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Manganese in PDB 6wb7: Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp

Enzymatic activity of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp

All present enzymatic activity of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp:
2.7.1.187;

Protein crystallography data

The structure of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp, PDB code: 6wb7 was solved by P.D.Jeffrey, J.N.Balaich, M.A.Estrella, M.S.Donia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.53 / 2.44
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 47.545, 50.268, 127.794, 89.06, 80.18, 71.81
R / Rfree (%) 18.7 / 25

Other elements in 6wb7:

The structure of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp (pdb code 6wb7). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp, PDB code: 6wb7:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 6wb7

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Manganese binding site 1 out of 5 in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:29.7
occ:1.00
 O2G A:ANP302 2.1 28.4 1.0
O A:HOH455 2.2 23.2 1.0
O A:HOH444 2.2 31.1 1.0
O A:HOH440 2.2 29.4 1.0
O2B A:ANP302 2.3 30.4 1.0
ND1 A:HIS164 2.3 28.3 1.0
CE1 A:HIS164 3.1 22.4 1.0
PG A:ANP302 3.3 49.8 1.0
CG A:HIS164 3.4 27.7 1.0
PB A:ANP302 3.6 52.8 1.0
O3G A:ANP302 3.6 33.5 1.0
CB A:HIS164 3.8 23.0 1.0
CA A:HIS164 3.8 28.5 1.0
N3B A:ANP302 4.0 38.0 1.0
OD1 A:ASP162 4.0 31.2 1.0
OD2 A:ASP162 4.2 23.0 1.0
O1B A:ANP302 4.2 45.1 1.0
O B:HOH458 4.3 30.6 1.0
NE2 A:HIS164 4.3 24.4 1.0
CG A:ASP162 4.4 26.0 1.0
CD2 A:HIS164 4.5 24.7 1.0
O1G A:ANP302 4.5 34.4 1.0
O6B E:AC13 4.5 33.2 1.0
CA A:GLY247 4.7 25.3 1.0
N A:HIS164 4.7 25.6 1.0
OD1 A:ASP248 4.7 23.7 1.0
O3A A:ANP302 4.8 44.4 1.0
C A:HIS164 4.8 27.7 1.0

Manganese binding site 2 out of 5 in 6wb7

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Manganese binding site 2 out of 5 in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:26.3
occ:1.00
 O2G B:ANP302 2.0 28.2 1.0
O B:HOH442 2.2 21.6 1.0
O B:HOH437 2.2 27.0 1.0
O B:HOH461 2.2 24.4 1.0
ND1 B:HIS164 2.2 24.1 1.0
O2B B:ANP302 2.3 30.0 1.0
CE1 B:HIS164 3.0 20.3 1.0
PG B:ANP302 3.3 51.9 1.0
CG B:HIS164 3.4 26.7 1.0
PB B:ANP302 3.7 49.2 1.0
O3G B:ANP302 3.7 28.9 1.0
CB B:HIS164 3.8 22.4 1.0
CA B:HIS164 3.9 27.3 1.0
N3B B:ANP302 4.0 34.1 1.0
O B:HOH466 4.1 21.5 1.0
OD2 B:ASP162 4.1 20.5 1.0
OD1 B:ASP162 4.2 23.4 1.0
NE2 B:HIS164 4.2 22.1 1.0
CD2 B:HIS164 4.4 20.9 1.0
O A:HOH424 4.4 26.2 1.0
O1G B:ANP302 4.5 38.4 1.0
O1B B:ANP302 4.5 51.8 1.0
CG B:ASP162 4.5 24.3 1.0
N B:HIS164 4.7 23.9 1.0
O3A B:ANP302 4.7 42.6 1.0
OD1 B:ASP248 4.7 27.9 1.0
CA B:GLY247 4.8 22.5 1.0
CB B:SER186 4.9 29.0 1.0
C B:HIS164 4.9 28.3 1.0

