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Manganese in PDB 7lox: The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site

Enzymatic activity of The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site

All present enzymatic activity of The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site:
3.5.3.11;

Protein crystallography data

The structure of The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site, PDB code: 7lox was solved by P.Maturana, M.Figueroa, F.Gonzalez-Ordenes, P.Villalobos, J.Martinez-Oyanedel, E.A.Uribe, V.Castro-Fernandez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.51 / 3.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 129.028, 129.028, 88.29, 90, 90, 120
R / Rfree (%) 17.2 / 21.8

Manganese Binding Sites:

The binding sites of Manganese atom in the The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site (pdb code 7lox). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site, PDB code: 7lox:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 7lox

Go back to Manganese Binding Sites List in 7lox
Manganese binding site 1 out of 6 in the The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:68.7
occ:0.82
 OD2 A:ASP232 1.9 69.5 1.0
OD1 A:ASP149 2.0 69.7 1.0
ND1 A:HIS151 2.2 73.0 1.0
OD2 A:ASP230 2.3 80.0 1.0
N2 A:GAI403 2.3 58.4 1.0
CG A:ASP232 2.6 70.8 1.0
OD1 A:ASP232 2.7 73.9 1.0
MN A:MN402 2.9 65.2 0.8
C A:GAI403 2.9 63.4 1.0
CG A:ASP149 3.0 71.8 1.0
CE1 A:HIS151 3.0 68.2 1.0
CG A:ASP230 3.1 66.5 1.0
CG A:HIS151 3.3 70.2 1.0
OD2 A:ASP149 3.4 73.2 1.0
N1 A:GAI403 3.5 64.2 1.0
OD1 A:ASP230 3.6 67.3 1.0
CB A:HIS151 3.7 67.5 1.0
N3 A:GAI403 3.7 74.0 1.0
N A:HIS151 4.0 68.8 1.0
CB A:ASP232 4.1 69.8 1.0
CB A:ASP230 4.1 62.8 1.0
N A:ALA150 4.1 64.1 1.0
NE2 A:HIS151 4.2 61.0 1.0
CB A:ASP149 4.3 64.8 1.0
CD2 A:HIS151 4.3 61.9 1.0
OG1 A:THR244 4.4 75.8 1.0
OD1 A:ASP153 4.5 80.0 1.0
CA A:HIS151 4.5 69.8 1.0
C A:ALA150 4.7 68.0 1.0
CA A:ALA150 4.8 65.4 1.0
CA A:ASP149 4.8 66.3 1.0
CB A:ALA150 4.8 62.7 1.0
OD2 A:ASP153 4.8 77.3 1.0
C A:ASP149 4.9 64.7 1.0

Manganese binding site 2 out of 6 in 7lox

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Manganese binding site 2 out of 6 in the The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:65.2
occ:0.82
 OD2 A:ASP149 2.0 73.2 1.0
N1 A:GAI403 2.0 64.2 1.0
OD1 A:ASP153 2.0 80.0 1.0
OD2 A:ASP230 2.1 80.0 1.0
ND1 A:HIS126 2.4 71.3 1.0
C A:GAI403 2.7 63.4 1.0
CG A:ASP149 2.7 71.8 1.0
MN A:MN401 2.9 68.7 0.8
OD1 A:ASP149 2.9 69.7 1.0
CG A:ASP153 3.1 77.4 1.0
CG A:ASP230 3.2 66.5 1.0
CE1 A:HIS126 3.2 65.4 1.0
N2 A:GAI403 3.2 58.4 1.0
N3 A:GAI403 3.5 74.0 1.0
OD2 A:ASP153 3.5 77.3 1.0
CG A:HIS126 3.6 75.8 1.0
CB A:ASP230 3.6 62.8 1.0
CB A:HIS126 4.0 70.2 1.0
CB A:ASP149 4.2 64.8 1.0
OD1 A:ASP230 4.2 67.3 1.0
CB A:ASP153 4.4 71.1 1.0
NE2 A:HIS126 4.4 63.4 1.0
CE1 A:HIS147 4.4 77.0 1.0
CB A:HIS151 4.4 67.5 1.0
ND1 A:HIS151 4.4 73.0 1.0
OD2 A:ASP232 4.4 69.5 1.0
CD2 A:HIS126 4.6 71.4 1.0
O A:HIS151 4.7 65.2 1.0
NE2 A:HIS147 4.8 73.4 1.0
CG A:HIS151 4.9 70.2 1.0

Manganese binding site 3 out of 6 in 7lox

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Manganese binding site 3 out of 6 in the The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:79.9
occ:0.87
 OD2 B:ASP232 1.9 85.3 1.0
OD1 B:ASP149 2.0 84.9 1.0
N2 B:GAI403 2.0 83.1 1.0
OD2 B:ASP230 2.2 85.8 1.0
ND1 B:HIS151 2.3 74.6 1.0
CG B:ASP232 2.6 79.7 1.0
OD1 B:ASP232 2.7 77.9 1.0
CG B:ASP149 2.9 86.2 1.0
CG B:ASP230 2.9 81.2 1.0
C B:GAI403 3.0 85.8 1.0
MN B:MN402 3.0 79.7 0.8
CE1 B:HIS151 3.1 73.8 1.0
OD2 B:ASP149 3.2 91.3 1.0
CG B:HIS151 3.3 82.5 1.0
OD1 B:ASP230 3.5 77.5 1.0
N3 B:GAI403 3.6 84.7 1.0
CB B:HIS151 3.7 82.0 1.0
N1 B:GAI403 3.8 83.4 1.0
N B:HIS151 3.9 76.0 1.0
CB B:ASP230 3.9 82.0 1.0
N B:ALA150 4.1 81.0 1.0
CB B:ASP232 4.1 78.2 1.0
CB B:ASP149 4.2 77.0 1.0
NE2 B:HIS151 4.3 74.7 1.0
CD2 B:HIS151 4.4 80.7 1.0
CA B:HIS151 4.5 77.0 1.0
OG1 B:THR244 4.5 78.5 1.0
CA B:ASP149 4.6 75.3 1.0
OD2 B:ASP153 4.6 83.6 1.0
OD1 B:ASP153 4.7 86.4 1.0
CA B:ALA150 4.8 74.2 1.0
C B:ALA150 4.8 74.7 1.0
C B:ASP149 4.8 78.2 1.0
CB B:ALA150 4.8 68.8 1.0
ND1 B:HIS126 4.9 84.3 1.0
CA B:ASP232 5.0 75.3 1.0

Manganese binding site 4 out of 6 in 7lox

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Manganese binding site 4 out of 6 in the The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:79.7
occ:0.83
 OD2 B:ASP149 2.0 91.3 1.0
N3 B:GAI403 2.0 84.7 1.0
OD2 B:ASP230 2.1 85.8 1.0
OD2 B:ASP153 2.2 83.6 1.0
ND1 B:HIS126 2.2 84.3 1.0
CE1 B:HIS126 2.8 83.9 1.0
C B:GAI403 2.8 85.8 1.0
CG B:ASP149 2.8 86.2 1.0
MN B:MN401 3.0 79.9 0.9
CG B:ASP230 3.1 81.2 1.0
OD1 B:ASP149 3.1 84.9 1.0
N2 B:GAI403 3.2 83.1 1.0
CG B:ASP153 3.2 84.8 1.0
CG B:HIS126 3.4 89.8 1.0
CB B:ASP230 3.5 82.0 1.0
OD1 B:ASP153 3.5 86.4 1.0
N1 B:GAI403 3.9 83.4 1.0
NE2 B:HIS126 4.0 80.8 1.0
CB B:HIS126 4.1 87.8 1.0
OD1 B:ASP230 4.2 77.5 1.0
CB B:ASP149 4.2 77.0 1.0
CD2 B:HIS126 4.4 86.4 1.0
NE2 B:HIS147 4.4 81.7 1.0
CB B:ASP153 4.5 81.3 1.0
OD2 B:ASP232 4.5 85.3 1.0
CB B:HIS151 4.6 82.0 1.0
ND1 B:HIS151 4.6 74.6 1.0
CA B:ASP230 4.8 81.5 1.0
CE B:MET166 4.8 89.4 1.0

