Manganese in PDB 6qaf: Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Cb- 1158/INCB001158

Enzymatic activity of Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Cb- 1158/INCB001158

All present enzymatic activity of Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Cb- 1158/INCB001158:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Cb- 1158/INCB001158, PDB code: 6qaf was solved by Y.Grobben, J.C.M.Uitdehaag, W.W.A.Tabak, G.J.R.Zaman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.74 / 1.61
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 90.130, 90.130, 69.111, 90.00, 90.00, 120.00
R / Rfree (%) 14.7 / 17.7

Other elements in 6qaf:

The structure of Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Cb- 1158/INCB001158 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Cb- 1158/INCB001158 (pdb code 6qaf). 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-1 at pH 9.0 in Complex with Cb- 1158/INCB001158, PDB code: 6qaf:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6qaf

Go back to Manganese Binding Sites List in 6qaf
Manganese binding site 1 out of 4 in the Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Cb- 1158/INCB001158


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-1 at pH 9.0 in Complex with Cb- 1158/INCB001158 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:17.1
occ:1.00
 OD2 A:ASP128 2.1 16.7 1.0
OD2 A:ASP124 2.2 15.1 1.0
O12 A:XC3403 2.2 18.5 1.0
ND1 A:HIS101 2.2 15.1 1.0
OD2 A:ASP232 2.3 16.8 1.0
O10 A:XC3403 2.3 18.7 1.0
B9 A:XC3403 2.8 18.8 1.0
CG A:ASP128 3.1 15.6 1.0
CG A:ASP124 3.1 14.1 1.0
CG A:HIS101 3.2 14.3 1.0
CE1 A:HIS101 3.2 14.7 1.0
CG A:ASP232 3.3 14.9 1.0
OD1 A:ASP128 3.3 15.9 1.0
MN A:MN402 3.3 18.1 1.0
CB A:HIS101 3.4 15.1 1.0
OD1 A:ASP124 3.4 15.3 1.0
CB A:ASP232 3.6 15.0 1.0
O11 A:XC3403 3.7 18.0 1.0
C8 A:XC3403 4.1 18.7 1.0
CD2 A:HIS101 4.3 15.3 1.0
NE2 A:HIS101 4.3 14.3 1.0
OD1 A:ASP232 4.4 15.9 1.0
NA A:NA404 4.4 30.0 1.0
NE1 A:TRP122 4.4 14.7 1.0
CB A:ASP128 4.4 16.0 1.0
O A:HIS141 4.5 16.8 1.0
CB A:ASP124 4.5 13.6 1.0
CZ2 A:TRP122 4.6 14.8 1.0
CG A:GLU277 4.8 17.0 1.0
CE2 A:TRP122 4.8 14.2 1.0
OE2 A:GLU277 4.9 17.3 1.0
CA A:HIS101 5.0 15.2 1.0
OD2 A:ASP234 5.0 15.2 1.0
CA A:ASP232 5.0 15.0 1.0

Manganese binding site 2 out of 4 in 6qaf

Go back to Manganese Binding Sites List in 6qaf
Manganese binding site 2 out of 4 in the Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Cb- 1158/INCB001158


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-1 at pH 9.0 in Complex with Cb- 1158/INCB001158 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:18.1
occ:1.00
 OD2 A:ASP234 2.2 15.2 1.0
ND1 A:HIS126 2.2 16.1 1.0
O12 A:XC3403 2.2 18.5 1.0
OD1 A:ASP124 2.2 15.3 1.0
OD2 A:ASP232 2.4 16.8 1.0
OD1 A:ASP234 2.5 15.7 1.0
O11 A:XC3403 2.6 18.0 1.0
CG A:ASP234 2.7 15.0 1.0
B9 A:XC3403 2.9 18.8 1.0
CE1 A:HIS126 3.1 15.2 1.0
CG A:ASP124 3.2 14.1 1.0
CG A:HIS126 3.2 14.4 1.0
CG A:ASP232 3.3 14.9 1.0
NA A:NA404 3.3 30.0 1.0
MN A:MN401 3.3 17.1 1.0
OD2 A:ASP124 3.5 15.1 1.0
CB A:HIS126 3.7 14.1 1.0
OD1 A:ASP232 3.8 15.9 1.0
O10 A:XC3403 3.8 18.7 1.0
OG1 A:THR246 4.0 18.0 1.0
N A:HIS126 4.0 12.7 1.0
C8 A:XC3403 4.2 18.7 1.0
CB A:ASP234 4.2 15.0 1.0
NE2 A:HIS126 4.2 15.2 1.0
N A:ALA125 4.3 14.1 1.0
CB A:ASP232 4.3 15.0 1.0
CD2 A:HIS126 4.3 15.2 1.0
C7 A:XC3403 4.3 19.5 1.0
OD1 A:ASP128 4.4 15.9 1.0
CA A:HIS126 4.5 13.8 1.0
CB A:ASP124 4.6 13.6 1.0
O A:HOH586 4.6 19.6 1.0
CB A:ALA125 4.7 14.2 1.0
CA A:ALA125 4.8 13.7 1.0
CA A:ASP124 4.9 13.4 1.0
C A:ALA125 4.9 13.7 1.0
OD2 A:ASP128 4.9 16.7 1.0
O A:THR246 4.9 17.3 1.0

