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Manganese in PDB 6ah7: D45W/H226G Mutant of Marine Bacterial Prolidase

Enzymatic activity of D45W/H226G Mutant of Marine Bacterial Prolidase

All present enzymatic activity of D45W/H226G Mutant of Marine Bacterial Prolidase:
3.4.13.9;

Protein crystallography data

The structure of D45W/H226G Mutant of Marine Bacterial Prolidase, PDB code: 6ah7 was solved by Y.Jian, X.Yunzhu, L.Lijuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.29 / 2.38
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.632, 183.632, 371.306, 90.00, 90.00, 120.00
R / Rfree (%) 23.3 / 26.9

Other elements in 6ah7:

The structure of D45W/H226G Mutant of Marine Bacterial Prolidase also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the D45W/H226G Mutant of Marine Bacterial Prolidase (pdb code 6ah7). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the D45W/H226G Mutant of Marine Bacterial Prolidase, PDB code: 6ah7:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 6ah7

Go back to Manganese Binding Sites List in 6ah7
Manganese binding site 1 out of 8 in the D45W/H226G Mutant of Marine Bacterial Prolidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of D45W/H226G Mutant of Marine Bacterial Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:46.1
occ:1.00
 OD2 A:ASP255 2.1 41.2 1.0
NE2 A:HIS336 2.3 37.5 1.0
OE2 A:GLU420 2.3 46.2 1.0
OE1 A:GLU381 2.8 44.3 1.0
CE1 A:HIS336 3.0 36.1 1.0
CG A:ASP255 3.1 40.7 1.0
CD A:GLU420 3.2 45.3 1.0
MN A:MN502 3.2 50.1 1.0
CD A:GLU381 3.3 41.7 1.0
CD2 A:HIS336 3.3 38.0 1.0
OE1 A:GLU420 3.4 44.6 1.0
OE2 A:GLU381 3.5 40.9 1.0
OD1 A:ASP255 3.7 38.2 1.0
OG1 A:THR379 3.8 34.3 1.0
CG2 A:THR379 3.8 32.5 1.0
CB A:THR379 4.0 35.8 1.0
ND1 A:HIS336 4.1 43.1 1.0
CB A:ASP255 4.3 38.2 1.0
CG A:HIS336 4.3 40.6 1.0
CG A:GLU381 4.5 40.5 1.0
CG A:GLU420 4.6 39.2 1.0
CE1 A:HIS343 4.6 41.8 0.4
NE2 A:HIS343 4.8 40.0 0.4
O A:ASP255 4.9 35.2 1.0

Manganese binding site 2 out of 8 in 6ah7

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Manganese binding site 2 out of 8 in the D45W/H226G Mutant of Marine Bacterial Prolidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of D45W/H226G Mutant of Marine Bacterial Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:50.1
occ:1.00
 OD1 A:ASP255 2.1 38.2 1.0
OE1 A:GLU420 2.3 44.6 1.0
OD1 A:ASP244 2.4 38.6 1.0
OD2 A:ASP244 2.4 39.8 1.0
CG A:ASP244 2.7 38.9 1.0
CG A:ASP255 2.9 40.7 1.0
OD2 A:ASP255 3.1 41.2 1.0
MN A:MN501 3.2 46.1 1.0
CD A:GLU420 3.2 45.3 1.0
OE2 A:GLU420 3.5 46.2 1.0
OG1 A:THR257 3.6 36.3 1.0
OH A:TYR212 3.8 32.4 1.0
OE2 A:GLU381 4.1 40.9 1.0
CZ A:TYR212 4.2 34.1 1.0
CB A:ASP244 4.2 35.9 1.0
CB A:ASP255 4.3 38.2 1.0
C A:ASP255 4.5 33.9 1.0
CE2 A:TYR212 4.5 38.5 1.0
O A:ASP255 4.5 35.2 1.0
CG A:GLU420 4.6 39.2 1.0
CA A:ASP255 4.7 32.8 1.0
NE A:ARG418 4.9 41.6 1.0
N A:ILE256 4.9 32.0 1.0
CD A:GLU381 4.9 41.7 1.0
CE1 A:TYR212 4.9 34.8 1.0
NH2 A:ARG418 5.0 36.1 1.0

