.6 1.0
O A:HIS227 4.4 40.5 1.0
CB A:ASN65 4.5 27.7 1.0
ND1 A:HIS66 4.5 28.7 1.0
C A:HIS227 4.5 40.7 1.0
CB A:ASP37 4.5 27.5 1.0
O A:GLY226 4.8 39.0 1.0
CG A:ASP8 5.0 30.6 1.0

Manganese binding site 2 out of 4 in 2dfj

Go back to Manganese Binding Sites List in 2dfj
Manganese binding site 2 out of 4 in the Crystal Structure of the Diadenosine Tetraphosphate Hydrolase From Shigella Flexneri 2A


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 the Diadenosine Tetraphosphate Hydrolase From Shigella Flexneri 2A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1002

b:64.7
occ:1.00
 O A:HOH1029 1.9 54.1 1.0
NE2 A:HIS10 2.1 30.0 1.0
OD2 A:ASP8 2.2 32.1 1.0
O A:HOH1023 2.3 49.4 1.0
OD2 A:ASP37 2.4 31.9 1.0
O A:HOH1022 2.5 49.0 1.0
CE1 A:HIS10 2.8 31.0 1.0
O A:HOH1021 3.1 57.7 1.0
CG A:ASP8 3.3 30.6 1.0
CG A:ASP37 3.3 28.8 1.0
CD2 A:HIS10 3.4 30.4 1.0
MN A:MN1001 3.4 64.6 1.0
CB A:ASP37 3.5 27.5 1.0
CB A:ASP8 3.9 30.1 1.0
OD2 A:ASP244 3.9 36.0 1.0
ND1 A:HIS10 4.0 32.1 1.0
ND1 A:HIS66 4.3 28.7 1.0
CG A:HIS10 4.3 31.8 1.0
OD1 A:ASP8 4.3 31.0 1.0
OD1 A:ASP37 4.5 28.7 1.0
CE1 A:HIS66 4.5 29.1 1.0
O A:HOH1016 4.6 38.9 1.0
O A:HIS227 4.6 40.5 1.0
CE1 A:HIS120 4.6 28.2 1.0
NE2 A:HIS120 4.7 29.0 1.0
ND1 A:HIS227 4.9 41.1 1.0
OD1 A:ASN65 4.9 32.7 1.0
O A:GLY226 5.0 39.0 1.0

Manganese binding site 3 out of 4 in 2dfj

Go back to Manganese Binding Sites List in 2dfj
Manganese binding site 3 out of 4 in the Crystal Structure of the Diadenosine Tetraphosphate Hydrolase From Shigella Flexneri 2A


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 the Diadenosine Tetraphosphate Hydrolase From Shigella Flexneri 2A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2001

b:51.4
occ:1.00
 OD1 B:ASN65 2.1 33.6 1.0
OD2 B:ASP37 2.3 40.9 1.0
ND1 B:HIS227 2.3 36.7 1.0
NE2 B:HIS120 2.5 31.5 1.0
O B:HOH2025 2.5 50.4 1.0
O B:HOH2023 2.6 40.7 1.0
CB B:HIS227 2.7 36.8 1.0
CG B:HIS227 2.9 36.7 1.0
CG B:ASN65 3.0 32.0 1.0
CG B:ASP37 3.3 38.2 1.0
ND2 B:ASN65 3.3 31.4 1.0
CE1 B:HIS120 3.3 31.9 1.0
MN B:MN2002 3.4 59.2 1.0
CE1 B:HIS227 3.6 35.7 1.0
CA B:HIS227 3.6 37.0 1.0
CD2 B:HIS120 3.6 30.8 1.0
OD1 B:ASP37 3.8 37.2 1.0
OD2 B:ASP8 3.9 39.4 1.0
O B:HIS227 4.0 36.8 1.0
C B:HIS227 4.2 36.8 1.0
CD2 B:HIS227 4.2 36.2 1.0
CB B:ASN65 4.4 29.8 1.0
O B:THR181 4.4 29.8 1.0
CB B:ASP37 4.4 37.8 1.0
NE2 B:HIS227 4.5 35.8 1.0
ND1 B:HIS120 4.5 31.9 1.0
N B:ASN65 4.5 29.4 1.0
ND1 B:HIS66 4.6 33.2 1.0
CG B:HIS120 4.7 30.6 1.0
O B:HOH2017 4.8 52.5 1.0
O B:GLY226 4.8 39.5 1.0
N B:HIS227 4.9 37.4 1.0

Manganese binding site 4 out of 4 in 2dfj

Go back to Manganese Binding Sites List in 2dfj
Manganese binding site 4 out of 4 in the Crystal Structure of the Diadenosine Tetraphosphate Hydrolase From Shigella Flexneri 2A


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 the Diadenosine Tetraphosphate Hydrolase From Shigella Flexneri 2A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2002

b:59.2
occ:1.00
 O B:HOH2025 2.1 50.4 1.0
NE2 B:HIS10 2.2 39.5 1.0
OD2 B:ASP37 2.4 40.9 1.0
O B:HOH2007 2.4 36.5 1.0
O B:HOH2017 2.5 52.5 1.0
OD2 B:ASP8 2.6 39.4 1.0
CE1 B:HIS10 3.1 41.0 1.0
CG B:ASP37 3.3 38.2 1.0
CD2 B:HIS10 3.3 39.4 1.0
CB B:ASP37 3.4 37.8 1.0
MN B:MN2001 3.4 51.4 1.0
O B:HOH2023 3.5 40.7 1.0
CG B:ASP8 3.5 37.5 1.0
CB B:ASP8 3.9 37.4 1.0
OD2 B:ASP244 3.9 35.8 1.0
ND1 B:HIS10 4.2 41.9 1.0
O B:HIS227 4.4 36.8 1.0
CG B:HIS10 4.4 40.4 1.0
OD1 B:ASP37 4.5 37.2 1.0
ND1 B:HIS66 4.5 33.2 1.0
CA B:HIS227 4.5 37.0 1.0
OD1 B:ASP8 4.7 38.4 1.0
OD1 B:ASN65 4.8 33.6 1.0
CB B:HIS227 4.8 36.8 1.0
CG B:ASP244 4.8 35.8 1.0
CE1 B:HIS120 4.8 31.9 1.0
CA B:ASP37 4.9 37.6 1.0
C B:HIS227 4.9 36.8 1.0
CE1 B:HIS66 4.9 34.7 1.0
NE2 B:HIS120 4.9 31.5 1.0

Reference:

Q.H.Wang, W.X.Hu, W.Gao, R.C.Bi. Crystal Structure of the Diadenosine Tetraphosphate Hydrolase From Shigella Flexneri 2A Proteins V. 65 1032 2006.
ISSN: ISSN 0887-3585
PubMed: 17006950
DOI: 10.1002/PROT.21106
Page generated: Sat Oct 5 13:45:26 2024

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