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Potassium in PDB 7zrh: Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+

Enzymatic activity of Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+

All present enzymatic activity of Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 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 A Nucleotide-Free E1 Conformation Loaded with K+ (pdb code 7zrh). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+, PDB code: 7zrh:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 7zrh

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Potassium binding site 1 out of 7 in the Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+


Mono view


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 A Nucleotide-Free E1 Conformation Loaded with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K601

b:17.1
occ:1.00
 CG2 A:ILE421 3.4 9.6 1.0
CD1 A:LEU389 3.8 11.9 1.0
CB B:ALA227 4.2 6.8 1.0
CB A:ILE421 4.4 9.6 1.0
CG1 A:VAL538 4.6 13.3 1.0
CD2 B:LEU228 4.6 7.9 1.0
CG B:LEU228 4.8 7.9 1.0
CG1 A:ILE421 4.8 9.6 1.0
CG2 A:VAL538 4.9 13.3 1.0
N B:LEU228 5.0 7.9 1.0

Potassium binding site 2 out of 7 in 7zrh

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Potassium binding site 2 out of 7 in the Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 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 A Nucleotide-Free E1 Conformation Loaded with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:34.5
occ:1.00
 O A:GLY468 2.9 10.9 1.0
O A:GLY345 3.4 8.2 1.0
O A:ASN114 3.5 13.6 1.0
ND2 A:ASN239 3.5 8.8 1.0
O A:GLY232 3.6 7.3 1.0
CG A:ASN239 3.8 8.8 1.0
C A:GLY468 3.9 10.9 1.0
OD1 A:ASN239 4.2 8.8 1.0
C A:GLY345 4.3 8.2 1.0
N A:GLN116 4.4 10.8 1.0
CB A:ASN239 4.4 8.8 1.0
CB A:GLN116 4.4 10.8 1.0
CG A:GLN116 4.4 10.8 1.0
CA A:GLY345 4.5 8.2 1.0
C A:ASN114 4.6 13.6 1.0
NE2 A:GLN116 4.7 10.8 1.0
N A:SER469 4.7 10.5 1.0
CA A:GLY468 4.7 10.9 1.0
C A:GLY232 4.8 7.3 1.0
CA A:TRP115 4.8 10.6 1.0
CA A:SER469 4.8 10.5 1.0
C A:TRP115 5.0 10.6 1.0

Potassium binding site 3 out of 7 in 7zrh

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Potassium binding site 3 out of 7 in the Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 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 A Nucleotide-Free E1 Conformation Loaded with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:55.1
occ:1.00
 OD1 A:ASN466 3.9 17.9 1.0
O A:GLY492 4.1 20.1 1.0
CB A:SER378 4.2 12.2 1.0
CG2 A:VAL496 4.2 20.1 1.0
NH1 A:ARG493 4.2 20.1 1.0
CB A:VAL496 4.3 20.1 1.0
CG1 A:VAL496 4.3 20.1 1.0
OG A:SER378 4.6 12.2 1.0
O A:ASN465 4.7 17.9 1.0
CB A:ASN466 4.7 17.9 1.0
CG A:ASN466 4.7 17.9 1.0
CA A:ARG493 4.8 20.1 1.0

Potassium binding site 4 out of 7 in 7zrh

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Potassium binding site 4 out of 7 in the Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 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 A Nucleotide-Free E1 Conformation Loaded with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:25.2
occ:1.00
 CG A:PRO425 3.4 17.4 1.0
CG1 A:VAL538 3.5 13.3 1.0
O A:VAL538 4.2 13.3 1.0
O A:ILE421 4.3 9.6 1.0
CG2 A:ILE421 4.3 9.6 1.0
CD A:PRO425 4.3 17.4 1.0
CZ A:PHE386 4.4 9.6 1.0
OG1 A:THR542 4.4 11.3 1.0
CB A:PRO425 4.5 17.4 1.0
C A:VAL538 4.5 13.3 1.0
CE1 A:PHE386 4.6 9.6 1.0
CA A:GLY539 4.7 12.6 1.0
N A:GLY539 4.8 12.6 1.0
CG2 A:THR542 4.8 11.3 1.0
CB A:VAL538 4.8 13.3 1.0
O A:ILE368 4.8 12.1 1.0

Potassium binding site 5 out of 7 in 7zrh

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Potassium binding site 5 out of 7 in the Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 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 A Nucleotide-Free E1 Conformation Loaded with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K605

b:15.1
occ:1.00
 O A:ASN231 2.8 9.4 1.0
O A:ASN112 2.8 17.6 1.0
O A:SER343 2.8 11.6 1.0
O A:ASN467 2.9 12.3 1.0
O A:THR113 3.0 15.2 1.0
O A:THR230 3.1 7.0 1.0
C A:THR113 3.6 15.2 1.0
C A:ASN231 3.6 9.4 1.0
CA A:THR113 3.7 15.2 1.0
C A:ASN467 3.8 12.3 1.0
C A:ASN112 3.8 17.6 1.0
O A:ASN466 3.8 17.9 1.0
C A:SER343 3.8 11.6 1.0
N A:GLY345 3.8 8.2 1.0
CA A:ASN231 3.9 9.4 1.0
CA A:CYS344 4.0 10.0 1.0
C A:THR230 4.1 7.0 1.0
N A:THR113 4.2 15.2 1.0
OG A:SER343 4.2 11.6 1.0
C A:CYS344 4.3 10.0 1.0
N A:CYS344 4.3 10.0 1.0
CA A:ASN467 4.3 12.3 1.0
N A:ASN231 4.5 9.4 1.0
C A:ASN466 4.5 17.9 1.0
ND2 A:ASN114 4.6 13.6 1.0
N A:ASN114 4.7 13.6 1.0
CA A:GLY345 4.7 8.2 1.0
OD1 A:ASN112 4.7 17.6 1.0
N A:GLY468 4.7 10.9 1.0
N A:GLY232 4.8 7.3 1.0
N A:ASN467 4.8 12.3 1.0
CB A:ASN114 4.9 13.6 1.0
CA A:SER343 5.0 11.6 1.0
CA A:ASN112 5.0 17.6 1.0

Potassium binding site 6 out of 7 in 7zrh

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Potassium binding site 6 out of 7 in the Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 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 A Nucleotide-Free E1 Conformation Loaded with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K606

b:41.1
occ:1.00
 OG1 A:THR424 3.0 16.7 1.0
O A:ALA420 3.9 9.3 1.0
CB A:THR424 4.1 16.7 1.0
CG2 A:THR424 4.1 16.7 1.0
CA A:GLY369 4.2 12.0 1.0
O A:ILE421 4.5 9.6 1.0
CD1 A:ILE421 4.7 9.6 1.0
CA A:ILE421 4.7 9.6 1.0
C A:ALA420 5.0 9.3 1.0

Potassium binding site 7 out of 7 in 7zrh

Go back to Potassium Binding Sites List in 7zrh
Potassium binding site 7 out of 7 in the Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 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 A Nucleotide-Free E1 Conformation Loaded with K+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:21.8
occ:1.00
 NZ B:LYS586 3.1 10.8 1.0
OD1 B:ASP583 3.3 12.8 1.0
O B:CYS261 3.5 8.3 1.0
O B:SER579 3.5 14.7 1.0
OD1 B:ASN624 3.7 11.6 1.0
O B:ILE263 3.8 7.5 1.0
CB B:ASN582 3.9 15.1 1.0
ND2 B:ASN582 4.4 15.1 1.0
CE B:LYS586 4.4 10.8 1.0
C B:SER579 4.5 14.7 1.0
C B:CYS261 4.5 8.3 1.0
CG B:ASP583 4.6 12.8 1.0
CA B:SER579 4.6 14.7 1.0
O B:LEU262 4.6 7.9 1.0
N B:THR265 4.7 9.0 1.0
C B:ILE263 4.7 7.5 1.0
CA B:PRO264 4.7 7.8 1.0
CG B:ASN582 4.7 15.1 1.0
CG B:LYS586 4.7 10.8 1.0
CB B:SER579 4.8 14.7 1.0
CG B:ASN624 4.9 11.6 1.0
C B:LEU262 4.9 7.9 1.0
N B:ASP583 4.9 12.8 1.0
C B:ASN582 5.0 15.1 1.0
CA B:ASN582 5.0 15.1 1.0
OG1 B:THR266 5.0 9.5 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: Mon Aug 12 21:54:09 2024

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