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Manganese in PDB 1hpu: 5'-Nucleotidase (Closed Form), Complex with Ampcp

Enzymatic activity of 5'-Nucleotidase (Closed Form), Complex with Ampcp

All present enzymatic activity of 5'-Nucleotidase (Closed Form), Complex with Ampcp:
3.1.3.5; 3.6.1.45;

Protein crystallography data

The structure of 5'-Nucleotidase (Closed Form), Complex with Ampcp, PDB code: 1hpu was solved by T.Knoefel, N.Straeter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.59 / 1.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 89.400, 89.960, 96.260, 110.79, 106.43, 107.76
R / Rfree (%) 20.7 / 23.4

Manganese Binding Sites:

The binding sites of Manganese atom in the 5'-Nucleotidase (Closed Form), Complex with Ampcp (pdb code 1hpu). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the 5'-Nucleotidase (Closed Form), Complex with Ampcp, PDB code: 1hpu:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1hpu

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Manganese binding site 1 out of 8 in the 5'-Nucleotidase (Closed Form), Complex with Ampcp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 5'-Nucleotidase (Closed Form), Complex with Ampcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn600

b:26.1
occ:1.00
O1B A:A121602 2.2 28.5 1.0
OD1 A:ASN116 2.2 26.9 1.0
NE2 A:HIS217 2.2 25.3 1.0
O A:HOH1669 2.3 25.6 1.0
ND1 A:HIS252 2.3 24.9 1.0
OD2 A:ASP84 2.4 22.4 1.0
CE1 A:HIS252 3.1 25.5 1.0
CG A:ASN116 3.2 27.9 1.0
CE1 A:HIS217 3.2 22.6 1.0
CG A:ASP84 3.2 24.6 1.0
CD2 A:HIS217 3.2 24.0 1.0
OD1 A:ASP84 3.5 25.5 1.0
MN A:MN601 3.5 47.0 1.0
CG A:HIS252 3.5 23.1 1.0
ND2 A:ASN116 3.5 27.9 1.0
PB A:A121602 3.5 34.1 1.0
O2B A:A121602 3.8 35.5 1.0
CA A:HIS252 3.8 21.3 1.0
CB A:HIS252 4.0 22.2 1.0
CD2 A:HIS117 4.0 26.0 1.0
OD1 A:ASP41 4.2 21.5 1.0
NE2 A:HIS252 4.3 26.9 1.0
O A:HIS252 4.3 25.8 1.0
ND1 A:HIS217 4.3 22.1 1.0
CG A:HIS217 4.4 26.6 1.0
CB A:ASP84 4.5 22.2 1.0
CD2 A:HIS252 4.5 28.2 1.0
C3A A:A121602 4.5 35.5 1.0
N A:ASN116 4.5 25.8 1.0
O3B A:A121602 4.5 30.9 1.0
C A:HIS252 4.6 21.5 1.0
CB A:ASN116 4.6 28.4 1.0
NE2 A:HIS117 4.7 27.3 1.0
N A:HIS252 4.8 20.3 1.0

Manganese binding site 2 out of 8 in 1hpu

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Manganese binding site 2 out of 8 in the 5'-Nucleotidase (Closed Form), Complex with Ampcp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 5'-Nucleotidase (Closed Form), Complex with Ampcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:47.0
occ:1.00
OD1 A:ASP41 2.1 21.5 1.0
O A:HOH1669 2.2 25.6 1.0
NE2 A:HIS43 2.3 27.2 1.0
OE1 A:GLN254 2.3 28.9 1.0
OD2 A:ASP84 2.4 22.4 1.0
CE1 A:HIS43 3.2 25.4 1.0
CG A:ASP41 3.2 25.1 1.0
CD2 A:HIS43 3.3 25.2 1.0
CD A:GLN254 3.3 27.0 1.0
CG A:ASP84 3.4 24.6 1.0
MN A:MN600 3.5 26.1 1.0
CB A:ASP84 3.6 22.2 1.0
O2B A:A121602 3.7 35.5 1.0
CB A:ASP41 3.8 21.9 1.0
CG A:GLN254 3.9 24.8 1.0
CE1 A:HIS217 4.2 22.6 1.0
O1B A:A121602 4.2 28.5 1.0
OD2 A:ASP41 4.2 22.4 1.0
O A:HIS252 4.2 25.8 1.0
ND1 A:HIS43 4.3 23.8 1.0
NE2 A:HIS217 4.4 25.3 1.0
NE2 A:GLN254 4.4 25.3 1.0
CG A:HIS43 4.4 26.3 1.0
CA A:ASP41 4.4 19.0 1.0
CA A:HIS252 4.5 21.3 1.0
OD1 A:ASP84 4.5 25.5 1.0
PB A:A121602 4.5 34.1 1.0
CD2 A:HIS117 4.6 26.0 1.0
C A:HIS252 4.8 21.5 1.0
N A:HIS252 4.9 20.3 1.0

