Potassium in PDB 7zrk: Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P_ADP Conformation, Under Turnover Conditions

Enzymatic activity of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P_ADP Conformation, Under Turnover Conditions

All present enzymatic activity of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P_ADP Conformation, Under Turnover Conditions:
7.2.2.6;

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Potassium atom in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P_ADP Conformation, Under Turnover Conditions (pdb code 7zrk). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 12 binding sites of Potassium where determined in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P_ADP Conformation, Under Turnover Conditions, PDB code: 7zrk:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 12 in 7zrk

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Potassium binding site 1 out of 12 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P_ADP Conformation, Under Turnover Conditions


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_ADP Conformation, Under Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K601

b:50.7
occ:1.00
 CG2 A:ILE421 3.3 22.8 1.0
K A:K602 4.0 41.1 1.0
CG1 B:VAL231 4.1 22.8 1.0
CG2 B:VAL231 4.3 22.8 1.0
O B:ALA227 4.3 21.9 1.0
CD2 B:LEU228 4.4 23.8 1.0
CB B:ALA227 4.4 21.9 1.0
C B:ALA227 4.4 21.9 1.0
CG1 A:VAL538 4.4 29.4 1.0
CG B:LEU228 4.6 23.8 1.0
N B:LEU228 4.6 23.8 1.0
CB A:ILE421 4.7 22.8 1.0
CA B:LEU228 4.7 23.8 1.0
CB B:VAL231 4.9 22.8 1.0

Potassium binding site 2 out of 12 in 7zrk

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Potassium binding site 2 out of 12 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P_ADP Conformation, Under Turnover Conditions


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_ADP Conformation, Under Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:41.1
occ:1.00
 K A:K603 2.9 41.0 1.0
OG1 A:THR542 3.3 25.7 1.0
CG1 A:VAL538 3.4 29.4 1.0
CG A:PRO425 3.5 22.7 1.0
CG2 A:ILE421 3.9 22.8 1.0
K A:K601 4.0 50.7 1.0
CG1 B:VAL231 4.3 22.8 1.0
CB A:THR542 4.3 25.7 1.0
O A:ILE421 4.3 22.8 1.0
CG2 A:THR542 4.3 25.7 1.0
CB A:PRO425 4.4 22.7 1.0
O A:VAL538 4.4 29.4 1.0
K A:K609 4.5 39.9 1.0
CD A:PRO425 4.5 22.7 1.0
C A:VAL538 4.8 29.4 1.0
CB A:VAL538 4.8 29.4 1.0
CB B:VAL231 5.0 22.8 1.0

Potassium binding site 3 out of 12 in 7zrk

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Potassium binding site 3 out of 12 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P_ADP Conformation, Under Turnover Conditions


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_ADP Conformation, Under Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:41.0
occ:1.00
 K A:K602 2.9 41.1 1.0
K A:K609 2.9 39.9 1.0
O A:ILE368 3.4 25.4 1.0
C A:ILE368 3.7 25.4 1.0
CG A:PRO425 3.8 22.7 1.0
O A:GLN367 3.8 23.5 1.0
CZ A:PHE386 3.9 26.7 1.0
CA A:ILE368 4.1 25.4 1.0
N A:GLY369 4.3 27.7 1.0
CG1 A:VAL538 4.3 29.4 1.0
CD A:PRO425 4.5 22.7 1.0
CA A:GLY369 4.6 27.7 1.0
CE2 A:PHE386 4.6 26.7 1.0
C A:GLN367 4.8 23.5 1.0
CA A:GLY539 4.9 27.3 1.0
OG1 A:THR542 4.9 25.7 1.0
CE2 A:PHE543 4.9 24.1 1.0
CE1 A:PHE386 4.9 26.7 1.0
O A:ILE421 5.0 22.8 1.0
N A:ILE368 5.0 25.4 1.0

Potassium binding site 4 out of 12 in 7zrk

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Potassium binding site 4 out of 12 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P_ADP Conformation, Under Turnover Conditions


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_ADP Conformation, Under Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:50.9
occ:1.00
 K A:K609 3.0 39.9 1.0
O A:GLY369 3.5 27.7 1.0
CA A:GLY369 3.7 27.7 1.0
K A:K605 3.7 37.8 1.0
K A:K611 3.7 36.8 1.0
C A:GLY369 4.1 27.7 1.0
OG1 A:THR424 4.3 22.9 1.0
O A:ALA420 4.5 22.0 1.0
CA A:GLY382 4.7 24.9 1.0
CD1 A:LEU385 4.8 24.5 1.0
CE2 A:PHE386 4.8 26.7 1.0
CB A:THR424 4.9 22.9 1.0
N A:GLY369 5.0 27.7 1.0
CG1 A:VAL496 5.0 20.3 1.0

