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Rubidium in PDB 7nnp: Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex.

Enzymatic activity of Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex.

All present enzymatic activity of Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex.:
7.2.2.6;

Rubidium Binding Sites:

The binding sites of Rubidium atom in the Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex. (pdb code 7nnp). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 8 binding sites of Rubidium where determined in the Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex., PDB code: 7nnp:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Rubidium binding site 1 out of 8 in 7nnp

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Rubidium binding site 1 out of 8 in the Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex.


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb601

b:74.6
occ:1.00
 CG2 A:ILE421 3.4 18.2 1.0
CG1 A:VAL538 3.4 23.7 1.0
CG1 B:VAL231 3.9 17.8 1.0
RB A:RB602 4.0 61.4 1.0
RB B:RB701 4.1 81.7 1.0
OG1 A:THR542 4.2 19.4 1.0
CG2 B:VAL231 4.5 17.8 1.0
CB B:VAL231 4.6 17.8 1.0
CG A:PRO425 4.7 17.5 1.0
CB A:VAL538 4.8 23.7 1.0
CB A:ILE421 4.8 18.2 1.0
O A:ILE421 4.9 18.2 1.0

Rubidium binding site 2 out of 8 in 7nnp

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Rubidium binding site 2 out of 8 in the Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex.


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb602

b:61.4
occ:1.00
 CG A:PRO425 3.8 17.5 1.0
O A:ILE368 3.8 19.4 1.0
O A:GLN367 3.9 18.1 1.0
RB A:RB601 4.0 74.6 1.0
CZ A:PHE386 4.0 20.9 1.0
CG1 A:VAL538 4.0 23.7 1.0
C A:ILE368 4.1 19.4 1.0
CA A:ILE368 4.4 19.4 1.0
CD A:PRO425 4.6 17.5 1.0
OG1 A:THR542 4.6 19.4 1.0
CE2 A:PHE543 4.7 18.3 1.0
CE1 A:PHE386 4.7 20.9 1.0
N A:GLY369 4.8 21.6 1.0
CG2 A:ILE421 4.8 18.2 1.0
CA A:GLY539 4.8 21.6 1.0
CE2 A:PHE386 4.9 20.9 1.0
C A:GLN367 4.9 18.1 1.0
CB A:PRO425 5.0 17.5 1.0

Rubidium binding site 3 out of 8 in 7nnp

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Rubidium binding site 3 out of 8 in the Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex.


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb603

b:93.1
occ:1.00
 O A:GLY369 3.0 21.6 1.0
C A:GLY369 4.0 21.6 1.0
CA A:GLY382 4.1 20.0 1.0
CA A:GLY369 4.2 21.6 1.0
CG1 A:VAL496 4.5 14.7 1.0
RB A:RB604 4.7 75.4 1.0
O A:SER378 4.7 18.8 1.0
CG2 A:THR424 4.8 17.6 1.0
OG1 A:THR424 4.9 17.6 1.0

Rubidium binding site 4 out of 8 in 7nnp

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Rubidium binding site 4 out of 8 in the Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex.


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 4 of Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb604

b:75.4
occ:1.00
 O A:ASN465 3.0 17.7 1.0
OG A:SER378 3.3 18.8 1.0
CB A:GLU370 3.7 20.2 1.0
CG A:GLU370 3.8 20.2 1.0
OG A:SER343 3.8 19.4 1.0
C A:ASN465 3.9 17.7 1.0
CB A:SER343 4.0 19.4 1.0
CB A:SER378 4.0 18.8 1.0
CB A:ASN466 4.1 18.4 1.0
OD1 A:ASN466 4.3 18.4 1.0
O A:GLY369 4.4 21.6 1.0
CG A:ASN466 4.7 18.4 1.0
CA A:ASN465 4.7 17.7 1.0
RB A:RB603 4.7 93.1 1.0
N A:ASN466 4.7 18.4 1.0
CA A:ASN466 4.8 18.4 1.0
RB A:RB605 4.9 41.1 1.0
CD A:GLU370 4.9 20.2 1.0
O A:GLU370 4.9 20.2 1.0
N A:GLY375 4.9 18.9 1.0
O A:ASN466 5.0 18.4 1.0

Rubidium binding site 5 out of 8 in 7nnp

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Rubidium binding site 5 out of 8 in the Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex.


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 5 of Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb605

b:41.1
occ:1.00
 OG A:SER343 2.8 19.4 1.0
ND2 A:ASN112 2.9 17.5 1.0
O A:SER343 3.4 19.4 1.0
O A:ASN466 3.5 18.4 1.0
O A:ASN112 3.5 17.5 1.0
CG A:ASN112 3.5 17.5 1.0
CB A:ASN112 3.9 17.5 1.0
CB A:SER343 3.9 19.4 1.0
OG1 A:THR230 3.9 17.7 1.0
O A:THR230 4.0 17.7 1.0
RB A:RB606 4.1 26.5 1.0
CA A:GLY375 4.1 18.9 1.0
NH1 A:ARG493 4.2 15.2 1.0
OG A:SER378 4.2 18.8 1.0
CB A:ASN466 4.2 18.4 1.0
C A:ASN112 4.3 17.5 1.0
OD1 A:ASN112 4.4 17.5 1.0
C A:SER343 4.5 19.4 1.0
C A:ASN466 4.6 18.4 1.0
N A:VAL376 4.6 17.5 1.0
CA A:ASN112 4.7 17.5 1.0
CA A:SER343 4.8 19.4 1.0
C A:GLY375 4.8 18.9 1.0
RB A:RB604 4.9 75.4 1.0

Rubidium binding site 6 out of 8 in 7nnp

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Rubidium binding site 6 out of 8 in the Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex.


