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Manganese in PDB 4gwd: Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex

Enzymatic activity of Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex

All present enzymatic activity of Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex, PDB code: 4gwd was solved by E.L.D'antonio, Y.Hai, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.53
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 91.082, 91.082, 69.903, 90.00, 90.00, 120.00
R / Rfree (%) 16 / 21.5

Other elements in 4gwd:

The structure of Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex (pdb code 4gwd). 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 MN2+2,ZN2+-Human Arginase I-Abh Complex, PDB code: 4gwd:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4gwd

Go back to Manganese Binding Sites List in 4gwd
Manganese binding site 1 out of 4 in the Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex


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 MN2+2,ZN2+-Human Arginase I-Abh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:16.1
occ:1.00
 OD1 A:ASP124 2.1 13.9 1.0
OD2 A:ASP234 2.2 17.5 1.0
OD2 A:ASP232 2.3 15.4 1.0
ND1 A:HIS126 2.3 15.9 1.0
OD1 A:ASP234 2.3 14.8 1.0
O1 A:ABH404 2.4 17.2 1.0
CG A:ASP234 2.6 15.3 1.0
O3 A:ABH404 3.0 17.6 1.0
CE1 A:HIS126 3.1 16.2 1.0
CG A:ASP124 3.1 13.7 1.0
CG A:ASP232 3.2 18.1 1.0
B A:ABH404 3.3 15.3 1.0
MN A:MN402 3.3 16.1 1.0
CG A:HIS126 3.4 15.8 1.0
OD2 A:ASP124 3.4 15.1 1.0
OD1 A:ASP232 3.7 16.5 1.0
CB A:HIS126 3.8 15.4 1.0
OG1 A:THR246 4.0 15.1 1.0
N A:HIS126 4.0 14.0 1.0
N A:ALA125 4.1 13.8 1.0
CB A:ASP234 4.1 14.8 1.0
O2 A:ABH404 4.1 15.8 1.0
CB A:ASP232 4.2 18.8 1.0
NE2 A:HIS126 4.3 15.7 1.0
CD2 A:HIS126 4.4 14.7 1.0
CB A:ASP124 4.4 13.8 1.0
CE A:ABH404 4.5 14.3 1.0
CD A:ABH404 4.5 14.8 1.0
OD2 A:ASP128 4.5 13.8 1.0
CA A:HIS126 4.5 14.9 1.0
O A:HOH502 4.6 15.0 1.0
CB A:ALA125 4.7 14.2 1.0
C A:ALA125 4.8 13.9 1.0
CA A:ALA125 4.8 14.5 1.0
CA A:ASP124 4.8 13.8 1.0
O A:THR246 4.9 16.9 1.0
OD1 A:ASP128 4.9 12.3 1.0
C A:ASP124 4.9 12.2 1.0
CA A:ASP234 5.0 14.3 1.0

Manganese binding site 2 out of 4 in 4gwd

Go back to Manganese Binding Sites List in 4gwd
Manganese binding site 2 out of 4 in the Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex


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 MN2+2,ZN2+-Human Arginase I-Abh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:16.1
occ:1.00
 OD2 A:ASP124 2.1 15.1 1.0
OD1 A:ASP128 2.2 12.3 1.0
OD2 A:ASP232 2.3 15.4 1.0
O1 A:ABH404 2.3 17.2 1.0
ND1 A:HIS101 2.3 14.9 1.0
O2 A:ABH404 2.5 15.8 1.0
B A:ABH404 2.9 15.3 1.0
CG A:ASP124 3.1 13.7 1.0
CG A:ASP128 3.1 12.6 1.0
CG A:HIS101 3.2 15.8 1.0
CG A:ASP232 3.2 18.1 1.0
CE1 A:HIS101 3.3 14.8 1.0
MN A:MN401 3.3 16.1 1.0
OD2 A:ASP128 3.4 13.8 1.0
CB A:HIS101 3.4 16.3 1.0
OD1 A:ASP124 3.4 13.9 1.0
O3 A:ABH404 3.6 17.6 1.0
CB A:ASP232 3.6 18.8 1.0
CE A:ABH404 4.2 14.3 1.0
OD1 A:ASP232 4.3 16.5 1.0
CD2 A:HIS101 4.4 15.8 1.0
NE2 A:HIS101 4.4 13.8 1.0
O A:HIS141 4.4 13.2 1.0
NE1 A:TRP122 4.4 16.8 1.0
CB A:ASP124 4.4 13.8 1.0
CB A:ASP128 4.5 13.9 1.0
OE2 A:GLU277 4.5 19.9 1.0
ZN A:ZN403 4.5 20.0 1.0
CZ2 A:TRP122 4.5 14.0 1.0
CE2 A:TRP122 4.8 13.2 1.0
CG A:GLU277 4.9 16.5 1.0
OD2 A:ASP234 4.9 17.5 1.0
CA A:ASP232 4.9 16.0 1.0
CA A:HIS101 4.9 19.0 1.0