Manganese binding site 5 out of 6 in 7lox

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Manganese binding site 5 out of 6 in the The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:83.0
occ:0.84
 OD2 C:ASP232 2.0 79.7 1.0
OD1 C:ASP149 2.0 84.1 1.0
N1 C:GAI403 2.0 74.7 1.0
OD1 C:ASP232 2.0 83.1 1.0
OD1 C:ASP230 2.2 84.3 1.0
CG C:ASP232 2.3 79.0 1.0
ND1 C:HIS151 2.4 78.2 1.0
CG C:ASP149 2.9 84.0 1.0
CG C:ASP230 3.1 79.1 1.0
CE1 C:HIS151 3.2 73.4 1.0
C C:GAI403 3.3 80.4 1.0
OD2 C:ASP149 3.3 81.4 1.0
MN C:MN402 3.5 83.0 1.0
CG C:HIS151 3.5 84.0 1.0
OD2 C:ASP230 3.7 82.8 1.0
CB C:ASP232 3.8 71.6 1.0
N C:ALA150 3.9 72.2 1.0
N3 C:GAI403 3.9 81.1 1.0
CB C:HIS151 3.9 76.3 1.0
N C:HIS151 4.0 74.0 1.0
CB C:ASP230 4.1 74.4 1.0
OG1 C:THR244 4.2 78.0 1.0
CB C:ASP149 4.2 72.6 1.0
N2 C:GAI403 4.2 83.3 1.0
NE2 C:HIS151 4.4 70.3 1.0
CA C:ASP149 4.5 74.5 1.0
CD2 C:HIS151 4.6 76.0 1.0
CA C:ALA150 4.6 74.4 1.0
CA C:HIS151 4.6 76.2 1.0
CA C:ASP232 4.7 72.1 1.0
CB C:ALA150 4.7 70.1 1.0
C C:ASP149 4.7 73.5 1.0
C C:ALA150 4.7 72.5 1.0
C C:ASP232 4.9 76.2 1.0
O C:THR244 5.0 70.4 1.0

Manganese binding site 6 out of 6 in 7lox

Go back to Manganese Binding Sites List in 7lox
Manganese binding site 6 out of 6 in the The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Structure of Agmatinase From E. Coli at 3.2 A Displaying Guanidine in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:83.0
occ:0.98
 OD2 C:ASP149 2.0 81.4 1.0
OD2 C:ASP153 2.0 91.9 1.0
N3 C:GAI403 2.0 81.1 1.0
ND1 C:HIS126 2.2 79.2 1.0
C C:GAI403 2.4 80.4 1.0
OD1 C:ASP230 2.7 84.3 1.0
CE1 C:HIS126 2.9 78.0 1.0
CG C:ASP149 3.0 84.0 1.0
N1 C:GAI403 3.0 74.7 1.0
CG C:ASP153 3.0 84.8 1.0
N2 C:GAI403 3.2 83.3 1.0
OD1 C:ASP149 3.3 84.1 1.0
CG C:HIS126 3.3 83.0 1.0
OD1 C:ASP153 3.4 76.8 1.0
MN C:MN401 3.5 83.0 0.8
CG C:ASP230 3.6 79.1 1.0
CB C:ASP230 3.8 74.4 1.0
CB C:HIS126 3.9 86.4 1.0
NE2 C:HIS126 4.1 75.1 1.0
NE2 C:HIS147 4.2 83.0 1.0
CB C:ASP149 4.3 72.6 1.0
CB C:ASP153 4.3 84.4 1.0
CD2 C:HIS126 4.3 78.6 1.0
O C:HIS163 4.6 87.8 1.0
OD2 C:ASP230 4.8 82.8 1.0
CB C:HIS151 4.8 76.3 1.0
CE1 C:HIS147 4.8 79.1 1.0
O C:HIS151 4.8 84.4 1.0

Reference:

P.Maturana, M.S.Orellana, S.M.Herrera, I.Martinez, M.Figueroa, J.Martinez-Oyanedel, V.Castro-Fernandez, E.Uribe. Crystal Structure of Escherichia Coli Agmatinase: Catalytic Mechanism and Residues Relevant For Substrate Specificity Int J Mol Sci V. 22 2021.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS22094769
Page generated: Sun Oct 6 09:55:28 2024

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