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Manganese in PDB 7euq: Crystal Structure of C86H-Y124N-G126H-H196S Mutant of N(Omega)- Hydroxy-L-Arginine Hydrolase

Enzymatic activity of Crystal Structure of C86H-Y124N-G126H-H196S Mutant of N(Omega)- Hydroxy-L-Arginine Hydrolase

All present enzymatic activity of Crystal Structure of C86H-Y124N-G126H-H196S Mutant of N(Omega)- Hydroxy-L-Arginine Hydrolase:
3.5.3.25;

Protein crystallography data

The structure of Crystal Structure of C86H-Y124N-G126H-H196S Mutant of N(Omega)- Hydroxy-L-Arginine Hydrolase, PDB code: 7euq 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) 39.26 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 42.491, 49.755, 60.515, 89.97, 72.2, 89.91
R / Rfree (%) 18.1 / 21.1

Other elements in 7euq:

The structure of Crystal Structure of C86H-Y124N-G126H-H196S Mutant of N(Omega)- Hydroxy-L-Arginine Hydrolase also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of C86H-Y124N-G126H-H196S Mutant of N(Omega)- Hydroxy-L-Arginine Hydrolase (pdb code 7euq). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of C86H-Y124N-G126H-H196S Mutant of N(Omega)- Hydroxy-L-Arginine Hydrolase, PDB code: 7euq:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7euq

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Manganese binding site 1 out of 4 in the Crystal Structure of C86H-Y124N-G126H-H196S Mutant 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 Crystal Structure of C86H-Y124N-G126H-H196S Mutant of N(Omega)- Hydroxy-L-Arginine Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:16.6
occ:1.00
 OD2 A:ASP109 2.2 15.5 1.0
NE2 A:HIS126 2.2 16.4 1.0
OD2 A:ASP113 2.2 19.5 1.0
ND1 A:HIS86 2.3 14.4 1.0
O A:HOH529 2.3 14.7 1.0
OD2 A:ASP198 2.3 15.0 1.0
CD2 A:HIS126 3.1 17.6 1.0
CG A:ASP109 3.1 15.3 1.0
CE1 A:HIS126 3.2 16.7 1.0
CG A:ASP113 3.2 18.8 1.0
CE1 A:HIS86 3.2 15.7 1.0
CG A:HIS86 3.2 16.1 1.0
CG A:ASP198 3.2 16.9 1.0
MN A:MN402 3.3 26.4 1.0
OD1 A:ASP109 3.4 17.7 1.0
OD1 A:ASP113 3.5 21.1 1.0
CB A:ASP198 3.5 15.5 1.0
CB A:HIS86 3.5 16.4 1.0
OH A:TYR107 4.1 13.8 1.0
CG A:HIS126 4.2 18.8 1.0
ND1 A:HIS126 4.2 16.4 1.0
NE2 A:HIS86 4.3 16.7 1.0
CD2 A:HIS86 4.4 16.4 1.0
OD1 A:ASP198 4.4 15.6 1.0
CE1 A:TYR107 4.4 14.7 1.0
CB A:ASP109 4.5 14.9 1.0
CB A:ASP113 4.5 17.2 1.0
CZ A:TYR107 4.6 13.4 1.0
OD2 A:ASP200 4.9 26.3 1.0
CA A:ASP198 5.0 15.1 1.0

Manganese binding site 2 out of 4 in 7euq

Go back to Manganese Binding Sites List in 7euq
Manganese binding site 2 out of 4 in the Crystal Structure of C86H-Y124N-G126H-H196S Mutant 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 Crystal Structure of C86H-Y124N-G126H-H196S Mutant of N(Omega)- Hydroxy-L-Arginine Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:26.4
occ:1.00
 O A:HOH529 1.9 14.7 1.0
OD1 A:ASP109 2.2 17.7 1.0
OD2 A:ASP200 2.2 26.3 1.0
OD2 A:ASP198 2.3 15.0 1.0
ND1 A:HIS111 2.4 27.9 1.0
OD1 A:ASP200 2.5 22.6 1.0
CG A:ASP200 2.7 23.9 1.0
CG A:ASP109 3.2 15.3 1.0
CG A:ASP198 3.2 16.9 1.0
CE1 A:HIS111 3.2 29.3 1.0
MN A:MN401 3.3 16.6 1.0
CG A:HIS111 3.5 27.2 1.0
OD2 A:ASP109 3.5 15.5 1.0
OD1 A:ASP198 3.8 15.6 1.0
CB A:HIS111 3.8 24.3 1.0
N A:HIS111 4.0 20.0 1.0
N A:GLY110 4.1 18.6 1.0
NE2 A:HIS126 4.2 16.4 1.0
CB A:ASP200 4.2 20.5 1.0
CE1 A:HIS126 4.2 16.7 1.0
CB A:ASP198 4.2 15.5 1.0
OD1 A:ASP113 4.3 21.1 1.0
O A:HOH549 4.4 21.3 1.0
NE2 A:HIS111 4.4 28.5 1.0
CB A:ASP109 4.5 14.9 1.0
CA A:HIS111 4.5 22.4 1.0
CD2 A:HIS111 4.6 27.4 1.0
CA A:GLY110 4.6 20.0 1.0
C A:GLY110 4.6 20.4 1.0
OD2 A:ASP113 4.7 19.5 1.0
O A:HOH612 4.8 42.1 1.0
CA A:ASP109 4.8 14.9 1.0
C A:ASP109 4.9 15.3 1.0
CG A:ASP113 4.9 18.8 1.0

