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Manganese in PDB 1hqg: Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea

Enzymatic activity of Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea

All present enzymatic activity of Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea, PDB code: 1hqg was solved by J.D.Cox, E.Cama, D.M.Colleluori, D.E.Ash, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 88.200, 88.200, 106.500, 90.00, 90.00, 120.00
R / Rfree (%) 24.3 / 23.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea (pdb code 1hqg). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea, PDB code: 1hqg:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 1hqg

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Manganese binding site 1 out of 6 in the Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:17.9
occ:1.00
 O A:URE1901 1.8 61.6 1.0
OD2 A:ASP124 2.1 15.5 1.0
OD2 A:ASP128 2.1 17.4 1.0
ND1 A:HIS101 2.2 16.5 1.0
O A:HOH604 2.3 27.1 1.0
OD2 A:ASP232 2.3 18.4 1.0
C A:URE1901 2.9 61.5 1.0
CG A:ASP124 3.1 15.8 1.0
CG A:ASP128 3.1 18.4 1.0
CG A:HIS101 3.2 17.9 1.0
CE1 A:HIS101 3.2 16.8 1.0
CG A:ASP232 3.3 20.1 1.0
MN A:MN501 3.3 19.3 1.0
CB A:HIS101 3.5 20.5 1.0
OD1 A:ASP124 3.5 15.1 1.0
OD1 A:ASP128 3.5 17.6 1.0
CB A:ASP232 3.6 15.8 1.0
N1 A:URE1901 3.6 61.4 1.0
N2 A:URE1901 3.8 62.0 1.0
NE1 A:TRP122 4.3 16.4 1.0
NE2 A:HIS101 4.3 17.1 1.0
CD2 A:HIS101 4.3 17.6 1.0
CB A:ASP124 4.4 13.1 1.0
OD1 A:ASP232 4.4 15.4 1.0
CB A:ASP128 4.4 16.2 1.0
CZ2 A:TRP122 4.5 14.5 1.0
NE A:ORN801 4.6 48.6 1.0
O A:CME141 4.7 22.7 1.0
CG A:GLU277 4.7 20.8 1.0
CE2 A:TRP122 4.7 15.6 1.0
OE2 A:GLU277 4.8 22.0 1.0
OD2 A:ASP234 4.9 16.7 1.0
CA A:ASP232 5.0 16.2 1.0
CA A:HIS101 5.0 20.6 1.0

Manganese binding site 2 out of 6 in 1hqg

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Manganese binding site 2 out of 6 in the Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:19.3
occ:1.00
 O A:HOH604 2.0 27.1 1.0
OD1 A:ASP124 2.1 15.1 1.0
OD2 A:ASP234 2.2 16.7 1.0
ND1 A:HIS126 2.3 15.2 1.0
OD2 A:ASP232 2.3 18.4 1.0
OD1 A:ASP234 2.5 16.8 1.0
CG A:ASP234 2.6 17.8 1.0
CG A:ASP124 3.0 15.8 1.0
CE1 A:HIS126 3.1 16.0 1.0
N1 A:URE1901 3.2 61.4 1.0
CG A:ASP232 3.2 20.1 1.0
OD2 A:ASP124 3.3 15.5 1.0
MN A:MN500 3.3 17.9 1.0
CG A:HIS126 3.4 16.4 1.0
O A:URE1901 3.6 61.6 1.0
C A:URE1901 3.7 61.5 1.0
OD1 A:ASP232 3.8 15.4 1.0
CB A:HIS126 3.8 16.8 1.0
NE A:ORN801 3.9 48.6 1.0
N A:HIS126 4.0 16.1 1.0
N A:ALA125 4.1 14.2 1.0
CB A:ASP234 4.2 14.3 1.0
CB A:ASP232 4.2 15.8 1.0
NE2 A:HIS126 4.2 13.7 1.0
CB A:ASP124 4.4 13.1 1.0
CD2 A:HIS126 4.4 16.9 1.0
CA A:HIS126 4.5 15.5 1.0
OD1 A:ASP128 4.6 17.6 1.0
O A:HOH606 4.6 13.4 1.0
OD2 A:ASP128 4.7 17.4 1.0
CA A:ASP124 4.8 15.5 1.0
CB A:ALA125 4.8 15.9 1.0
C A:ALA125 4.8 16.0 1.0
CA A:ALA125 4.9 15.7 1.0
CD A:ORN801 4.9 49.6 1.0
N2 A:URE1901 4.9 62.0 1.0
C A:ASP124 4.9 15.5 1.0