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 6 of Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb606

b:26.5
occ:1.00
 O A:ASN112 2.8 17.5 1.0
O A:CYS344 2.8 18.1 1.0
O A:SER343 2.8 19.4 1.0
O A:ASN467 2.8 17.7 1.0
O A:THR113 3.1 17.6 1.0
O A:THR230 3.1 17.7 1.0
O A:ASN466 3.3 18.4 1.0
N A:ASP232 3.5 18.0 1.0
C A:CYS344 3.6 18.1 1.0
C A:THR113 3.7 17.6 1.0
CA A:ASN231 3.7 17.5 1.0
C A:ASN467 3.8 17.7 1.0
C A:SER343 3.9 19.4 1.0
C A:ASN112 3.9 17.5 1.0
C A:ASN231 3.9 17.5 1.0
CA A:THR113 3.9 17.6 1.0
CA A:CYS344 4.0 18.1 1.0
RB A:RB605 4.1 41.1 1.0
C A:THR230 4.1 17.7 1.0
OG A:SER343 4.3 19.4 1.0
CA A:ASN467 4.3 17.7 1.0
C A:ASN466 4.3 18.4 1.0
N A:ASN231 4.3 17.5 1.0
N A:CYS344 4.4 18.1 1.0
N A:THR113 4.4 17.6 1.0
CB A:ASP232 4.4 18.0 1.0
OD1 A:ASN114 4.5 17.6 1.0
CA A:ASP232 4.5 18.0 1.0
N A:GLY345 4.6 17.4 1.0
N A:ASN114 4.6 17.6 1.0
CB A:ASN114 4.7 17.6 1.0
N A:ASN467 4.7 17.7 1.0
CB A:ASN231 4.8 17.5 1.0
N A:GLY468 4.8 17.8 1.0
CG A:ASN114 4.8 17.6 1.0
O A:ASN231 4.9 17.5 1.0

Rubidium binding site 7 out of 8 in 7nnp

Go back to Rubidium Binding Sites List in 7nnp
Rubidium binding site 7 out of 8 in the Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex.


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 7 of Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb701

b:81.7
occ:1.00
 CD1 A:LEU389 3.8 21.7 1.0
CG B:LEU228 3.9 18.5 1.0
CD2 B:LEU228 4.0 18.5 1.0
RB A:RB601 4.1 74.6 1.0
CD1 B:LEU228 4.5 18.5 1.0
CB B:ALA227 4.7 17.6 1.0
CG2 A:VAL538 4.8 23.7 1.0
C67 B:CDL703 4.8 34.7 1.0
O B:LEU224 4.8 19.5 1.0
N B:LEU228 4.9 18.5 1.0
CD2 B:LEU224 4.9 19.5 1.0

Rubidium binding site 8 out of 8 in 7nnp

Go back to Rubidium Binding Sites List in 7nnp
Rubidium binding site 8 out of 8 in the Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex.


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 8 of Rb-Loaded Cryo-Em Structure of the E1-Atp Kdpfabc Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb704

b:39.3
occ:1.00
 O B:ILE263 2.9 19.0 1.0
ND2 B:ASN624 3.0 21.9 1.0
OG1 B:THR265 3.3 22.0 1.0
O B:CYS261 3.4 20.0 1.0
N B:THR265 3.7 22.0 1.0
NZ B:LYS586 4.0 20.2 1.0
C B:CYS261 4.0 20.0 1.0
O B:VAL260 4.0 19.6 1.0
C B:ILE263 4.0 19.0 1.0
CG B:ASN624 4.1 21.9 1.0
CB B:THR265 4.3 22.0 1.0
CA B:PRO264 4.4 19.9 1.0
OD1 B:ASP583 4.4 21.8 1.0
O B:LEU262 4.4 19.0 1.0
CG2 B:THR265 4.4 22.0 1.0
C B:LEU262 4.5 19.0 1.0
OD1 B:ASN624 4.5 21.9 1.0
C B:PRO264 4.6 19.9 1.0
CA B:THR265 4.6 22.0 1.0
CA B:CYS261 4.6 20.0 1.0
N B:PRO264 4.7 19.9 1.0
N B:LEU262 4.7 19.0 1.0
N B:THR266 4.7 24.0 1.0
N B:ILE263 4.7 19.0 1.0
OG1 B:THR266 4.8 24.0 1.0
O B:SER579 4.8 24.2 1.0
CA B:LEU262 5.0 19.0 1.0

Reference:

J.M.Silberberg, R.A.Corey, L.Hielkema, C.Stock, P.J.Stansfeld, C.Paulino, I.Hanelt. Deciphering Ion Transport and Atpase Coupling in the Intersubunit Tunnel of Kdpfabc Biorxiv 2021.
DOI: 10.1101/2021.05.18.444724
Page generated: Thu Oct 10 12:18:44 2024

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