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Manganese in PDB 8oxg: Crystal Structure of Human Methionine Aminopeptidase-2 Complexed with (3R,4S,5S,6R)-5-Methoxy-4-[(2R,3R)-2-Methyl-3-(3-Methyl-2-Buten-1- Yl)-2-Oxiranyl]-1-Oxaspiro[2.5]Oct-6-Yl N-(Trans-4-Aminocyclohexyl) Carbamate

Enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 Complexed with (3R,4S,5S,6R)-5-Methoxy-4-[(2R,3R)-2-Methyl-3-(3-Methyl-2-Buten-1- Yl)-2-Oxiranyl]-1-Oxaspiro[2.5]Oct-6-Yl N-(Trans-4-Aminocyclohexyl) Carbamate

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase-2 Complexed with (3R,4S,5S,6R)-5-Methoxy-4-[(2R,3R)-2-Methyl-3-(3-Methyl-2-Buten-1- Yl)-2-Oxiranyl]-1-Oxaspiro[2.5]Oct-6-Yl N-(Trans-4-Aminocyclohexyl) Carbamate:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Human Methionine Aminopeptidase-2 Complexed with (3R,4S,5S,6R)-5-Methoxy-4-[(2R,3R)-2-Methyl-3-(3-Methyl-2-Buten-1- Yl)-2-Oxiranyl]-1-Oxaspiro[2.5]Oct-6-Yl N-(Trans-4-Aminocyclohexyl) Carbamate, PDB code: 8oxg was solved by S.Moss, P.Cornelius, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.84 / 1.73
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 119.05, 101.127, 83.737, 90, 98.76, 90
R / Rfree (%) 18.1 / 21.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Methionine Aminopeptidase-2 Complexed with (3R,4S,5S,6R)-5-Methoxy-4-[(2R,3R)-2-Methyl-3-(3-Methyl-2-Buten-1- Yl)-2-Oxiranyl]-1-Oxaspiro[2.5]Oct-6-Yl N-(Trans-4-Aminocyclohexyl) Carbamate (pdb code 8oxg). 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 Methionine Aminopeptidase-2 Complexed with (3R,4S,5S,6R)-5-Methoxy-4-[(2R,3R)-2-Methyl-3-(3-Methyl-2-Buten-1- Yl)-2-Oxiranyl]-1-Oxaspiro[2.5]Oct-6-Yl N-(Trans-4-Aminocyclohexyl) Carbamate, PDB code: 8oxg:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 8oxg

Go back to Manganese Binding Sites List in 8oxg
Manganese binding site 1 out of 4 in the Crystal Structure of Human Methionine Aminopeptidase-2 Complexed with (3R,4S,5S,6R)-5-Methoxy-4-[(2R,3R)-2-Methyl-3-(3-Methyl-2-Buten-1- Yl)-2-Oxiranyl]-1-Oxaspiro[2.5]Oct-6-Yl N-(Trans-4-Aminocyclohexyl) Carbamate


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 Methionine Aminopeptidase-2 Complexed with (3R,4S,5S,6R)-5-Methoxy-4-[(2R,3R)-2-Methyl-3-(3-Methyl-2-Buten-1- Yl)-2-Oxiranyl]-1-Oxaspiro[2.5]Oct-6-Yl N-(Trans-4-Aminocyclohexyl) Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:18.6
occ:1.00
 O A:HOH676 2.0 24.1 1.0
OD1 A:ASP262 2.1 16.9 1.0
OD2 A:ASP251 2.1 21.1 1.0
OE1 A:GLU459 2.1 19.2 1.0
O A:HOH812 2.2 18.4 1.0
OD1 A:ASP251 2.2 21.2 1.0
CG A:ASP251 2.5 19.6 1.0
CD A:GLU459 3.0 21.3 1.0
CG A:ASP262 3.0 20.3 1.0
OE2 A:GLU459 3.2 19.6 1.0
HE22 A:GLN457 3.3 18.0 0.0
OD2 A:ASP262 3.3 20.6 1.0
MN A:MN503 3.3 19.6 1.0
HZ A:PHE219 3.7 21.6 1.0
HB2 A:ALA264 3.8 19.2 1.0
O A:HOH728 3.9 23.2 1.0
H22 A:W5N501 3.9 20.1 0.0
OE1 A:GLU364 4.0 19.9 1.0
CB A:ASP251 4.0 18.8 1.0
NE2 A:GLN457 4.0 18.0 1.0
O A:HOH860 4.1 30.2 1.0
O A:HOH743 4.1 25.9 1.0
HE21 A:GLN457 4.2 18.0 0.0
CZ A:PHE219 4.2 22.2 1.0
HE1 A:PHE219 4.2 21.2 1.0
O3 A:W5N501 4.3 20.4 1.0
H A:CYS263 4.3 20.9 1.0
CB A:ASP262 4.4 22.0 1.0
HB3 A:ASP251 4.4 19.0 1.0
CG A:GLU459 4.4 18.1 1.0
HB2 A:ASP251 4.4 19.0 1.0
HE2 A:HIS331 4.4 15.4 0.0
CE1 A:PHE219 4.4 21.9 1.0
N A:CYS263 4.5 20.4 1.0
HA A:ASP262 4.5 21.8 1.0
C A:ASP262 4.6 20.7 1.0
HB3 A:GLU459 4.6 18.3 1.0
OE2 A:GLU364 4.7 23.1 1.0
HG2 A:GLU459 4.7 18.9 1.0
CD A:GLU364 4.7 22.9 1.0
CB A:ALA264 4.7 19.3 1.0
CA A:ASP262 4.7 22.8 1.0
H20 A:W5N501 4.8 18.5 1.0
HB3 A:ASP262 4.8 21.8 1.0
HA A:ASP251 4.8 19.3 1.0
HB2 A:GLU459 4.9 18.3 1.0
CB A:GLU459 4.9 18.4 1.0
CA A:ASP251 4.9 18.7 1.0
H24 A:W5N501 4.9 21.2 1.0
HB1 A:ALA264 5.0 19.2 1.0
HB2 A:ASP262 5.0 21.8 1.0

Manganese binding site 2 out of 4 in 8oxg

Go back to Manganese Binding Sites List in 8oxg
Manganese binding site 2 out of 4 in the Crystal Structure of Human Methionine Aminopeptidase-2 Complexed with (3R,4S,5S,6R)-5-Methoxy-4-[(2R,3R)-2-Methyl-3-(3-Methyl-2-Buten-1- Yl)-2-Oxiranyl]-1-Oxaspiro[2.5]Oct-6-Yl N-(Trans-4-Aminocyclohexyl) Carbamate


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 Methionine Aminopeptidase-2 Complexed with (3R,4S,5S,6R)-5-Methoxy-4-[(2R,3R)-2-Methyl-3-(3-Methyl-2-Buten-1- Yl)-2-Oxiranyl]-1-Oxaspiro[2.5]Oct-6-Yl N-(Trans-4-Aminocyclohexyl) Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:19.6
occ:1.00
 HE2 A:HIS331 1.2 15.4 0.0
NE2 A:HIS331 2.1 15.4 1.0
O A:HOH676 2.1 24.1 1.0
OE2 A:GLU459 2.1 19.6 1.0
OD2 A:ASP262 2.2 20.6 1.0
OE2 A:GLU364 2.2 23.1 1.0
HB1 A:ALA362 2.9 20.0 1.0
CG A:ASP262 3.0 20.3 1.0
H22 A:W5N501 3.0 20.1 0.0
CE1 A:HIS331 3.0 21.4 1.0
CD A:GLU364 3.0 22.9 1.0
CD2 A:HIS331 3.1 18.1 1.0
CD A:GLU459 3.2 21.3 1.0
HE1 A:HIS331 3.2 18.2 1.0
OE1 A:GLU364 3.3 19.9 1.0
HD2 A:HIS331 3.3 17.0 1.0
MN A:MN502 3.3 18.6 1.0
O3 A:W5N501 3.4 20.4 1.0
OD1 A:ASP262 3.4 16.9 1.0
HB2 A:ALA362 3.4 20.0 1.0
CB A:ALA362 3.5 20.1 1.0
OE1 A:GLU459 3.6 19.2 1.0
O A:HOH728 3.7 23.2 1.0
HB3 A:ALA362 3.7 20.0 1.0
H26 A:W5N501 4.0 21.4 1.0
H6 A:W5N501 4.0 17.6 1.0
HB3 A:ASP262 4.1 21.8 1.0
ND1 A:HIS331 4.2 15.0 1.0
CG A:HIS331 4.2 16.0 1.0
CB A:ASP262 4.2 22.0 1.0
H4 A:W5N501 4.2 20.0 1.0
O A:HOH812 4.3 18.4 1.0
CG A:GLU364 4.3 23.0 1.0
HG2 A:GLU364 4.3 22.8 1.0
HB3 A:GLU364 4.3 22.6 1.0
HA2 A:GLY330 4.4 19.3 1.0
CG A:GLU459 4.5 18.1 1.0
HG3 A:GLU459 4.5 18.9 1.0
HB2 A:ASP262 4.7 21.8 1.0
C12 A:W5N501 4.8 19.5 1.0
C15 A:W5N501 4.9 22.2 1.0
CB A:GLU364 4.9 22.2 1.0
C5 A:W5N501 4.9 16.6 1.0
HD1 A:HIS331 4.9 15.0 0.0
CA A:ALA362 5.0 19.8 1.0
H24 A:W5N501 5.0 21.2 1.0
HG2 A:GLU459 5.0 18.9 1.0
H7 A:W5N501 5.0 17.6 1.0
OD2 A:ASP251 5.0 21.1 1.0
HD13 A:ILE338 5.0 28.0 1.0

Manganese binding site 3 out of 4 in 8oxg

Go back to Manganese Binding Sites List in 8oxg
Manganese binding site 3 out of 4 in the Crystal Structure of Human Methionine Aminopeptidase-2 Complexed with (3R,4S,5S,6R)-5-Methoxy-4-[(2R,3R)-2-Methyl-3-(3-Methyl-2-Buten-1- Yl)-2-Oxiranyl]-1-Oxaspiro[2.5]Oct-6-Yl N-(Trans-4-Aminocyclohexyl) Carbamate


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 Methionine Aminopeptidase-2 Complexed with (3R,4S,5S,6R)-5-Methoxy-4-[(2R,3R)-2-Methyl-3-(3-Methyl-2-Buten-1- Yl)-2-Oxiranyl]-1-Oxaspiro[2.5]Oct-6-Yl N-(Trans-4-Aminocyclohexyl) Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:19.1
occ:1.00
 OD1 B:ASP262 2.0 19.7 1.0
OD2 B:ASP251 2.1 21.5 1.0
OE1 B:GLU459 2.1 19.6 1.0
O B:HOH788 2.1 20.3 1.0
O B:HOH634 2.1 24.5 1.0
OD1 B:ASP251 2.3 21.1 1.0
CG B:ASP251 2.5 19.6 1.0
CD B:GLU459 3.0 19.3 1.0
CG B:ASP262 3.0 20.6 1.0
MN B:MN503 3.3 21.6 1.0
OE2 B:GLU459 3.3 19.1 1.0
HE22 B:GLN457 3.3 16.9 0.0
OD2 B:ASP262 3.4 22.6 1.0
HZ B:PHE219 3.6 18.7 1.0
HB2 B:ALA264 3.8 19.7 1.0
O B:HOH728 3.9 29.7 1.0
H22 B:W5N501 3.9 18.6 0.0
OE1 B:GLU364 4.0 24.5 1.0
CB B:ASP251 4.0 20.1 1.0
NE2 B:GLN457 4.0 17.0 1.0
O B:HOH659 4.0 26.7 1.0
CZ B:PHE219 4.1 17.9 1.0
O B:HOH832 4.1 41.0 1.0
HE21 B:GLN457 4.1 16.9 0.0
HE1 B:PHE219 4.2 19.4 1.0
O3 B:W5N501 4.3 18.5 1.0
HB3 B:ASP251 4.4 19.9 1.0
CB B:ASP262 4.4 17.7 1.0
H B:CYS263 4.4 19.1 1.0
HB2 B:ASP251 4.4 19.9 1.0
CG B:GLU459 4.4 16.3 1.0
CE1 B:PHE219 4.4 20.2 1.0
HE2 B:HIS331 4.4 19.9 1.0
HA B:ASP262 4.5 18.5 1.0
N B:CYS263 4.6 18.7 1.0
HB3 B:GLU459 4.6 16.3 1.0
CD B:GLU364 4.7 22.7 1.0
HG2 B:GLU459 4.7 16.8 1.0
OE2 B:GLU364 4.7 25.1 1.0
CB B:ALA264 4.7 20.4 1.0
C B:ASP262 4.7 18.8 1.0
CA B:ASP262 4.8 18.1 1.0
HB2 B:GLU459 4.8 16.3 1.0
HA B:ASP251 4.8 19.8 1.0
HB3 B:ASP262 4.8 18.4 1.0
CB B:GLU459 4.9 15.7 1.0
CA B:ASP251 4.9 19.8 1.0
CE2 B:PHE219 5.0 18.8 1.0
HB1 B:ALA264 5.0 19.7 1.0
HB2 B:ASP262 5.0 18.4 1.0
H24 B:W5N501 5.0 24.9 1.0

Manganese binding site 4 out of 4 in 8oxg

Go back to Manganese Binding Sites List in 8oxg
Manganese binding site 4 out of 4 in the Crystal Structure of Human Methionine Aminopeptidase-2 Complexed with (3R,4S,5S,6R)-5-Methoxy-4-[(2R,3R)-2-Methyl-3-(3-Methyl-2-Buten-1- Yl)-2-Oxiranyl]-1-Oxaspiro[2.5]Oct-6-Yl N-(Trans-4-Aminocyclohexyl) Carbamate


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 Methionine Aminopeptidase-2 Complexed with (3R,4S,5S,6R)-5-Methoxy-4-[(2R,3R)-2-Methyl-3-(3-Methyl-2-Buten-1- Yl)-2-Oxiranyl]-1-Oxaspiro[2.5]Oct-6-Yl N-(Trans-4-Aminocyclohexyl) Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:21.6
occ:1.00
 HE2 B:HIS331 1.4 19.9 1.0
O B:HOH634 2.0 24.5 1.0
OE2 B:GLU459 2.1 19.1 1.0
NE2 B:HIS331 2.2 17.9 1.0
OE2 B:GLU364 2.2 25.1 1.0
OD2 B:ASP262 2.2 22.6 1.0
CG B:ASP262 3.0 20.6 1.0
HB1 B:ALA362 3.0 19.7 1.0
H22 B:W5N501 3.0 18.6 0.0
CD B:GLU364 3.1 22.7 1.0
CD B:GLU459 3.1 19.3 1.0
CD2 B:HIS331 3.1 22.4 1.0
CE1 B:HIS331 3.2 21.7 1.0
OD1 B:ASP262 3.3 19.7 1.0
MN B:MN502 3.3 19.1 1.0
HD2 B:HIS331 3.3 20.9 1.0
HE1 B:HIS331 3.4 20.9 1.0
OE1 B:GLU364 3.4 24.5 1.0
O3 B:W5N501 3.4 18.5 1.0
OE1 B:GLU459 3.5 19.6 1.0
HB2 B:ALA362 3.5 19.7 1.0
CB B:ALA362 3.6 19.5 1.0
O B:HOH728 3.7 29.7 1.0
HB3 B:ALA362 3.7 19.7 1.0
H6 B:W5N501 4.0 26.3 1.0
HB3 B:ASP262 4.1 18.4 1.0
H26 B:W5N501 4.2 24.8 1.0
CB B:ASP262 4.2 17.7 1.0
O B:HOH788 4.2 20.3 1.0
ND1 B:HIS331 4.2 22.1 1.0
CG B:HIS331 4.3 20.6 1.0
CG B:GLU364 4.3 27.3 1.0
HB3 B:GLU364 4.3 24.9 1.0
H4 B:W5N501 4.4 26.5 1.0
CG B:GLU459 4.4 16.3 1.0
HG2 B:GLU364 4.4 25.4 1.0
HG3 B:GLU459 4.4 16.8 1.0
HA2 B:GLY330 4.4 25.3 1.0
HB2 B:ASP262 4.6 18.4 1.0
HD13 B:ILE338 4.7 26.0 1.0
C12 B:W5N501 4.8 23.7 1.0
HG2 B:GLU459 4.9 16.8 1.0
CB B:GLU364 4.9 24.3 1.0
OD2 B:ASP251 4.9 21.5 1.0
CA B:ALA362 5.0 20.2 1.0
C5 B:W5N501 5.0 26.0 1.0

Reference:

P.Cornelius, B.A.Mayes, J.S.Petersen, D.J.Turnquist, P.J.Dufour, A.J.Dannenberg, J.M.Shanahan, B.J.Carver. Pharmacological Characterization of Sdx-7320/Evexomostat: A Novel Methionine Aminopeptidase Type 2 Inhibitor with Anti-Tumor and Anti-Metastatic Activity. Mol.Cancer Ther. 2024.
ISSN: ESSN 1538-8514
PubMed: 38530115
DOI: 10.1158/1535-7163.MCT-23-0574
Page generated: Sun Oct 6 13:30:51 2024

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