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Manganese in PDB 6luh: High Resolution Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase

Enzymatic activity of High Resolution Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase

All present enzymatic activity of High Resolution Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase:
3.5.3.25;

Protein crystallography data

The structure of High Resolution Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase, PDB code: 6luh was solved by K.Oda, Y.Matoba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.09 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.326, 47.057, 59.261, 83.57, 84.63, 70.13
R / Rfree (%) 20 / 23

Other elements in 6luh:

The structure of High Resolution Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the High Resolution Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase (pdb code 6luh). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the High Resolution Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase, PDB code: 6luh:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6luh

Go back to Manganese Binding Sites List in 6luh
Manganese binding site 1 out of 4 in the High Resolution Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of High Resolution Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:5.7
occ:1.00
 OD2 A:ASP109 2.2 5.2 1.0
OD2 A:ASP198 2.2 5.5 1.0
O A:HOH623 2.2 8.0 1.0
OD2 A:ASP113 2.3 7.6 1.0
O A:HOH549 2.4 5.8 1.0
SG A:CYS86 2.5 6.2 1.0
CG A:ASP198 3.2 6.9 1.0
CG A:ASP113 3.2 5.8 1.0
CG A:ASP109 3.2 4.1 1.0
CB A:CYS86 3.4 4.4 1.0
OD1 A:ASP113 3.4 6.9 1.0
MN A:MN402 3.4 5.7 1.0
CB A:ASP198 3.5 6.8 1.0
OD1 A:ASP109 3.5 2.8 1.0
O A:HOH503 3.9 18.5 1.0
OH A:TYR107 4.0 5.6 1.0
OE2 A:GLU241 4.2 7.3 1.0
OD1 A:ASP198 4.3 7.2 1.0
O A:GLY126 4.3 10.1 1.0
CD A:GLU241 4.4 6.7 1.0
CE1 A:TYR107 4.4 5.1 1.0
CB A:ASP109 4.5 4.4 1.0
CB A:ASP113 4.5 4.5 1.0
OE1 A:GLU241 4.6 8.8 1.0
CZ A:TYR107 4.7 3.3 1.0
CA A:CYS86 4.8 5.0 1.0
NE2 A:HIS196 4.9 5.8 1.0
CA A:ASP198 4.9 6.8 1.0
O B:HOH732 4.9 16.9 1.0
OD2 A:ASP200 5.0 4.8 1.0

Manganese binding site 2 out of 4 in 6luh

Go back to Manganese Binding Sites List in 6luh
Manganese binding site 2 out of 4 in the High Resolution Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of High Resolution Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:5.7
occ:1.00
 OD1 A:ASP109 2.0 2.8 1.0
O A:HOH549 2.1 5.8 1.0
OD2 A:ASP198 2.2 5.5 1.0
OD2 A:ASP200 2.2 4.8 1.0
ND1 A:HIS111 2.3 8.2 1.0
OD1 A:ASP200 2.4 3.9 1.0
CG A:ASP200 2.6 5.0 1.0
CG A:ASP109 3.0 4.1 1.0
CG A:ASP198 3.0 6.9 1.0
CE1 A:HIS111 3.2 6.7 1.0
CG A:HIS111 3.3 7.4 1.0
OD2 A:ASP109 3.4 5.2 1.0
MN A:MN401 3.4 5.7 1.0
OD1 A:ASP198 3.6 7.2 1.0
CB A:HIS111 3.6 6.8 1.0
N A:HIS111 3.7 7.2 1.0
CB A:ASP198 4.1 6.8 1.0
CB A:ASP200 4.2 6.7 1.0
N A:GLY110 4.2 5.2 1.0
CA A:HIS111 4.3 7.1 1.0
O A:HOH595 4.3 15.8 1.0
OD1 A:ASP113 4.3 6.9 1.0
NE2 A:HIS111 4.3 4.2 1.0
O A:HOH525 4.4 13.5 1.0
O A:HOH623 4.4 8.0 1.0
CB A:ASP109 4.4 4.4 1.0
CD2 A:HIS111 4.4 7.2 1.0
O B:HOH732 4.5 16.9 1.0
C A:GLY110 4.6 7.1 1.0
O A:HOH503 4.7 18.5 1.0
CA A:GLY110 4.7 6.0 1.0
CA A:ASP109 4.8 4.1 1.0
C A:ASP109 4.8 4.6 1.0
OD2 A:ASP113 4.8 7.6 1.0
CG A:ASP113 5.0 5.8 1.0