Potassium binding site 5 out of 12 in 7zrk

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Potassium binding site 5 out of 12 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P_ADP Conformation, Under Turnover Conditions


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_ADP Conformation, Under Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K605

b:37.8
occ:1.00
 O A:SER378 2.9 24.5 1.0
K A:K611 2.9 36.8 1.0
O A:GLY369 3.3 27.7 1.0
CA A:GLY382 3.4 24.9 1.0
N A:GLY382 3.7 24.9 1.0
K A:K604 3.7 50.9 1.0
C A:SER378 3.8 24.5 1.0
O A:GLU370 4.1 24.8 1.0
CE1 A:TYR381 4.2 23.8 1.0
CD1 A:TYR381 4.3 23.8 1.0
C A:GLY369 4.5 27.7 1.0
CA A:SER378 4.5 24.5 1.0
CB A:SER378 4.6 24.5 1.0
N A:GLY379 4.6 23.9 1.0
C A:GLY382 4.7 24.9 1.0
CA A:GLY379 4.7 23.9 1.0
CG1 A:VAL496 4.8 20.3 1.0
C A:TYR381 4.8 23.8 1.0
C A:GLU370 4.9 24.8 1.0

Potassium binding site 6 out of 12 in 7zrk

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Potassium binding site 6 out of 12 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P_ADP Conformation, Under Turnover Conditions


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_ADP Conformation, Under Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K606

b:22.2
occ:1.00
 OG A:SER343 2.9 22.6 1.0
O A:ASN112 3.0 20.0 1.0
ND2 A:ASN112 3.0 20.0 1.0
O A:ASN466 3.2 20.9 1.0
K A:K610 3.5 34.4 1.0
CG A:ASN112 3.5 20.0 1.0
O A:SER343 3.5 22.6 1.0
CB A:SER343 3.6 22.6 1.0
CB A:ASN112 3.7 20.0 1.0
C A:ASN112 4.0 20.0 1.0
CB A:ASN466 4.1 20.9 1.0
NH1 A:ARG493 4.1 19.3 1.0
K A:K607 4.1 22.0 1.0
OG1 A:THR230 4.2 21.0 1.0
O A:THR230 4.3 21.0 1.0
OD1 A:ASN112 4.4 20.0 1.0
C A:ASN466 4.4 20.9 1.0
CA A:GLY375 4.4 22.4 1.0
C A:SER343 4.5 22.6 1.0
CA A:ASN112 4.5 20.0 1.0
OG A:SER378 4.6 24.5 1.0
CA A:SER343 4.7 22.6 1.0
CB A:SER378 4.8 24.5 1.0
CA A:ASN466 4.9 20.9 1.0
O A:GLY374 4.9 24.6 1.0

Potassium binding site 7 out of 12 in 7zrk

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Potassium binding site 7 out of 12 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P_ADP Conformation, Under Turnover Conditions


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_ADP Conformation, Under Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K607

b:22.0
occ:1.00
 O A:SER343 2.8 22.6 1.0
O A:ASN231 2.8 20.3 1.0
O A:ASN112 2.8 20.0 1.0
O A:ASN467 2.9 21.5 1.0
O A:THR113 2.9 20.8 1.0
O A:THR230 3.2 21.0 1.0
O A:ASN466 3.3 20.9 1.0
C A:THR113 3.5 20.8 1.0
CA A:THR113 3.6 20.8 1.0
C A:ASN112 3.7 20.0 1.0
C A:ASN231 3.7 20.3 1.0
C A:ASN467 3.7 21.5 1.0
C A:SER343 3.8 22.6 1.0
N A:GLY345 3.9 22.9 1.0
CA A:CYS344 4.0 21.8 1.0
CA A:ASN231 4.0 20.3 1.0
N A:THR113 4.0 20.8 1.0
CA A:ASN467 4.1 21.5 1.0
K A:K606 4.1 22.2 1.0
C A:ASN466 4.2 20.9 1.0
ND2 A:ASN114 4.2 20.9 1.0
C A:THR230 4.3 21.0 1.0
C A:CYS344 4.3 21.8 1.0
N A:CYS344 4.3 21.8 1.0
OG A:SER343 4.4 22.6 1.0
N A:ASN114 4.5 20.9 1.0
N A:ASN467 4.6 21.5 1.0
CB A:ASN114 4.6 20.9 1.0
N A:ASN231 4.6 20.3 1.0
CA A:GLY345 4.7 22.9 1.0
N A:GLY468 4.7 22.1 1.0
OD1 A:ASN112 4.8 20.0 1.0
N A:GLY232 4.8 21.1 1.0
CG A:ASN114 4.9 20.9 1.0
CA A:ASN112 4.9 20.0 1.0
CG A:ASN112 5.0 20.0 1.0
CA A:SER343 5.0 22.6 1.0

