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Manganese in PDB 6ah8: Marine Bacterial Prolidase with Promiscuous Organophosphorus Hydrolase Activity

Enzymatic activity of Marine Bacterial Prolidase with Promiscuous Organophosphorus Hydrolase Activity

All present enzymatic activity of Marine Bacterial Prolidase with Promiscuous Organophosphorus Hydrolase Activity:
3.4.13.9;

Protein crystallography data

The structure of Marine Bacterial Prolidase with Promiscuous Organophosphorus Hydrolase Activity, PDB code: 6ah8 was solved by Y.Jian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.53 / 2.61
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 178.854, 178.854, 371.586, 90.00, 90.00, 120.00
R / Rfree (%) 22.6 / 27.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Marine Bacterial Prolidase with Promiscuous Organophosphorus Hydrolase Activity (pdb code 6ah8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Marine Bacterial Prolidase with Promiscuous Organophosphorus Hydrolase Activity, PDB code: 6ah8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 6ah8

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Manganese binding site 1 out of 8 in the Marine Bacterial Prolidase with Promiscuous Organophosphorus Hydrolase Activity


Mono view


Stereo pair view

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

b:64.5
occ:1.00
 OE2 A:GLU381 1.8 73.0 1.0
NE2 A:HIS336 2.1 56.2 1.0
OE2 A:GLU420 2.2 51.8 1.0
OD2 A:ASP255 2.4 49.7 1.0
CD A:GLU381 3.0 69.9 1.0
CE1 A:HIS336 3.0 52.5 1.0
CD2 A:HIS336 3.1 58.9 1.0
MN A:MN502 3.2 80.9 1.0
CD A:GLU420 3.2 55.1 1.0
CG A:ASP255 3.2 48.7 1.0
OE1 A:GLU420 3.5 54.9 1.0
OD1 A:ASP255 3.6 50.9 1.0
OE1 A:GLU381 3.7 77.0 1.0
CG2 A:THR379 3.8 61.9 1.0
OG1 A:THR379 4.0 58.4 1.0
CG A:GLU381 4.0 69.6 1.0
CB A:THR379 4.1 58.8 1.0
ND1 A:HIS336 4.1 53.0 1.0
CG A:HIS336 4.2 54.9 1.0
CB A:ASP255 4.4 51.1 1.0
CG A:GLU420 4.5 58.0 1.0
NE2 A:HIS343 4.7 53.1 1.0
CD2 A:HIS343 4.8 53.8 1.0
CG1 A:VAL342 4.9 44.8 1.0

Manganese binding site 2 out of 8 in 6ah8

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Manganese binding site 2 out of 8 in the Marine Bacterial Prolidase with Promiscuous Organophosphorus Hydrolase Activity


Mono view


Stereo pair view

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

b:80.9
occ:1.00
 OD1 A:ASP255 2.1 50.9 1.0
OE1 A:GLU420 2.2 54.9 1.0
OD1 A:ASP244 2.4 52.9 1.0
OD2 A:ASP244 2.4 50.6 1.0
CG A:ASP244 2.8 53.1 1.0
CD A:GLU420 3.0 55.1 1.0
CG A:ASP255 3.0 48.7 1.0
MN A:MN501 3.2 64.5 1.0
OE2 A:GLU420 3.2 51.8 1.0
OD2 A:ASP255 3.3 49.7 1.0
OG1 A:THR257 3.7 52.2 1.0
OE2 A:GLU381 3.8 73.0 1.0
OH A:TYR212 4.2 46.2 1.0
CB A:ASP244 4.3 53.4 1.0
CG A:GLU420 4.4 58.0 1.0
CB A:ASP255 4.4 51.1 1.0
CD A:GLU381 4.4 69.9 1.0
C A:ASP255 4.5 55.1 1.0
O A:ASP255 4.5 53.3 1.0
CZ A:TYR212 4.6 45.1 1.0
CE2 A:TYR212 4.7 44.1 1.0
OE1 A:GLU381 4.8 77.0 1.0
CA A:ASP255 4.8 53.1 1.0
N A:ILE256 4.8 54.9 1.0
NH2 A:ARG418 4.8 46.2 1.0
NE A:ARG418 4.9 50.8 1.0
CB A:GLU420 4.9 58.0 1.0

Manganese binding site 3 out of 8 in 6ah8

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Manganese binding site 3 out of 8 in the Marine Bacterial Prolidase with Promiscuous Organophosphorus Hydrolase Activity


Mono view


Stereo pair view

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

b:85.7
occ:1.00
 OD1 B:ASP255 2.1 53.7 1.0
OD2 B:ASP244 2.3 55.8 1.0
OD1 B:ASP244 2.3 54.5 1.0
CG B:ASP244 2.6 54.6 1.0
OE1 B:GLU420 2.6 59.2 1.0
CG B:ASP255 3.0 55.2 1.0
MN B:MN502 3.1 80.4 1.0
OD2 B:ASP255 3.2 56.3 1.0
CD B:GLU420 3.4 59.6 1.0
OE2 B:GLU420 3.5 61.0 1.0
OG1 B:THR257 3.7 59.2 1.0
OE1 B:GLU381 4.0 82.3 1.0
OH B:TYR212 4.0 49.7 1.0
CB B:ASP244 4.1 56.9 1.0
CZ B:TYR212 4.2 51.9 1.0
CE2 B:TYR212 4.3 51.3 1.0
CB B:ASP255 4.4 53.1 1.0
CD B:GLU381 4.7 80.2 1.0
C B:ASP255 4.7 51.9 1.0
O B:ASP255 4.9 52.8 1.0
CG B:GLU420 4.9 58.2 1.0
CA B:ASP255 4.9 51.2 1.0
NE B:ARG418 4.9 49.1 1.0
CA B:ASP244 5.0 55.6 1.0
CE1 B:TYR212 5.0 52.6 1.0

Manganese binding site 4 out of 8 in 6ah8

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Manganese binding site 4 out of 8 in the Marine Bacterial Prolidase with Promiscuous Organophosphorus Hydrolase Activity


Mono view


Stereo pair view

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

b:80.4
occ:1.00
 OE1 B:GLU381 1.8 82.3 1.0
OD2 B:ASP255 2.3 56.3 1.0
NE2 B:HIS336 2.3 63.1 1.0
OE2 B:GLU420 2.4 61.0 1.0
CD B:GLU381 3.0 80.2 1.0
MN B:MN501 3.1 85.7 1.0
CG B:ASP255 3.1 55.2 1.0
CD B:GLU420 3.2 59.6 1.0
CD2 B:HIS336 3.3 64.9 1.0
CE1 B:HIS336 3.3 62.2 1.0
OE1 B:GLU420 3.4 59.2 1.0
OD1 B:ASP255 3.5 53.7 1.0
OE2 B:GLU381 3.9 93.9 1.0
CG B:GLU381 3.9 74.6 1.0
CG2 B:THR379 4.0 59.2 1.0
OG1 B:THR379 4.2 58.0 1.0
CB B:THR379 4.2 61.4 1.0
CB B:ASP255 4.4 53.1 1.0
ND1 B:HIS336 4.4 60.5 1.0
CG B:HIS336 4.4 62.1 1.0
CG B:GLU420 4.5 58.2 1.0
NE2 B:HIS343 4.7 61.5 1.0
CD2 B:HIS343 4.9 59.2 1.0

Manganese binding site 5 out of 8 in 6ah8

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Manganese binding site 5 out of 8 in the Marine Bacterial Prolidase with Promiscuous Organophosphorus Hydrolase Activity


Mono view


Stereo pair view

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

b:70.8
occ:1.00
 OE2 C:GLU420 2.0 56.2 1.0
OD2 C:ASP255 2.1 64.5 1.0
NE2 C:HIS336 2.1 70.7 1.0
OE2 C:GLU381 2.2 88.9 1.0
CD C:GLU420 3.0 57.0 1.0
CE1 C:HIS336 3.0 67.9 1.0
CG C:ASP255 3.1 64.7 1.0
MN C:MN502 3.1 92.7 1.0
CD2 C:HIS336 3.1 68.4 1.0
CD C:GLU381 3.2 81.6 1.0
OE1 C:GLU420 3.3 58.0 1.0
OD1 C:ASP255 3.6 68.8 1.0
OE1 C:GLU381 4.0 85.1 1.0
CG2 C:THR379 4.0 65.3 1.0
OG1 C:THR379 4.0 59.8 1.0
CG C:GLU381 4.1 78.0 1.0
ND1 C:HIS336 4.2 69.7 1.0
CB C:THR379 4.2 62.9 1.0
CG C:HIS336 4.2 68.2 1.0
CB C:ASP255 4.4 61.4 1.0
CG C:GLU420 4.4 59.2 1.0
NE2 C:HIS343 4.7 68.2 1.0
CD2 C:HIS343 4.8 68.4 1.0
CG1 C:VAL342 4.9 48.3 1.0

Manganese binding site 6 out of 8 in 6ah8

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Manganese binding site 6 out of 8 in the Marine Bacterial Prolidase with Promiscuous Organophosphorus Hydrolase Activity


