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

Protein crystallography data

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

Other elements in 4xym:

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

Calcium Binding Sites:

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 4xym

Go back to Calcium Binding Sites List in 4xym
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 4xym

Go back to Calcium Binding Sites List in 4xym
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

Reference:

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
Page generated: Sat Dec 12 05:12:40 2020

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