Manganese binding site 3 out of 5 in 6wb7

Go back to Manganese Binding Sites List in 6wb7
Manganese binding site 3 out of 5 in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn303

b:35.1
occ:1.00
 O2B C:ANP302 2.1 32.2 1.0
O2G C:ANP302 2.1 37.5 0.7
O C:HOH452 2.2 24.5 1.0
O C:HOH439 2.2 30.0 1.0
ND1 C:HIS164 2.3 29.7 1.0
CE1 C:HIS164 3.1 26.9 1.0
CG C:HIS164 3.4 27.5 1.0
PG C:ANP302 3.4 51.6 0.7
PB C:ANP302 3.5 38.7 0.7
CB C:HIS164 3.8 25.5 1.0
O3G C:ANP302 3.9 23.8 0.7
CA C:HIS164 4.0 31.9 1.0
N3B C:ANP302 4.0 35.6 1.0
O C:HOH474 4.0 28.5 1.0
O1B C:ANP302 4.0 38.0 1.0
OD2 C:ASP162 4.2 30.2 1.0
NE2 C:HIS164 4.3 29.0 1.0
OD1 C:ASP162 4.3 30.0 1.0
CD2 C:HIS164 4.4 25.4 1.0
O6B G:AC13 4.4 34.9 1.0
CG C:ASP162 4.6 31.4 1.0
O1G C:ANP302 4.6 36.4 0.7
O3A C:ANP302 4.6 41.9 1.0
CA C:GLY247 4.7 25.8 1.0
N C:HIS164 4.9 31.8 1.0
OD1 C:ASP248 4.9 23.9 1.0

Manganese binding site 4 out of 5 in 6wb7

Go back to Manganese Binding Sites List in 6wb7
Manganese binding site 4 out of 5 in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn305

b:42.6
occ:1.00
 O C:ASP202 2.6 39.3 1.0
O C:GLY204 2.9 29.9 1.0
C C:ASP202 3.5 37.9 1.0
O C:ILE201 3.6 37.2 1.0
C C:GLY204 4.1 30.9 1.0
CA C:ASP202 4.2 31.6 1.0
NH2 C:ARG223 4.2 29.2 1.0
C C:ARG203 4.3 35.3 1.0
N C:GLY204 4.3 36.3 1.0
N C:ARG203 4.4 37.3 1.0
C C:ILE201 4.6 35.8 1.0
O C:ARG203 4.6 32.6 1.0
CA C:ARG203 4.6 33.2 1.0
NH1 C:ARG223 4.6 28.5 1.0
CA C:GLY204 4.8 31.4 1.0
N C:ASP202 4.9 33.4 1.0
CZ C:ARG223 4.9 31.3 1.0

Manganese binding site 5 out of 5 in 6wb7

Go back to Manganese Binding Sites List in 6wb7
Manganese binding site 5 out of 5 in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn303

b:38.7
occ:1.00
 O2G D:ANP302 1.8 51.1 0.4
O2B D:ANP302 2.1 49.9 1.0
O D:HOH402 2.2 37.0 1.0
O D:HOH442 2.2 27.4 1.0
ND1 D:HIS164 2.2 29.1 1.0
PG D:ANP302 3.1 82.2 0.4
CE1 D:HIS164 3.2 26.5 1.0
CG D:HIS164 3.3 34.6 1.0
PB D:ANP302 3.3 60.5 1.0
CB D:HIS164 3.6 30.6 1.0
O3G D:ANP302 3.6 46.2 0.4
CA D:HIS164 3.7 30.1 1.0
O1B D:ANP302 3.8 62.3 1.0
N3B D:ANP302 3.8 48.6 1.0
OD1 D:ASP162 4.1 34.2 1.0
O1G D:ANP302 4.3 59.0 0.4
NE2 D:HIS164 4.3 33.9 1.0
OD2 D:ASP162 4.3 27.6 1.0
CD2 D:HIS164 4.4 36.0 1.0
CG D:ASP162 4.6 29.8 1.0
O6B H:AC13 4.6 35.9 0.8
O3A D:ANP302 4.6 38.5 1.0
N D:HIS164 4.6 29.0 1.0
CA D:GLY247 4.7 29.3 1.0
C D:HIS164 4.8 38.4 1.0
OD1 D:ASP248 4.9 33.9 1.0

Reference:

J.N.Balaich, M.A.Estrella, P.D.Jeffrey, A.Biswas, A.Korennykh, M.S.Donia. Acarbose Sugar Kinases Encoded By the Human Microbiome Mediates Microbial Competition For Complex Carbohydrates To Be Published.
Page generated: Sun Oct 6 07:41:46 2024

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