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Manganese in PDB 7e5c: Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I

Enzymatic activity of Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I

All present enzymatic activity of Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I:
3.4.13.9;

Protein crystallography data

The structure of Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I, PDB code: 7e5c was solved by Y.Jian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.45 / 2.22
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 182.965, 182.965, 372.079, 90, 90, 120
R / Rfree (%) 20.3 / 23.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I (pdb code 7e5c). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I, PDB code: 7e5c:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 7e5c

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Manganese binding site 1 out of 8 in the Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:71.6
occ:1.00
 OD1 A:ASP255 2.2 43.8 1.0
OD2 A:ASP244 2.3 44.4 1.0
OE1 A:GLU420 2.4 47.1 1.0
OD1 A:ASP244 2.4 45.8 1.0
CG A:ASP244 2.7 42.9 1.0
CG A:ASP255 3.0 43.4 1.0
CD A:GLU420 3.2 46.1 1.0
MN A:MN502 3.2 71.3 1.0
OD2 A:ASP255 3.3 48.3 1.0
OE2 A:GLU420 3.4 45.4 1.0
OG1 A:THR257 3.6 38.5 1.0
OE1 A:GLU381 3.8 57.9 1.0
OH A:TYR212 4.0 42.5 1.0
CB A:ASP244 4.2 41.6 1.0
CZ A:TYR212 4.4 44.5 1.0
CB A:ASP255 4.4 43.7 1.0
C A:ASP255 4.6 40.2 1.0
CE2 A:TYR212 4.6 46.2 1.0
CD A:GLU381 4.6 54.0 1.0
CG A:GLU420 4.6 43.6 1.0
O A:ASP255 4.7 40.7 1.0
OE2 A:GLU381 4.8 57.8 1.0
NE A:ARG418 4.8 44.8 1.0
CA A:ASP255 4.8 41.4 1.0
NH2 A:ARG418 4.8 44.6 1.0
N A:ILE256 4.9 41.0 1.0
CA A:ASP244 5.0 40.3 1.0
CB A:THR257 5.0 39.1 1.0

Manganese binding site 2 out of 8 in 7e5c

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Manganese binding site 2 out of 8 in the Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:71.3
occ:1.00
 OD2 A:ASP255 2.2 48.3 1.0
OE2 A:GLU420 2.3 45.4 1.0
NE2 A:HIS336 2.5 42.3 1.0
OE2 A:GLU381 2.5 57.8 1.0
CG A:ASP255 3.1 43.4 1.0
CE1 A:HIS336 3.1 42.1 1.0
MN A:MN501 3.2 71.6 1.0
CD A:GLU381 3.3 54.0 1.0
CD A:GLU420 3.3 46.1 1.0
OE1 A:GLU381 3.4 57.9 1.0
OD1 A:ASP255 3.5 43.8 1.0
CD2 A:HIS336 3.6 43.6 1.0
OE1 A:GLU420 3.6 47.1 1.0
OG1 A:THR379 3.7 41.3 1.0
CG2 A:THR379 3.8 41.3 1.0
CB A:THR379 3.9 41.7 1.0
CB A:ASP255 4.3 43.7 1.0
ND1 A:HIS336 4.3 43.4 1.0
CG A:HIS336 4.5 45.8 1.0
CG A:GLU381 4.6 54.5 1.0
CG A:GLU420 4.6 43.6 1.0
O A:ASP255 5.0 40.7 1.0

Manganese binding site 3 out of 8 in 7e5c

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Manganese binding site 3 out of 8 in the Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:68.1
occ:1.00
 OD2 B:ASP255 2.1 50.9 1.0
OE2 B:GLU420 2.4 46.0 1.0
NE2 B:HIS336 2.4 47.0 1.0
OE2 B:GLU381 2.5 53.1 1.0
CE1 B:HIS336 3.0 44.6 1.0
CG B:ASP255 3.1 42.6 1.0
MN B:MN502 3.1 71.6 1.0
CD B:GLU381 3.3 51.6 1.0
CD B:GLU420 3.3 46.2 1.0
OE1 B:GLU381 3.4 56.4 1.0
OD1 B:ASP255 3.5 41.8 1.0
CD2 B:HIS336 3.6 45.2 1.0
OE1 B:GLU420 3.6 49.2 1.0
OG1 B:THR379 3.8 39.1 1.0
CG2 B:THR379 3.9 41.0 1.0
CB B:THR379 4.1 41.1 1.0
ND1 B:HIS336 4.2 49.1 1.0
CB B:ASP255 4.3 42.7 1.0
CG B:HIS336 4.5 47.2 1.0
CG B:GLU381 4.6 49.4 1.0
CG B:GLU420 4.7 45.7 1.0
O B:ASP255 5.0 40.4 1.0

Manganese binding site 4 out of 8 in 7e5c

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Manganese binding site 4 out of 8 in the Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:71.6
occ:1.00
 OD1 B:ASP255 2.2 41.8 1.0
OE1 B:GLU420 2.4 49.2 1.0
OD2 B:ASP244 2.4 40.4 1.0
OD1 B:ASP244 2.5 44.4 1.0
CG B:ASP244 2.8 43.4 1.0
CG B:ASP255 3.0 42.6 1.0
MN B:MN501 3.1 68.1 1.0
OD2 B:ASP255 3.2 50.9 1.0
CD B:GLU420 3.3 46.2 1.0
OE2 B:GLU420 3.4 46.0 1.0
OG1 B:THR257 3.7 37.8 1.0
OE1 B:GLU381 3.8 56.4 1.0
OH B:TYR212 4.0 40.4 1.0
CB B:ASP244 4.3 40.9 1.0
CZ B:TYR212 4.3 40.7 1.0
CB B:ASP255 4.4 42.7 1.0
CD B:GLU381 4.6 51.6 1.0
CE2 B:TYR212 4.6 42.3 1.0
OE2 B:GLU381 4.6 53.1 1.0
C B:ASP255 4.6 39.8 1.0
O B:ASP255 4.7 40.4 1.0
CG B:GLU420 4.7 45.7 1.0
NE B:ARG418 4.8 48.4 1.0
CA B:ASP255 4.8 42.4 1.0
NH2 B:ARG418 4.9 50.6 1.0
N B:ILE256 4.9 41.6 1.0

Manganese binding site 5 out of 8 in 7e5c

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Manganese binding site 5 out of 8 in the Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:85.4
occ:1.00
 OE2 C:GLU420 2.3 45.7 1.0
OD2 C:ASP255 2.3 55.0 1.0
NE2 C:HIS336 2.4 56.2 1.0
OE2 C:GLU381 2.5 61.8 1.0
MN C:MN502 3.1 85.7 1.0
CE1 C:HIS336 3.1 53.6 1.0
CD C:GLU381 3.2 59.9 1.0
CG C:ASP255 3.2 47.4 1.0
CD C:GLU420 3.3 48.6 1.0
OE1 C:GLU381 3.3 58.9 1.0
CD2 C:HIS336 3.5 52.9 1.0
OE1 C:GLU420 3.6 53.8 1.0
OD1 C:ASP255 3.6 49.1 1.0
OG1 C:THR379 3.8 44.2 1.0
CG2 C:THR379 3.8 46.3 1.0
CB C:THR379 4.0 46.2 1.0
ND1 C:HIS336 4.2 54.2 1.0
CB C:ASP255 4.4 47.8 1.0
CG C:HIS336 4.5 52.8 1.0
CG C:GLU381 4.5 53.4 1.0
CG C:GLU420 4.6 50.8 1.0
O C:ASP255 5.0 48.1 1.0

Manganese binding site 6 out of 8 in 7e5c

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Manganese binding site 6 out of 8 in the Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn502