Manganese binding site 3 out of 6 in 1hqg

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Manganese binding site 3 out of 6 in the Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:17.9
occ:1.00
 O B:URE1902 1.8 61.6 1.0
OD2 B:ASP124 2.1 15.5 1.0
OD2 B:ASP128 2.1 17.4 1.0
ND1 B:HIS101 2.2 16.5 1.0
O B:HOH660 2.3 27.1 1.0
OD2 B:ASP232 2.3 18.4 1.0
C B:URE1902 2.9 61.5 1.0
CG B:ASP124 3.1 15.8 1.0
CG B:ASP128 3.1 18.4 1.0
CG B:HIS101 3.2 17.9 1.0
CE1 B:HIS101 3.2 16.8 1.0
CG B:ASP232 3.3 20.1 1.0
MN B:MN503 3.3 19.3 1.0
CB B:HIS101 3.5 20.5 1.0
OD1 B:ASP124 3.5 15.1 1.0
OD1 B:ASP128 3.5 17.6 1.0
CB B:ASP232 3.6 15.8 1.0
N1 B:URE1902 3.6 61.4 1.0
N2 B:URE1902 3.8 62.0 1.0
NE1 B:TRP122 4.3 16.4 1.0
NE2 B:HIS101 4.3 17.1 1.0
CD2 B:HIS101 4.3 17.6 1.0
CB B:ASP124 4.4 13.1 1.0
OD1 B:ASP232 4.4 15.4 1.0
CB B:ASP128 4.4 16.2 1.0
CZ2 B:TRP122 4.5 14.5 1.0
NE B:ORN902 4.6 48.6 1.0
O B:CME141 4.7 22.7 1.0
CG B:GLU277 4.7 20.8 1.0
CE2 B:TRP122 4.7 15.6 1.0
OE2 B:GLU277 4.8 22.0 1.0
OD2 B:ASP234 4.9 16.7 1.0
CA B:ASP232 5.0 16.2 1.0
CA B:HIS101 5.0 20.6 1.0

Manganese binding site 4 out of 6 in 1hqg

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Manganese binding site 4 out of 6 in the Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:19.3
occ:1.00
 O B:HOH660 2.0 27.1 1.0
OD1 B:ASP124 2.1 15.1 1.0
OD2 B:ASP234 2.2 16.7 1.0
ND1 B:HIS126 2.3 15.2 1.0
OD2 B:ASP232 2.3 18.4 1.0
OD1 B:ASP234 2.5 16.8 1.0
CG B:ASP234 2.6 17.8 1.0
CG B:ASP124 3.0 15.8 1.0
CE1 B:HIS126 3.1 16.0 1.0
N1 B:URE1902 3.2 61.4 1.0
CG B:ASP232 3.2 20.1 1.0
OD2 B:ASP124 3.3 15.5 1.0
MN B:MN502 3.3 17.9 1.0
CG B:HIS126 3.4 16.4 1.0
O B:URE1902 3.6 61.6 1.0
C B:URE1902 3.7 61.5 1.0
OD1 B:ASP232 3.8 15.4 1.0
CB B:HIS126 3.8 16.8 1.0
NE B:ORN902 3.9 48.6 1.0
N B:HIS126 4.0 16.1 1.0
N B:ALA125 4.1 14.2 1.0
CB B:ASP234 4.2 14.3 1.0
CB B:ASP232 4.2 15.8 1.0
NE2 B:HIS126 4.2 13.7 1.0
CB B:ASP124 4.4 13.1 1.0
CD2 B:HIS126 4.4 16.9 1.0
CA B:HIS126 4.5 15.5 1.0
OD1 B:ASP128 4.6 17.6 1.0
O B:HOH662 4.6 13.4 1.0
OD2 B:ASP128 4.7 17.4 1.0
CA B:ASP124 4.8 15.5 1.0
CB B:ALA125 4.8 15.9 1.0
C B:ALA125 4.8 16.0 1.0
CA B:ALA125 4.9 15.7 1.0
CD B:ORN902 4.9 49.6 1.0
N2 B:URE1902 4.9 62.0 1.0
C B:ASP124 4.9 15.5 1.0