Manganese binding site 3 out of 8 in 1hpu

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Manganese binding site 3 out of 8 in the 5'-Nucleotidase (Closed Form), Complex with Ampcp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 5'-Nucleotidase (Closed Form), Complex with Ampcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn600

b:24.0
occ:1.00
O1B B:A121603 2.2 27.1 1.0
OD1 B:ASN116 2.2 25.0 1.0
ND1 B:HIS252 2.2 23.5 1.0
O B:HOH1690 2.2 23.3 1.0
NE2 B:HIS217 2.3 23.6 1.0
OD2 B:ASP84 2.3 21.7 1.0
CE1 B:HIS252 3.0 26.9 1.0
CG B:ASP84 3.2 23.5 1.0
CE1 B:HIS217 3.2 23.0 1.0
CG B:ASN116 3.2 26.4 1.0
CD2 B:HIS217 3.2 22.7 1.0
CG B:HIS252 3.4 25.3 1.0
MN B:MN601 3.4 45.4 1.0
PB B:A121603 3.5 27.9 1.0
OD1 B:ASP84 3.6 24.1 1.0
ND2 B:ASN116 3.6 22.5 1.0
CA B:HIS252 3.8 22.9 1.0
CB B:HIS252 3.9 22.0 1.0
O2B B:A121603 3.9 29.6 1.0
CD2 B:HIS117 4.1 26.0 1.0
OD1 B:ASP41 4.2 19.1 1.0
NE2 B:HIS252 4.2 26.0 1.0
O B:HIS252 4.2 21.9 1.0
ND1 B:HIS217 4.3 23.0 1.0
CG B:HIS217 4.4 22.4 1.0
CD2 B:HIS252 4.4 27.7 1.0
CB B:ASP84 4.4 19.9 1.0
C3A B:A121603 4.5 31.4 1.0
O3B B:A121603 4.5 28.6 1.0
C B:HIS252 4.5 23.1 1.0
CB B:ASN116 4.6 25.1 1.0
N B:ASN116 4.6 25.7 1.0
NE2 B:HIS117 4.7 24.6 1.0
N B:HIS252 4.9 22.1 1.0

Manganese binding site 4 out of 8 in 1hpu

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Manganese binding site 4 out of 8 in the 5'-Nucleotidase (Closed Form), Complex with Ampcp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of 5'-Nucleotidase (Closed Form), Complex with Ampcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn601

b:45.4
occ:1.00
OD1 B:ASP41 2.1 19.1 1.0
O B:HOH1690 2.1 23.3 1.0
OE1 B:GLN254 2.2 31.6 1.0
NE2 B:HIS43 2.3 20.1 1.0
OD2 B:ASP84 2.5 21.7 1.0
CG B:ASP41 3.2 18.8 1.0
CD B:GLN254 3.2 29.0 1.0
CE1 B:HIS43 3.2 19.5 1.0
CD2 B:HIS43 3.3 20.8 1.0
CG B:ASP84 3.4 23.5 1.0
MN B:MN600 3.4 24.0 1.0
CB B:ASP84 3.6 19.9 1.0
O2B B:A121603 3.7 29.6 1.0
CG B:GLN254 3.7 26.1 1.0
CB B:ASP41 3.7 17.4 1.0
O1B B:A121603 4.1 27.1 1.0
O B:HOH1723 4.1 39.4 1.0
O B:HIS252 4.2 21.9 1.0
CE1 B:HIS217 4.2 23.0 1.0
OD2 B:ASP41 4.2 19.6 1.0
NE2 B:GLN254 4.3 27.3 1.0
NE2 B:HIS217 4.3 23.6 1.0
ND1 B:HIS43 4.4 21.0 1.0
CA B:ASP41 4.4 19.2 1.0
CG B:HIS43 4.5 20.3 1.0
CD2 B:HIS117 4.5 26.0 1.0
PB B:A121603 4.5 27.9 1.0
CA B:HIS252 4.5 22.9 1.0
OD1 B:ASP84 4.6 24.1 1.0
C B:HIS252 4.8 23.1 1.0
ND1 B:HIS252 4.9 23.5 1.0
N B:HIS252 5.0 22.1 1.0
O B:HOH1768 5.0 36.7 1.0

Manganese binding site 5 out of 8 in 1hpu

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Manganese binding site 5 out of 8 in the 5'-Nucleotidase (Closed Form), Complex with Ampcp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of 5'-Nucleotidase (Closed Form), Complex with Ampcp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn600

b:20.0
occ:1.00
OD1 C:ASN116 2.2 19.9 1.0
O1B C:A121604 2.2 24.7 1.0
NE2 C:HIS217 2.2 18.4 1.0
O C:HOH1681 2.3 19.7 1.0
OD2 C:ASP84 2.3 19.6 1.0
ND1 C:HIS252 2.3 17.6 1.0
CE1 C:HIS252 3.0 22.4 1.0
CE1 C:HIS217 3.2 17.4 1.0
CG C:ASP84 3.2 18.9 1.0
CG C:ASN116 3.2 19.6 1.0
CD2 C:HIS217 3.3 19.8 1.0
CG C:HIS252 3.4 20.3 1.0
MN C:MN601 3.5 30.4 1.0
OD1 C:ASP84 3.5 21.6 1.0
PB C:A121604 3.5 24.5 1.0
ND2 C:ASN116 3.6 20.9 1.0
CA C:HIS252 3.8 19.9 1.0
O2B C:A121604 3.9 23.2 1.0
CB C:HIS252 3.9 20.9 1.0
CD2 C:HIS117 4.0 23.2 1.0
O C:HOH1885 4.1 36.8 1.0
OD2 C:ASP41 4.1 18.8 1.0
NE2 C:HIS252 4.2 19.5 1.0
O C:HIS252 4.3 21.1 1.0
ND1 C:HIS217 4.3 19.4 1.0
CG C:HIS217 4.4 19.1 1.0
CD2 C:HIS252 4.5 19.4 1.0
CB C:ASP84 4.5 20.5 1.0
O3B C:A121604 4.5 25.7 1.0
N C:ASN116 4.5 19.9 1.0
C C:HIS252 4.6 21.1 1.0
CB C:ASN116 4.6 19.3 1.0
C3A C:A121604 4.6 27.6 1.0
NE2 C:HIS117 4.7 28.4 1.0
N C:HIS252 4.8 18.7 1.0

Manganese binding site 6 out of 8 in 1hpu

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Manganese binding site 6 out of 8 in the 5'-Nucleotidase (Closed Form), Complex with Ampcp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of 5'-Nucleotidase (Closed Form), Complex with Ampcp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn601

b:30.4
occ:1.00
OD2 C:ASP41 2.1 18.8 1.0
O C:HOH1681 2.2 19.7 1.0
OE1 C:GLN254 2.2 24.2 1.0
NE2 C:HIS43 2.2 20.6 1.0
OD2 C:ASP84 2.3 19.6 1.0
O C:HOH1885 2.4 36.8 1.0
CE1 C:HIS43 3.0 22.8 1.0
CG C:ASP41 3.3 20.2 1.0
CD C:GLN254 3.3 24.9 1.0
CG C:ASP84 3.3 18.9 1.0
CD2 C:HIS43 3.3 23.2 1.0
MN C:MN600 3.5 20.0 1.0
CB C:ASP84 3.5 20.5 1.0
CB C:ASP41 3.8 20.7 1.0
CG C:GLN254 3.9 24.2 1.0
O2B C:A121604 3.9 23.2 1.0
O1B C:A121604 4.1 24.7 1.0
ND1 C:HIS43 4.2 20.5 1.0
CE1 C:HIS217 4.2 17.4 1.0
CD2 C:HIS117 4.3 23.2 1.0
OD1 C:ASP41 4.3 20.6 1.0
O C:HIS252 4.3 21.1 1.0
NE2 C:GLN254 4.4 24.2 1.0
CG C:HIS43 4.4 21.8 1.0
NE2 C:HIS217 4.4 18.4 1.0
O C:HOH1788 4.4 34.3 1.0
OD1 C:ASP84 4.4 21.6 1.0
CA C:ASP41 4.5 18.4 1.0
PB C:A121604 4.5 24.5 1.0
CA C:HIS252 4.6 19.9 1.0
NE2 C:HIS117 4.8 28.4 1.0
C C:HIS252 4.9 21.1 1.0
O3B C:A121604 4.9 25.7 1.0

