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Potassium in PDB 7zrj: 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 7zrj). 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: 7zrj:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 7zrj

Go back to Potassium Binding Sites List in 7zrj
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:11.4
occ:1.00
 CG2 A:ILE421 3.4 12.3 1.0
CB A:ILE421 4.2 12.3 1.0
CB B:ALA227 4.4 11.9 1.0
CD2 B:LEU228 4.5 12.2 1.0
CG2 B:VAL231 4.6 10.9 1.0
CD1 A:LEU389 4.6 12.4 1.0
CD1 A:ILE421 4.6 12.3 1.0
CG B:LEU228 4.7 12.2 1.0
C B:ALA227 4.9 11.9 1.0
O B:ALA227 4.9 11.9 1.0
N B:LEU228 5.0 12.2 1.0

Potassium binding site 2 out of 7 in 7zrj

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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:18.7
occ:1.00
 O A:GLY468 3.0 13.9 1.0
ND2 A:ASN239 3.0 15.4 1.0
CB A:ALA470 3.7 11.9 1.0
O A:GLY345 3.9 15.3 1.0
N A:ALA470 3.9 11.9 1.0
CG A:ASN239 3.9 15.4 1.0
OD1 A:ASN239 4.0 15.4 1.0
C A:GLY468 4.1 13.9 1.0
CA A:SER469 4.2 12.2 1.0
C A:SER469 4.3 12.2 1.0
CA A:ALA470 4.5 11.9 1.0
N A:GLN116 4.6 13.5 1.0
N A:SER469 4.6 12.2 1.0
O A:GLN116 4.9 13.5 1.0
CB A:GLN116 4.9 13.5 1.0

Potassium binding site 3 out of 7 in 7zrj

Go back to Potassium Binding Sites List in 7zrj
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:13.3
occ:1.00
 OG A:SER378 4.1 14.0 1.0
O A:GLY492 4.2 26.8 1.0
O A:ASN465 4.4 13.6 1.0
CG A:GLU370 4.5 17.6 1.0
ND2 A:ASN466 4.5 17.0 1.0
CG2 A:VAL496 4.5 30.6 1.0
CG1 A:VAL496 4.5 30.6 1.0
K A:K605 4.6 18.7 1.0
CB A:GLU370 4.7 17.6 1.0
CB A:VAL496 4.8 30.6 1.0
C A:ASN465 4.8 13.6 1.0
N A:GLU370 4.9 17.6 1.0
OG1 A:THR424 5.0 14.9 1.0
CA A:ASN465 5.0 13.6 1.0

Potassium binding site 4 out of 7 in 7zrj

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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:33.8
occ:1.00
 O A:ILE421 3.3 12.3 1.0
CG A:PRO425 3.4 11.3 1.0
CD A:PRO425 3.6 11.3 1.0
CG2 A:ILE421 4.0 12.3 1.0
CB A:THR424 4.2 14.9 1.0
C A:ILE421 4.3 12.3 1.0
O A:ILE368 4.3 14.6 1.0
CZ A:PHE386 4.4 12.0 1.0
O A:GLN367 4.4 14.0 1.0
CG2 A:THR424 4.5 14.9 1.0
N A:PRO425 4.6 11.3 1.0
K A:K605 4.6 18.7 1.0
C A:ILE368 4.6 14.6 1.0
CA A:ILE421 4.7 12.3 1.0
CB A:PRO425 4.8 11.3 1.0
N A:GLY369 4.9 15.1 1.0
OG1 A:THR424 4.9 14.9 1.0
CB A:ILE421 5.0 12.3 1.0