Manganese binding site 5 out of 6 in 1hqg

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Manganese binding site 5 out of 6 in the Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn504

b:17.9
occ:1.00
 O C:URE1903 1.8 61.6 1.0
OD2 C:ASP124 2.1 15.5 1.0
OD2 C:ASP128 2.1 17.4 1.0
ND1 C:HIS101 2.2 16.5 1.0
O C:HOH714 2.3 27.1 1.0
OD2 C:ASP232 2.3 18.4 1.0
C C:URE1903 2.9 61.5 1.0
CG C:ASP124 3.1 15.8 1.0
CG C:ASP128 3.1 18.4 1.0
CG C:HIS101 3.2 17.9 1.0
CE1 C:HIS101 3.2 16.8 1.0
CG C:ASP232 3.3 20.1 1.0
MN C:MN505 3.3 19.3 1.0
CB C:HIS101 3.5 20.5 1.0
OD1 C:ASP124 3.5 15.1 1.0
OD1 C:ASP128 3.5 17.6 1.0
CB C:ASP232 3.6 15.8 1.0
N1 C:URE1903 3.6 61.4 1.0
N2 C:URE1903 3.8 62.0 1.0
NE1 C:TRP122 4.3 16.4 1.0
NE2 C:HIS101 4.3 17.1 1.0
CD2 C:HIS101 4.3 17.6 1.0
CB C:ASP124 4.4 13.1 1.0
OD1 C:ASP232 4.4 15.4 1.0
CB C:ASP128 4.4 16.2 1.0
CZ2 C:TRP122 4.5 14.5 1.0
NE C:ORN903 4.6 48.6 1.0
O C:CME141 4.7 22.7 1.0
CG C:GLU277 4.7 20.8 1.0
CE2 C:TRP122 4.7 15.6 1.0
OE2 C:GLU277 4.8 22.0 1.0
OD2 C:ASP234 4.9 16.7 1.0
CA C:ASP232 5.0 16.2 1.0
CA C:HIS101 5.0 20.6 1.0

Manganese binding site 6 out of 6 in 1hqg

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Manganese binding site 6 out of 6 in the Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of the H141C Arginase Variant Complexed with Products Ornithine and Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn505

b:19.3
occ:1.00
 O C:HOH714 2.0 27.1 1.0
OD1 C:ASP124 2.1 15.1 1.0
OD2 C:ASP234 2.2 16.7 1.0
ND1 C:HIS126 2.3 15.2 1.0
OD2 C:ASP232 2.3 18.4 1.0
OD1 C:ASP234 2.5 16.8 1.0
CG C:ASP234 2.6 17.8 1.0
CG C:ASP124 3.0 15.8 1.0
CE1 C:HIS126 3.1 16.0 1.0
N1 C:URE1903 3.2 61.4 1.0
CG C:ASP232 3.2 20.1 1.0
OD2 C:ASP124 3.3 15.5 1.0
MN C:MN504 3.3 17.9 1.0
CG C:HIS126 3.4 16.4 1.0
O C:URE1903 3.6 61.6 1.0
C C:URE1903 3.7 61.5 1.0
OD1 C:ASP232 3.8 15.4 1.0
CB C:HIS126 3.8 16.8 1.0
NE C:ORN903 3.9 48.6 1.0
N C:HIS126 4.0 16.1 1.0
N C:ALA125 4.1 14.2 1.0
CB C:ASP234 4.2 14.3 1.0
CB C:ASP232 4.2 15.8 1.0
NE2 C:HIS126 4.2 13.7 1.0
CB C:ASP124 4.4 13.1 1.0
CD2 C:HIS126 4.4 16.9 1.0
CA C:HIS126 4.5 15.5 1.0
OD1 C:ASP128 4.6 17.6 1.0
O C:HOH716 4.6 13.4 1.0
OD2 C:ASP128 4.7 17.4 1.0
CA C:ASP124 4.8 15.5 1.0
CB C:ALA125 4.8 15.9 1.0
C C:ALA125 4.8 16.0 1.0
CA C:ALA125 4.9 15.7 1.0
CD C:ORN903 4.9 49.6 1.0
N2 C:URE1903 4.9 62.0 1.0
C C:ASP124 4.9 15.5 1.0

Reference:

J.D.Cox, E.Cama, D.M.Colleluori, S.Pethe, J.L.Boucher, D.Mansuy, D.E.Ash, D.W.Christianson. Mechanistic and Metabolic Inferences From the Binding of Substrate Analogues and Products to Arginase. Biochemistry V. 40 2689 2001.
ISSN: ISSN 0006-2960
PubMed: 11258880
DOI: 10.1021/BI002318+
Page generated: Sat Oct 5 10:54:02 2024

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