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Manganese in PDB 1d3v: Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog

Enzymatic activity of Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog

All present enzymatic activity of Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog, PDB code: 1d3v was solved by J.D.Cox, N.N.Kim, A.M.Traish, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 91.300, 91.300, 69.900, 90.00, 90.00, 120.00
R / Rfree (%) 15.7 / 17.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog (pdb code 1d3v). 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 the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog, PDB code: 1d3v:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1d3v

Go back to Manganese Binding Sites List in 1d3v
Manganese binding site 1 out of 4 in the Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog


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 Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:9.5
occ:1.00
 OD2 A:ASP124 2.1 7.5 1.0
ND1 A:HIS101 2.2 10.8 1.0
O1 A:ABH551 2.2 20.0 1.0
OD2 A:ASP128 2.2 8.2 1.0
O2 A:ABH551 2.4 17.6 1.0
OD2 A:ASP232 2.4 10.4 1.0
B A:ABH551 2.8 18.4 1.0
CE1 A:HIS101 3.1 10.3 1.0
CG A:ASP124 3.2 6.7 1.0
CG A:ASP128 3.2 6.8 1.0
CG A:HIS101 3.2 11.6 1.0
CG A:ASP232 3.3 9.6 1.0
MN A:MN501 3.4 10.5 1.0
OD1 A:ASP124 3.5 5.8 1.0
OD1 A:ASP128 3.5 5.6 1.0
CB A:HIS101 3.5 11.7 1.0
O3 A:ABH551 3.6 19.9 1.0
CB A:ASP232 3.6 9.5 1.0
CE A:ABH551 4.1 18.6 1.0
NE2 A:HIS101 4.3 9.9 1.0
CD2 A:HIS101 4.3 11.6 1.0
NE1 A:TRP122 4.3 10.4 1.0
CB A:ASP124 4.5 6.8 1.0
OD1 A:ASP232 4.5 9.3 1.0
O A:HIS141 4.5 10.7 1.0
CB A:ASP128 4.6 7.3 1.0
CZ2 A:TRP122 4.6 10.4 1.0
CE2 A:TRP122 4.8 10.6 1.0
CG A:GLU277 4.8 11.0 1.0
CA A:ASP232 5.0 9.8 1.0

Manganese binding site 2 out of 4 in 1d3v

Go back to Manganese Binding Sites List in 1d3v
Manganese binding site 2 out of 4 in the Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog


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 Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:10.5
occ:1.00
 OD2 A:ASP234 2.2 9.1 1.0
O1 A:ABH551 2.2 20.0 1.0
OD2 A:ASP232 2.3 10.4 1.0
OD1 A:ASP124 2.3 5.8 1.0
ND1 A:HIS126 2.5 9.0 1.0
OD1 A:ASP234 2.6 10.4 1.0
CG A:ASP234 2.7 10.3 1.0
O3 A:ABH551 2.9 19.9 1.0
B A:ABH551 3.1 18.4 1.0
CG A:ASP124 3.2 6.7 1.0
CG A:ASP232 3.2 9.6 1.0
CE1 A:HIS126 3.4 7.5 1.0
MN A:MN500 3.4 9.5 1.0
OD2 A:ASP124 3.5 7.5 1.0
CG A:HIS126 3.6 8.7 1.0
OD1 A:ASP232 3.8 9.3 1.0
CB A:HIS126 3.9 8.3 1.0
O2 A:ABH551 4.1 17.6 1.0
N A:HIS126 4.2 7.9 1.0
CB A:ASP232 4.2 9.5 1.0
CE A:ABH551 4.2 18.6 1.0
CB A:ASP234 4.2 9.4 1.0
CD A:ABH551 4.3 17.3 1.0
N A:ALA125 4.3 8.9 1.0
NE2 A:HIS126 4.6 8.2 1.0
O A:HOH555 4.6 8.5 1.0
CB A:ASP124 4.6 6.8 1.0
OD1 A:ASP128 4.7 5.6 1.0
CA A:HIS126 4.7 8.4 1.0
CD2 A:HIS126 4.7 7.5 1.0
OD2 A:ASP128 4.9 8.2 1.0
CB A:ALA125 4.9 8.2 1.0
CA A:ASP124 5.0 8.4 1.0
C A:ALA125 5.0 7.8 1.0
O A:HOH645 5.0 18.6 1.0

Manganese binding site 3 out of 4 in 1d3v

Go back to Manganese Binding Sites List in 1d3v
Manganese binding site 3 out of 4 in the Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog


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 Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:9.6
occ:1.00
 OD2 B:ASP128 2.2 8.7 1.0
OD2 B:ASP124 2.2 8.8 1.0
O1 B:ABH552 2.2 16.9 1.0
ND1 B:HIS101 2.2 9.9 1.0
OD2 B:ASP232 2.3 11.2 1.0
O2 B:ABH552 2.4 15.9 1.0
B B:ABH552 2.9 15.8 1.0
CG B:ASP128 3.1 7.3 1.0
CE1 B:HIS101 3.2 8.6 1.0
CG B:ASP124 3.2 8.8 1.0
CG B:HIS101 3.2 10.2 1.0
CG B:ASP232 3.3 10.4 1.0
OD1 B:ASP128 3.4 6.3 1.0
MN B:MN503 3.4 9.3 1.0
CB B:HIS101 3.5 11.3 1.0
OD1 B:ASP124 3.6 7.5 1.0
CB B:ASP232 3.7 9.6 1.0
O3 B:ABH552 3.7 14.7 1.0
CE B:ABH552 4.1 15.8 1.0
NE2 B:HIS101 4.4 9.2 1.0
NE1 B:TRP122 4.4 9.0 1.0
CD2 B:HIS101 4.4 9.9 1.0
OD1 B:ASP232 4.4 10.4 1.0
O B:HIS141 4.4 8.8 1.0
CB B:ASP124 4.5 8.3 1.0
CB B:ASP128 4.5 7.2 1.0
CZ2 B:TRP122 4.6 10.1 1.0
CE2 B:TRP122 4.8 9.3 1.0
CG B:GLU277 4.9 11.2 1.0
CA B:ASP232 5.0 9.2 1.0

Manganese binding site 4 out of 4 in 1d3v

Go back to Manganese Binding Sites List in 1d3v
Manganese binding site 4 out of 4 in the Crystal Structure of the Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog


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 Binuclear Manganese Metalloenzyme Arginase Complexed with 2(S)-Amino-6-Boronohexanoic Acid, An L-Arginine Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:9.3
occ:1.00
 OD1 B:ASP234 2.1 10.4 1.0
O1 B:ABH552 2.2 16.9 1.0
OD1 B:ASP124 2.3 7.5 1.0
OD2 B:ASP232 2.3 11.2 1.0
ND1 B:HIS126 2.4 9.0 1.0
OD2 B:ASP234 2.6 9.1 1.0
CG B:ASP234 2.7 10.2 1.0
O3 B:ABH552 3.0 14.7 1.0
B B:ABH552 3.2 15.8 1.0
CG B:ASP124 3.2 8.8 1.0
CE1 B:HIS126 3.2 7.9 1.0
CG B:ASP232 3.3 10.4 1.0
MN B:MN502 3.4 9.6 1.0
OD2 B:ASP124 3.4 8.8 1.0
CG B:HIS126 3.5 7.3 1.0
OD1 B:ASP232 3.8 10.4 1.0
CB B:HIS126 3.9 8.3 1.0
N B:HIS126 4.1 7.7 1.0
O2 B:ABH552 4.1 15.9 1.0
CB B:ASP234 4.2 9.6 1.0
N B:ALA125 4.2 8.3 1.0
CE B:ABH552 4.3 15.8 1.0
CB B:ASP232 4.3 9.6 1.0
CD B:ABH552 4.4 16.0 1.0
NE2 B:HIS126 4.4 8.6 1.0
OD1 B:ASP128 4.6 6.3 1.0
CD2 B:HIS126 4.6 7.2 1.0
CB B:ASP124 4.6 8.3 1.0
O B:HOH667 4.6 10.9 1.0
CA B:HIS126 4.6 8.1 1.0
CB B:ALA125 4.8 8.2 1.0
C B:ALA125 4.9 7.1 1.0
CA B:ALA125 4.9 7.9 1.0
OD2 B:ASP128 4.9 8.7 1.0
CA B:ASP124 5.0 9.3 1.0

Reference:

J.D.Cox, N.N.Kim, A.M.Traish, D.W.Christianson. Arginase-Boronic Acid Complex Highlights A Physiological Role in Erectile Function. Nat.Struct.Biol. V. 6 1043 1999.
ISSN: ISSN 1072-8368
PubMed: 10542097
DOI: 10.1038/14929
Page generated: Sat Oct 5 10:03:36 2024

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