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Manganese in PDB 2aeb: Crystal Structure of Human Arginase I at 1.29 A Resolution and Exploration of Inhibition in Immune Response.

Enzymatic activity of Crystal Structure of Human Arginase I at 1.29 A Resolution and Exploration of Inhibition in Immune Response.

All present enzymatic activity of Crystal Structure of Human Arginase I at 1.29 A Resolution and Exploration of Inhibition in Immune Response.:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Arginase I at 1.29 A Resolution and Exploration of Inhibition in Immune Response., PDB code: 2aeb was solved by L.Di Costanzo, G.Sabio, A.Mora, P.C.Rodriguez, A.C.Ochoa, F.Centeno, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 1.29
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 91.422, 91.422, 69.637, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 17.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Arginase I at 1.29 A Resolution and Exploration of Inhibition in Immune Response. (pdb code 2aeb). 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 Human Arginase I at 1.29 A Resolution and Exploration of Inhibition in Immune Response., PDB code: 2aeb:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2aeb

Go back to Manganese Binding Sites List in 2aeb
Manganese binding site 1 out of 4 in the Crystal Structure of Human Arginase I at 1.29 A Resolution and Exploration of Inhibition in Immune Response.


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 Human Arginase I at 1.29 A Resolution and Exploration of Inhibition in Immune Response. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2362

b:7.7
occ:1.00
 O1 A:ABH551 2.1 11.8 1.0
OD1 A:ASP234 2.2 8.5 1.0
OD1 A:ASP124 2.2 7.6 1.0
ND1 A:HIS126 2.2 8.0 1.0
OD2 A:ASP232 2.3 7.4 1.0
OD2 A:ASP234 2.4 8.6 1.0
CG A:ASP234 2.7 9.6 1.0
HO1 A:ABH551 2.7 17.7 1.0
O3 A:ABH551 2.8 13.7 1.0
HB2 A:HIS126 3.0 8.9 1.0
B A:ABH551 3.1 10.9 1.0
CG A:ASP232 3.1 6.5 1.0
CG A:ASP124 3.1 6.5 1.0
CE1 A:HIS126 3.2 7.7 1.0
CG A:HIS126 3.3 10.7 1.0
HE1 A:HIS126 3.3 9.3 1.0
MN A:MN2363 3.3 7.9 1.0
OD2 A:ASP124 3.5 8.4 1.0
HO3 A:ABH551 3.5 20.6 1.0
H A:HIS126 3.6 9.6 1.0
CB A:HIS126 3.6 7.4 1.0
OD1 A:ASP232 3.7 7.9 1.0
HCD1 A:ABH551 3.7 20.1 1.0
H A:ALA125 3.8 10.1 1.0
O2 A:ABH551 3.9 12.2 1.0
HB3 A:ALA125 3.9 11.3 1.0
HB3 A:ASP232 4.0 8.4 1.0
N A:HIS126 4.1 8.0 1.0
CB A:ASP234 4.2 9.0 1.0
CB A:ASP232 4.2 7.0 1.0
CE A:ABH551 4.2 14.1 1.0
HB3 A:HIS126 4.3 8.9 1.0
NE2 A:HIS126 4.3 8.5 1.0
N A:ALA125 4.3 8.4 1.0
CD2 A:HIS126 4.4 8.0 1.0
CD A:ABH551 4.4 16.8 1.0
HB A:THR246 4.4 13.4 1.0
HB2 A:ASP232 4.4 8.4 1.0
HA A:ASP124 4.4 7.4 1.0
CB A:ASP124 4.5 7.9 1.0
HB3 A:ASP234 4.5 10.8 1.0
OD1 A:ASP128 4.5 8.9 1.0
CA A:HIS126 4.5 8.9 1.0
HO2 A:ABH551 4.6 18.2 1.0
HCE2 A:ABH551 4.6 17.0 1.0
HB2 A:ASP234 4.6 10.8 1.0
O A:HOH2465 4.6 9.4 1.0
HG3 A:GLU277 4.6 14.0 1.0
CB A:ALA125 4.7 7.5 1.0
HCD2 A:ABH551 4.8 20.1 1.0
OD2 A:ASP128 4.8 7.1 1.0
CA A:ASP124 4.8 6.2 1.0
H A:ASP234 4.8 10.8 1.0
O A:HOH2391 4.9 15.2 1.0
CA A:ALA125 4.9 7.6 1.0
HB3 A:ASP124 4.9 9.5 1.0
HCE1 A:ABH551 4.9 17.0 1.0
C A:ALA125 4.9 6.7 1.0
C A:ASP124 5.0 7.5 1.0

Manganese binding site 2 out of 4 in 2aeb

Go back to Manganese Binding Sites List in 2aeb
Manganese binding site 2 out of 4 in the Crystal Structure of Human Arginase I at 1.29 A Resolution and Exploration of Inhibition in Immune Response.


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 Human Arginase I at 1.29 A Resolution and Exploration of Inhibition in Immune Response. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2363

b:7.9
occ:1.00
 OD2 A:ASP124 2.1 8.4 1.0
OD2 A:ASP128 2.1 7.1 1.0
ND1 A:HIS101 2.2 6.8 1.0
O1 A:ABH551 2.2 11.8 1.0
OD2 A:ASP232 2.2 7.4 1.0
O2 A:ABH551 2.3 12.2 1.0
HO1 A:ABH551 2.4 17.7 1.0
HO2 A:ABH551 2.7 18.2 1.0
B A:ABH551 2.8 10.9 1.0
CG A:ASP128 3.0 5.9 1.0
CG A:ASP124 3.0 6.5 1.0
HB2 A:ASP232 3.0 8.4 1.0
CE1 A:HIS101 3.2 8.3 1.0
CG A:HIS101 3.2 9.1 1.0
CG A:ASP232 3.3 6.5 1.0
HB2 A:HIS101 3.3 10.7 1.0
MN A:MN2362 3.3 7.7 1.0
HE1 A:HIS101 3.3 10.0 1.0
OD1 A:ASP128 3.4 8.9 1.0
OD1 A:ASP124 3.4 7.6 1.0
HB3 A:HIS101 3.4 10.7 1.0
CB A:HIS101 3.5 8.9 1.0
O3 A:ABH551 3.5 13.7 1.0
CB A:ASP232 3.6 7.0 1.0
HE1 A:TRP122 3.7 10.4 1.0
HB3 A:ASP232 3.8 8.4 1.0
HB2 A:HIS126 3.9 8.9 1.0
HZ2 A:TRP122 4.0 10.6 1.0
HCE2 A:ABH551 4.1 17.0 1.0
HG3 A:GLU277 4.1 14.0 1.0
CE A:ABH551 4.1 14.1 1.0
NE2 A:HIS101 4.3 9.8 1.0
HO3 A:ABH551 4.3 20.6 1.0
CD2 A:HIS101 4.3 8.5 1.0
OD1 A:ASP232 4.4 7.9 1.0
NE1 A:TRP122 4.4 8.7 1.0
CB A:ASP124 4.4 7.9 1.0
CB A:ASP128 4.4 10.7 1.0
HB2 A:ASP124 4.5 9.5 1.0
O A:HIS141 4.5 9.3 1.0
HCE1 A:ABH551 4.6 17.0 1.0
HB2 A:ASP128 4.6 12.8 1.0
CZ2 A:TRP122 4.6 8.8 1.0
HB3 A:ASP128 4.7 12.8 1.0
CE2 A:TRP122 4.9 7.9 1.0
HB3 A:ASP124 4.9 9.5 1.0
CB A:HIS126 4.9 7.4 1.0
HG2 A:GLU277 4.9 14.0 1.0
CG A:GLU277 4.9 11.6 1.0
CA A:ASP232 5.0 4.6 1.0

Manganese binding site 3 out of 4 in 2aeb

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Manganese binding site 3 out of 4 in the Crystal Structure of Human Arginase I at 1.29 A Resolution and Exploration of Inhibition in Immune Response.


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 Human Arginase I at 1.29 A Resolution and Exploration of Inhibition in Immune Response. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1362

b:10.6
occ:1.00
 OD2 B:ASP234 2.1 12.0 1.0
O1 B:ABH552 2.2 10.9 1.0
OD1 B:ASP124 2.2 9.9 1.0
ND1 B:HIS126 2.3 11.0 1.0
OD2 B:ASP232 2.3 10.7 1.0
OD1 B:ASP234 2.4 12.7 1.0
CG B:ASP234 2.6 14.3 1.0
O3 B:ABH552 2.7 15.2 1.0
HO1 B:ABH552 2.9 16.3 1.0
B B:ABH552 3.1 15.7 1.0
CG B:ASP232 3.1 13.6 1.0
HB2 B:HIS126 3.1 14.1 1.0
CG B:ASP124 3.2 8.4 1.0
CE1 B:HIS126 3.2 10.0 1.0
HE1 B:HIS126 3.3 12.0 1.0
CG B:HIS126 3.3 9.1 1.0
MN B:MN1363 3.3 11.2 1.0
HO3 B:ABH552 3.5 22.8 1.0
OD2 B:ASP124 3.6 9.8 1.0
OD1 B:ASP232 3.6 12.7 1.0
H B:HIS126 3.7 13.9 1.0
CB B:HIS126 3.7 11.7 1.0
HCD1 B:ABH552 3.7 21.3 1.0
H B:ALA125 3.8 10.3 1.0
O2 B:ABH552 3.9 15.4 1.0
HB3 B:ALA125 4.0 15.1 1.0
HB3 B:ASP232 4.0 15.5 1.0
CB B:ASP234 4.1 9.0 1.0
CB B:ASP232 4.2 12.9 1.0
CE B:ABH552 4.2 18.8 1.0
N B:HIS126 4.2 11.6 1.0
NE2 B:HIS126 4.3 13.7 1.0
CD B:ABH552 4.3 17.8 1.0
N B:ALA125 4.4 8.6 1.0
HB B:THR246 4.4 17.5 1.0
CD2 B:HIS126 4.4 10.9 1.0
HB2 B:ASP232 4.4 15.5 1.0
HCD2 B:ABH552 4.4 21.3 1.0
HB3 B:HIS126 4.4 14.1 1.0
HA B:ASP124 4.5 10.9 1.0
HB2 B:ASP234 4.5 10.8 1.0
CB B:ASP124 4.5 11.2 1.0
HB3 B:ASP234 4.5 10.8 1.0
OD2 B:ASP128 4.6 10.8 1.0
O B:HOH1383 4.6 12.9 1.0
HG3 B:GLU277 4.6 16.3 1.0
CA B:HIS126 4.6 10.9 1.0
HCE2 B:ABH552 4.6 22.5 1.0
HO2 B:ABH552 4.6 23.1 1.0
CB B:ALA125 4.8 10.1 1.0
CA B:ASP124 4.8 9.1 1.0
H B:ASP234 4.8 12.3 1.0
OD1 B:ASP128 4.9 10.1 1.0
O B:HOH1453 4.9 18.6 1.0
HCE1 B:ABH552 4.9 22.5 1.0
CA B:ALA125 4.9 10.5 1.0
C B:ALA125 4.9 9.1 1.0
HB3 B:ASP124 5.0 13.5 1.0
C B:ASP124 5.0 9.1 1.0

