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

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

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

Other elements in 7zrm:

The structure of Cryo-Em Map of the Unphosphorylated Kdpfabc Complex in the E1-P_ADP Conformation, Under Turnover Conditions also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Potassium Binding Sites:

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

Potassium binding site 1 out of 5 in 7zrm

Go back to Potassium Binding Sites List in 7zrm
Potassium binding site 1 out of 5 in the Cryo-Em Map of the Unphosphorylated 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 Unphosphorylated 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:19.3
occ:1.00
 CD2 B:LEU228 3.8 14.2 1.0
CG2 A:ILE421 3.9 14.1 1.0
CD2 A:LEU389 3.9 15.4 1.0
CB B:ALA227 4.4 13.7 1.0
CG B:LEU228 4.5 14.2 1.0
CD2 A:LEU422 4.6 12.9 1.0
CB A:ILE421 4.8 14.1 1.0
N B:LEU228 4.8 14.2 1.0
CG2 A:VAL538 4.9 15.0 1.0
O B:LEU224 4.9 15.4 1.0
C B:ALA227 4.9 13.7 1.0
CG1 A:VAL538 5.0 15.0 1.0

Potassium binding site 2 out of 5 in 7zrm

Go back to Potassium Binding Sites List in 7zrm
Potassium binding site 2 out of 5 in the Cryo-Em Map of the Unphosphorylated 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 Unphosphorylated 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:21.5
occ:1.00
 CG1 A:VAL538 3.4 15.0 1.0
CG A:PRO425 3.7 12.7 1.0
O A:VAL538 3.7 15.0 1.0
OG1 A:THR542 3.8 14.2 1.0
C A:VAL538 4.2 15.0 1.0
O A:ILE368 4.5 14.0 1.0
CA A:GLY539 4.5 14.5 1.0
CB A:THR542 4.5 14.2 1.0
N A:GLY539 4.5 14.5 1.0
O A:GLN367 4.6 14.1 1.0
CB A:PRO425 4.6 12.7 1.0
CB A:VAL538 4.7 15.0 1.0
CG2 A:THR542 4.8 14.2 1.0
CD A:PRO425 4.8 12.7 1.0
C A:ILE368 4.8 14.0 1.0
CZ A:PHE386 4.8 14.2 1.0
CG2 A:ILE421 4.9 14.1 1.0
O A:ILE421 4.9 14.1 1.0

Potassium binding site 3 out of 5 in 7zrm

Go back to Potassium Binding Sites List in 7zrm
Potassium binding site 3 out of 5 in the Cryo-Em Map of the Unphosphorylated 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 Unphosphorylated 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:25.5
occ:1.00
 O A:GLY369 2.9 15.1 1.0
K A:K605 3.3 32.6 1.0
C A:GLY369 4.1 15.1 1.0
O A:SER378 4.2 16.0 1.0
CG2 A:THR424 4.4 13.4 1.0
CG1 A:VAL496 4.4 13.2 1.0
CA A:GLY369 4.7 15.1 1.0
CA A:GLY382 4.7 14.8 1.0
O A:GLU370 4.7 14.4 1.0
CG2 A:VAL496 4.8 13.2 1.0
OD1 A:ASN465 4.9 12.6 1.0
CB A:GLU370 4.9 14.4 1.0
CE1 A:TYR381 5.0 15.2 1.0

Potassium binding site 4 out of 5 in 7zrm

Go back to Potassium Binding Sites List in 7zrm
Potassium binding site 4 out of 5 in the Cryo-Em Map of the Unphosphorylated 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 Unphosphorylated 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:20.4
occ:1.00
 ND2 A:ASN239 3.0 15.4 1.0
O A:GLY468 3.2 14.4 1.0
O A:GLY345 3.2 14.8 1.0
CG A:ASN239 4.0 15.4 1.0
O A:ASN114 4.1 15.8 1.0
C A:GLY468 4.1 14.4 1.0
CB A:ASN239 4.1 15.4 1.0
C A:GLY345 4.2 14.8 1.0
CB A:GLN116 4.4 17.2 1.0
CA A:SER469 4.4 14.2 1.0
CG A:GLN116 4.4 17.2 1.0
N A:GLY233 4.4 15.4 1.0
N A:GLN116 4.5 17.2 1.0
CA A:GLY345 4.5 14.8 1.0
CA A:GLY233 4.5 15.4 1.0
NE2 A:GLN116 4.6 17.2 1.0
N A:SER469 4.6 14.2 1.0
N A:ALA470 4.8 14.8 1.0

Potassium binding site 5 out of 5 in 7zrm

Go back to Potassium Binding Sites List in 7zrm
Potassium binding site 5 out of 5 in the Cryo-Em Map of the Unphosphorylated 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 Unphosphorylated 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:32.6
occ:1.00
 K A:K603 3.3 25.5 1.0
ND2 A:ASN466 3.5 13.4 1.0
CB A:SER378 4.2 16.0 1.0
O A:ASN465 4.3 12.6 1.0
OG A:SER378 4.4 16.0 1.0
CB A:ASN466 4.4 13.4 1.0
CG A:ASN466 4.5 13.4 1.0
OH A:TYR381 4.5 15.2 1.0
O A:SER378 4.6 16.0 1.0
C A:ASN465 4.7 12.6 1.0
CG1 A:VAL496 4.8 13.2 1.0
CE1 A:TYR381 4.9 15.2 1.0
CB A:VAL496 4.9 13.2 1.0
CG2 A:THR424 5.0 13.4 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: Mon Aug 12 21:56:09 2024

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