Manganese binding site 3 out of 4 in 4gwd

Go back to Manganese Binding Sites List in 4gwd
Manganese binding site 3 out of 4 in the Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex


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 MN2+2,ZN2+-Human Arginase I-Abh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:18.5
occ:1.00
 OD2 B:ASP234 2.1 18.5 1.0
OD1 B:ASP124 2.2 15.0 1.0
OD2 B:ASP232 2.3 17.1 1.0
O1 B:ABH404 2.4 24.0 1.0
OD1 B:ASP234 2.4 15.2 1.0
ND1 B:HIS126 2.5 18.0 1.0
CG B:ASP234 2.6 18.0 1.0
O3 B:ABH404 2.9 24.3 1.0
B B:ABH404 3.1 24.7 1.0
CG B:ASP232 3.2 17.4 1.0
CG B:ASP124 3.2 12.9 1.0
MN B:MN402 3.3 19.3 1.0
CE1 B:HIS126 3.3 18.2 1.0
OD2 B:ASP124 3.5 14.3 1.0
CG B:HIS126 3.6 19.1 1.0
OD1 B:ASP232 3.7 16.7 1.0
OG1 B:THR246 3.8 19.8 1.0
O2 B:ABH404 3.8 22.6 1.0
CB B:HIS126 3.9 18.9 1.0
N B:HIS126 4.0 16.6 1.0
CB B:ASP234 4.1 16.8 1.0
CB B:ASP232 4.1 18.0 1.0
N B:ALA125 4.2 15.3 1.0
CE B:ABH404 4.4 23.8 1.0
NE2 B:HIS126 4.5 17.0 1.0
CB B:ASP124 4.5 15.1 1.0
CD B:ABH404 4.5 25.1 1.0
OD2 B:ASP128 4.6 20.1 1.0
CA B:HIS126 4.6 18.2 1.0
O B:HOH503 4.6 16.7 1.0
CD2 B:HIS126 4.6 16.6 1.0
CB B:ALA125 4.7 13.2 1.0
O B:THR246 4.7 19.2 1.0
ZN B:ZN403 4.8 26.7 1.0
CA B:ALA125 4.9 15.4 1.0
C B:ALA125 4.9 16.0 1.0
OD1 B:ASP128 4.9 19.1 1.0
CA B:ASP124 4.9 13.8 1.0
CA B:ASP234 5.0 17.3 1.0

Manganese binding site 4 out of 4 in 4gwd

Go back to Manganese Binding Sites List in 4gwd
Manganese binding site 4 out of 4 in the Crystal Structure of the MN2+2,ZN2+-Human Arginase I-Abh Complex


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 MN2+2,ZN2+-Human Arginase I-Abh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:19.3
occ:1.00
 OD1 B:ASP128 2.2 19.1 1.0
ND1 B:HIS101 2.2 21.5 1.0
OD2 B:ASP124 2.3 14.3 1.0
OD2 B:ASP232 2.3 17.1 1.0
O2 B:ABH404 2.5 22.6 1.0
O1 B:ABH404 2.5 24.0 1.0
B B:ABH404 3.0 24.7 1.0
CG B:ASP128 3.2 20.0 1.0
CG B:HIS101 3.2 20.7 1.0
CG B:ASP124 3.2 12.9 1.0
CE1 B:HIS101 3.2 18.9 1.0
CG B:ASP232 3.3 17.4 1.0
MN B:MN401 3.3 18.5 1.0
CB B:HIS101 3.4 19.4 1.0
OD2 B:ASP128 3.5 20.1 1.0
OD1 B:ASP124 3.5 15.0 1.0
CB B:ASP232 3.6 18.0 1.0
O3 B:ABH404 3.8 24.3 1.0
CE B:ABH404 4.3 23.8 1.0
CD2 B:HIS101 4.3 21.0 1.0
NE2 B:HIS101 4.3 17.8 1.0
O B:HIS141 4.4 18.7 1.0
OD1 B:ASP232 4.4 16.7 1.0
NE1 B:TRP122 4.4 17.4 1.0
ZN B:ZN403 4.5 26.7 1.0
CZ2 B:TRP122 4.5 17.5 1.0
CB B:ASP128 4.5 19.1 1.0
CB B:ASP124 4.6 15.1 1.0
OE2 B:GLU277 4.7 26.8 1.0
CG B:GLU277 4.8 19.4 1.0
CE2 B:TRP122 4.8 17.8 1.0
OD2 B:ASP234 4.9 18.5 1.0
CA B:HIS101 4.9 19.3 1.0
CA B:ASP232 4.9 17.5 1.0

Reference:

E.L.D'antonio, Y.Hai, D.W.Christianson. Structure and Function of Non-Native Metal Clusters in Human Arginase I. Biochemistry V. 51 8399 2012.
ISSN: ISSN 0006-2960
PubMed: 23061982
DOI: 10.1021/BI301145N
Page generated: Sat Oct 5 19:40:14 2024

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