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Potassium in PDB 6gvs: Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+

Protein crystallography data

The structure of Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+, PDB code: 6gvs was solved by J.Zarzycki, D.Trudeau, M.Scheffen, T.J.Erb, D.S.Tawfik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.13 / 2.58
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 362.202, 123.183, 165.096, 90.00, 109.25, 90.00
R / Rfree (%) 19.2 / 21

Potassium Binding Sites:

The binding sites of Potassium atom in the Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+ (pdb code 6gvs). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 10 binding sites of Potassium where determined in the Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+, PDB code: 6gvs:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 10 in 6gvs

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Potassium binding site 1 out of 10 in the Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:63.3
occ:1.00
 O A:GLU416 2.6 63.8 1.0
O A:LYS332 2.6 60.9 1.0
OE1 A:GLU333 2.7 60.4 1.0
O A:VAL414 2.7 58.6 1.0
OD1 A:ASN298 2.7 60.2 1.0
O A:PHE413 2.8 47.3 1.0
C A:VAL414 3.4 58.1 1.0
CG A:ASN298 3.5 55.7 1.0
ND2 A:ASN298 3.5 53.9 1.0
C A:LYS332 3.6 61.9 1.0
CB A:LYS332 3.7 37.3 1.0
CA A:VAL414 3.7 53.2 1.0
C A:GLU416 3.8 53.5 1.0
CD A:GLU333 3.8 57.7 1.0
C A:PHE413 3.8 51.5 1.0
CB A:GLU333 4.3 46.1 1.0
N A:GLU416 4.3 52.7 1.0
N A:VAL414 4.3 58.0 1.0
CA A:LYS332 4.3 51.8 1.0
N A:GLN415 4.5 54.5 1.0
N A:GLU333 4.6 55.6 1.0
C A:GLN415 4.6 63.1 1.0
CG A:GLU333 4.6 43.4 1.0
CA A:GLU416 4.7 52.8 1.0
N A:GLU417 4.7 45.8 1.0
OE2 A:GLU333 4.7 63.6 1.0
CA A:GLU417 4.8 39.0 1.0
CA A:GLU333 4.9 55.0 1.0
CB A:ASN298 4.9 50.1 1.0
CG A:LYS332 5.0 49.5 1.0

Potassium binding site 2 out of 10 in 6gvs

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Potassium binding site 2 out of 10 in the Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K602

b:64.9
occ:1.00
 O B:GLU416 2.5 75.1 1.0
O B:PHE413 2.5 61.3 1.0
O B:VAL414 2.7 71.7 1.0
OD1 B:ASN298 2.9 58.7 1.0
OE1 B:GLU333 2.9 58.7 1.0
O B:LYS332 2.9 62.2 1.0
C B:VAL414 3.4 64.2 1.0
C B:GLU416 3.7 62.4 1.0
C B:PHE413 3.7 56.8 1.0
CG B:ASN298 3.7 50.4 1.0
CB B:LYS332 3.8 45.2 1.0
C B:LYS332 3.8 54.5 1.0
ND2 B:ASN298 3.8 45.5 1.0
CA B:VAL414 3.8 54.1 1.0
CD B:GLU333 4.1 60.1 1.0
N B:VAL414 4.2 52.2 1.0
N B:GLU416 4.3 55.2 1.0
CB B:GLU333 4.3 33.4 1.0
CA B:LYS332 4.4 51.6 1.0
N B:GLN415 4.4 64.3 1.0
C B:GLN415 4.5 61.6 1.0
N B:GLU417 4.5 59.4 1.0
CA B:GLU417 4.6 58.4 1.0
CA B:GLU416 4.6 54.8 1.0
N B:GLU333 4.7 42.1 1.0
CG B:GLU333 4.7 40.8 1.0
N B:LEU418 4.8 72.9 1.0
O B:HOH717 4.8 61.1 1.0
O B:GLN415 4.8 64.7 1.0
CG B:PRO424 4.9 57.8 1.0
CA B:PHE413 4.9 57.6 1.0
CG B:LYS332 5.0 54.3 1.0
CA B:GLN415 5.0 61.9 1.0

Potassium binding site 3 out of 10 in 6gvs

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Potassium binding site 3 out of 10 in the Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K602

b:67.3
occ:1.00
 OE1 C:GLU333 2.4 67.7 1.0
O C:GLU416 2.6 60.1 1.0
OD1 C:ASN298 2.7 56.1 1.0
O C:LYS332 2.8 54.7 1.0
O C:PHE413 2.8 67.0 1.0
O C:VAL414 2.8 51.0 1.0
C C:VAL414 3.6 59.0 1.0
CG C:ASN298 3.6 51.3 1.0
CB C:LYS332 3.6 43.2 1.0
CD C:GLU333 3.7 64.5 1.0
C C:GLU416 3.7 58.2 1.0
ND2 C:ASN298 3.7 46.5 1.0
C C:LYS332 3.7 58.3 1.0
C C:PHE413 3.9 66.0 1.0
CA C:VAL414 3.9 58.8 1.0
N C:GLU416 4.2 58.5 1.0
CA C:LYS332 4.3 50.9 1.0
N C:VAL414 4.4 62.5 1.0
OE2 C:GLU333 4.4 59.4 1.0
CB C:GLU333 4.5 56.1 1.0
N C:GLU417 4.5 51.9 1.0
N C:GLN415 4.5 53.9 1.0
CA C:GLU416 4.6 62.4 1.0
C C:GLN415 4.6 62.0 1.0
CA C:GLU417 4.6 55.2 1.0
CG C:GLU333 4.7 53.8 1.0
N C:GLU333 4.7 52.8 1.0
CG C:LYS332 4.8 47.1 1.0
N C:LEU418 4.9 50.6 1.0
CD C:LYS332 4.9 51.8 1.0

Potassium binding site 4 out of 10 in 6gvs

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Potassium binding site 4 out of 10 in the Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K602

b:76.5
occ:1.00
 O D:LYS332 2.5 76.9 1.0
OE1 D:GLU333 2.5 67.7 1.0
OD1 D:ASN298 2.8 76.1 1.0
O D:GLU416 2.9 73.4 1.0
O D:PHE413 3.0 66.3 1.0
O D:VAL414 3.1 73.7 1.0
CB D:LYS332 3.3 41.4 1.0
C D:LYS332 3.4 58.6 1.0
CG D:ASN298 3.7 66.6 1.0
CD D:GLU333 3.8 66.0 1.0
C D:VAL414 3.8 71.4 1.0
C D:GLU416 3.9 69.5 1.0
ND2 D:ASN298 3.9 66.7 1.0
CA D:LYS332 4.0 47.0 1.0
CA D:VAL414 4.1 64.3 1.0
C D:PHE413 4.1 67.2 1.0
CB D:GLU333 4.2 50.5 1.0
N D:GLU333 4.4 50.4 1.0
N D:GLU416 4.5 74.7 1.0
CG D:GLU333 4.6 60.6 1.0
CG D:LYS332 4.6 52.8 1.0
N D:VAL414 4.6 63.2 1.0
OE2 D:GLU333 4.7 65.0 1.0
N D:GLU417 4.7 67.8 1.0
CA D:GLU417 4.7 73.6 1.0
N D:LEU418 4.7 76.9 1.0
CD D:LYS332 4.8 61.0 1.0
CA D:GLU333 4.8 50.6 1.0
N D:GLN415 4.8 73.6 1.0
CA D:GLU416 4.9 71.8 1.0

Potassium binding site 5 out of 10 in 6gvs

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Potassium binding site 5 out of 10 in the Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K602

b:60.6
occ:1.00
 OE1 E:GLU333 2.5 54.0 1.0
O E:VAL414 2.6 49.0 1.0
O E:GLU416 2.6 55.6 1.0
O E:PHE413 2.6 46.7 1.0
OD1 E:ASN298 2.7 50.6 1.0
O E:LYS332 2.8 57.3 1.0
C E:VAL414 3.4 47.4 1.0
CG E:ASN298 3.5 51.1 1.0
ND2 E:ASN298 3.6 43.6 1.0
C E:LYS332 3.6 43.5 1.0
CD E:GLU333 3.7 48.2 1.0
CB E:LYS332 3.7 30.8 1.0
C E:GLU416 3.7 44.5 1.0
CA E:VAL414 3.7 48.9 1.0
C E:PHE413 3.7 50.5 1.0
CB E:GLU333 4.1 35.3 1.0
N E:GLU416 4.2 43.3 1.0
N E:VAL414 4.2 45.1 1.0
CA E:LYS332 4.3 32.6 1.0
N E:GLU333 4.5 49.4 1.0
CG E:GLU333 4.5 43.5 1.0
N E:GLN415 4.5 49.5 1.0
N E:GLU417 4.6 44.7 1.0
OE2 E:GLU333 4.6 50.0 1.0
CA E:GLU416 4.6 46.3 1.0
CA E:GLU417 4.7 43.1 1.0
C E:GLN415 4.7 48.2 1.0
CA E:GLU333 4.8 42.3 1.0
CG E:LYS332 4.9 49.9 1.0
CG E:PRO424 4.9 36.9 1.0
CB E:ASN298 5.0 31.2 1.0
CA E:PHE413 5.0 54.6 1.0

