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Potassium in PDB 8g6x: Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe

Other elements in 8g6x:

The structure of Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Magnesium (Mg) 223 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe (pdb code 8g6x). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe, PDB code: 8g6x:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 8g6x

Go back to Potassium Binding Sites List in 8g6x
Potassium binding site 1 out of 7 in the Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe within 5.0Å range:
probe atom residue distance (Å) B Occ
a:K6215

b:31.2
occ:1.00
 O2' a:G2250 2.6 8.4 1.0
OP2 a:A2497 2.7 8.4 1.0
OP2 a:OMG2251 3.0 8.4 1.0
N7 a:A2497 3.0 8.4 1.0
OP2 a:C2496 3.1 8.4 1.0
O5' a:C2496 3.3 8.4 1.0
C8 a:A2497 3.4 8.4 1.0
P a:C2496 3.6 8.4 1.0
O a:HOH6737 3.7 7.1 1.0
O3' a:G2250 3.7 8.4 1.0
C2' a:G2250 3.8 8.4 1.0
OP1 a:C2496 3.9 8.4 1.0
P a:OMG2251 3.9 8.4 1.0
O a:HOH6635 3.9 8.4 1.0
P a:A2497 4.1 8.4 1.0
C3' a:C2496 4.2 8.4 1.0
O a:HOH8454 4.3 8.4 1.0
C5 a:A2497 4.3 8.4 1.0
C3' a:G2250 4.4 8.4 1.0
C1' a:G2250 4.4 8.4 1.0
C5' a:C2496 4.4 8.4 1.0
O3' a:C2496 4.5 8.4 1.0
O5' a:A2497 4.7 8.4 1.0
CD l:4D481 4.7 8.4 1.0
OP1 a:OMG2251 4.7 8.4 1.0
N9 a:A2497 4.8 8.4 1.0
C4' a:C2496 4.9 8.4 1.0

Potassium binding site 2 out of 7 in 8g6x

Go back to Potassium Binding Sites List in 8g6x
Potassium binding site 2 out of 7 in the Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe within 5.0Å range:
probe atom residue distance (Å) B Occ
a:K6218

b:31.2
occ:1.00
 O a:HOH8598 2.7 10.3 1.0
O6 a:G26 2.8 8.4 1.0
OP2 a:U25 2.9 8.4 1.0
O6 a:G27 3.3 8.4 1.0
N7 a:G26 3.3 8.4 1.0
C6 a:G26 3.6 8.4 1.0
O a:HOH8240 3.6 8.4 1.0
C5 a:G26 3.8 8.4 1.0
P a:U25 4.2 8.4 1.0
C6 a:G27 4.2 8.4 1.0
O a:HOH6627 4.2 10.5 1.0
C5 a:U25 4.3 8.4 1.0
O5' a:U25 4.5 8.4 1.0
C8 a:G26 4.5 8.4 1.0
C6 a:U25 4.6 8.4 1.0
N1 a:G27 4.7 8.4 1.0
O a:HOH6731 4.8 5.2 1.0
N1 a:G26 4.9 8.4 1.0
OP1 a:U25 5.0 8.4 1.0

Potassium binding site 3 out of 7 in 8g6x

Go back to Potassium Binding Sites List in 8g6x
Potassium binding site 3 out of 7 in the Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe within 5.0Å range:
probe atom residue distance (Å) B Occ
a:K6219

