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Manganese in PDB 4zng: X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase

Enzymatic activity of X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase

All present enzymatic activity of X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase:
3.4.13.9;

Protein crystallography data

The structure of X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase, PDB code: 4zng was solved by O.Kgosisejo, P.Grochulski, T.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.83 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 212.130, 76.990, 88.920, 90.00, 112.39, 90.00
R / Rfree (%) 22 / 28

Other elements in 4zng:

The structure of X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase also contains other interesting chemical elements:

Arsenic (As) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase (pdb code 4zng). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase, PDB code: 4zng:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 4zng

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Manganese binding site 1 out of 5 in the X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:58.8
occ:1.00
 OD1 C:ASP232 2.0 56.8 1.0
OE1 C:GLU339 2.0 71.1 1.0
OD1 C:ASP221 2.1 52.6 1.0
CD C:GLU339 2.7 80.3 1.0
CG C:ASP232 2.7 60.3 1.0
CG C:ASP221 2.8 62.0 1.0
OD2 C:ASP221 2.8 61.5 1.0
OE2 C:GLU339 2.8 65.5 1.0
OD2 C:ASP232 2.8 49.3 1.0
OG1 C:THR234 3.5 62.5 1.0
OE1 C:GLU325 3.6 96.1 1.0
O C:ALA233 3.8 87.7 1.0
N C:ALA233 4.0 72.3 1.0
C C:ALA233 4.1 78.0 1.0
CZ C:PHE190 4.2 66.1 1.0
CG C:GLU339 4.2 84.2 1.0
CB C:ASP221 4.2 65.0 1.0
CB C:ASP232 4.2 60.7 1.0
CA C:ALA233 4.4 73.6 1.0
C C:ASP232 4.5 69.9 1.0
CD C:GLU325 4.6 95.6 1.0
CE2 C:PHE190 4.7 67.6 1.0
N C:THR234 4.7 75.1 1.0
CB C:GLU339 4.7 88.3 1.0
CA C:ASP232 4.7 64.6 1.0
CA C:ASP221 4.7 66.9 1.0
CE1 C:PHE190 4.8 61.3 1.0
CB C:THR234 4.8 72.5 1.0

Manganese binding site 2 out of 5 in 4zng

Go back to Manganese Binding Sites List in 4zng
Manganese binding site 2 out of 5 in the X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:37.3
occ:1.00
 O1 B:CAC401 1.7 44.5 1.0
OD1 B:ASP232 1.9 28.9 1.0
OE1 B:GLU339 2.0 41.8 1.0
OD1 B:ASP221 2.0 32.0 1.0
CG B:ASP221 2.8 34.0 1.0
CG B:ASP232 2.8 36.0 1.0
CD B:GLU339 2.8 40.5 1.0
OD2 B:ASP221 2.9 32.8 1.0
OE2 B:GLU339 3.0 33.7 1.0
OD2 B:ASP232 3.0 33.7 1.0
MN B:MN403 3.2 40.2 1.0
AS B:CAC401 3.2 75.5 1.0
OG1 B:THR234 3.5 43.8 1.0
C2 B:CAC401 3.8 67.6 1.0
CZ B:PHE190 3.9 39.3 1.0
OE1 B:GLU325 4.2 59.1 1.0
CE2 B:PHE190 4.3 37.5 1.0
CB B:ASP221 4.3 33.0 1.0
CB B:ASP232 4.3 34.2 1.0
CG B:GLU339 4.3 47.0 1.0
C1 B:CAC401 4.3 85.6 1.0
N B:ALA233 4.4 38.1 1.0
O B:ALA233 4.4 39.4 1.0
O2 B:CAC401 4.4 81.1 1.0
C B:ALA233 4.5 40.4 1.0
CE1 B:PHE190 4.6 39.6 1.0
OE2 B:GLU325 4.6 41.0 1.0
C B:ASP232 4.6 39.9 1.0
CD B:GLU325 4.7 55.3 1.0
CA B:ASP232 4.8 35.9 1.0
CA B:ASP221 4.8 36.4 1.0
CA B:ALA233 4.9 41.0 1.0
N B:THR234 4.9 40.4 1.0
N B:LEU222 4.9 34.8 1.0
NE B:ARG337 4.9 44.6 1.0
CB B:THR234 4.9 44.3 1.0
CB B:GLU339 5.0 44.6 1.0
C B:ASP221 5.0 36.5 1.0

