Calcium in PDB 4xym: Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+

The structure of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+, PDB code: 4xym 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)	85.02 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.560, 114.416, 127.040, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.7

The structure of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+ also contains other interesting chemical elements:

Mercury	(Hg)	8 atoms
Chlorine	(Cl)	6 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+ (pdb code 4xym). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+, PDB code: 4xym:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:32.2 occ:1.00 O B:ASN211 2.3 29.6 1.0 O3B B:A12300 2.3 36.1 1.0 O1A B:A12300 2.3 33.8 1.0 O B:HOH413 2.5 39.0 1.0 O B:HOH409 2.5 33.5 1.0 OD2 B:ASP224 2.5 38.5 1.0 O B:HOH412 2.5 34.0 1.0 HB3 B:ASP224 3.3 38.5 1.0 HD3 B:PRO212 3.4 33.3 1.0 C B:ASN211 3.4 26.5 1.0 CG B:ASP224 3.5 36.2 1.0 PA B:A12300 3.5 30.8 1.0 PB B:A12300 3.6 37.0 1.0 CB B:ASP224 3.7 32.1 1.0 HB2 B:ASP224 3.7 38.5 1.0 HB3 B:ASN211 3.8 39.7 1.0 O B:HOH410 4.0 34.8 1.0 CD B:PRO212 4.0 27.8 1.0 HD2 B:PRO212 4.0 33.3 1.0 O B:HOH414 4.1 46.2 1.0 C3A B:A12300 4.2 30.6 1.0 N B:PRO212 4.2 29.0 1.0 O2A B:A12300 4.4 36.4 1.0 H5'1 B:A12300 4.4 41.5 1.0 O2B B:A12300 4.4 34.4 1.0 CB B:ASN211 4.4 33.0 1.0 CG B:ASN211 4.4 33.4 1.0 O B:HOH447 4.5 50.6 1.0 CA B:ASN211 4.5 29.7 1.0 O3' B:A12300 4.5 33.6 1.0 OD1 B:ASN211 4.5 32.9 1.0 H3' B:A12300 4.6 43.5 1.0 O D:HOH447 4.6 57.3 1.0 OD1 B:ASP224 4.7 37.0 1.0 H B:ASN211 4.7 37.5 1.0 O1B B:A12300 4.7 37.0 1.0 O5' B:A12300 4.7 36.0 1.0 H3A2 B:A12300 4.8 36.8 1.0 HZ1 B:LYS69 5.0 45.7 1.0 ND2 B:ASN211 5.0 38.9 1.0 H3A1 B:A12300 5.0 36.8 1.0

Calcium binding site 2 out of 2 in the Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ca. Korarchaeum Cryptofilum Dinucleotide Forming Acetyl-Coenzyme A Synthetase 1 in Complex with Coenzyme A, Ca-Ampcp and Hgcl+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:41.4 occ:1.00 O2B D:A12302 2.3 46.2 1.0 O2A D:A12302 2.3 43.6 1.0 O D:ASN211 2.4 36.9 1.0 O D:HOH431 2.5 48.6 1.0 O D:HOH417 2.6 48.4 1.0 OD2 D:ASP224 2.6 45.8 1.0 O D:HOH411 2.8 44.7 1.0 HB3 D:ASP224 3.3 49.3 1.0 PA D:A12302 3.5 45.0 1.0 PB D:A12302 3.5 50.1 1.0 CG D:ASP224 3.5 45.5 1.0 C D:ASN211 3.6 33.9 1.0 HD3 D:PRO212 3.6 43.0 1.0 HB3 D:ASN211 3.8 44.0 1.0 CB D:ASP224 3.8 41.1 1.0 HB2 D:ASP224 3.8 49.3 1.0 O D:HOH433 4.0 56.4 1.0 C3A D:A12302 4.1 43.0 1.0 O D:HOH427 4.1 35.2 1.0 CD D:PRO212 4.2 35.8 1.0 O1B D:A12302 4.2 44.5 1.0 O D:HOH446 4.2 59.2 1.0 HD2 D:PRO212 4.2 43.0 1.0 O1A D:A12302 4.3 46.7 1.0 H5'1 D:A12302 4.4 57.5 1.0 N D:PRO212 4.4 36.6 1.0 CB D:ASN211 4.4 36.7 1.0 CG D:ASN211 4.5 39.5 1.0 O D:HOH440 4.5 52.4 1.0 H3' D:A12302 4.5 58.4 1.0 CA D:ASN211 4.6 38.3 1.0 HZ1 D:LYS69 4.6 60.6 1.0 OD1 D:ASN211 4.6 36.1 1.0 O D:HOH435 4.6 64.5 1.0 O3' D:A12302 4.7 46.4 1.0 OD1 D:ASP224 4.7 42.6 1.0 O5' D:A12302 4.7 51.0 1.0 H D:ASN211 4.8 41.7 1.0 O3B D:A12302 4.8 52.3 1.0 H3A2 D:A12302 4.8 51.6 1.0 H3A1 D:A12302 4.9 51.6 1.0 HZ3 D:LYS69 4.9 60.6 1.0 ND2 D:ASN211 5.0 37.6 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