b:85.7
occ:1.00
 OD1 C:ASP255 2.2 49.1 1.0
OD2 C:ASP244 2.5 46.4 1.0
OE1 C:GLU420 2.5 53.8 1.0
OD1 C:ASP244 2.6 48.8 1.0
CG C:ASP244 2.9 46.4 1.0
CG C:ASP255 2.9 47.4 1.0
OD2 C:ASP255 3.0 55.0 1.0
MN C:MN501 3.1 85.4 1.0
CD C:GLU420 3.3 48.6 1.0
OE2 C:GLU420 3.3 45.7 1.0
OG1 C:THR257 3.9 44.7 1.0
OE1 C:GLU381 3.9 58.9 1.0
OH C:TYR212 4.0 42.1 1.0
CB C:ASP255 4.4 47.8 1.0
CB C:ASP244 4.4 43.8 1.0
CZ C:TYR212 4.4 43.1 1.0
CE2 C:TYR212 4.6 43.5 1.0
O C:ASP255 4.7 48.1 1.0
C C:ASP255 4.7 45.5 1.0
CD C:GLU381 4.7 59.9 1.0
CG C:GLU420 4.7 50.8 1.0
OE2 C:GLU381 4.8 61.8 1.0
CA C:ASP255 4.8 43.5 1.0
NE C:ARG418 4.9 53.6 1.0
NH2 C:ARG418 5.0 51.2 1.0

Manganese binding site 7 out of 8 in 7e5c

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Manganese binding site 7 out of 8 in the Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:64.0
occ:1.00
 OE2 D:GLU420 2.3 46.4 1.0
OD2 D:ASP255 2.3 47.7 1.0
NE2 D:HIS336 2.4 47.8 1.0
OE2 D:GLU381 2.5 53.7 1.0
CE1 D:HIS336 3.1 46.1 1.0
CG D:ASP255 3.1 43.4 1.0
MN D:MN502 3.2 67.8 1.0
CD D:GLU381 3.2 51.1 1.0
CD D:GLU420 3.3 43.0 1.0
OE1 D:GLU381 3.3 49.2 1.0
CD2 D:HIS336 3.5 44.5 1.0
OD1 D:ASP255 3.5 45.6 1.0
OE1 D:GLU420 3.6 44.9 1.0
OG1 D:THR379 3.8 38.9 1.0
CG2 D:THR379 3.8 42.0 1.0
CB D:THR379 4.0 41.9 1.0
ND1 D:HIS336 4.2 45.9 1.0
CB D:ASP255 4.3 43.7 1.0
CG D:HIS336 4.5 47.2 1.0
CG D:GLU381 4.6 50.5 1.0
CG D:GLU420 4.6 43.4 1.0
O D:ASP255 5.0 41.3 1.0

Manganese binding site 8 out of 8 in 7e5c

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Manganese binding site 8 out of 8 in the Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Bacterial Prolidase Mutant D45W/L225Y/H226L/H343I within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn502

b:67.8
occ:1.00
 OD1 D:ASP255 2.2 45.6 1.0
OD1 D:ASP244 2.3 43.0 1.0
OD2 D:ASP244 2.4 44.0 1.0
OE1 D:GLU420 2.5 44.9 1.0
CG D:ASP244 2.7 42.2 1.0
CG D:ASP255 3.0 43.4 1.0
MN D:MN501 3.2 64.0 1.0
OD2 D:ASP255 3.2 47.7 1.0
CD D:GLU420 3.3 43.0 1.0
OE2 D:GLU420 3.4 46.4 1.0
OG1 D:THR257 3.7 41.3 1.0
OE1 D:GLU381 3.9 49.2 1.0
OH D:TYR212 4.0 43.7 1.0
CB D:ASP244 4.2 41.8 1.0
O D:HOH683 4.2 60.5 1.0
O D:HOH694 4.3 55.6 1.0
CZ D:TYR212 4.3 42.5 1.0
CB D:ASP255 4.4 43.7 1.0
CE2 D:TYR212 4.5 42.9 1.0
C D:ASP255 4.6 41.3 1.0
O D:ASP255 4.7 41.3 1.0
CD D:GLU381 4.7 51.1 1.0
CG D:GLU420 4.7 43.4 1.0
CA D:ASP255 4.8 42.7 1.0
NH2 D:ARG418 4.9 46.3 1.0
OE2 D:GLU381 4.9 53.7 1.0
NE D:ARG418 4.9 43.5 1.0
N D:ILE256 4.9 41.4 1.0
CA D:ASP244 5.0 41.5 1.0

Reference:

Y.Jian, Y.Jian. N/A N/A.
Page generated: Sun Oct 6 08:29:13 2024

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