Manganese binding site 3 out of 5 in 4zng

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Manganese binding site 3 out of 5 in the X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:40.2
occ:1.00
 OD2 B:ASP232 2.1 33.7 1.0
NE2 B:HIS296 2.1 41.7 1.0
OE2 B:GLU325 2.2 41.0 1.0
OE2 B:GLU339 2.2 33.7 1.0
O1 B:CAC401 2.6 44.5 1.0
O2 B:CAC401 2.8 81.1 1.0
AS B:CAC401 2.9 75.5 1.0
CD B:GLU325 3.0 55.3 1.0
CG B:ASP232 3.0 36.0 1.0
CD2 B:HIS296 3.1 42.6 1.0
CE1 B:HIS296 3.2 41.5 1.0
MN B:MN402 3.2 37.3 1.0
OE1 B:GLU325 3.2 59.1 1.0
CD B:GLU339 3.2 40.5 1.0
OD1 B:ASP232 3.5 28.9 1.0
C2 B:CAC401 3.5 67.6 1.0
OE1 B:GLU339 3.7 41.8 1.0
OG B:SER323 4.0 40.0 1.0
CB B:ASP232 4.2 34.2 1.0
CG B:HIS296 4.2 42.8 1.0
ND1 B:HIS296 4.3 39.5 1.0
CB B:SER323 4.3 44.5 1.0
CG B:GLU325 4.4 52.2 1.0
NE2 B:HIS303 4.4 50.7 1.0
CG B:GLU339 4.6 47.0 1.0
C1 B:CAC401 4.9 85.6 1.0

Manganese binding site 4 out of 5 in 4zng

Go back to Manganese Binding Sites List in 4zng
Manganese binding site 4 out of 5 in the X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:31.3
occ:1.00
 OE2 A:GLU339 2.0 26.9 1.0
OD2 A:ASP232 2.1 27.8 1.0
OE2 A:GLU325 2.1 31.2 1.0
NE2 A:HIS296 2.2 32.0 1.0
O1 A:CAC403 2.3 51.0 1.0
O2 A:CAC403 2.6 57.1 1.0
CD A:GLU325 3.0 38.5 1.0
AS A:CAC403 3.0 66.5 1.0
CD2 A:HIS296 3.1 33.8 1.0
CG A:ASP232 3.1 29.2 1.0
OE1 A:GLU325 3.2 42.0 1.0
CE1 A:HIS296 3.2 33.8 1.0
CD A:GLU339 3.2 29.3 1.0
MN A:MN402 3.3 27.3 1.0
OD1 A:ASP232 3.5 27.6 1.0
OE1 A:GLU339 3.8 28.6 1.0
OG A:SER323 3.9 31.4 1.0
C2 A:CAC403 4.1 54.9 1.0
CB A:SER323 4.2 31.4 1.0
CG A:HIS296 4.3 36.5 1.0
ND1 A:HIS296 4.3 34.0 1.0
CG A:GLU325 4.3 33.2 1.0
CB A:ASP232 4.4 27.6 1.0
CG A:GLU339 4.4 29.2 1.0
C1 A:CAC403 4.6 65.7 1.0
NE2 A:HIS303 4.6 53.9 1.0
CB A:GLU325 5.0 30.5 1.0

Manganese binding site 5 out of 5 in 4zng

Go back to Manganese Binding Sites List in 4zng
Manganese binding site 5 out of 5 in the X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:27.3
occ:1.00
 OD1 A:ASP232 2.0 27.6 1.0
OE1 A:GLU339 2.0 28.6 1.0
OD1 A:ASP221 2.1 23.3 1.0
O1 A:CAC403 2.1 51.0 1.0
OD2 A:ASP221 2.6 23.2 1.0
CG A:ASP221 2.7 25.6 1.0
CD A:GLU339 2.8 29.3 1.0
CG A:ASP232 2.9 29.2 1.0
OE2 A:GLU339 3.0 26.9 1.0
AS A:CAC403 3.1 66.5 1.0
C2 A:CAC403 3.2 54.9 1.0
OD2 A:ASP232 3.2 27.8 1.0
MN A:MN401 3.3 31.3 1.0
OG1 A:THR234 3.5 22.6 1.0
CZ A:PHE190 3.9 32.6 1.0
OE1 A:GLU325 4.2 42.0 1.0
CG A:GLU339 4.2 29.2 1.0
CB A:ASP221 4.3 23.5 1.0
O2 A:CAC403 4.3 57.1 1.0
C1 A:CAC403 4.3 65.7 1.0
O A:ALA233 4.3 27.7 1.0
CB A:ASP232 4.3 27.6 1.0
CE1 A:PHE190 4.4 33.0 1.0
N A:ALA233 4.4 24.5 1.0
C A:ALA233 4.5 25.1 1.0
CE2 A:PHE190 4.5 31.8 1.0
NE A:ARG337 4.7 28.1 1.0
C A:ASP232 4.7 26.7 1.0
OE2 A:GLU325 4.8 31.2 1.0
CA A:ASP232 4.8 25.8 1.0
CD A:GLU325 4.8 38.5 1.0
CA A:ASP221 4.9 23.5 1.0
CB A:THR234 4.9 23.6 1.0
CA A:ALA233 4.9 25.1 1.0
CB A:GLU339 4.9 30.6 1.0

Reference:

O.Kgosisejo, P.Grochulski, T.Tanaka. X-Ray Crystallography of Recombinant Lactococcus Lactis Prolidase To Be Published.
Page generated: Sat Oct 5 23:14:27 2024

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