Potassium binding site 5 out of 7 in 7zrj

Go back to Potassium Binding Sites List in 7zrj
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:18.7
occ:1.00
 OG1 A:THR424 3.3 14.9 1.0
O A:ALA420 3.9 12.4 1.0
CD1 A:LEU385 4.1 12.1 1.0
CB A:THR424 4.2 14.9 1.0
K A:K604 4.6 33.8 1.0
K A:K603 4.6 13.3 1.0
O A:ILE421 4.6 12.3 1.0
CA A:ILE421 4.7 12.3 1.0
CA A:GLY369 4.7 15.1 1.0
CG1 A:VAL496 4.7 30.6 1.0
CG2 A:VAL496 4.7 30.6 1.0
CG2 A:THR424 4.8 14.9 1.0
C A:ALA420 4.9 12.4 1.0

Potassium binding site 6 out of 7 in 7zrj

Go back to Potassium Binding Sites List in 7zrj
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:21.2
occ:1.00
 O A:ASN231 2.8 13.0 1.0
O A:SER343 2.8 19.6 1.0
O A:ASN112 2.8 16.7 1.0
O A:ASN466 2.9 17.0 1.0
O A:ASN467 2.9 17.0 1.0
O A:THR230 3.0 13.9 1.0
O A:CYS344 3.0 18.3 1.0
O A:THR113 3.1 15.7 1.0
C A:ASN467 3.6 17.0 1.0
C A:THR113 3.7 15.7 1.0
C A:ASN112 3.7 16.7 1.0
C A:ASN231 3.8 13.0 1.0
C A:ASN466 3.8 17.0 1.0
CA A:THR113 3.8 15.7 1.0
OG A:SER343 3.8 19.6 1.0
C A:CYS344 3.9 18.3 1.0
C A:SER343 3.9 19.6 1.0
CA A:ASN467 4.0 17.0 1.0
N A:THR113 4.1 15.7 1.0
OD1 A:ASN112 4.1 16.7 1.0
C A:THR230 4.1 13.9 1.0
CA A:ASN231 4.2 13.0 1.0
N A:ASN467 4.3 17.0 1.0
CA A:CYS344 4.3 18.3 1.0
CB A:ASN114 4.6 14.9 1.0
N A:CYS344 4.6 18.3 1.0
N A:ASN114 4.7 14.9 1.0
N A:ASN231 4.7 13.0 1.0
N A:GLY468 4.7 13.9 1.0
CG A:ASN112 4.7 16.7 1.0
CA A:ASN112 4.8 16.7 1.0
N A:GLY232 4.8 13.8 1.0
N A:GLY345 4.9 15.3 1.0
CA A:ASN466 4.9 17.0 1.0
ND2 A:ASN114 4.9 14.9 1.0
CB A:SER343 4.9 19.6 1.0
ND2 A:ASN467 5.0 17.0 1.0
CA A:SER343 5.0 19.6 1.0

Potassium binding site 7 out of 7 in 7zrj

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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:K901

b:21.0
occ:1.00
 O B:CYS261 3.0 15.1 1.0
NZ B:LYS586 3.3 17.7 1.0
O B:ILE263 3.5 12.7 1.0
CE B:LYS586 3.7 17.7 1.0
OD1 B:ASN624 3.8 20.9 1.0
O B:SER579 4.0 17.6 1.0
N B:THR265 4.2 15.5 1.0
CD B:LYS586 4.2 17.7 1.0
OD1 B:ASP583 4.2 17.9 1.0
C B:CYS261 4.2 15.1 1.0
C B:ILE263 4.5 12.7 1.0
OG1 B:THR265 4.5 15.5 1.0
CA B:PRO264 4.5 12.9 1.0
CG2 B:THR266 4.6 15.5 1.0
CG B:ASN624 4.6 20.9 1.0
CB B:ASN582 4.8 18.5 1.0
CB B:THR265 4.8 15.5 1.0
O B:LEU262 4.8 13.6 1.0
C B:SER579 4.8 17.6 1.0
CA B:SER579 4.9 17.6 1.0
C B:PRO264 4.9 12.9 1.0
CB B:SER579 4.9 17.6 1.0
C B:LEU262 4.9 13.6 1.0
N B:PRO264 5.0 12.9 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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