Manganese binding site 3 out of 8 in 6ah7

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Manganese binding site 3 out of 8 in the D45W/H226G Mutant of Marine Bacterial Prolidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of D45W/H226G Mutant of Marine Bacterial Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:50.5
occ:1.00
 OE2 B:GLU420 2.1 38.5 1.0
OD2 B:ASP255 2.1 44.1 1.0
O B:HOH625 2.1 45.5 1.0
NE2 B:HIS336 2.3 37.3 1.0
OE2 B:GLU381 2.7 43.6 1.0
CE1 B:HIS336 3.0 38.8 1.0
CG B:ASP255 3.1 38.3 1.0
CD B:GLU420 3.2 37.8 1.0
MN B:MN502 3.3 48.6 1.0
CD B:GLU381 3.3 45.2 1.0
CD2 B:HIS336 3.4 37.7 1.0
OE1 B:GLU381 3.5 45.0 1.0
OD1 B:ASP255 3.6 37.9 1.0
OE1 B:GLU420 3.6 42.7 1.0
CG2 B:THR379 3.7 33.5 1.0
OG1 B:THR379 3.8 38.8 1.0
CB B:THR379 3.9 37.1 1.0
ND1 B:HIS336 4.1 40.9 1.0
CB B:ASP255 4.2 38.0 1.0
CG B:HIS336 4.4 39.2 1.0
CG B:GLU420 4.4 38.5 1.0
CG B:GLU381 4.5 39.3 1.0
NE2 B:HIS343 4.6 41.1 0.5
O B:HOH703 4.7 62.5 1.0
O B:ASP255 4.9 40.8 1.0

Manganese binding site 4 out of 8 in 6ah7

Go back to Manganese Binding Sites List in 6ah7
Manganese binding site 4 out of 8 in the D45W/H226G Mutant of Marine Bacterial Prolidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of D45W/H226G Mutant of Marine Bacterial Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:48.6
occ:1.00
 OD1 B:ASP255 2.1 37.9 1.0
OD1 B:ASP244 2.3 39.2 1.0
O B:HOH625 2.3 45.5 1.0
OE1 B:GLU420 2.5 42.7 1.0
OD2 B:ASP244 2.6 40.5 1.0
CG B:ASP244 2.8 41.6 1.0
CG B:ASP255 2.9 38.3 1.0
O B:HOH703 3.1 62.5 1.0
OD2 B:ASP255 3.1 44.1 1.0
CD B:GLU420 3.3 37.8 1.0
MN B:MN501 3.3 50.5 1.0
OE2 B:GLU420 3.3 38.5 1.0
OG1 B:THR257 3.6 34.7 1.0
OH B:TYR212 3.7 37.9 1.0
OE1 B:GLU381 4.1 45.0 1.0
CZ B:TYR212 4.2 37.6 1.0
CB B:ASP244 4.3 39.8 1.0
CB B:ASP255 4.3 38.0 1.0
O B:HOH700 4.4 53.5 1.0
CE2 B:TYR212 4.4 40.5 1.0
C B:ASP255 4.5 37.7 1.0
O B:ASP255 4.7 40.8 1.0
CA B:ASP255 4.7 33.2 1.0
CG B:GLU420 4.7 38.5 1.0
N B:ILE256 4.7 33.8 1.0
CD B:GLU381 4.8 45.2 1.0
O B:ILE256 4.8 39.1 1.0
CE1 B:TYR212 4.9 33.6 1.0
NE B:ARG418 4.9 42.1 1.0
OE2 B:GLU381 4.9 43.6 1.0
C B:ILE256 5.0 39.3 1.0

Manganese binding site 5 out of 8 in 6ah7

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Manganese binding site 5 out of 8 in the D45W/H226G Mutant of Marine Bacterial Prolidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of D45W/H226G Mutant of Marine Bacterial Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:52.8
occ:1.00
 NE2 C:HIS336 2.2 44.5 1.0
OE2 C:GLU420 2.2 41.4 1.0
OD2 C:ASP255 2.3 45.3 1.0
OE1 C:GLU381 2.7 52.8 1.0
CE1 C:HIS336 2.9 46.5 1.0
CD C:GLU381 2.9 50.6 1.0
OE2 C:GLU381 2.9 45.6 1.0
MN C:MN502 3.1 53.9 1.0
CD C:GLU420 3.2 47.5 1.0
CG C:ASP255 3.3 44.3 1.0
CD2 C:HIS336 3.3 45.3 1.0
OE1 C:GLU420 3.6 51.2 1.0
CG2 C:THR379 3.7 40.6 1.0
OD1 C:ASP255 3.8 43.8 1.0
CG C:GLU381 3.9 45.7 1.0
CB C:THR379 4.1 37.0 1.0
ND1 C:HIS336 4.1 49.6 1.0
OG1 C:THR379 4.1 44.4 1.0
CG C:HIS336 4.3 44.0 1.0
CE1 C:HIS343 4.5 46.9 0.4
CB C:ASP255 4.5 43.1 1.0
CG C:GLU420 4.5 47.8 1.0
O C:HOH692 4.9 46.8 1.0
O C:HOH660 4.9 59.3 1.0
CG1 C:VAL342 5.0 43.8 1.0

Manganese binding site 6 out of 8 in 6ah7

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Manganese binding site 6 out of 8 in the D45W/H226G Mutant of Marine Bacterial Prolidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of D45W/H226G Mutant of Marine Bacterial Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn502

b:53.9
occ:1.00
 OE1 C:GLU420 2.2 51.2 1.0
OD1 C:ASP255 2.3 43.8 1.0
OD2 C:ASP244 2.3 50.4 1.0
OD1 C:ASP244 2.4 47.4 1.0
CG C:ASP244 2.7 45.9 1.0
CG C:ASP255 3.0 44.3 1.0
CD C:GLU420 3.0 47.5 1.0
OD2 C:ASP255 3.1 45.3 1.0
MN C:MN501 3.1 52.8 1.0
OE2 C:GLU420 3.2 41.4 1.0
OE1 C:GLU381 3.2 52.8 1.0
OG1 C:THR257 3.6 42.7 1.0
O C:HOH665 4.0 49.8 1.0
OH C:TYR212 4.1 38.6 1.0
CB C:ASP244 4.2 43.0 1.0
CD C:GLU381 4.3 50.6 1.0
O C:HOH692 4.4 46.8 1.0
CB C:ASP255 4.5 43.1 1.0
CG C:GLU420 4.5 47.8 1.0
CZ C:TYR212 4.5 37.8 1.0
NH2 C:ARG418 4.6 45.1 1.0
CE2 C:TYR212 4.7 42.5 1.0
C C:ASP255 4.7 43.9 1.0
O C:ASP255 4.8 48.5 1.0
NE C:ARG418 4.9 49.2 1.0
N C:ILE256 4.9 41.7 1.0
CB C:GLU420 4.9 47.6 1.0
CA C:ASP255 4.9 41.6 1.0
OE2 C:GLU381 5.0 45.6 1.0

Manganese binding site 7 out of 8 in 6ah7

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Manganese binding site 7 out of 8 in the D45W/H226G Mutant of Marine Bacterial Prolidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of D45W/H226G Mutant of Marine Bacterial Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:44.1
occ:1.00
 OE2 D:GLU420 1.5 44.3 1.0
OE2 D:GLU381 2.1 43.2 1.0
NE2 D:HIS336 2.1 37.4 1.0
OD2 D:ASP255 2.1 40.4 1.0
CD D:GLU381 2.3 46.2 1.0
OE1 D:GLU381 2.3 43.7 1.0
CD D:GLU420 2.8 39.2 1.0
O D:HOH601 2.8 58.7 1.0
CE1 D:HIS336 2.8 39.1 1.0
CG D:ASP255 3.1 40.2 1.0
MN D:MN502 3.2 50.4 1.0
CD2 D:HIS336 3.2 35.7 1.0
OE1 D:GLU420 3.4 42.4 1.0
CG D:GLU381 3.6 36.9 1.0
OD1 D:ASP255 3.6 35.9 1.0
OG1 D:THR379 3.7 30.8 1.0
CG2 D:THR379 3.9 36.4 1.0
ND1 D:HIS336 4.0 39.9 1.0
CG D:GLU420 4.0 40.1 1.0
CB D:THR379 4.1 35.9 1.0
CG D:HIS336 4.2 37.9 1.0
CB D:ASP255 4.3 37.1 1.0
CE1 D:HIS343 4.5 38.1 0.5
O D:HOH646 4.8 49.3 1.0
NE2 D:HIS343 4.8 39.0 0.5
CG1 D:VAL342 4.9 43.6 1.0
CB D:GLU381 4.9 38.9 1.0

Manganese binding site 8 out of 8 in 6ah7

Go back to Manganese Binding Sites List in 6ah7
Manganese binding site 8 out of 8 in the D45W/H226G Mutant of Marine Bacterial Prolidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of D45W/H226G Mutant of Marine Bacterial Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn502

b:50.4
occ:1.00
 OE1 D:GLU420 1.8 42.4 1.0
OD1 D:ASP255 2.1 35.9 1.0
O D:HOH601 2.3 58.7 1.0
OD2 D:ASP244 2.4 41.1 1.0
OD1 D:ASP244 2.6 40.1 1.0
CD D:GLU420 2.7 39.2 1.0
CG D:ASP244 2.8 39.7 1.0
CG D:ASP255 2.9 40.2 1.0
OE2 D:GLU420 2.9 44.3 1.0
OD2 D:ASP255 3.0 40.4 1.0
MN D:MN501 3.2 44.1 1.0
OE1 D:GLU381 3.4 43.7 1.0
OG1 D:THR257 3.5 37.1 1.0
CD D:GLU381 3.9 46.2 1.0
OH D:TYR212 4.0 39.8 1.0
CG D:GLU420 4.1 40.1 1.0
CB D:ASP255 4.3 37.1 1.0
CG D:GLU381 4.3 36.9 1.0
CB D:ASP244 4.3 35.5 1.0
CZ D:TYR212 4.4 39.3 1.0
O D:ASP255 4.5 37.5 1.0
C D:ASP255 4.5 39.4 1.0
CE2 D:TYR212 4.6 40.4 1.0
CB D:GLU420 4.7 39.7 1.0
OE2 D:GLU381 4.7 43.2 1.0
CA D:ASP255 4.7 34.8 1.0
NE D:ARG418 4.8 43.2 1.0
N D:ILE256 4.9 36.9 1.0
CB D:THR257 5.0 40.3 1.0

Reference:

Y.Jian, X.Yunzhu. D45W/H226G Mutant of Marine Bacterial Prolidase To Be Published.
Page generated: Sun Oct 6 03:49:52 2024

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