Potassium in PDB 7zrd: Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate

Enzymatic activity of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate

All present enzymatic activity of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate:
7.2.2.6;

Other elements in 7zrd:

The structure of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate also contains other interesting chemical elements:

Vanadium (V) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate (pdb code 7zrd). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate, PDB code: 7zrd:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Potassium binding site 1 out of 9 in 7zrd

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Potassium binding site 1 out of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K601

b:26.2
occ:1.00
 CG1 A:VAL538 3.5 17.4 1.0
CG A:PRO425 3.6 13.1 1.0
O A:ILE368 4.0 13.4 1.0
K A:K605 4.1 24.2 1.0
CZ A:PHE386 4.2 14.2 1.0
OG1 A:THR542 4.3 14.6 1.0
O A:GLN367 4.4 12.0 1.0
O A:ILE421 4.5 12.7 1.0
CD A:PRO425 4.5 13.1 1.0
C A:ILE368 4.5 13.4 1.0
CG2 A:ILE421 4.6 12.7 1.0
CB A:PRO425 4.8 13.1 1.0
O A:VAL538 4.8 17.4 1.0
CE1 A:PHE386 4.8 14.2 1.0
CB A:THR542 4.9 14.6 1.0
CA A:ILE368 4.9 13.4 1.0
CG2 A:THR542 4.9 14.6 1.0
K A:K602 4.9 63.3 1.0
CB A:VAL538 4.9 17.4 1.0
C A:VAL538 4.9 17.4 1.0

Potassium binding site 2 out of 9 in 7zrd

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Potassium binding site 2 out of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:63.3
occ:1.00
 CA A:GLY369 3.4 14.7 1.0
CE2 A:PHE386 3.8 14.2 1.0
O A:GLY369 3.9 14.7 1.0
O A:ILE368 4.1 13.4 1.0
C A:GLY369 4.1 14.7 1.0
CZ A:PHE386 4.2 14.2 1.0
OG1 A:THR424 4.3 12.9 1.0
N A:GLY369 4.5 14.7 1.0
CG1 A:VAL371 4.5 13.5 1.0
K A:K603 4.6 45.3 1.0
CD2 A:PHE386 4.7 14.2 1.0
C A:ILE368 4.7 13.4 1.0
CA A:GLY382 4.8 14.2 1.0
O A:ALA420 4.8 11.9 1.0
CA A:ILE421 4.9 12.7 1.0
K A:K601 4.9 26.2 1.0
O A:GLY382 5.0 14.2 1.0
O A:ILE421 5.0 12.7 1.0

Potassium binding site 3 out of 9 in 7zrd

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Potassium binding site 3 out of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:45.3
occ:1.00
 K A:K604 3.3 28.3 1.0
O A:GLY369 3.4 14.7 1.0
CG2 A:THR424 3.9 12.9 1.0
C A:GLY369 4.3 14.7 1.0
ND2 A:ASN465 4.3 10.5 1.0
OG1 A:THR424 4.5 12.9 1.0
O A:SER378 4.5 13.9 1.0
K A:K602 4.6 63.3 1.0
O A:ASN465 4.7 10.5 1.0
CA A:GLY369 4.7 14.7 1.0
CB A:THR424 4.7 12.9 1.0
CG1 A:VAL496 4.8 10.0 1.0
CA A:ASN465 4.8 10.5 1.0
CG2 A:VAL496 4.9 10.0 1.0
O A:GLY492 4.9 8.9 1.0

Potassium binding site 4 out of 9 in 7zrd

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Potassium binding site 4 out of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:28.3
occ:1.00
 OD1 A:ASN466 3.3 9.5 1.0
K A:K603 3.3 45.3 1.0
O A:GLY492 3.4 8.9 1.0
OH A:TYR381 3.8 13.1 1.0
O A:SER378 4.1 13.9 1.0
CG A:ASN466 4.3 9.5 1.0
CD A:ARG493 4.3 9.1 1.0
CB A:SER378 4.3 13.9 1.0
C A:GLY492 4.5 8.9 1.0
OG A:SER378 4.5 13.9 1.0
CB A:ASN466 4.5 9.5 1.0
NE A:ARG493 4.6 9.1 1.0
CA A:ARG493 4.6 9.1 1.0
CE1 A:TYR381 4.6 13.1 1.0
CB A:VAL496 4.6 10.0 1.0
CZ A:TYR381 4.7 13.1 1.0
CG1 A:VAL496 4.8 10.0 1.0
O A:ASN465 4.8 10.5 1.0
CG2 A:VAL496 4.9 10.0 1.0
C A:SER378 4.9 13.9 1.0
N A:ARG493 5.0 9.1 1.0

Potassium binding site 5 out of 9 in 7zrd

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Potassium binding site 5 out of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K605

b:24.2
occ:1.00
 CG2 A:ILE421 3.4 12.7 1.0
K B:K701 3.5 23.8 1.0
CG1 B:VAL231 3.6 12.5 1.0
CG2 B:VAL231 3.8 12.5 1.0
CG1 A:VAL538 3.8 17.4 1.0
OG1 A:THR542 4.1 14.6 1.0
K A:K601 4.1 26.2 1.0
CB B:VAL231 4.2 12.5 1.0
CB A:ILE421 4.9 12.7 1.0
CD2 B:LEU228 4.9 12.7 1.0
CD2 A:LEU422 4.9 12.4 1.0
O A:ILE421 5.0 12.7 1.0
CB A:VAL538 5.0 17.4 1.0
O B:ALA227 5.0 12.5 1.0