Manganese binding site 7 out of 8 in 1hpu

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Manganese binding site 7 out of 8 in the 5'-Nucleotidase (Closed Form), Complex with Ampcp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of 5'-Nucleotidase (Closed Form), Complex with Ampcp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn600

b:22.5
occ:1.00
OD1 D:ASN116 2.2 20.6 1.0
O D:HOH1652 2.2 20.2 1.0
O1B D:A121605 2.3 27.5 1.0
ND1 D:HIS252 2.3 24.2 1.0
OD2 D:ASP84 2.3 19.0 1.0
NE2 D:HIS217 2.3 23.6 1.0
CE1 D:HIS252 3.0 25.9 1.0
CG D:ASN116 3.2 22.3 1.0
CG D:ASP84 3.2 23.6 1.0
CD2 D:HIS217 3.3 23.6 1.0
CE1 D:HIS217 3.3 20.6 1.0
MN D:MN601 3.4 36.7 1.0
CG D:HIS252 3.5 23.8 1.0
OD1 D:ASP84 3.5 20.2 1.0
PB D:A121605 3.6 27.8 1.0
ND2 D:ASN116 3.6 23.0 1.0
O2B D:A121605 3.8 27.8 1.0
CA D:HIS252 3.8 23.1 1.0
CB D:HIS252 4.0 24.5 1.0
CD2 D:HIS117 4.0 22.7 1.0
OD2 D:ASP41 4.1 21.3 1.0
O D:HOH1812 4.2 37.1 1.0
NE2 D:HIS252 4.2 23.2 1.0
O D:HIS252 4.3 23.7 1.0
ND1 D:HIS217 4.4 21.8 1.0
CG D:HIS217 4.4 23.2 1.0
CD2 D:HIS252 4.5 22.6 1.0
CB D:ASP84 4.5 19.2 1.0
O3B D:A121605 4.5 28.1 1.0
CB D:ASN116 4.6 21.9 1.0
N D:ASN116 4.6 21.1 1.0
C D:HIS252 4.6 21.8 1.0
C3A D:A121605 4.6 32.8 1.0
NE2 D:HIS117 4.7 23.7 1.0
N D:HIS252 4.9 21.3 1.0

Manganese binding site 8 out of 8 in 1hpu

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Manganese binding site 8 out of 8 in the 5'-Nucleotidase (Closed Form), Complex with Ampcp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of 5'-Nucleotidase (Closed Form), Complex with Ampcp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn601

b:36.7
occ:1.00
OD2 D:ASP41 2.1 21.3 1.0
O D:HOH1652 2.2 20.2 1.0
NE2 D:HIS43 2.2 20.6 1.0
OD2 D:ASP84 2.3 19.0 1.0
OE1 D:GLN254 2.3 24.2 1.0
O D:HOH1812 2.5 37.1 1.0
CE1 D:HIS43 3.0 21.4 1.0
CG D:ASP41 3.2 19.4 1.0
CG D:ASP84 3.2 23.6 1.0
CD D:GLN254 3.3 23.4 1.0
CD2 D:HIS43 3.4 17.6 1.0
MN D:MN600 3.4 22.5 1.0
CB D:ASP84 3.5 19.2 1.0
CB D:ASP41 3.7 20.5 1.0
O2B D:A121605 3.8 27.8 1.0
CG D:GLN254 3.9 24.7 1.0
O1B D:A121605 4.2 27.5 1.0
ND1 D:HIS43 4.2 20.2 1.0
CE1 D:HIS217 4.2 20.6 1.0
OD1 D:ASP41 4.3 21.3 1.0
O D:HIS252 4.3 23.7 1.0
NE2 D:HIS217 4.3 23.6 1.0
CD2 D:HIS117 4.3 22.7 1.0
O D:HOH1795 4.3 33.9 1.0
OD1 D:ASP84 4.4 20.2 1.0
NE2 D:GLN254 4.4 23.0 1.0
CG D:HIS43 4.4 17.3 1.0
CA D:ASP41 4.5 19.5 1.0
PB D:A121605 4.6 27.8 1.0
CA D:HIS252 4.6 23.1 1.0
C D:HIS252 4.9 21.8 1.0
NE2 D:HIS117 4.9 23.7 1.0

Reference:

T.Knofel, N.Strater. Mechanism of Hydrolysis of Phosphate Esters By the Dimetal Center of 5'-Nucleotidase Based on Crystal Structures. J.Mol.Biol. V. 309 239 2001.
ISSN: ISSN 0022-2836
PubMed: 11491293
DOI: 10.1006/JMBI.2001.4656
Page generated: Tue Dec 15 03:48:58 2020

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