Atomistry » Calcium » PDB 6zpt-7apy » 7a0s
Atomistry »
  Calcium »
    PDB 6zpt-7apy »
      7a0s »

Calcium in PDB 7a0s: 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I

Protein crystallography data

The structure of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I, PDB code: 7a0s was solved by E.Breiner, Z.Eyal, D.Matzov, Y.Halfon, G.Cimicata, H.Rozenberg, E.Zimmerman, A.Bashan, A.Yonath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.67 / 3.22
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 169.995, 410.736, 697.778, 90, 90, 90
R / Rfree (%) 22.4 / 25.3

Other elements in 7a0s:

The structure of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I also contains other interesting chemical elements:

Sodium (Na) 1 atom
Magnesium (Mg) 367 atoms
Potassium (K) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I (pdb code 7a0s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I, PDB code: 7a0s:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 7a0s

Go back to Calcium Binding Sites List in 7a0s
Calcium binding site 1 out of 5 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca3251

b:78.6
occ:1.00
OP2 X:A1278 2.5 78.0 1.0
OP1 X:U2594 2.6 77.9 1.0
P X:A1278 3.4 77.9 1.0
OP1 X:A1278 3.5 77.6 1.0
P X:U2594 3.9 78.2 1.0
O5' X:U2594 4.1 78.4 1.0
O2' X:U1280 4.1 77.2 1.0
OP1 X:A2593 4.2 76.5 1.0
O5' X:A1278 4.5 78.1 1.0
O3' X:G1277 4.5 78.3 1.0
C5' X:A1278 4.5 78.1 1.0
C3' X:A2593 4.5 77.7 1.0
O3' X:A2593 4.7 78.1 1.0
C5' X:A2593 4.7 77.1 1.0
C5' X:U2594 4.8 78.8 1.0
C4' X:A2593 5.0 77.5 1.0

Calcium binding site 2 out of 5 in 7a0s

Go back to Calcium Binding Sites List in 7a0s
Calcium binding site 2 out of 5 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca3252

b:100.2
occ:1.00
OP2 X:U2594 2.7 78.6 1.0
OP2 X:C2595 2.8 79.7 1.0
P X:U2594 3.9 78.2 1.0
OP1 X:U2594 4.1 77.9 1.0
P X:C2595 4.2 80.1 1.0
O2' X:A2593 4.6 78.1 1.0
O3' X:A2593 4.7 78.1 1.0
OP1 X:C2595 4.9 80.5 1.0

Calcium binding site 3 out of 5 in 7a0s

Go back to Calcium Binding Sites List in 7a0s
Calcium binding site 3 out of 5 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca3253

b:72.6
occ:1.00
O6 X:G1993 3.9 76.5 1.0
O6 X:G1992 4.1 76.3 1.0
N7 X:G1992 4.1 77.0 1.0
N7 X:G1993 4.3 77.2 1.0
OP2 X:U1280 4.6 77.6 1.0
C6 X:G1992 4.7 76.6 1.0
C5 X:G1992 4.7 76.9 1.0
O4 X:U1994 4.7 77.0 1.0
OP1 X:U1280 4.8 77.8 1.0
C6 X:G1993 4.8 76.7 1.0
N4 X:C1991 4.8 76.0 1.0
C5 X:G1993 5.0 77.0 1.0

Calcium binding site 4 out of 5 in 7a0s

Go back to Calcium Binding Sites List in 7a0s
Calcium binding site 4 out of 5 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca3254

b:82.5
occ:1.00
OP1 X:U1280 2.2 77.8 1.0
P X:U1280 3.5 77.7 1.0
C3' X:G1279 4.1 78.1 1.0
O5' X:U1280 4.2 77.5 1.0
O3' X:G1279 4.2 77.7 1.0
C5' X:U1280 4.3 77.6 1.0
OP2 X:C1991 4.4 77.3 1.0
OP2 X:U1280 4.8 77.6 1.0

Calcium binding site 5 out of 5 in 7a0s

Go back to Calcium Binding Sites List in 7a0s
Calcium binding site 5 out of 5 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Ca3255

b:78.1
occ:1.00
OP2 X:A1682 2.3 81.8 1.0
OP1 X:A1681 2.9 80.2 1.0
O5' X:A1681 3.6 80.7 1.0
P X:A1682 3.6 82.3 1.0
P X:A1681 3.7 80.1 1.0
OP1 X:A1682 4.0 82.8 1.0
C5' X:A1681 4.4 80.6 1.0
O5' X:A1682 4.5 82.8 1.0
OP2 X:A1681 4.5 80.0 1.0
O3' X:A1681 4.7 82.1 1.0
OP2 X:G1683 5.0 83.4 1.0
O3' X:U1680 5.0 79.7 1.0

Reference:

E.Breiner, Z.Eyal, D.Matzov, Y.Halfon, G.Cimicata, H.Rozenberg, E.Zimmerman, A.Bashan, A.Yonath. 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I To Be Published.
Page generated: Sat Aug 21 12:35:16 2021

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy