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

Potassium binding site 1 out of 7 in 7zri

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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:19.3
occ:1.00
 O A:GLY468 2.9 14.1 1.0
O A:GLY345 2.9 12.1 1.0
ND2 A:ASN239 3.0 12.3 1.0
O A:ASN114 3.0 13.4 1.0
C A:GLY468 3.6 14.1 1.0
N A:GLY233 3.7 12.3 1.0
CA A:GLY233 3.7 12.3 1.0
CG A:ASN239 3.9 12.3 1.0
C A:GLY345 3.9 12.1 1.0
C A:ASN114 4.1 13.4 1.0
CA A:GLY468 4.2 14.1 1.0
OD1 A:ASN239 4.2 12.3 1.0
N A:SER469 4.3 14.0 1.0
N A:GLN116 4.4 13.8 1.0
CA A:TRP115 4.5 14.4 1.0
C A:GLY232 4.6 11.1 1.0
CA A:SER469 4.6 14.0 1.0
CA A:GLY345 4.6 12.1 1.0
N A:TRP115 4.7 14.4 1.0
CB A:GLN116 4.8 13.8 1.0
N A:ALA346 4.8 11.5 1.0
C A:TRP115 4.9 14.4 1.0
OE1 A:GLN116 4.9 13.8 1.0

Potassium binding site 2 out of 7 in 7zri

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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:49.3
occ:1.00
 OD1 A:ASN466 3.8 14.1 1.0
K A:K604 4.0 88.0 1.0
O A:SER378 4.1 11.4 1.0
O A:GLY492 4.1 26.6 1.0
O A:ASN465 4.2 15.6 1.0
CG A:ASN466 4.5 14.1 1.0
C A:ASN465 4.5 15.6 1.0
CB A:ASN466 4.5 14.1 1.0
CA A:ASN465 4.9 15.6 1.0
CG2 A:VAL496 4.9 12.7 1.0
CG1 A:VAL496 5.0 12.7 1.0

Potassium binding site 3 out of 7 in 7zri

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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:23.7
occ:1.00
 CG A:PRO425 3.4 12.0 1.0
CG1 A:VAL538 3.4 16.7 1.0
CG2 A:THR542 3.8 14.8 1.0
O A:VAL538 3.9 16.7 1.0
C A:VAL538 4.3 16.7 1.0
CD A:PRO425 4.4 12.0 1.0
CB A:PRO425 4.5 12.0 1.0
O A:ILE368 4.5 14.5 1.0
CG2 A:ILE421 4.6 9.7 1.0
CA A:GLY539 4.6 15.2 1.0
CZ A:PHE386 4.6 12.0 1.0
N A:GLY539 4.7 15.2 1.0
O A:ILE421 4.7 9.7 1.0
O A:GLN367 4.7 14.5 1.0
CB A:VAL538 4.8 16.7 1.0
CE2 A:PHE543 4.9 14.7 1.0
C A:ILE368 4.9 14.5 1.0
CE1 A:PHE386 5.0 12.0 1.0
CB A:THR542 5.0 14.8 1.0

Potassium binding site 4 out of 7 in 7zri

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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:88.0
occ:1.00
 K A:K602 4.0 49.3 1.0
CA A:GLY369 4.1 14.9 1.0
OG1 A:THR424 4.2 13.2 1.0
N A:GLU370 4.3 13.4 1.0
CG2 A:THR424 4.4 13.2 1.0
C A:GLY369 4.5 14.9 1.0
CA A:GLY382 4.5 11.8 1.0
OD1 A:ASN465 4.7 15.6 1.0
CG1 A:VAL496 4.8 12.7 1.0
CB A:THR424 4.9 13.2 1.0

Potassium binding site 5 out of 7 in 7zri

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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:26.6
occ:1.00
 O A:ASN112 2.8 11.8 1.0
O A:ASN231 2.8 12.0 1.0
O A:SER343 2.8 12.4 1.0
O A:ASN467 2.9 13.2 1.0
O A:CYS344 2.9 12.0 1.0
O A:THR113 3.0 13.2 1.0
O A:ASN466 3.1 14.1 1.0
O A:THR230 3.5 12.8 1.0
C A:THR113 3.5 13.2 1.0
C A:ASN467 3.7 13.2 1.0
C A:CYS344 3.7 12.0 1.0
C A:ASN112 3.8 11.8 1.0
C A:ASN231 3.8 12.0 1.0
CA A:THR113 3.8 13.2 1.0
C A:SER343 3.9 12.4 1.0
C A:ASN466 4.0 14.1 1.0
CA A:ASN467 4.1 13.2 1.0
CA A:CYS344 4.1 12.0 1.0
N A:THR113 4.2 13.2 1.0
CA A:ASN231 4.3 12.0 1.0
N A:ASN467 4.5 13.2 1.0
N A:CYS344 4.5 12.0 1.0
CB A:ASN114 4.5 13.4 1.0
C A:THR230 4.5 12.8 1.0
N A:ASN114 4.5 13.4 1.0
N A:GLY345 4.7 12.1 1.0
N A:GLY468 4.7 14.1 1.0
N A:GLY232 4.8 11.1 1.0
ND2 A:ASN114 4.8 13.4 1.0
ND2 A:ASN112 4.9 11.8 1.0
N A:ASN231 4.9 12.0 1.0
CA A:ASN112 5.0 11.8 1.0
CA A:SER343 5.0 12.4 1.0
CG A:ASN112 5.0 11.8 1.0
CB A:SER343 5.0 12.4 1.0

Potassium binding site 6 out of 7 in 7zri

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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
B:K701

b:42.2
occ:1.00
 CG2 A:ILE421 3.6 9.7 1.0
CB B:ALA227 3.7 12.1 1.0
CD1 B:LEU224 4.0 12.8 1.0
CB A:ILE421 4.4 9.7 1.0
CG B:LEU228 4.4 13.3 1.0
C B:ALA227 4.5 12.1 1.0
N B:LEU228 4.6 13.3 1.0
CD2 A:LEU389 4.7 14.0 1.0
CD2 B:LEU228 4.7 13.3 1.0
CA B:ALA227 4.8 12.1 1.0
O B:LEU224 4.8 12.8 1.0
O B:ALA227 4.8 12.1 1.0
CG1 A:ILE421 4.9 9.7 1.0
CA B:LEU228 5.0 13.3 1.0

Potassium binding site 7 out of 7 in 7zri

Go back to Potassium Binding Sites List in 7zri
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:K703

b:18.0
occ:1.00
 O B:CYS261 3.0 13.6 1.0
O B:ILE263 3.1 13.2 1.0
OG B:SER579 3.7 18.5 1.0
OG1 B:THR265 3.8 14.9 1.0
OD1 B:ASP583 3.9 18.6 1.0
OD1 B:ASN624 3.9 17.8 1.0
N B:THR265 4.0 14.9 1.0
C B:CYS261 4.0 13.6 1.0
C B:ILE263 4.1 13.2 1.0
ND2 B:ASN624 4.1 17.8 1.0
CG B:ASN624 4.2 17.8 1.0
NZ B:LYS586 4.2 16.6 1.0
OG1 B:THR266 4.3 15.4 1.0
CA B:PRO264 4.4 13.5 1.0
O B:LEU262 4.4 13.2 1.0
CE B:LYS586 4.4 16.6 1.0
C B:LEU262 4.5 13.2 1.0
O B:SER579 4.5 18.5 1.0
O B:VAL260 4.6 12.2 1.0
N B:PRO264 4.7 13.5 1.0
C B:PRO264 4.7 13.5 1.0
ND2 B:ASN582 4.7 19.7 1.0
CB B:THR265 4.8 14.9 1.0
N B:ILE263 4.8 13.2 1.0
N B:THR266 4.8 15.4 1.0
CA B:CYS261 4.8 13.6 1.0
CG B:ASP583 4.9 18.6 1.0
CA B:THR265 4.9 14.9 1.0
N B:LEU262 4.9 13.2 1.0
CG2 B:THR265 5.0 14.9 1.0
CB B:SER579 5.0 18.5 1.0
CA B:LEU262 5.0 13.2 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 10:31:06 2023

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