Atomistry » Manganese » PDB 6a9v-6bh4 » 6ah8
Atomistry »
  Manganese »
    PDB 6a9v-6bh4 »
      6ah8 »

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

Go back to Manganese Binding Sites List in 6ah8
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

Go back to Manganese Binding Sites List in 6ah8
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

Go back to Manganese Binding Sites List in 6ah8
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

Go back to Manganese Binding Sites List in 6ah8
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

Go back to Manganese Binding Sites List in 6ah8
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

Go back to Manganese Binding Sites List in 6ah8
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

Go back to Manganese Binding Sites List in 6ah8
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

Go back to Manganese Binding Sites List in 6ah8
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy