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Manganese in PDB 6npz: Crystal Structure of AKT1 (Aa 123-480) Kinase with A Bisubstrate

Enzymatic activity of Crystal Structure of AKT1 (Aa 123-480) Kinase with A Bisubstrate

All present enzymatic activity of Crystal Structure of AKT1 (Aa 123-480) Kinase with A Bisubstrate:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of AKT1 (Aa 123-480) Kinase with A Bisubstrate, PDB code: 6npz was solved by N.Chu, P.A.Cole, S.B.Gabelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.82 / 2.12
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.321, 56.088, 92.019, 90.00, 104.56, 90.00
R / Rfree (%) 18.5 / 24.1

Other elements in 6npz:

The structure of Crystal Structure of AKT1 (Aa 123-480) Kinase with A Bisubstrate also contains other interesting chemical elements:

Vanadium (V) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of AKT1 (Aa 123-480) Kinase with A Bisubstrate (pdb code 6npz). 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 AKT1 (Aa 123-480) Kinase with A Bisubstrate, PDB code: 6npz:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6npz

Go back to Manganese Binding Sites List in 6npz
Manganese binding site 1 out of 4 in the Crystal Structure of AKT1 (Aa 123-480) Kinase with A Bisubstrate


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 AKT1 (Aa 123-480) Kinase with A Bisubstrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:48.3
occ:1.00
NE2 A:HIS354 2.2 42.5 1.0
O A:HOH749 2.5 37.2 1.0
O A:HOH706 2.5 50.2 1.0
OE2 A:GLU314 2.6 30.0 1.0
CE1 A:HIS354 3.1 45.5 1.0
CD2 A:HIS354 3.4 44.0 1.0
CD A:GLU314 3.4 30.4 1.0
OE1 A:GLU314 3.5 31.1 1.0
ND1 A:HIS354 4.3 36.8 1.0
CG A:HIS354 4.4 40.2 1.0
O F:HOH212 4.4 56.1 1.0
O A:HOH777 4.6 65.3 1.0
O F:HOH208 4.6 41.3 1.0
O F:HOH204 4.7 43.8 1.0
CG A:GLU314 4.8 31.9 1.0
CB A:PRO313 4.8 28.2 1.0
CG2 F:THR5 4.9 32.8 1.0
CG A:PRO313 4.9 30.8 1.0
O A:GLN352 4.9 34.5 1.0

Manganese binding site 2 out of 4 in 6npz

Go back to Manganese Binding Sites List in 6npz
Manganese binding site 2 out of 4 in the Crystal Structure of AKT1 (Aa 123-480) Kinase with A Bisubstrate


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 AKT1 (Aa 123-480) Kinase with A Bisubstrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:76.2
occ:1.00
O B:HOH722 2.5 43.0 1.0
OE2 B:GLU314 2.7 40.3 1.0
O B:HOH731 2.8 55.8 1.0
O B:HOH709 2.8 50.3 1.0
NE2 B:HIS354 2.9 34.2 1.0
O B:HOH665 3.0 55.9 1.0
CD B:GLU314 3.5 36.3 1.0
CD2 B:HIS354 3.6 39.6 1.0
OE1 B:GLU314 3.7 29.9 1.0
O G:HOH604 3.8 46.6 1.0
O B:HOH601 3.9 41.7 1.0
CE1 B:HIS354 4.0 33.1 1.0
O G:HOH610 4.7 55.0 1.0
CG2 G:THR5 4.8 40.5 1.0
CG B:HIS354 4.8 29.4 1.0
CG B:GLU314 4.9 32.4 1.0
O B:GLN352 4.9 33.9 1.0

Manganese binding site 3 out of 4 in 6npz

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Manganese binding site 3 out of 4 in the Crystal Structure of AKT1 (Aa 123-480) Kinase with A Bisubstrate


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 AKT1 (Aa 123-480) Kinase with A Bisubstrate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn101

b:53.9
occ:1.00
O2A F:ZXW7 1.9 74.0 1.0
OD2 A:ASP292 2.1 41.6 1.0
O A:HOH631 2.2 37.1 1.0
O F:HOH202 2.4 36.4 1.0
O2B F:ZXW7 2.4 51.7 1.0
O3B F:ZXW7 2.6 71.0 1.0
CG A:ASP292 2.9 43.9 1.0
PB F:ZXW7 3.1 51.3 1.0
OD1 A:ASP292 3.1 43.4 1.0
PA F:ZXW7 3.1 57.8 1.0
O3A F:ZXW7 3.6 54.6 1.0
PG F:ZXW7 3.8 65.5 1.0
OD1 A:ASN279 3.9 28.7 1.0
S2G F:ZXW7 4.0 65.0 1.0
O5' F:ZXW7 4.0 56.8 1.0
O F:HOH205 4.1 40.5 1.0
C5' F:ZXW7 4.1 45.7 1.0
O1A F:ZXW7 4.2 55.4 1.0
O F:HOH207 4.2 60.9 1.0
O A:HOH677 4.2 52.6 1.0
CB A:ASP292 4.4 37.8 1.0
O1B F:ZXW7 4.5 58.5 1.0
NH1 F:ARG4 4.6 35.6 1.0
O A:HOH723 4.6 38.8 1.0
O3G F:ZXW7 4.8 55.7 1.0
O1G F:ZXW7 4.9 53.8 1.0
CG A:ASN279 4.9 22.6 1.0

Manganese binding site 4 out of 4 in 6npz

Go back to Manganese Binding Sites List in 6npz
Manganese binding site 4 out of 4 in the Crystal Structure of AKT1 (Aa 123-480) Kinase with A Bisubstrate


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 AKT1 (Aa 123-480) Kinase with A Bisubstrate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn501

b:87.0
occ:1.00
O1A G:ZXW7 1.8 85.3 1.0
OD2 B:ASP292 2.0 55.4 1.0
O G:HOH606 2.1 45.9 1.0
O1G G:ZXW7 2.2 0.5 1.0
O1B G:ZXW7 2.8 77.0 1.0
CG B:ASP292 2.8 46.3 1.0
OD1 B:ASP292 3.1 51.9 1.0
PA G:ZXW7 3.2 79.2 1.0
OD1 B:ASN279 3.3 31.1 1.0
PG G:ZXW7 3.3 86.9 1.0
PB G:ZXW7 3.6 65.5 1.0
O G:HOH601 3.7 57.5 1.0
O G:HOH605 3.7 51.8 1.0
O2A G:ZXW7 3.9 65.0 1.0
O3B G:ZXW7 3.9 78.1 1.0
O3A G:ZXW7 3.9 83.9 1.0
S2G G:ZXW7 4.0 85.9 1.0
O G:HOH603 4.1 66.4 1.0
CB B:ASP292 4.3 34.5 1.0
O5' G:ZXW7 4.4 81.1 1.0
CG B:ASN279 4.4 26.4 1.0
C5' G:ZXW7 4.6 63.5 1.0
O3G G:ZXW7 4.7 74.1 1.0
NH1 G:ARG4 4.7 40.5 1.0
ND2 B:ASN279 4.9 29.5 1.0

Reference:

N.Chu, A.L.Salguero, A.Z.Liu, Z.Chen, D.R.Dempsey, S.B.Ficarro, W.M.Alexander, J.A.Marto, Y.Li, L.M.Amzel, S.B.Gabelli, P.A.Cole. Akt Kinase Activation Mechanisms Revealed Using Protein Semisynthesis. Cell V. 174 897 2018.
ISSN: ISSN 1097-4172
PubMed: 30078705
DOI: 10.1016/J.CELL.2018.07.003
Page generated: Tue Dec 15 04:57:59 2020

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