Atomistry » Magnesium » PDB 6c7y-6cfv » 6cap
Atomistry »
  Magnesium »
    PDB 6c7y-6cfv »
      6cap »

Magnesium in PDB 6cap: Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin

Protein crystallography data

The structure of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin, PDB code: 6cap was solved by H.Demirci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.91 / 3.40
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 400.970, 400.970, 175.050, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23

Other elements in 6cap:

The structure of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 252 in 6cap

Go back to Magnesium Binding Sites List in 6cap
Magnesium binding site 1 out of 252 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:98.7
occ:1.00
N3 A:C381 3.8 0.2 1.0
O2 A:C381 3.9 0.7 1.0
C2 A:C381 4.3 1.0 1.0
O4 A:U65 4.4 0.7 1.0
O2' A:A382 4.8 0.9 1.0
C4 A:C381 4.8 0.8 1.0
N3 A:A382 4.9 0.1 1.0
N4 A:C381 4.9 0.7 1.0

Magnesium binding site 2 out of 252 in 6cap

Go back to Magnesium Binding Sites List in 6cap
Magnesium binding site 2 out of 252 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1602

b:0.6
occ:1.00
O A:HOH2080 2.1 0.1 1.0
O A:HOH2028 2.1 0.9 1.0
O6 A:G377 3.1 0.2 1.0
N7 A:G376 3.4 0.9 1.0
O6 A:G376 3.4 0.7 1.0
C5 A:G376 3.9 0.7 1.0
C6 A:G376 3.9 0.1 1.0
C6 A:G377 4.0 0.8 1.0
C8 A:G376 4.4 1.0 1.0
N7 A:G377 4.5 0.3 1.0
O4 A:U375 4.6 0.2 1.0
C5 A:G377 4.6 0.5 1.0
C5 A:U375 4.7 0.6 1.0
C4 A:U375 4.7 0.9 1.0

Magnesium binding site 3 out of 252 in 6cap

Go back to Magnesium Binding Sites List in 6cap
Magnesium binding site 3 out of 252 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:0.6
occ:1.00
O A:HOH2022 2.1 0.5 1.0
O O:HOH101 2.1 0.1 1.0
OP2 A:A753 3.3 0.6 1.0
O6 A:G650 3.6 0.9 1.0
N7 A:G650 4.0 0.1 1.0
P A:A753 4.2 0.5 1.0
O6 A:G649 4.3 0.0 1.0
OP1 A:A753 4.3 0.5 1.0
C6 A:G650 4.5 0.6 1.0
N7 A:G649 4.5 0.3 1.0
C5 A:G650 4.6 0.5 1.0
C6 A:G649 4.9 0.9 1.0
O5' A:A753 4.9 0.0 1.0
C5 A:G649 5.0 0.6 1.0

Magnesium binding site 4 out of 252 in 6cap

Go back to Magnesium Binding Sites List in 6cap
Magnesium binding site 4 out of 252 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1604

b:0.5
occ:1.00
O A:HOH1907 2.1 0.5 1.0
O A:HOH2035 2.1 0.1 1.0
OP2 A:G750 2.8 0.3 1.0
OP1 A:C749 3.1 0.8 1.0
OP2 A:C749 3.2 0.3 1.0
P A:C749 3.6 0.7 1.0
P A:G750 3.9 0.8 1.0
OP1 A:G750 4.2 0.6 1.0
O6 A:G752 4.6 0.1 1.0
O3' A:C748 4.7 1.0 1.0
O2' A:C748 4.9 0.8 1.0
O5' A:G750 4.9 0.2 1.0
O5' A:C749 4.9 1.0 1.0

Magnesium binding site 5 out of 252 in 6cap

Go back to Magnesium Binding Sites List in 6cap
Magnesium binding site 5 out of 252 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1605

b:89.2
occ:1.00
O6 A:G742 3.4 0.3 1.0
O6 A:G741 3.4 0.9 1.0
MG A:MG1730 3.4 0.4 1.0
O6 A:G664 3.8 1.0 1.0
N6 A:A663 4.2 0.4 1.0
C6 A:G742 4.3 0.9 1.0
C6 A:G741 4.3 1.0 1.0
N7 A:G741 4.5 0.5 1.0
O4 A:U740 4.7 0.6 1.0
C5 A:G741 4.8 0.3 1.0
C6 A:G664 4.9 0.2 1.0

Magnesium binding site 6 out of 252 in 6cap

Go back to Magnesium Binding Sites List in 6cap
Magnesium binding site 6 out of 252 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1606

b:0.4
occ:1.00
O A:HOH1905 2.1 0.9 1.0
O A:HOH1909 2.1 0.6 1.0
O A:HOH1925 2.1 0.6 1.0
O A:HOH1928 2.1 0.2 1.0
OP2 A:G117 2.7 0.1 1.0
OP2 A:G289 3.1 0.6 1.0
OP1 A:A116 3.5 0.7 1.0
P A:G117 3.8 0.1 1.0
O4 A:U118 4.0 88.2 1.0
O5' A:A288 4.0 0.3 1.0
C3' A:A288 4.1 0.1 1.0
P A:G289 4.2 0.8 1.0
OP1 A:G117 4.2 0.3 1.0
O3' A:A116 4.2 0.0 1.0
C8 A:A288 4.2 0.1 1.0
OP2 A:A116 4.3 1.0 1.0
OP2 A:A288 4.4 0.9 1.0
C5 A:U118 4.4 89.0 1.0
N7 A:G117 4.4 0.6 1.0
P A:A116 4.4 0.6 1.0
O3' A:A288 4.5 0.9 1.0
C4 A:U118 4.6 89.0 1.0
OP1 A:G289 4.6 95.9 1.0
N7 A:A288 4.6 0.2 1.0
C3' A:A116 4.6 0.8 1.0
P A:A288 4.8 0.7 1.0
C8 A:G117 4.8 0.1 1.0
C2' A:A288 4.9 0.1 1.0
N9 A:A288 4.9 0.8 1.0

Magnesium binding site 7 out of 252 in 6cap

Go back to Magnesium Binding Sites List in 6cap
Magnesium binding site 7 out of 252 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1607

b:90.6
occ:1.00
OP2 A:C48 2.9 0.9 1.0
OP1 A:G115 2.9 0.2 1.0
OP2 A:U49 3.3 0.9 1.0
O5' A:C48 3.6 0.7 1.0
P A:C48 3.8 0.5 1.0
OP1 A:A51 3.9 0.6 1.0
P A:G115 4.2 0.8 1.0
O3' A:C47 4.2 0.9 1.0
O3' A:U114 4.3 1.0 1.0
C5' A:G115 4.6 0.3 1.0
C5' A:C48 4.7 0.5 1.0
P A:U49 4.8 0.4 1.0
O2' A:C47 4.8 0.0 1.0
O5' A:G115 4.9 0.2 1.0

Magnesium binding site 8 out of 252 in 6cap

Go back to Magnesium Binding Sites List in 6cap
Magnesium binding site 8 out of 252 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1608

b:0.0
occ:1.00
O A:HOH2017 2.1 0.4 1.0
O A:HOH2013 2.1 0.8 1.0
O A:HOH2026 2.1 0.2 1.0
O A:HOH2062 2.1 0.7 1.0
N7 A:G752 3.8 0.1 1.0
OP2 A:U652 4.1 0.8 1.0
OP2 A:U751 4.1 0.4 1.0
OP1 A:C651 4.4 0.0 1.0
C8 A:G752 4.5 0.2 1.0
OP1 A:U751 4.6 0.8 1.0
OP2 A:G752 4.8 0.0 1.0
P A:U751 4.8 0.9 1.0
C5 A:G752 4.9 0.7 1.0
O6 A:G752 4.9 0.1 1.0

Magnesium binding site 9 out of 252 in 6cap

Go back to Magnesium Binding Sites List in 6cap
Magnesium binding site 9 out of 252 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1609

b:84.6
occ:1.00
O A:HOH2059 2.1 73.2 1.0
O A:HOH2075 2.1 83.8 1.0
O A:HOH2076 2.1 94.2 1.0
O6 A:G799 3.4 0.3 1.0
O6 A:G800 3.5 0.3 1.0
C6 A:G800 4.1 0.1 1.0
O A:HOH2012 4.1 0.5 1.0
N7 A:G799 4.2 0.7 1.0
OP2 A:A781 4.3 0.4 1.0
C6 A:G799 4.3 0.5 1.0
N1 A:G800 4.4 0.5 1.0
OP1 A:A781 4.6 0.3 1.0
C5 A:G799 4.6 0.7 1.0
N7 A:G798 4.8 98.1 1.0
O6 A:G798 4.8 99.5 1.0
P A:A781 5.0 1.0 1.0

Magnesium binding site 10 out of 252 in 6cap

Go back to Magnesium Binding Sites List in 6cap
Magnesium binding site 10 out of 252 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Sisomicin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1610

b:0.1
occ:1.00
O2 A:U1506 3.0 0.2 1.0
O2' A:C795 3.3 0.8 1.0
O3' A:C795 3.3 0.9 1.0
OP1 A:C796 3.7 0.6 1.0
C1' A:U1506 3.9 0.7 1.0
C2 A:U1506 3.9 0.3 1.0
O4' A:U1506 4.2 0.4 1.0
P A:C796 4.2 0.0 1.0
C3' A:C795 4.2 97.6 1.0
NZ K:LYS123 4.3 0.5 1.0
C2' A:C795 4.3 0.3 1.0
N1 A:U1506 4.4 99.2 1.0
O3' A:U1506 4.6 0.7 1.0
C4' A:C795 4.7 95.9 1.0
CE K:LYS123 4.7 0.4 1.0
N3 A:U1506 5.0 0.6 1.0
C4' A:U1506 5.0 0.6 1.0

Reference:

H.Demirci, H.Demirci. N/A N/A.
Page generated: Mon Sep 30 20:24:44 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy