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Magnesium 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:

Manganese (Mn) 4 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 7euq

Go back to Magnesium Binding Sites List in 7euq
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg403

b:32.2
occ:1.00
 O A:HOH594 1.9 33.6 1.0
O A:HOH546 2.0 29.0 1.0
O A:HOH617 2.0 25.6 1.0
O A:HOH614 2.1 37.2 1.0
O A:HOH622 2.1 29.7 1.0
O A:HOH599 2.2 28.9 1.0
O A:HOH541 3.9 20.4 1.0
O A:HOH607 4.0 43.7 1.0
O A:ASN77 4.1 21.8 1.0
O A:HOH618 4.1 36.3 1.0
O A:ASP76 4.1 28.9 1.0
C A:ASP76 4.3 27.2 1.0
O A:HOH548 4.3 25.6 1.0
O A:GLY75 4.3 27.1 1.0
CA A:ASP76 4.5 30.2 1.0
C A:ASN77 4.6 23.9 1.0
O A:LEU234 4.7 22.2 1.0
N A:ASN77 4.8 25.6 1.0
O A:ILE235 4.8 22.8 1.0

Magnesium binding site 2 out of 4 in 7euq

Go back to Magnesium Binding Sites List in 7euq
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg404

b:22.7
occ:1.00
 O A:HOH575 3.0 39.2 1.0
NE A:ARG59 3.2 19.9 0.6
O A:HOH560 3.3 25.5 1.0
O A:HOH539 3.5 31.5 1.0
CD A:ARG59 3.9 20.2 0.6
CA A:PRO56 4.0 25.4 1.0
NH2 A:ARG59 4.1 20.8 0.6
CZ A:ARG59 4.1 20.1 0.6
CD A:ARG59 4.1 22.2 0.4
CB A:ARG59 4.3 21.9 0.4
CB A:ARG59 4.3 20.8 0.6
CG A:ARG59 4.4 22.4 0.4
O A:PRO56 4.6 26.8 1.0
N A:PRO56 4.7 23.1 1.0
CB A:PRO56 4.7 27.0 1.0
CG A:ARG59 4.7 20.7 0.6
C A:PRO56 4.9 25.4 1.0
O A:LEU55 5.0 23.2 1.0

Magnesium binding site 3 out of 4 in 7euq

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Magnesium 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 Magnesium with other atoms in the Mg 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
A:Mg405

b:22.8
occ:1.00
 O B:HOH571 3.0 35.3 1.0
NE B:ARG59 3.1 31.0 1.0
ND2 A:ASN243 3.2 23.0 1.0
O B:HOH560 3.2 24.4 1.0
O B:HOH559 3.4 32.6 1.0
N A:ALA16 3.5 23.8 1.0
CZ3 A:TRP17 3.8 32.4 1.0
CD B:ARG59 3.8 26.5 1.0
CE3 A:TRP17 3.9 28.9 1.0
CA A:ALA15 3.9 23.2 1.0
CB A:ALA15 3.9 25.6 1.0
CZ B:ARG59 4.0 32.5 1.0
NH2 B:ARG59 4.0 32.5 1.0
CA B:PRO56 4.0 23.8 1.0
CG A:ASN243 4.1 21.3 1.0
OD1 A:ASN243 4.1 23.7 1.0
CB A:ALA16 4.1 25.7 1.0
C A:ALA15 4.2 23.9 1.0
CB B:ARG59 4.3 22.1 1.0
CA A:ALA16 4.4 24.0 1.0
O B:PRO56 4.5 23.4 1.0
CB B:PRO56 4.7 25.3 1.0
CG B:ARG59 4.7 24.4 1.0
N B:PRO56 4.7 22.7 1.0
CH2 A:TRP17 4.7 29.7 1.0
C B:PRO56 4.9 23.8 1.0
CD2 A:TRP17 4.9 26.6 1.0
O B:LEU55 4.9 20.1 1.0
N A:TRP17 4.9 21.0 1.0

Magnesium binding site 4 out of 4 in 7euq

Go back to Magnesium Binding Sites List in 7euq
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg403

b:33.8
occ:1.00
 O B:HOH611 1.9 29.5 1.0
O B:HOH558 2.0 34.5 1.0
O B:HOH618 2.0 30.0 1.0
O B:HOH598 2.1 27.1 1.0
O B:HOH548 2.2 28.4 1.0
O B:HOH610 2.2 36.6 1.0
O B:HOH541 3.9 21.1 1.0
O B:ASN77 4.3 21.7 1.0
O B:HOH538 4.3 23.4 1.0
O B:ASP76 4.4 30.1 1.0
O B:GLY75 4.5 27.6 1.0
C B:ASP76 4.5 27.5 1.0
O B:LEU234 4.6 21.7 1.0
O B:ILE235 4.7 21.3 1.0
CA B:ASP76 4.8 29.3 1.0
C B:ASN77 4.8 21.9 1.0
CA B:ILE235 4.9 21.0 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: Wed Oct 2 20:59:49 2024

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