Potassium binding site 6 out of 9 in 7zrd

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Potassium binding site 6 out of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K606

b:15.8
occ:1.00
 O A:ASN112 2.8 8.6 1.0
O A:ASN231 2.8 9.3 1.0
O A:SER343 2.8 10.6 1.0
O A:ASN467 2.8 10.1 1.0
O A:ASN466 2.9 9.5 1.0
O A:THR113 3.2 8.6 1.0
O A:THR230 3.3 9.8 1.0
C A:ASN467 3.6 10.1 1.0
C A:THR113 3.7 8.6 1.0
CA A:THR113 3.7 8.6 1.0
C A:SER343 3.7 10.6 1.0
C A:ASN112 3.7 8.6 1.0
C A:ASN231 3.8 9.3 1.0
C A:ASN466 3.8 9.5 1.0
OG A:SER343 3.9 10.6 1.0
CA A:ASN467 3.9 10.1 1.0
CA A:CYS344 4.1 10.3 1.0
N A:GLY345 4.1 10.2 1.0
N A:THR113 4.1 8.6 1.0
CA A:ASN231 4.2 9.3 1.0
N A:CYS344 4.2 10.3 1.0
N A:ASN467 4.3 10.1 1.0
C A:THR230 4.4 9.8 1.0
C A:CYS344 4.4 10.3 1.0
ND2 A:ASN114 4.6 8.9 1.0
N A:GLY468 4.6 9.9 1.0
N A:ASN114 4.7 8.9 1.0
ND2 A:ASN112 4.7 8.6 1.0
CA A:SER343 4.8 10.6 1.0
N A:ASN231 4.8 9.3 1.0
CB A:ASN114 4.8 8.9 1.0
CG A:ASN112 4.9 8.6 1.0
CB A:SER343 4.9 10.6 1.0
OD1 A:ASN467 4.9 10.1 1.0
CA A:ASN112 4.9 8.6 1.0
N A:GLY232 5.0 9.9 1.0

Potassium binding site 7 out of 9 in 7zrd

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Potassium binding site 7 out of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K607

b:19.6
occ:1.00
 O A:ASN114 3.0 8.9 1.0
ND2 A:ASN239 3.0 10.6 1.0
O A:GLY468 3.0 9.9 1.0
O A:GLY232 3.3 9.9 1.0
N A:GLN116 3.8 11.5 1.0
O A:GLY345 3.8 10.2 1.0
CG A:GLN116 4.0 11.5 1.0
C A:GLY468 4.0 9.9 1.0
C A:ASN114 4.1 8.9 1.0
CG A:ASN239 4.1 10.6 1.0
CB A:GLN116 4.2 11.5 1.0
CA A:TRP115 4.2 10.4 1.0
C A:GLY345 4.4 10.2 1.0
C A:GLY232 4.5 9.9 1.0
C A:TRP115 4.5 10.4 1.0
CA A:GLY345 4.5 10.2 1.0
CA A:GLN116 4.6 11.5 1.0
N A:TRP115 4.7 10.4 1.0
OD1 A:ASN239 4.8 10.6 1.0
CA A:GLY468 4.8 9.9 1.0
N A:SER469 4.9 10.5 1.0

Potassium binding site 8 out of 9 in 7zrd

Go back to Potassium Binding Sites List in 7zrd
Potassium binding site 8 out of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K701

b:23.8
occ:1.00
 K A:K605 3.5 24.2 1.0
CG2 A:ILE421 3.9 12.7 1.0
CD2 B:LEU228 4.0 12.7 1.0
CB B:ALA227 4.0 12.5 1.0
CD2 A:LEU389 4.4 14.7 1.0
CG B:LEU228 4.4 12.7 1.0
CD1 A:ILE421 4.5 12.7 1.0
CD1 A:LEU389 4.6 14.7 1.0
N B:LEU228 4.7 12.7 1.0
C B:ALA227 4.8 12.5 1.0
O B:LEU224 4.8 14.6 1.0
CB A:ILE421 4.9 12.7 1.0

Potassium binding site 9 out of 9 in 7zrd

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Potassium binding site 9 out of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Stabilised with the Inhibitor Orthovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K702

b:23.2
occ:1.00
 OD1 B:ASP583 3.3 17.5 1.0
O B:SER579 3.3 19.1 1.0
O B:ILE263 3.5 15.5 1.0
O B:CYS261 3.9 15.4 1.0
NZ B:LYS586 4.0 16.2 1.0
CA B:PRO264 4.0 16.5 1.0
CB B:ASN582 4.1 18.9 1.0
C B:SER579 4.2 19.1 1.0
O B:LEU262 4.2 14.9 1.0
CA B:SER579 4.2 19.1 1.0
N B:THR265 4.3 17.6 1.0
C B:ILE263 4.3 15.5 1.0
OG1 B:THR266 4.4 18.6 1.0
CG B:ASP583 4.4 17.5 1.0
CB B:SER579 4.5 19.1 1.0
OG1 B:THR265 4.5 17.6 1.0
N B:PRO264 4.5 16.5 1.0
C B:PRO264 4.7 16.5 1.0
ND2 B:ASN582 4.7 18.9 1.0
C B:LEU262 4.7 14.9 1.0
OD1 B:ASN624 4.8 16.2 1.0
OD2 B:ASP583 4.9 17.5 1.0
C B:CYS261 4.9 15.4 1.0
CG B:ASN582 4.9 18.9 1.0
N B:THR266 5.0 18.6 1.0

Reference:

J.M.Silberberg, C.Stock, L.Hielkema, R.A.Corey, J.Rheinberger, D.Wunnicke, V.R.A.Dubach, P.J.Stansfeld, I.Hanelt, C.Paulino. Inhibited Kdpfabc Transitions Into An E1 Off-Cycle State. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 36255052
DOI: 10.7554/ELIFE.80988
Page generated: Wed Apr 5 10:31:11 2023

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