Manganese binding site 3 out of 4 in 6qaf

Go back to Manganese Binding Sites List in 6qaf
Manganese binding site 3 out of 4 in the Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Cb- 1158/INCB001158


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-1 at pH 9.0 in Complex with Cb- 1158/INCB001158 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:18.0
occ:1.00
 OD2 B:ASP124 2.1 13.7 1.0
OD2 B:ASP128 2.1 17.5 1.0
ND1 B:HIS101 2.3 15.8 1.0
O12 B:XC3403 2.3 17.8 1.0
OD2 B:ASP232 2.3 16.6 1.0
O10 B:XC3403 2.3 19.3 1.0
B9 B:XC3403 2.8 18.2 1.0
CG B:ASP128 3.1 16.5 1.0
CG B:ASP124 3.1 13.9 1.0
CG B:HIS101 3.2 16.0 1.0
CE1 B:HIS101 3.2 15.4 1.0
CG B:ASP232 3.3 16.3 1.0
MN B:MN402 3.3 18.9 1.0
OD1 B:ASP128 3.4 17.5 1.0
OD1 B:ASP124 3.4 15.6 1.0
CB B:HIS101 3.4 16.6 1.0
O11 B:XC3403 3.6 19.2 1.0
CB B:ASP232 3.6 16.2 1.0
C8 B:XC3403 4.1 19.1 1.0
CD2 B:HIS101 4.3 15.7 1.0
NE2 B:HIS101 4.3 16.1 1.0
NA B:NA404 4.4 30.0 1.0
NE1 B:TRP122 4.4 16.9 1.0
OD1 B:ASP232 4.4 15.3 1.0
O B:HIS141 4.4 22.0 1.0
CB B:ASP128 4.5 16.5 1.0
CB B:ASP124 4.5 13.7 1.0
CZ2 B:TRP122 4.5 17.9 1.0
CE2 B:TRP122 4.8 17.4 1.0
CG B:GLU277 4.8 20.3 1.0
CA B:ASP232 4.9 16.4 1.0
CA B:HIS101 5.0 17.4 1.0
OE2 B:GLU277 5.0 21.6 1.0

Manganese binding site 4 out of 4 in 6qaf

Go back to Manganese Binding Sites List in 6qaf
Manganese binding site 4 out of 4 in the Crystal Structure of Human Arginase-1 at pH 9.0 in Complex with Cb- 1158/INCB001158


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-1 at pH 9.0 in Complex with Cb- 1158/INCB001158 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:18.9
occ:1.00
 OD2 B:ASP234 2.2 14.9 1.0
OD1 B:ASP124 2.2 15.6 1.0
O12 B:XC3403 2.2 17.8 1.0
OD2 B:ASP232 2.3 16.6 1.0
ND1 B:HIS126 2.4 16.4 1.0
OD1 B:ASP234 2.5 13.8 1.0
O11 B:XC3403 2.5 19.2 1.0
CG B:ASP234 2.7 14.7 1.0
B9 B:XC3403 2.9 18.2 1.0
NA B:NA404 3.2 30.0 1.0
CG B:ASP232 3.2 16.3 1.0
CG B:ASP124 3.2 13.9 1.0
CE1 B:HIS126 3.2 15.5 1.0
MN B:MN401 3.3 18.0 1.0
CG B:HIS126 3.4 16.4 1.0
OD2 B:ASP124 3.5 13.7 1.0
OD1 B:ASP232 3.7 15.3 1.0
CB B:HIS126 3.8 15.8 1.0
O10 B:XC3403 3.8 19.3 1.0
OG1 B:THR246 4.0 20.7 1.0
N B:HIS126 4.1 14.2 1.0
CB B:ASP232 4.2 16.2 1.0
C8 B:XC3403 4.2 19.1 1.0
CB B:ASP234 4.2 14.0 1.0
N B:ALA125 4.2 14.0 1.0
C7 B:XC3403 4.4 18.5 1.0
NE2 B:HIS126 4.4 16.6 1.0
CD2 B:HIS126 4.5 16.7 1.0
OD1 B:ASP128 4.5 17.5 1.0
CB B:ASP124 4.6 13.7 1.0
CA B:HIS126 4.6 15.4 1.0
O B:HOH531 4.7 19.7 1.0
CB B:ALA125 4.8 13.4 1.0
CA B:ALA125 4.8 13.8 1.0
OD2 B:ASP128 4.9 17.5 1.0
CA B:ASP124 4.9 14.0 1.0
C B:ALA125 4.9 13.6 1.0
O B:THR246 4.9 18.0 1.0

Reference:

Y.Grobben, J.C.M.Uitdehaag, W.W.A.Tabak, G.J.R.Zaman. Structural Insights Into Human Arginase-1 pH Dependence and Its Inhibition By the Small Molecule Inhibitor Cb-1158 Journal of Structural 2019BIOLOGY: X.
ISSN: ESSN 2590-1524
DOI: 10.1016/J.YJSBX.2019.100014
Page generated: Tue Dec 15 04:59:04 2020

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