Manganese binding site 3 out of 4 in 7euq

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Manganese binding site 3 out of 4 in the Crystal Structure of C86H-Y124N-G126H-H196S Mutant 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 Crystal Structure of C86H-Y124N-G126H-H196S Mutant of N(Omega)- Hydroxy-L-Arginine Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:16.1
occ:1.00
 OD2 B:ASP109 2.1 17.1 1.0
NE2 B:HIS126 2.2 16.3 1.0
OD2 B:ASP113 2.2 18.5 1.0
ND1 B:HIS86 2.2 15.7 1.0
OD2 B:ASP198 2.3 16.9 1.0
O B:HOH527 2.4 17.0 1.0
CG B:ASP109 3.1 15.8 1.0
CD2 B:HIS126 3.1 18.1 1.0
CG B:ASP113 3.2 18.8 1.0
CE1 B:HIS86 3.2 15.9 1.0
CE1 B:HIS126 3.2 17.1 1.0
CG B:ASP198 3.2 18.0 1.0
CG B:HIS86 3.3 17.4 1.0
MN B:MN402 3.3 25.1 1.0
OD1 B:ASP109 3.4 16.5 1.0
OD1 B:ASP113 3.5 20.3 1.0
CB B:ASP198 3.5 17.0 1.0
CB B:HIS86 3.6 17.9 1.0
OH B:TYR107 4.1 13.4 1.0
ND1 B:HIS126 4.2 15.3 1.0
CG B:HIS126 4.3 18.0 1.0
NE2 B:HIS86 4.3 17.7 1.0
OD1 B:ASP198 4.4 18.2 1.0
CD2 B:HIS86 4.4 18.4 1.0
CB B:ASP109 4.4 16.1 1.0
CE1 B:TYR107 4.5 13.6 1.0
CB B:ASP113 4.5 16.9 1.0
CZ B:TYR107 4.6 13.4 1.0
OD2 B:ASP200 4.8 24.0 1.0
CA B:ASP198 5.0 16.2 1.0
O B:HIS126 5.0 17.4 1.0

Manganese binding site 4 out of 4 in 7euq

Go back to Manganese Binding Sites List in 7euq
Manganese binding site 4 out of 4 in the Crystal Structure of C86H-Y124N-G126H-H196S Mutant 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 Crystal Structure of C86H-Y124N-G126H-H196S Mutant of N(Omega)- Hydroxy-L-Arginine Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:25.1
occ:1.00
 O B:HOH527 2.0 17.0 1.0
OD2 B:ASP200 2.2 24.0 1.0
OD1 B:ASP109 2.2 16.5 1.0
ND1 B:HIS111 2.3 22.3 1.0
OD2 B:ASP198 2.3 16.9 1.0
OD1 B:ASP200 2.4 22.4 1.0
CG B:ASP200 2.6 24.2 1.0
CG B:ASP109 3.2 15.8 1.0
CE1 B:HIS111 3.2 26.5 1.0
CG B:ASP198 3.2 18.0 1.0
MN B:MN401 3.3 16.1 1.0
CG B:HIS111 3.5 23.1 1.0
OD2 B:ASP109 3.5 17.1 1.0
OD1 B:ASP198 3.8 18.2 1.0
CB B:HIS111 3.8 22.0 1.0
N B:HIS111 3.9 20.2 1.0
N B:GLY110 4.1 18.6 1.0
CB B:ASP200 4.1 21.5 1.0
CB B:ASP198 4.2 17.0 1.0
NE2 B:HIS126 4.2 16.3 1.0
CE1 B:HIS126 4.2 17.1 1.0
OD1 B:ASP113 4.3 20.3 1.0
NE2 B:HIS111 4.4 25.8 1.0
O B:HOH545 4.5 22.7 1.0
CB B:ASP109 4.5 16.1 1.0
CA B:HIS111 4.5 21.2 1.0
CD2 B:HIS111 4.5 25.5 1.0
CA B:GLY110 4.6 19.6 1.0
C B:GLY110 4.7 20.4 1.0
OD2 B:ASP113 4.7 18.5 1.0
CA B:ASP109 4.7 15.4 1.0
O B:HOH607 4.8 43.5 1.0
C B:ASP109 4.8 16.4 1.0
CG B:ASP113 4.9 18.8 1.0

Reference:

K.Oda, T.Sakaguchi, Y.Matoba. Catalytic Mechanism of Dcsb: Arginase Framework Used For Hydrolyzing Its Inhibitor. Protein Sci. V. 31 E4338 2022.
ISSN: ESSN 1469-896X
PubMed: 35634777
DOI: 10.1002/PRO.4338
Page generated: Sun Oct 6 08:34:30 2024

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