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Potassium in PDB 7nnl: Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+

Enzymatic activity of Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+

All present enzymatic activity of Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+:
7.2.2.6;

Potassium Binding Sites:

The binding sites of Potassium atom in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+ (pdb code 7nnl). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 10 binding sites of Potassium where determined in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+, PDB code: 7nnl:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 10 in 7nnl

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Potassium binding site 1 out of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K601

b:47.6
occ:1.00
 CG1 A:VAL538 3.4 38.9 1.0
K A:K602 3.6 44.8 1.0
O A:ILE421 3.8 33.9 1.0
K B:K701 3.9 42.3 1.0
CG1 B:VAL231 3.9 33.7 1.0
CG A:PRO425 4.1 30.3 1.0
OG1 A:THR542 4.1 35.5 1.0
CG1 A:ILE421 4.3 33.9 1.0
CG2 A:ILE421 4.5 33.9 1.0
O A:VAL538 4.6 38.9 1.0
CG2 B:VAL231 4.6 33.7 1.0
CB B:VAL231 4.6 33.7 1.0
C A:ILE421 4.7 33.9 1.0
CD1 A:ILE421 4.8 33.9 1.0
CB A:VAL538 4.8 38.9 1.0
CB A:ILE421 5.0 33.9 1.0
CB A:PRO425 5.0 30.3 1.0

Potassium binding site 2 out of 10 in 7nnl

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Potassium binding site 2 out of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:44.8
occ:1.00
 CG A:PRO425 3.4 30.3 1.0
K A:K601 3.6 47.6 1.0
O A:GLN367 3.8 31.9 1.0
O A:ILE368 4.0 33.5 1.0
CD A:PRO425 4.0 30.3 1.0
C A:ILE368 4.2 33.5 1.0
O A:ILE421 4.2 33.9 1.0
CZ A:PHE386 4.3 36.2 1.0
CA A:ILE368 4.4 33.5 1.0
CB A:PRO425 4.5 30.3 1.0
CE2 A:PHE543 4.6 32.4 1.0
CG1 A:ILE421 4.7 33.9 1.0
CG1 A:VAL538 4.7 38.9 1.0
N A:GLY369 4.8 34.9 1.0
C A:GLN367 4.8 31.9 1.0
CA A:GLY539 4.8 37.2 1.0

Potassium binding site 3 out of 10 in 7nnl

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Potassium binding site 3 out of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:45.2
occ:1.00
 OG1 A:THR424 2.9 31.4 1.0
O A:ALA420 3.0 32.0 1.0
CG2 A:THR424 3.5 31.4 1.0
CB A:THR424 3.8 31.4 1.0
CG2 A:VAL496 4.0 30.1 1.0
C A:ALA420 4.1 32.0 1.0
CG1 A:VAL496 4.2 30.1 1.0
CA A:ILE421 4.2 33.9 1.0
N A:THR424 4.2 31.4 1.0
K A:K604 4.3 50.4 1.0
C A:ILE421 4.6 33.9 1.0
N A:ILE421 4.6 33.9 1.0
O A:ILE421 4.6 33.9 1.0
CA A:THR424 4.7 31.4 1.0
CB A:VAL496 4.8 30.1 1.0
CD1 A:LEU385 4.8 34.2 1.0
CD A:PRO425 4.9 30.3 1.0

Potassium binding site 4 out of 10 in 7nnl

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Potassium binding site 4 out of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:50.4
occ:1.00
 O A:GLY369 2.9 34.9 1.0
O A:SER378 3.3 32.8 1.0
CA A:GLY382 3.5 33.1 1.0
C A:GLY369 4.1 34.9 1.0
K A:K605 4.2 46.4 1.0
N A:GLY382 4.3 33.1 1.0
K A:K603 4.3 45.2 1.0
C A:SER378 4.4 32.8 1.0
CG1 A:VAL496 4.5 30.1 1.0
C A:GLY382 4.6 33.1 1.0
CA A:GLY369 4.7 34.9 1.0
CB A:SER378 4.7 32.8 1.0
O A:GLU370 4.7 33.2 1.0
CA A:SER378 5.0 32.8 1.0
CG1 A:VAL371 5.0 34.0 1.0
O A:GLY382 5.0 33.1 1.0

Potassium binding site 5 out of 10 in 7nnl

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Potassium binding site 5 out of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K605

b:46.4
occ:1.00
 OH A:TYR381 3.0 32.4 1.0
CB A:SER378 3.5 32.8 1.0
CE1 A:TYR381 3.5 32.4 1.0
CZ A:TYR381 3.6 32.4 1.0
CB A:VAL496 4.0 30.1 1.0
O A:GLY492 4.1 27.4 1.0
CG1 A:VAL496 4.2 30.1 1.0
K A:K604 4.2 50.4 1.0
OD1 A:ASN466 4.2 29.1 1.0
OG A:SER378 4.3 32.8 1.0
O A:ARG493 4.4 28.4 1.0
NH1 A:ARG493 4.4 28.4 1.0
CA A:ARG493 4.4 28.4 1.0
CA A:SER378 4.5 32.8 1.0
CG A:ARG493 4.5 28.4 1.0
CG2 A:VAL496 4.6 30.1 1.0
CD1 A:TYR381 4.7 32.4 1.0
C A:ARG493 4.9 28.4 1.0
CE2 A:TYR381 4.9 32.4 1.0
CG1 A:ILE497 5.0 29.4 1.0

Potassium binding site 6 out of 10 in 7nnl

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Potassium binding site 6 out of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K606

b:37.9
occ:1.00
 OG A:SER343 3.0 30.9 1.0
ND2 A:ASN112 3.1 29.3 1.0
OG A:SER378 3.2 32.8 1.0
NH1 A:ARG493 3.4 28.4 1.0
O A:ASN466 3.6 29.1 1.0
O A:ASN112 3.6 29.3 1.0
CB A:ASN466 3.9 29.1 1.0
CG A:ASN112 3.9 29.3 1.0
CB A:SER343 3.9 30.9 1.0
CB A:ASN112 3.9 29.3 1.0
CB A:SER378 4.3 32.8 1.0
CA A:GLY375 4.3 31.9 1.0
O A:SER343 4.3 30.9 1.0
CZ A:ARG493 4.5 28.4 1.0
C A:ASN466 4.6 29.1 1.0
C A:ASN112 4.6 29.3 1.0
NH2 A:ARG493 4.7 28.4 1.0
CA A:ASN466 4.9 29.1 1.0
CG A:ASN466 4.9 29.1 1.0
OG1 A:THR230 4.9 29.7 1.0
CA A:ASN112 4.9 29.3 1.0
N A:VAL376 5.0 30.7 1.0
O A:THR111 5.0 28.9 1.0
C A:GLY375 5.0 31.9 1.0
OD1 A:ASN112 5.0 29.3 1.0
OD1 A:ASN466 5.0 29.1 1.0

Potassium binding site 7 out of 10 in 7nnl

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Potassium binding site 7 out of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K607

b:30.2
occ:1.00
 O A:ASN112 2.8 29.3 1.0
O A:ASN231 2.8 29.3 1.0
O A:SER343 2.8 30.9 1.0
O A:ASN467 2.8 29.7 1.0
O A:CYS344 2.9 29.6 1.0
O A:THR113 2.9 29.9 1.0
O A:ASN466 3.2 29.1 1.0
C A:THR113 3.4 29.9 1.0
CA A:THR113 3.5 29.9 1.0
C A:ASN467 3.5 29.7 1.0
O A:THR230 3.6 29.7 1.0
C A:ASN112 3.6 29.3 1.0
C A:CYS344 3.7 29.6 1.0
C A:ASN231 3.8 29.3 1.0
CA A:ASN467 3.8 29.7 1.0
C A:SER343 3.8 30.9 1.0
C A:ASN466 3.9 29.1 1.0
N A:THR113 3.9 29.9 1.0
CA A:CYS344 4.1 29.6 1.0
OG A:SER343 4.2 30.9 1.0
N A:ASN467 4.2 29.7 1.0
CA A:ASN231 4.2 29.3 1.0
N A:CYS344 4.4 29.6 1.0
C A:THR230 4.5 29.7 1.0
N A:GLY468 4.5 30.2 1.0
N A:ASN114 4.5 30.9 1.0
N A:GLY345 4.7 29.9 1.0
CB A:ASN114 4.8 30.9 1.0
N A:ASN231 4.8 29.3 1.0
CB A:THR113 4.8 29.9 1.0
N A:GLY232 4.8 30.6 1.0
CA A:ASN112 4.9 29.3 1.0
OD1 A:ASN467 4.9 29.7 1.0
CA A:SER343 5.0 30.9 1.0

