Calcium in PDB 6ckk: N. Meningitidis Cmp-Sialic Acid Synthetase in the Presence of Ctp and CA2+

Enzymatic activity of N. Meningitidis Cmp-Sialic Acid Synthetase in the Presence of Ctp and CA2+

All present enzymatic activity of N. Meningitidis Cmp-Sialic Acid Synthetase in the Presence of Ctp and CA2+:
2.7.7.43;

Protein crystallography data

The structure of N. Meningitidis Cmp-Sialic Acid Synthetase in the Presence of Ctp and CA2+, PDB code: 6ckk was solved by M.M.Matthews, A.J.Fisher, X.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.11 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.190, 69.560, 158.210, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 25

Calcium Binding Sites:

The binding sites of Calcium atom in the N. Meningitidis Cmp-Sialic Acid Synthetase in the Presence of Ctp and CA2+ (pdb code 6ckk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the N. Meningitidis Cmp-Sialic Acid Synthetase in the Presence of Ctp and CA2+, PDB code: 6ckk:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6ckk

Go back to Calcium Binding Sites List in 6ckk
Calcium binding site 1 out of 3 in the N. Meningitidis Cmp-Sialic Acid Synthetase in the Presence of Ctp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of N. Meningitidis Cmp-Sialic Acid Synthetase in the Presence of Ctp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:28.0
occ:1.00
O A:HOH882 2.4 23.6 1.0
OD1 A:ASP211 2.4 28.0 1.0
O A:HOH1035 2.4 34.7 1.0
O A:HOH808 2.4 30.4 1.0
O2A A:CTP701 2.4 16.9 1.0
O A:HOH974 2.5 23.3 1.0
O A:HOH1047 2.8 31.7 1.0
CG A:ASP211 3.2 27.1 1.0
O1A A:CTP701 3.3 16.3 1.0
PA A:CTP701 3.4 16.5 1.0
OD2 A:ASP211 3.4 30.6 1.0
OD2 A:ASP209 3.9 25.9 0.5
NZ A:LYS21 4.2 15.5 1.0
O5' A:CTP701 4.4 14.5 1.0
O A:HOH937 4.5 23.3 1.0
O3A A:CTP701 4.5 15.0 1.0
OD1 A:ASP209 4.5 21.0 0.5
CB A:ASP211 4.6 24.8 1.0
CG A:ASP209 4.6 23.0 0.5
O A:HOH1038 4.7 47.7 1.0
C5' A:CTP701 4.7 14.7 1.0
O A:HOH1007 4.8 37.9 1.0
OD2 A:ASP209 4.9 22.9 0.5
O3G A:CTP701 4.9 16.6 1.0

Calcium binding site 2 out of 3 in 6ckk

Go back to Calcium Binding Sites List in 6ckk
Calcium binding site 2 out of 3 in the N. Meningitidis Cmp-Sialic Acid Synthetase in the Presence of Ctp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of N. Meningitidis Cmp-Sialic Acid Synthetase in the Presence of Ctp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:17.6
occ:1.00
O1A A:CTP701 2.4 16.3 1.0
O3G A:CTP701 2.4 16.6 1.0
O A:HOH937 2.4 23.3 1.0
O A:HOH1028 2.4 22.4 1.0
O A:HOH886 2.4 23.0 1.0
O A:HOH1040 2.4 22.8 1.0
O2B A:CTP701 2.4 14.9 1.0
PB A:CTP701 3.5 16.5 1.0
PA A:CTP701 3.6 16.5 1.0
PG A:CTP701 3.6 18.4 1.0
O3A A:CTP701 3.9 15.0 1.0
O1G A:CTP701 3.9 16.4 1.0
O3B A:CTP701 3.9 19.0 1.0
O A:HOH1025 4.1 31.9 1.0
O A:HOH974 4.3 23.3 1.0
O A:HOH859 4.4 16.9 1.0
O5' A:CTP701 4.4 14.5 1.0
O A:HOH1035 4.4 34.7 1.0
O A:ASP78 4.5 18.6 1.0
NH1 A:ARG12 4.6 14.5 1.0
O A:HOH1161 4.6 40.2 1.0
NE A:ARG12 4.7 14.1 1.0
O A:HOH981 4.8 38.8 1.0
O A:HOH834 4.8 16.8 1.0
O2A A:CTP701 4.8 16.9 1.0
O A:HOH852 4.9 25.9 1.0
O1B A:CTP701 4.9 17.1 1.0
O2G A:CTP701 4.9 17.5 1.0

Calcium binding site 3 out of 3 in 6ckk

Go back to Calcium Binding Sites List in 6ckk
Calcium binding site 3 out of 3 in the N. Meningitidis Cmp-Sialic Acid Synthetase in the Presence of Ctp and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of N. Meningitidis Cmp-Sialic Acid Synthetase in the Presence of Ctp and CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:45.8
occ:1.00
O B:HOH814 2.4 48.1 1.0
O B:HOH879 2.5 41.9 1.0
O B:HOH927 2.5 36.7 1.0
O B:HOH1000 2.5 46.9 1.0
OD1 B:ASP209 2.5 32.4 1.0
O A:HOH979 3.2 43.4 1.0
CG B:ASP209 3.5 29.6 1.0
OD2 B:ASP209 3.9 30.8 1.0
O B:ASP209 4.0 24.7 1.0
OD2 B:ASP211 4.1 40.6 1.0
OE2 A:GLU137 4.3 34.9 1.0
OD1 B:ASP215 4.5 33.7 1.0
OD2 B:ASP215 4.6 30.2 1.0
O B:HOH830 4.7 32.6 1.0
N B:ASP209 4.7 20.0 1.0
CB B:ASP209 4.8 23.0 1.0
C B:ASP209 4.8 21.7 1.0
NE2 A:HIS138 4.8 24.3 1.0
CG B:ASP215 4.9 29.6 1.0
CA B:ASP209 5.0 22.7 1.0

Reference:

M.M.Matthews, H.Yu, Y.Li, X.Chen, A.J.Fisher. Structural Insight Into the Mechanism of Cmp-Sialic Acid Synthetase To Be Published.
Page generated: Sat Dec 12 06:01:31 2020

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