Mono view


Stereo pair view

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

b:92.7
occ:1.00
 OE1 C:GLU420 2.0 58.0 1.0
OD1 C:ASP255 2.1 68.8 1.0
OD2 C:ASP244 2.3 64.5 1.0
OD1 C:ASP244 2.5 68.2 1.0
CG C:ASP244 2.7 64.7 1.0
CG C:ASP255 2.9 64.7 1.0
CD C:GLU420 2.9 57.0 1.0
OD2 C:ASP255 3.1 64.5 1.0
MN C:MN501 3.1 70.8 1.0
OE2 C:GLU420 3.3 56.2 1.0
OG1 C:THR257 3.7 48.8 1.0
OH C:TYR212 3.9 59.1 1.0
CB C:ASP244 4.2 62.0 1.0
CZ C:TYR212 4.3 56.4 1.0
OE2 C:GLU381 4.3 88.9 1.0
CG C:GLU420 4.3 59.2 1.0
CB C:ASP255 4.3 61.4 1.0
O C:ASP255 4.5 52.7 1.0
CD C:GLU381 4.5 81.6 1.0
C C:ASP255 4.6 55.2 1.0
OE1 C:GLU381 4.6 85.1 1.0
CE2 C:TYR212 4.6 54.3 1.0
CA C:ASP255 4.8 56.5 1.0
CB C:GLU420 4.8 58.9 1.0
NE C:ARG418 4.9 62.1 1.0
O C:ILE256 4.9 61.5 1.0

Manganese binding site 7 out of 8 in 6ah8

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Manganese binding site 7 out of 8 in the Marine Bacterial Prolidase with Promiscuous Organophosphorus Hydrolase Activity


Mono view


Stereo pair view

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

b:99.9
occ:1.00
 OD1 D:ASP255 2.2 66.1 1.0
OD2 D:ASP244 2.5 79.5 1.0
OD1 D:ASP244 2.5 73.5 1.0
OE1 D:GLU420 2.6 77.5 1.0
CG D:ASP244 2.8 73.2 1.0
CG D:ASP255 3.0 63.0 1.0
MN D:MN502 3.1 80.9 1.0
OD2 D:ASP255 3.3 58.7 1.0
OE2 D:GLU381 3.3 0.0 1.0
CD D:GLU420 3.4 81.2 1.0
OE2 D:GLU420 3.4 85.5 1.0
OG1 D:THR257 3.9 53.5 1.0
OH D:TYR212 4.1 66.0 1.0
CE2 D:TYR212 4.3 62.9 1.0
CZ D:TYR212 4.3 63.3 1.0
CB D:ASP244 4.3 67.9 1.0
CB D:ASP255 4.5 59.7 1.0
O D:ASP255 4.5 70.0 1.0
CD D:GLU381 4.6 0.8 1.0
C D:ASP255 4.6 67.0 1.0
CA D:ASP255 4.8 61.1 1.0
CG D:GLU420 4.9 77.4 1.0

Manganese binding site 8 out of 8 in 6ah8

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Manganese binding site 8 out of 8 in the Marine Bacterial Prolidase with Promiscuous Organophosphorus Hydrolase Activity


Mono view


Stereo pair view

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

b:80.9
occ:1.00
 OE2 D:GLU381 2.0 0.0 1.0
NE2 D:HIS336 2.3 64.5 1.0
OE2 D:GLU420 2.3 85.5 1.0
OD2 D:ASP255 2.5 58.7 1.0
CD D:GLU381 2.7 0.8 1.0
MN D:MN501 3.1 99.9 1.0
CD2 D:HIS336 3.2 67.9 1.0
OE1 D:GLU381 3.3 98.1 1.0
CE1 D:HIS336 3.3 67.9 1.0
CD D:GLU420 3.3 81.2 1.0
CG D:ASP255 3.4 63.0 1.0
OE1 D:GLU420 3.7 77.5 1.0
OD1 D:ASP255 3.7 66.1 1.0
CG D:GLU381 3.7 0.0 1.0
OG1 D:THR379 4.3 75.8 1.0
CG D:HIS336 4.4 70.1 1.0
CB D:THR379 4.4 80.3 1.0
ND1 D:HIS336 4.4 70.3 1.0
NE2 D:HIS343 4.5 77.9 1.0
CG2 D:THR379 4.5 79.1 1.0
CG D:GLU420 4.6 77.4 1.0
CD2 D:HIS343 4.7 76.3 1.0
CB D:ASP255 4.8 59.7 1.0
O D:ASP255 5.0 70.0 1.0

Reference:

Y.Jian, Y.Jian. N/A N/A.
Page generated: Sun Oct 6 03:50:28 2024

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