Potassium binding site 8 out of 10 in 7nnl

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Potassium binding site 8 out of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K608

b:35.9
occ:1.00
 O A:GLY468 2.9 30.2 1.0
O A:GLY232 3.0 30.6 1.0
ND2 A:ASN239 3.0 33.7 1.0
O A:ASN114 3.1 30.9 1.0
O A:GLY345 3.1 29.9 1.0
C A:GLY468 3.8 30.2 1.0
CG A:ASN239 4.0 33.7 1.0
OD1 A:ASN239 4.1 33.7 1.0
C A:ASN114 4.1 30.9 1.0
C A:GLY232 4.1 30.6 1.0
C A:GLY345 4.2 29.9 1.0
CA A:TRP115 4.2 30.8 1.0
N A:GLN116 4.4 33.0 1.0
N A:SER469 4.5 30.9 1.0
CG A:GLN116 4.5 33.0 1.0
CA A:GLY468 4.5 30.2 1.0
N A:TRP115 4.6 30.8 1.0
CA A:SER469 4.6 30.9 1.0
C A:TRP115 4.8 30.8 1.0
CA A:GLY233 4.9 31.9 1.0
CA A:GLY232 4.9 30.6 1.0
CA A:GLY345 4.9 29.9 1.0
N A:GLY233 4.9 31.9 1.0

Potassium binding site 9 out of 10 in 7nnl

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Potassium binding site 9 out of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K701

b:42.3
occ:1.00
 CG2 A:ILE421 3.8 33.9 1.0
CB B:ALA227 3.9 33.9 1.0
K A:K601 3.9 47.6 1.0
CD2 A:LEU389 4.0 37.6 1.0
CD2 B:LEU228 4.3 34.3 1.0
C B:ALA227 4.4 33.9 1.0
N B:LEU228 4.4 34.3 1.0
CG B:LEU228 4.5 34.3 1.0
O B:ALA227 4.7 33.9 1.0
CG1 A:VAL538 4.8 38.9 1.0
CA B:ALA227 4.8 33.9 1.0
CA B:LEU228 4.9 34.3 1.0
O B:LEU224 4.9 35.7 1.0
CD1 A:ILE421 4.9 33.9 1.0

Potassium binding site 10 out of 10 in 7nnl

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Potassium binding site 10 out of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K703

b:52.0
occ:1.00
 NZ B:LYS586 3.2 36.9 1.0
O B:CYS261 3.6 36.2 1.0
OD1 B:ASP583 3.7 37.9 1.0
O B:ILE263 3.7 35.8 1.0
O B:SER579 3.8 40.3 1.0
OG1 B:THR265 3.9 38.8 1.0
OG1 B:THR266 3.9 39.5 1.0
ND2 B:ASN624 4.0 38.5 1.0
CB B:ASN582 4.2 40.0 1.0
N B:THR265 4.3 38.8 1.0
CA B:SER579 4.5 40.3 1.0
C B:CYS261 4.5 36.2 1.0
ND2 B:ASN582 4.5 40.0 1.0
C B:SER579 4.6 40.3 1.0
CG B:ASN624 4.6 38.5 1.0
O B:LEU262 4.6 35.0 1.0
CA B:PRO264 4.6 36.3 1.0
N B:THR266 4.7 39.5 1.0
CB B:SER579 4.7 40.3 1.0
C B:ILE263 4.7 35.8 1.0
CE B:LYS586 4.7 36.9 1.0
OD1 B:ASN624 4.8 38.5 1.0
CG B:ASP583 4.9 37.9 1.0
CG B:ASN582 4.9 40.0 1.0
CB B:THR266 4.9 39.5 1.0
C B:LEU262 4.9 35.0 1.0
C B:PRO264 5.0 36.3 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: Mon Aug 12 19:32:59 2024

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