b:31.2
occ:1.00
 O6 a:G2061 2.8 0.0 1.0
O a:HOH8840 2.9 8.4 1.0
O6 a:G2447 3.0 0.0 1.0
O4' a:C2501 3.0 1.9 1.0
N7 a:G2447 3.0 0.0 1.0
N7 a:G2061 3.1 0.0 1.0
O2 a:PSU2504 3.2 0.4 1.0
O2 a:C2501 3.4 0.3 1.0
C6 a:G2061 3.4 0.0 1.0
C5 a:G2061 3.6 0.0 1.0
C6 a:G2447 3.6 0.0 1.0
C5 a:G2447 3.6 0.0 1.0
C1' a:C2501 3.7 0.0 1.0
N1 a:PSU2504 3.8 1.6 1.0
C4' a:C2501 3.8 1.6 1.0
C2 a:PSU2504 3.9 0.7 1.0
C2 a:C2501 4.0 1.2 1.0
N6 a:A2451 4.1 0.0 1.0
N1 a:C2501 4.1 0.0 1.0
C8 a:G2447 4.2 0.1 1.0
C5' a:C2501 4.2 0.0 1.0
C8 a:G2061 4.3 0.0 1.0
C2' a:U2500 4.5 0.9 1.0
N1 a:G2061 4.8 0.0 1.0
O2' a:U2500 4.8 2.9 1.0
C4 a:G2447 4.9 0.5 1.0
C4 a:G2061 4.9 1.1 1.0
N3 a:C2501 4.9 0.2 1.0
N1 a:G2447 4.9 0.0 1.0
C6 a:PSU2504 5.0 1.9 1.0
O2 a:U2500 5.0 0.0 1.0

Potassium binding site 4 out of 7 in 8g6x

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Potassium binding site 4 out of 7 in the Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe within 5.0Å range:
probe atom residue distance (Å) B Occ
a:K6220

b:31.2
occ:1.00
 O a:HOH7479 2.8 8.4 1.0
OP1 a:C2501 3.0 1.3 1.0
OP1 a:2MA2503 3.0 3.3 1.0
O3' a:A575 3.1 8.4 1.0
OP1 a:PSU2504 3.1 0.3 1.0
O a:HOH8901 3.2 6.9 1.0
OP1 a:U576 3.2 8.4 1.0
O5' a:2MA2503 3.3 1.0 1.0
O3' a:U2500 3.5 0.4 1.0
MG a:MG6077 3.7 8.4 1.0
P a:2MA2503 3.7 0.0 1.0
OP2 a:PSU2504 3.8 2.1 1.0
P a:U576 3.8 8.4 1.0
P a:C2501 3.9 0.0 1.0
P a:PSU2504 3.9 2.2 1.0
C3' a:A575 4.2 8.4 1.0
O a:HOH7361 4.3 8.4 1.0
O2' a:A575 4.4 8.4 1.0
C4' a:A575 4.4 8.4 1.0
C5' a:C2501 4.4 0.0 1.0
C5' a:2MA2503 4.4 0.0 1.0
C5' a:U576 4.5 8.4 1.0
C4' a:2MA2503 4.6 0.1 1.0
O5' a:C2501 4.6 2.4 1.0
O2' a:U2500 4.6 2.9 1.0
O a:HOH8239 4.6 5.8 1.0
O5' a:U576 4.7 8.4 1.0
OP2 a:2MA2503 4.7 0.0 1.0
C3' a:U2500 4.7 0.0 1.0
C3' a:2MA2503 4.8 1.2 1.0
O3' a:2MA2503 4.9 0.6 1.0
C2' a:A575 5.0 8.4 1.0
C5' a:A575 5.0 8.4 1.0
OP2 a:U576 5.0 8.4 1.0

Potassium binding site 5 out of 7 in 8g6x

Go back to Potassium Binding Sites List in 8g6x
Potassium binding site 5 out of 7 in the Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe within 5.0Å range:
probe atom residue distance (Å) B Occ
a:K6221

b:31.2
occ:1.00
 N1 a:A2614 2.8 8.4 1.0
O a:HOH6537 3.0 8.4 1.0
N7 a:G2053 3.0 8.4 1.0
O2' a:A2051 3.1 8.4 1.0
N3 a:A2051 3.3 8.4 1.0
O6 a:G2053 3.4 8.4 1.0
N6 a:A2052 3.5 8.4 1.0
C2 a:A2614 3.5 8.4 1.0
N7 a:A2052 3.5 8.4 1.0
C5 a:A2052 3.6 8.4 1.0
C6 a:A2052 3.7 8.4 1.0
C6 a:A2614 3.7 8.4 1.0
N6 a:A2577 3.8 8.4 1.0
C5 a:G2053 3.8 8.4 1.0
N6 a:A2614 3.8 8.4 1.0
C2 a:A2051 3.9 8.4 1.0
C6 a:G2053 4.0 8.4 1.0
C6 a:A2577 4.0 8.4 1.0
C8 a:G2053 4.0 8.4 1.0
C4 a:A2051 4.1 8.4 1.0
C2' a:A2051 4.2 8.4 1.0
C1' a:A2051 4.2 8.4 1.0
C5 a:A2577 4.3 8.4 1.0
C8 a:A2052 4.3 8.4 1.0
N9 a:A2051 4.5 8.4 1.0
N1 a:A2577 4.5 8.4 1.0
C4 a:A2052 4.6 8.4 1.0
N1 a:A2052 4.6 8.4 1.0
N7 a:A2577 4.6 8.4 1.0
N3 a:A2614 4.7 8.4 1.0
O3' a:A2051 4.9 8.4 1.0
C5 a:A2614 4.9 8.4 1.0
N9 a:A2052 4.9 8.4 1.0

Potassium binding site 6 out of 7 in 8g6x

Go back to Potassium Binding Sites List in 8g6x
Potassium binding site 6 out of 7 in the Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe within 5.0Å range:
probe atom residue distance (Å) B Occ
c:K302

b:55.1
occ:1.00
 O c:GLY237 2.7 13.8 1.0
O a:HOH7756 2.8 8.4 1.0
O c:HOH423 2.8 8.4 1.0
O c:GLY235 3.0 8.4 1.0
O c:GLY234 3.7 8.4 1.0
C c:GLY237 3.8 13.8 1.0
O a:HOH8297 3.8 8.4 1.0
O c:THR223 3.9 8.4 1.0
C c:GLY235 4.2 8.4 1.0
O c:HOH431 4.2 5.5 1.0
C c:GLY234 4.3 8.4 1.0
OP2 a:A2590 4.3 8.4 1.0
CA c:ARG238 4.6 16.4 1.0
OP1 a:A2590 4.6 8.4 1.0
N c:GLY237 4.6 13.8 1.0
N c:ARG238 4.6 16.4 1.0
O a:HOH8367 4.7 10.2 1.0
CA c:GLY237 4.8 13.8 1.0
N c:GLY235 4.8 8.4 1.0
CA c:GLY235 4.9 8.4 1.0
O a:HOH8538 4.9 8.4 1.0
O a:HOH8338 5.0 8.4 1.0

Potassium binding site 7 out of 7 in 8g6x

Go back to Potassium Binding Sites List in 8g6x
Potassium binding site 7 out of 7 in the Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh- Trnaphe within 5.0Å range:
probe atom residue distance (Å) B Occ
e:K301

b:31.2
occ:1.00
 NH2 e:ARG61 3.2 8.4 1.0
N e:ARG61 3.3 8.4 1.0
CB e:ARG61 3.8 8.4 1.0
CA e:TRP60 4.0 8.4 1.0
CB e:TRP60 4.0 8.4 1.0
CG e:ARG61 4.0 8.4 1.0
CD e:ARG61 4.1 8.4 1.0
CG2 e:THR65 4.1 8.4 1.0
C e:TRP60 4.1 8.4 1.0
CA e:ARG61 4.2 8.4 1.0
CZ e:ARG61 4.3 8.4 1.0
NE e:ARG61 4.6 8.4 1.0

Reference:

C.Majumdar, J.H.D.Cate. Structure of Wt E.Coli Ribosome 50S Subunit with Complexed with Mrna, P-Site Fmet-Nh-Trnafmet and A-Site Meta-Aminobenzoic Acid Charged Nh-Trnaphe To Be Published.
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