Potassium binding site 6 out of 10 in 6gvs

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Potassium binding site 6 out of 10 in the Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K602

b:70.0
occ:1.00
 O F:VAL414 2.6 76.2 1.0
O F:GLU416 2.8 80.7 1.0
OD1 F:ASN298 2.9 64.1 1.0
O F:PHE413 3.0 81.3 1.0
OE1 F:GLU333 3.0 78.1 1.0
O F:LYS332 3.3 69.9 1.0
CB F:LYS332 3.3 70.7 1.0
C F:VAL414 3.5 80.1 1.0
C F:GLU416 3.8 76.3 1.0
C F:LYS332 3.8 64.7 1.0
CG F:ASN298 3.9 64.3 1.0
CA F:VAL414 4.0 81.6 1.0
C F:PHE413 4.1 85.6 1.0
ND2 F:ASN298 4.2 51.0 1.0
CA F:LYS332 4.2 67.8 1.0
CD F:GLU333 4.2 73.0 1.0
N F:GLU416 4.3 73.8 1.0
CG F:LYS332 4.4 72.7 1.0
N F:GLN415 4.4 66.8 1.0
N F:VAL414 4.5 85.3 1.0
N F:GLU417 4.5 71.0 1.0
CB F:GLU333 4.5 52.2 1.0
C F:GLN415 4.6 75.5 1.0
CA F:GLU417 4.6 76.7 1.0
N F:GLU333 4.6 60.3 1.0
CA F:GLU416 4.7 75.9 1.0
N F:LEU418 4.7 64.8 1.0
CD F:LYS332 4.9 71.4 1.0
CA F:GLN415 4.9 70.5 1.0
CG F:GLU333 5.0 53.1 1.0

Potassium binding site 7 out of 10 in 6gvs

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Potassium binding site 7 out of 10 in the Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K602

b:51.9
occ:1.00
 O G:GLU416 2.6 61.1 1.0
OE1 G:GLU333 2.7 37.2 1.0
O G:PHE413 2.7 43.7 1.0
O G:LYS332 2.8 51.8 1.0
OD1 G:ASN298 2.8 52.7 1.0
O G:VAL414 3.1 40.5 1.0
CB G:LYS332 3.6 34.8 1.0
C G:LYS332 3.6 38.7 1.0
C G:VAL414 3.7 43.8 1.0
CG G:ASN298 3.8 46.5 1.0
C G:GLU416 3.8 50.5 1.0
CD G:GLU333 3.9 42.8 1.0
C G:PHE413 3.9 45.2 1.0
ND2 G:ASN298 4.0 39.6 1.0
CA G:VAL414 4.0 37.5 1.0
CB G:GLU333 4.2 31.6 1.0
CA G:LYS332 4.2 35.9 1.0
N G:VAL414 4.4 42.6 1.0
N G:GLU416 4.5 50.5 1.0
N G:GLU333 4.5 27.9 1.0
CA G:GLU417 4.5 46.5 1.0
N G:GLU417 4.5 49.5 1.0
CG G:GLU333 4.6 32.2 1.0
N G:GLN415 4.6 43.0 1.0
C G:GLN415 4.7 49.0 1.0
CA G:GLU416 4.7 39.9 1.0
N G:LEU418 4.8 45.0 1.0
OE2 G:GLU333 4.8 40.8 1.0
CG G:LYS332 4.8 39.3 1.0
CA G:GLU333 4.8 45.5 1.0
CD G:LYS332 4.9 43.2 1.0
CG G:PRO424 5.0 36.4 1.0

Potassium binding site 8 out of 10 in 6gvs

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Potassium binding site 8 out of 10 in the Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K602

b:58.5
occ:1.00
 O H:GLU416 2.4 54.0 1.0
O H:PHE413 2.7 60.2 1.0
OD1 H:ASN298 2.7 54.0 1.0
OE1 H:GLU333 2.9 63.8 1.0
O H:LYS332 2.9 43.7 1.0
O H:VAL414 3.0 57.9 1.0
C H:GLU416 3.5 52.4 1.0
CG H:ASN298 3.6 50.2 1.0
C H:VAL414 3.6 54.7 1.0
CB H:LYS332 3.7 30.7 1.0
ND2 H:ASN298 3.8 45.3 1.0
C H:LYS332 3.8 43.3 1.0
C H:PHE413 3.8 54.6 1.0
CA H:VAL414 4.0 53.5 1.0
N H:GLU416 4.0 54.5 1.0
CD H:GLU333 4.0 51.8 1.0
CA H:LYS332 4.3 44.4 1.0
N H:VAL414 4.4 59.2 1.0
CA H:GLU416 4.4 45.7 1.0
N H:GLU417 4.4 41.6 1.0
CB H:GLU333 4.4 49.5 1.0
N H:GLN415 4.5 50.2 1.0
CA H:GLU417 4.6 39.9 1.0
C H:GLN415 4.7 57.5 1.0
N H:GLU333 4.7 41.8 1.0
CG H:GLU333 4.8 39.4 1.0
N H:LEU418 4.9 46.9 1.0
OE2 H:GLU333 4.9 59.9 1.0
CG H:LYS332 4.9 35.0 1.0
CA H:PHE413 4.9 56.6 1.0
CD H:LYS332 5.0 48.0 1.0
CB H:ASN298 5.0 42.1 1.0