Manganese binding site 3 out of 4 in 6luh

Go back to Manganese Binding Sites List in 6luh
Manganese binding site 3 out of 4 in the High Resolution Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of High Resolution Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:6.7
occ:1.00
 OD2 B:ASP113 2.1 4.0 1.0
OD2 B:ASP109 2.2 7.1 1.0
O B:HOH588 2.2 7.5 1.0
O B:HOH521 2.2 6.2 1.0
OD2 B:ASP198 2.3 7.5 1.0
SG B:CYS86 2.5 7.4 1.0
O B:HOH501 3.1 18.2 1.0
CG B:ASP113 3.1 5.6 1.0
CG B:ASP109 3.2 4.8 1.0
CG B:ASP198 3.3 8.2 1.0
CB B:CYS86 3.3 9.4 1.0
OD1 B:ASP113 3.3 6.9 1.0
MN B:MN402 3.4 7.5 1.0
CB B:ASP198 3.5 7.8 1.0
OD1 B:ASP109 3.6 5.7 1.0
O B:HOH745 3.7 21.7 1.0
OH B:TYR107 4.0 6.2 1.0
OE2 B:GLU241 4.3 8.1 1.0
OD1 B:ASP198 4.4 6.1 1.0
O B:GLY126 4.4 9.3 1.0
CE1 B:TYR107 4.5 7.8 1.0
CD B:GLU241 4.5 7.5 1.0
CB B:ASP113 4.5 5.7 1.0
CB B:ASP109 4.5 6.7 1.0
CZ B:TYR107 4.7 5.4 1.0
CA B:CYS86 4.8 9.1 1.0
OE1 B:GLU241 4.8 8.1 1.0
OD2 B:ASP200 4.9 6.8 1.0
NE2 B:HIS196 4.9 8.1 1.0
CA B:ASP198 5.0 6.4 1.0
CG B:GLU241 5.0 7.8 1.0
O B:HOH699 5.0 18.4 1.0

Manganese binding site 4 out of 4 in 6luh

Go back to Manganese Binding Sites List in 6luh
Manganese binding site 4 out of 4 in the High Resolution Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of High Resolution Structure of N(Omega)-Hydroxy-L-Arginine Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:7.5
occ:1.00
 O B:HOH501 2.1 18.2 1.0
OD2 B:ASP200 2.1 6.8 1.0
OD2 B:ASP198 2.2 7.5 1.0
OD1 B:ASP109 2.2 5.7 1.0
O B:HOH521 2.2 6.2 1.0
ND1 B:HIS111 2.2 6.6 1.0
OD1 B:ASP200 2.4 6.6 1.0
CG B:ASP200 2.6 11.6 1.0
CG B:ASP109 3.1 4.8 1.0
CE1 B:HIS111 3.1 5.7 1.0
CG B:ASP198 3.1 8.2 1.0
CG B:HIS111 3.3 6.7 1.0
O B:HOH745 3.4 21.7 1.0
MN B:MN401 3.4 6.7 1.0
OD2 B:ASP109 3.4 7.1 1.0
OD1 B:ASP198 3.6 6.1 1.0
CB B:HIS111 3.7 5.7 1.0
N B:HIS111 3.9 6.3 1.0
N B:GLY110 4.1 7.0 1.0
CB B:ASP200 4.1 9.4 1.0
O B:HOH588 4.1 7.5 1.0
CB B:ASP198 4.2 7.8 1.0
OD1 B:ASP113 4.3 6.9 1.0
NE2 B:HIS111 4.3 7.9 1.0
CD2 B:HIS111 4.4 7.4 1.0
CA B:HIS111 4.4 8.6 1.0
CB B:ASP109 4.5 6.7 1.0
O B:HOH547 4.5 11.4 1.0
C B:GLY110 4.6 7.7 1.0
O B:HOH699 4.6 18.4 1.0
CA B:GLY110 4.6 6.5 1.0
OD2 B:ASP113 4.7 4.0 1.0
CA B:ASP109 4.8 6.8 1.0
C B:ASP109 4.8 6.3 1.0
CG B:ASP113 4.9 5.6 1.0

Reference:

K.Oda, N.Shimotani, T.Kuroda, Y.Matoba. Crystal Structure of An Nomega-Hydroxy-L-Arginine Hydrolase Found in the D-Cycloserine Biosynthetic Pathway. Acta Crystallogr D Struct V. 76 506 2020BIOL.
ISSN: ISSN 2059-7983
PubMed: 32496212
DOI: 10.1107/S2059798320004908
Page generated: Sun Oct 6 05:27:29 2024

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