Magnesium in PDB 4xz3: Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Se-Met Derivative) in Complex with Coenzyme A and Mg- Amppcp, Phosphohistidine Segment Pointing Towards Nucleotide Binding Site

The structure of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Se-Met Derivative) in Complex with Coenzyme A and Mg- Amppcp, Phosphohistidine Segment Pointing Towards Nucleotide Binding Site, PDB code: 4xz3 was solved by R.H.-J.Weisse, A.J.Scheidig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.84 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.170, 111.880, 127.590, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.4

The binding sites of Magnesium atom in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Se-Met Derivative) in Complex with Coenzyme A and Mg- Amppcp, Phosphohistidine Segment Pointing Towards Nucleotide Binding Site (pdb code 4xz3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Se-Met Derivative) in Complex with Coenzyme A and Mg- Amppcp, Phosphohistidine Segment Pointing Towards Nucleotide Binding Site, PDB code: 4xz3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Se-Met Derivative) in Complex with Coenzyme A and Mg- Amppcp, Phosphohistidine Segment Pointing Towards Nucleotide Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Se-Met Derivative) in Complex with Coenzyme A and Mg- Amppcp, Phosphohistidine Segment Pointing Towards Nucleotide Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:57.7 occ:1.00 O2B A:ACP502 2.2 90.1 1.0 O3G A:ACP502 2.8 65.0 1.0 H A:GLY354 2.9 59.5 1.0 HA A:THR353 3.1 53.4 1.0 PB A:ACP502 3.7 80.1 1.0 N A:GLY354 3.7 49.6 1.0 H3' A:ACP502 3.9 0.5 1.0 HB A:THR353 4.0 55.5 1.0 CA A:THR353 4.0 44.5 1.0 H A:GLY308 4.0 45.0 1.0 PG A:ACP502 4.1 80.4 1.0 O1B A:ACP502 4.2 80.6 1.0 OD2 A:ASP351 4.2 62.6 1.0 HA2 A:GLY307 4.2 55.8 1.0 HA3 A:GLY354 4.3 59.3 1.0 C3B A:ACP502 4.4 73.0 1.0 C A:THR353 4.4 46.1 1.0 O1G A:ACP502 4.5 71.2 1.0 CB A:THR353 4.5 46.2 1.0 O A:ASN306 4.5 54.7 1.0 OD1 A:ASP351 4.6 49.4 1.0 CA A:GLY354 4.6 49.4 1.0 H3B1 A:ACP502 4.6 87.6 1.0 HB2 C:ALA162 4.7 52.4 1.0 O3A A:ACP502 4.8 0.1 1.0 HG22 A:THR353 4.8 61.2 1.0 CG A:ASP351 4.8 55.3 1.0 N A:GLY308 4.9 37.5 1.0 H A:THR353 4.9 47.9 1.0 C3' A:ACP502 4.9 0.9 1.0 HA2 A:GLY354 5.0 59.3 1.0

Magnesium binding site 2 out of 5 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Se-Met Derivative) in Complex with Coenzyme A and Mg- Amppcp, Phosphohistidine Segment Pointing Towards Nucleotide Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Se-Met Derivative) in Complex with Coenzyme A and Mg- Amppcp, Phosphohistidine Segment Pointing Towards Nucleotide Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:57.9 occ:1.00 O2G B:ACP300 2.1 85.3 1.0 OD2 B:ASP224 2.2 74.5 1.0 O2B B:ACP300 2.3 78.2 1.0 O2A B:ACP300 2.3 70.0 1.0 O B:HOH411 2.5 57.7 1.0 HB3 B:ASP224 3.1 74.1 1.0 CG B:ASP224 3.1 69.9 1.0 HB2 B:ASP224 3.2 74.1 1.0 CB B:ASP224 3.3 61.8 1.0 PB B:ACP300 3.3 69.4 1.0 HZ1 B:LYS60 3.4 89.4 1.0 PG B:ACP300 3.4 80.9 1.0 PA B:ACP300 3.4 62.7 1.0 O3A B:ACP300 3.5 65.6 1.0 HZ3 B:LYS60 3.6 89.4 1.0 C3B B:ACP300 3.8 71.2 1.0 HD3 B:PRO212 3.8 61.6 1.0 NZ B:LYS60 3.9 74.5 1.0 O1G B:ACP300 3.9 82.6 1.0 O B:ASN211 4.0 47.0 1.0 H3B2 B:ACP300 4.1 85.4 1.0 O5' B:ACP300 4.2 61.5 1.0 H3' B:ACP300 4.2 82.2 1.0 HD2 B:PRO212 4.3 61.6 1.0 OD1 B:ASP224 4.3 71.2 1.0 HZ2 B:LYS60 4.4 89.4 1.0 O B:HOH402 4.5 50.6 1.0 CD B:PRO212 4.5 51.4 1.0 O3G B:ACP300 4.6 87.5 1.0 O1A B:ACP300 4.6 65.7 1.0 O1B B:ACP300 4.6 68.9 1.0 H3B1 B:ACP300 4.8 85.4 1.0 H8 B:ACP300 4.8 74.0 1.0 CA B:ASP224 4.8 56.4 1.0 HE2 B:LYS60 4.8 89.9 1.0 HH21 B:ARG226 4.9 0.4 1.0

Magnesium binding site 3 out of 5 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Se-Met Derivative) in Complex with Coenzyme A and Mg- Amppcp, Phosphohistidine Segment Pointing Towards Nucleotide Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Se-Met Derivative) in Complex with Coenzyme A and Mg- Amppcp, Phosphohistidine Segment Pointing Towards Nucleotide Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:62.5 occ:1.00 O1G C:ACP501 2.2 61.4 1.0 O1B C:ACP501 2.3 76.8 1.0 HA C:THR353 3.3 64.3 1.0 OD2 C:ASP351 3.3 58.0 1.0 H C:GLY308 3.3 47.0 1.0 HA2 C:GLY307 3.6 59.0 1.0 H C:GLY354 3.6 65.1 1.0 PG C:ACP501 3.7 63.2 1.0 PB C:ACP501 3.8 77.0 1.0 OD1 C:ASP351 3.9 57.1 1.0 CG C:ASP351 4.0 60.2 1.0 N C:GLY308 4.1 39.1 1.0 H3' C:ACP501 4.1 0.4 1.0 CA C:THR353 4.2 53.6 1.0 N C:GLY354 4.2 54.2 1.0 O C:ASN306 4.3 55.2 1.0 C3B C:ACP501 4.3 60.5 1.0 O2B C:ACP501 4.4 67.3 1.0 HB C:THR353 4.5 75.1 1.0 O2G C:ACP501 4.5 57.3 1.0 CA C:GLY307 4.5 49.2 1.0 HA3 C:GLY308 4.6 56.6 1.0 HB2 A:ALA162 4.6 45.0 1.0 O3G C:ACP501 4.6 53.8 1.0 H C:THR353 4.7 53.1 1.0 C C:THR353 4.7 51.6 1.0 H2' C:ACP501 4.7 0.5 1.0 O1A C:ACP501 4.7 69.2 1.0 O3A C:ACP501 4.8 82.8 1.0 C C:GLY307 4.8 47.9 1.0 H3B2 C:ACP501 4.8 72.5 1.0 O5' C:ACP501 4.8 82.4 1.0 HA3 C:GLY354 4.9 69.7 1.0 CA C:GLY308 4.9 47.2 1.0 CB C:THR353 4.9 62.6 1.0 O2' C:ACP501 4.9 78.3 1.0 HG22 C:THR353 4.9 76.9 1.0

Magnesium binding site 4 out of 5 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Se-Met Derivative) in Complex with Coenzyme A and Mg- Amppcp, Phosphohistidine Segment Pointing Towards Nucleotide Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Se-Met Derivative) in Complex with Coenzyme A and Mg- Amppcp, Phosphohistidine Segment Pointing Towards Nucleotide Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:59.9 occ:1.00 OD1 C:ASP66 2.6 61.3 1.0 OD2 C:ASP66 3.0 57.4 1.0 CG C:ASP66 3.2 55.5 1.0 HG C:SER11 3.8 71.0 1.0 HB2 C:SER11 3.8 67.1 1.0 HB2 C:ALA12 3.9 59.5 1.0 OG C:SER11 4.1 59.1 1.0 H C:LYS67 4.3 76.4 1.0 CB C:SER11 4.5 55.9 1.0 HG3 C:LYS41 4.5 61.5 1.0 O C:LYS67 4.6 56.7 1.0 CB C:ASP66 4.7 54.2 1.0 CB C:ALA12 4.7 49.5 1.0 HB3 C:ALA12 4.7 59.5 1.0 N C:LYS67 4.9 63.7 1.0 HH C:TYR43 4.9 72.2 1.0 HA C:ASP66 4.9 73.9 1.0 HB2 C:ASP66 5.0 65.1 1.0

Magnesium binding site 5 out of 5 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Se-Met Derivative) in Complex with Coenzyme A and Mg- Amppcp, Phosphohistidine Segment Pointing Towards Nucleotide Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 (Se-Met Derivative) in Complex with Coenzyme A and Mg- Amppcp, Phosphohistidine Segment Pointing Towards Nucleotide Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:93.6 occ:1.00 O1B D:ACP300 2.4 0.8 1.0 OD2 D:ASP224 2.5 99.8 1.0 O1A D:ACP300 2.6 0.9 1.0 HB3 D:ASP224 3.0 92.7 1.0 O1G D:ACP300 3.2 0.6 1.0 HB2 D:ASP224 3.2 92.7 1.0 CG D:ASP224 3.3 91.7 1.0 HD3 D:PRO212 3.3 79.3 1.0 CB D:ASP224 3.4 77.2 1.0 O2G D:ACP300 3.5 0.7 1.0 O D:ASN211 3.7 75.4 1.0 PB D:ACP300 3.8 0.7 1.0 PG D:ACP300 3.8 0.3 1.0 HD2 D:PRO212 3.8 79.3 1.0 PA D:ACP300 3.9 0.5 1.0 CD D:PRO212 4.0 66.0 1.0 H3' D:ACP300 4.0 0.9 1.0 O3A D:ACP300 4.1 0.3 1.0 C3B D:ACP300 4.4 0.6 1.0 OD1 D:ASP224 4.5 96.2 1.0 C D:ASN211 4.6 74.4 1.0 O2B D:ACP300 4.8 0.1 1.0 N D:PRO212 4.8 75.1 1.0 O2A D:ACP300 4.8 0.0 1.0 CA D:ASP224 4.9 71.2 1.0 HH21 D:ARG226 4.9 0.8 1.0 O5' D:ACP300 4.9 0.1 1.0

R.H.Weie, A.Faust, M.Schmidt, P.Schonheit, A.J.Scheidig. Structure of Ndp-Forming Acetyl-Coa Synthetase ACD1 Reveals A Large Rearrangement For Phosphoryl Transfer. Proc.Natl.Acad.Sci.Usa V. 113 E519 2016.
ISSN: ESSN 1091-6490
PubMed: 26787904
DOI: 10.1073/PNAS.1518614113