Manganese binding site 4 out of 4 in 2aeb

Go back to Manganese Binding Sites List in 2aeb
Manganese binding site 4 out of 4 in the Crystal Structure of Human Arginase I at 1.29 A Resolution and Exploration of Inhibition in Immune Response.


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 Human Arginase I at 1.29 A Resolution and Exploration of Inhibition in Immune Response. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1363

b:11.2
occ:1.00
 O1 B:ABH552 2.1 10.9 1.0
OD1 B:ASP128 2.1 10.1 1.0
OD2 B:ASP124 2.2 9.8 1.0
OD2 B:ASP232 2.2 10.7 1.0
ND1 B:HIS101 2.2 13.0 1.0
HO1 B:ABH552 2.3 16.3 1.0
O2 B:ABH552 2.3 15.4 1.0
HO2 B:ABH552 2.6 23.1 1.0
B B:ABH552 2.8 15.7 1.0
HB2 B:ASP232 3.0 15.5 1.0
CG B:ASP124 3.0 8.4 1.0
CG B:ASP128 3.1 9.2 1.0
CE1 B:HIS101 3.2 11.4 1.0
CG B:ASP232 3.2 13.6 1.0
CG B:HIS101 3.2 11.0 1.0
HB2 B:HIS101 3.2 16.4 1.0
HE1 B:HIS101 3.3 13.7 1.0
MN B:MN1362 3.3 10.6 1.0
OD1 B:ASP124 3.4 9.9 1.0
OD2 B:ASP128 3.4 10.8 1.0
HB3 B:HIS101 3.5 16.4 1.0
CB B:ASP232 3.5 12.9 1.0
CB B:HIS101 3.5 13.6 1.0
O3 B:ABH552 3.6 15.2 1.0
HE1 B:TRP122 3.6 13.3 1.0
HB3 B:ASP232 3.8 15.5 1.0
HZ2 B:TRP122 3.9 14.2 1.0
HCE2 B:ABH552 4.0 22.5 1.0
HB2 B:HIS126 4.0 14.1 1.0
HG3 B:GLU277 4.1 16.3 1.0
CE B:ABH552 4.1 18.8 1.0
NE2 B:HIS101 4.3 9.8 1.0
HO3 B:ABH552 4.3 22.8 1.0
NE1 B:TRP122 4.3 11.1 1.0
CD2 B:HIS101 4.4 10.9 1.0
OD1 B:ASP232 4.4 12.7 1.0
CB B:ASP124 4.4 11.2 1.0
HB2 B:ASP124 4.4 13.5 1.0
CB B:ASP128 4.5 10.4 1.0
O B:HIS141 4.6 11.7 1.0
HB2 B:ASP128 4.6 12.4 1.0
HCE1 B:ABH552 4.6 22.5 1.0
CZ2 B:TRP122 4.6 11.8 1.0
HB3 B:ASP128 4.7 12.4 1.0
CE2 B:TRP122 4.8 14.0 1.0
HB3 B:ASP124 4.9 13.5 1.0
OD1 B:ASP234 4.9 12.7 1.0
HG2 B:GLU277 4.9 16.3 1.0
CG B:GLU277 4.9 13.6 1.0
CA B:ASP232 4.9 10.0 1.0
CB B:HIS126 5.0 11.7 1.0
HCD1 B:ABH552 5.0 21.3 1.0
OD2 B:ASP234 5.0 12.0 1.0
OE2 B:GLU277 5.0 14.5 1.0

Reference:

L.Di Costanzo, G.Sabio, A.Mora, P.C.Rodriguez, A.C.Ochoa, F.Centeno, D.W.Christianson. Crystal Structure of Human Arginase I at 1.29 A Resolution and Exploration of Inhibition in the Immune Response. Proc.Natl.Acad.Sci.Usa V. 102 13058 2005.
ISSN: ISSN 0027-8424
PubMed: 16141327
DOI: 10.1073/PNAS.0504027102
Page generated: Sat Oct 5 13:24:20 2024

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