Potassium binding site 8 out of 12 in 7zrk

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Potassium binding site 8 out of 12 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P_ADP Conformation, Under Turnover Conditions


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_ADP Conformation, Under Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K608

b:27.8
occ:1.00
 O A:GLY345 3.0 22.9 1.0
O A:GLY232 3.0 21.1 1.0
O A:ASN114 3.1 20.9 1.0
O A:GLY468 3.2 22.1 1.0
ND2 A:ASN239 3.2 22.6 1.0
C A:GLY345 3.6 22.9 1.0
CA A:GLY345 3.8 22.9 1.0
C A:GLY468 3.9 22.1 1.0
OE1 A:GLN116 3.9 23.8 1.0
C A:GLY232 4.1 21.1 1.0
C A:ASN114 4.2 20.9 1.0
N A:SER469 4.4 22.5 1.0
CG A:ASN239 4.5 22.6 1.0
CA A:SER469 4.5 22.5 1.0
CA A:GLY468 4.6 22.1 1.0
N A:ALA346 4.7 21.9 1.0
N A:GLN116 4.7 23.8 1.0
CA A:TRP115 4.7 21.8 1.0
CA A:GLY233 4.7 21.6 1.0
N A:GLY234 4.8 22.1 1.0
CD A:GLN116 4.8 23.8 1.0
N A:TRP115 4.9 21.8 1.0
N A:GLY233 4.9 21.6 1.0

Potassium binding site 9 out of 12 in 7zrk

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Potassium binding site 9 out of 12 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P_ADP Conformation, Under Turnover Conditions


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_ADP Conformation, Under Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K609

b:39.9
occ:1.00
 K A:K603 2.9 41.0 1.0
K A:K604 3.0 50.9 1.0
O A:ILE421 3.3 22.8 1.0
CD A:PRO425 3.4 22.7 1.0
CG A:PRO425 3.8 22.7 1.0
CA A:GLY369 4.0 27.7 1.0
CB A:THR424 4.1 22.9 1.0
C A:ILE421 4.2 22.8 1.0
CA A:ILE421 4.3 22.8 1.0
OG1 A:THR424 4.3 22.9 1.0
K A:K602 4.5 41.1 1.0
N A:PRO425 4.6 22.7 1.0
O A:ILE368 4.6 25.4 1.0
N A:GLY369 4.6 27.7 1.0
O A:ALA420 4.7 22.0 1.0
CG2 A:ILE421 4.8 22.8 1.0
C A:ILE368 4.8 25.4 1.0
N A:THR424 4.8 22.9 1.0
CA A:THR424 4.9 22.9 1.0
CE2 A:PHE386 5.0 26.7 1.0

Potassium binding site 10 out of 12 in 7zrk

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Potassium binding site 10 out of 12 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P_ADP Conformation, Under Turnover Conditions


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P_ADP Conformation, Under Turnover Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K610

b:34.4
occ:1.00
 OG A:SER343 3.0 22.6 1.0
O A:ASN465 3.3 21.6 1.0
CB A:SER378 3.4 24.5 1.0
K A:K606 3.5 22.2 1.0
CB A:SER343 3.6 22.6 1.0
O A:GLY374 3.6 24.6 1.0
CB A:ASN466 3.6 20.9 1.0
OG A:SER378 3.9 24.5 1.0
K A:K611 4.1 36.8 1.0
O A:ASN466 4.1 20.9 1.0
OD1 A:ASN466 4.2 20.9 1.0
CB A:GLU370 4.3 24.8 1.0
C A:ASN465 4.3 21.6 1.0
CG A:ASN466 4.4 20.9 1.0
CG A:GLU370 4.5 24.8 1.0
CA A:ASN466 4.5 20.9 1.0
C A:ASN466 4.5 20.9 1.0
C A:GLY374 4.7 24.6 1.0
CA A:SER378 4.8 24.5 1.0
NH1 A:ARG493 4.8 19.3 1.0
N A:ASN466 4.8 20.9 1.0
C A:SER378 5.0 24.5 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 10:31:09 2023

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