Calcium in PDB 6wb4: Microbiome-Derived Acarbose Kinase MAK1 Labeled with Selenomethionine

The structure of Microbiome-Derived Acarbose Kinase MAK1 Labeled with Selenomethionine, PDB code: 6wb4 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)	29.60 / 2.59
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	113.831, 123.509, 102.443, 90, 90, 90
R / Rfree (%)	18.6 / 25.3

The binding sites of Calcium atom in the Microbiome-Derived Acarbose Kinase MAK1 Labeled with Selenomethionine (pdb code 6wb4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Microbiome-Derived Acarbose Kinase MAK1 Labeled with Selenomethionine, PDB code: 6wb4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Microbiome-Derived Acarbose Kinase MAK1 Labeled with Selenomethionine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Microbiome-Derived Acarbose Kinase MAK1 Labeled with Selenomethionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:78.0 occ:1.00 OG1 A:THR43 2.4 136.3 1.0 O A:THR43 3.3 109.7 1.0 C A:THR43 3.5 112.2 1.0 OG A:SER138 3.6 65.9 1.0 CB A:THR43 3.7 126.5 1.0 NE2 A:HIS136 3.8 56.3 1.0 N A:GLY44 4.0 90.8 1.0 NE2 A:HIS162 4.0 68.6 1.0 CB A:ASP160 4.1 57.7 1.0 CA A:GLY44 4.1 80.4 1.0 OD1 A:ASP247 4.1 106.3 1.0 CA A:THR43 4.2 111.3 1.0 CD2 A:HIS136 4.3 46.7 1.0 CB A:SER138 4.4 45.7 1.0 CE1 A:HIS162 4.4 71.7 1.0 CG2 A:THR43 4.4 119.5 1.0 OD2 A:ASP160 4.5 74.6 1.0 CG2 A:VAL47 4.5 52.8 1.0 CA A:SER138 4.6 44.7 1.0 CG A:ASP160 4.7 66.7 1.0 CG A:ASP247 4.9 99.2 1.0 CE1 A:HIS136 4.9 61.1 1.0

Calcium binding site 2 out of 5 in the Microbiome-Derived Acarbose Kinase MAK1 Labeled with Selenomethionine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Microbiome-Derived Acarbose Kinase MAK1 Labeled with Selenomethionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:98.5 occ:1.00 O2B A:ATP302 2.7 200.0 0.8 O3G A:ATP302 2.7 175.2 0.8 O3B A:ATP302 3.0 155.6 0.8 CE A:MSE210 3.1 167.5 1.0 O2G A:ATP302 3.1 176.1 0.8 PG A:ATP302 3.1 176.4 0.8 PB A:ATP302 3.4 202.5 0.8 OD1 A:ASP160 3.5 69.2 1.0 ND1 A:HIS162 3.6 79.9 1.0 OD2 A:ASP160 3.8 74.6 1.0 CG A:ASP160 4.1 66.7 1.0 CA A:HIS162 4.1 75.8 1.0 O3A A:ATP302 4.2 159.3 0.8 CB A:SER184 4.3 101.7 1.0 CE1 A:HIS162 4.3 71.7 1.0 CA A:GLY246 4.5 86.1 1.0 CG A:HIS162 4.5 80.5 1.0 N A:SER184 4.5 87.8 1.0 O1G A:ATP302 4.6 174.9 0.8 CA A:SER184 4.7 95.5 1.0 N A:HIS162 4.7 72.7 1.0 CB A:HIS162 4.7 78.6 1.0 O1B A:ATP302 4.7 201.3 0.8 SE A:MSE210 4.8 101.8 1.0

Calcium binding site 3 out of 5 in the Microbiome-Derived Acarbose Kinase MAK1 Labeled with Selenomethionine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Microbiome-Derived Acarbose Kinase MAK1 Labeled with Selenomethionine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:73.0 occ:1.00 O B:HOH405 2.1 58.7 1.0 O3B D:AC13 2.9 124.1 0.9 OG1 B:THR43 3.2 71.4 1.0 OD2 B:ASP15 3.4 73.2 1.0 OD1 B:ASP15 3.5 77.5 1.0 C3B D:AC13 3.7 117.5 0.9 N B:HIS42 3.8 63.5 1.0 CA B:GLY41 3.9 55.3 1.0 CG B:ASP15 3.9 66.6 1.0 NH2 B:ARG106 4.1 65.4 1.0 O2B D:AC13 4.1 126.2 0.9 C B:GLY41 4.3 66.3 1.0 N B:THR43 4.4 60.5 1.0 CD2 B:HIS42 4.4 77.8 1.0 CB B:THR43 4.4 71.0 1.0 NE2 B:HIS42 4.6 77.4 1.0 C2B D:AC13 4.6 122.4 0.9 CG B:HIS42 4.7 67.8 1.0 OG B:SER96 4.7 66.2 1.0 CA B:HIS42 4.9 65.0 1.0 O4 D:AC13 4.9 111.8 0.9 C4A D:AC13 4.9 108.7 0.9 CA B:THR43 5.0 74.9 1.0 CE1 B:HIS42 5.0 69.6 1.0

Calcium binding site 4 out of 5 in the Microbiome-Derived Acarbose Kinase MAK1 Labeled with Selenomethionine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Microbiome-Derived Acarbose Kinase MAK1 Labeled with Selenomethionine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:60.3 occ:1.00 O B:HOH402 2.2 74.9 1.0 O B:HOH413 2.4 55.7 1.0 O B:THR43 2.6 81.5 1.0 OG B:SER138 3.4 51.8 1.0 NE2 B:HIS136 3.7 45.9 1.0 C B:THR43 3.8 79.7 1.0 O B:HOH406 4.0 63.1 1.0 NE2 B:HIS162 4.1 48.7 1.0 CD2 B:HIS136 4.2 42.9 1.0 CB B:SER138 4.3 43.1 1.0 CG2 B:VAL47 4.3 52.2 1.0 CB B:ASP160 4.5 55.9 1.0 CA B:GLY44 4.5 69.2 1.0 CE1 B:HIS162 4.5 50.2 1.0 CA B:SER138 4.5 48.8 1.0 N B:GLY44 4.6 64.0 1.0 CG2 B:THR43 4.7 59.8 1.0 OD1 B:ASP247 4.8 69.7 1.0 CA B:THR43 4.8 74.9 1.0 CE1 B:HIS136 4.9 56.0 1.0

Calcium binding site 5 out of 5 in the Microbiome-Derived Acarbose Kinase MAK1 Labeled with Selenomethionine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Microbiome-Derived Acarbose Kinase MAK1 Labeled with Selenomethionine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca305 b:72.2 occ:1.00 O B:HOH401 2.2 66.4 1.0 O B:HOH407 2.3 76.3 1.0 O2B B:ATP302 2.4 198.3 0.8 O2G B:ATP302 2.7 196.2 0.8 O3B B:ATP302 2.8 221.0 0.8 PB B:ATP302 3.2 204.8 0.8 PG B:ATP302 3.2 197.0 0.8 ND1 B:HIS162 3.2 62.8 1.0 O3G B:ATP302 3.6 190.7 0.8 OD2 B:ASP160 3.8 68.0 1.0 OD1 B:ASP160 3.8 83.9 1.0 O3A B:ATP302 4.0 214.4 0.8 CA B:HIS162 4.0 62.2 1.0 CE1 B:HIS162 4.1 50.2 1.0 CG B:HIS162 4.2 63.3 1.0 CG B:ASP160 4.2 66.2 1.0 CB B:SER184 4.3 68.7 1.0 CB B:HIS162 4.4 52.5 1.0 O1B B:ATP302 4.5 204.8 0.8 CE B:MSE210 4.5 170.7 1.0 O1G B:ATP302 4.6 196.8 0.8 CA B:GLY246 4.7 44.5 1.0 N B:HIS162 4.8 59.9 1.0 C B:HIS162 4.9 63.3 1.0 N B:SER184 5.0 56.7 1.0 CA B:SER184 5.0 62.7 1.0 OG B:SER184 5.0 72.1 1.0

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.