Potassium binding site 9 out of 10 in 6gvs

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Potassium binding site 9 out of 10 in the Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+ within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K602

b:58.2
occ:1.00
 OE1 I:GLU333 2.4 71.6 1.0
O I:GLU416 2.6 58.1 1.0
O I:LYS332 2.6 58.4 1.0
O I:VAL414 2.7 61.4 1.0
O I:PHE413 2.7 67.9 1.0
OD1 I:ASN298 3.0 41.8 1.0
C I:VAL414 3.4 65.0 1.0
C I:LYS332 3.6 48.6 1.0
CD I:GLU333 3.7 55.9 1.0
CB I:LYS332 3.7 34.8 1.0
C I:GLU416 3.7 52.2 1.0
CA I:VAL414 3.7 56.1 1.0
C I:PHE413 3.8 59.6 1.0
CG I:ASN298 3.9 47.6 1.0
ND2 I:ASN298 4.1 42.3 1.0
N I:GLU416 4.2 51.1 1.0
CB I:GLU333 4.2 48.4 1.0
N I:VAL414 4.2 52.7 1.0
CA I:LYS332 4.3 45.3 1.0
N I:GLN415 4.4 56.6 1.0
OE2 I:GLU333 4.5 52.4 1.0
CG I:GLU333 4.6 40.7 1.0
N I:GLU417 4.6 48.9 1.0
N I:GLU333 4.6 50.1 1.0
CA I:GLU416 4.6 44.7 1.0
C I:GLN415 4.6 55.8 1.0
CA I:GLU417 4.7 43.2 1.0
CG I:LYS332 4.9 36.3 1.0
CA I:GLU333 4.9 56.1 1.0
N I:LEU418 4.9 41.8 1.0
CG I:PRO424 4.9 37.5 1.0
CA I:GLN415 5.0 55.2 1.0

Potassium binding site 10 out of 10 in 6gvs

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Potassium binding site 10 out of 10 in the Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Engineered Glycolyl-Coa Reductase Comprising 8 Mutations with Bound Nadp+ within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K602

b:64.0
occ:1.00
 O J:GLU416 2.4 52.3 1.0
OD1 J:ASN298 2.5 51.6 1.0
O J:VAL414 2.8 53.5 1.0
O J:PHE413 2.8 49.3 1.0
OE1 J:GLU333 2.9 60.2 1.0
O J:LYS332 3.2 65.4 1.0
CG J:ASN298 3.4 48.8 1.0
C J:GLU416 3.5 46.1 1.0
C J:VAL414 3.5 54.1 1.0
CB J:LYS332 3.6 50.9 1.0
ND2 J:ASN298 3.7 35.8 1.0
C J:PHE413 3.9 50.4 1.0
C J:LYS332 4.0 53.5 1.0
CA J:VAL414 4.0 49.6 1.0
CD J:GLU333 4.1 56.4 1.0
CA J:GLU417 4.2 55.2 1.0
N J:GLU417 4.2 49.8 1.0
N J:GLU416 4.2 54.8 1.0
C J:GLN415 4.4 56.7 1.0
CA J:LYS332 4.4 50.1 1.0
N J:GLN415 4.5 58.8 1.0
CA J:GLU416 4.5 44.2 1.0
N J:VAL414 4.5 49.4 1.0
CG J:LYS332 4.6 52.7 1.0
O J:GLN415 4.6 58.6 1.0
N J:LEU418 4.6 51.3 1.0
CB J:GLU333 4.7 32.1 1.0
CB J:ASN298 4.9 51.4 1.0
N J:GLU333 4.9 54.2 1.0
OE2 J:GLU333 4.9 51.9 1.0
CA J:GLN415 4.9 62.1 1.0
CG J:GLU333 5.0 43.9 1.0
C J:GLU417 5.0 54.0 1.0
CD J:LYS332 5.0 59.0 1.0

Reference:

D.L.Trudeau, C.Edlich-Muth, J.Zarzycki, M.Scheffen, M.Goldsmith, O.Khersonsky, Z.Avizemer, S.J.Fleishman, C.A.R.Cotton, T.J.Erb, D.S.Tawfik, A.Bar-Even. Design and in Vitro Realization of Carbon-Conserving Photorespiration. Proc. Natl. Acad. Sci. V. 115 11455 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30459276
DOI: 10.1073/PNAS.1812605115
Page generated: Mon Aug 12 16:13:58 2024

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