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Zinc in PDB 6m4u: Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin

Enzymatic activity of Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin

All present enzymatic activity of Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin:
2.7.11.1; 5.2.1.8;

Protein crystallography data

The structure of Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin, PDB code: 6m4u was solved by M.Kikuchi, D.Wu, T.Inoue, T.Umehara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.40 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.034, 67.419, 69.793, 90.00, 107.20, 90.00
R / Rfree (%) 19.8 / 25.8

Other elements in 6m4u:

The structure of Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin (pdb code 6m4u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin, PDB code: 6m4u:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 6m4u

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Zinc binding site 1 out of 14 in the Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:56.3
occ:1.00
 OE2 A:GLU55 2.0 33.8 1.0
OXT F:LYS2113 2.1 37.0 1.0
O F:HOH2346 2.5 32.8 1.0
CD A:GLU55 2.7 31.8 1.0
OE1 A:GLU55 2.9 32.7 1.0
O B:HOH2327 3.1 45.8 1.0
C F:LYS2113 3.2 36.2 1.0
NH2 B:ARG2109 3.7 27.2 1.0
CA F:LYS2113 3.8 35.3 1.0
CG A:GLU55 4.1 30.5 1.0
O F:LYS2113 4.2 37.9 1.0
O F:SER2112 4.5 33.1 1.0
CZ B:ARG2109 4.6 27.4 1.0
CB F:LYS2113 4.6 35.7 1.0
CD A:LYS53 4.6 34.9 1.0
N A:MET50 4.7 27.8 1.0
NH1 B:ARG2109 4.8 27.5 1.0
O B:HOH2355 4.8 30.6 1.0
CB A:MET50 4.9 32.3 1.0
N F:LYS2113 4.9 34.5 1.0

Zinc binding site 2 out of 14 in 6m4u

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Zinc binding site 2 out of 14 in the Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:36.1
occ:1.00
 OE2 E:GLU108 2.1 31.5 1.0
OXT A:GLU108 2.2 27.2 1.0
CL A:CL205 2.5 49.2 1.0
CL E:CL203 2.7 51.7 1.0
CD E:GLU108 2.9 31.6 1.0
OE1 E:GLU108 2.9 31.4 1.0
C A:GLU108 3.1 26.0 1.0
CA A:GLU108 3.2 25.3 1.0
NZ E:LYS48 3.5 31.4 1.0
CE E:LYS48 3.6 30.8 1.0
NZ E:LYS106 3.8 34.4 1.0
CB A:GLU108 4.0 25.0 1.0
O A:GLU108 4.2 26.4 1.0
CG E:GLU108 4.3 31.7 1.0
N A:GLU108 4.5 24.5 1.0
CD E:LYS106 4.5 32.7 1.0
CD E:LYS48 4.6 29.7 1.0
O A:LEU107 4.7 23.3 1.0
CE E:LYS106 4.8 33.5 1.0
CG2 E:VAL24 4.8 23.6 1.0
CG A:GLU108 4.9 24.6 1.0

Zinc binding site 3 out of 14 in 6m4u

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Zinc binding site 3 out of 14 in the Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:42.6
occ:1.00
 OE2 A:GLU108 2.1 23.9 1.0
OXT E:GLU108 2.2 35.0 1.0
NZ A:LYS48 2.9 32.4 1.0
CL E:CL204 2.9 58.5 1.0
CL A:CL206 2.9 62.1 1.0
CD A:GLU108 3.0 24.4 1.0
C E:GLU108 3.1 33.6 1.0
OE1 A:GLU108 3.3 25.0 1.0
CA E:GLU108 3.3 32.4 1.0
CE A:LYS48 3.6 31.6 1.0
CE A:LYS106 3.9 27.9 1.0
CB E:GLU108 4.1 31.8 1.0
NZ A:LYS106 4.2 28.5 1.0
O E:GLU108 4.2 34.7 1.0
CG A:GLU108 4.4 24.6 1.0
N E:GLU108 4.5 32.0 1.0
CD A:LYS48 4.5 30.3 1.0
O E:LEU107 4.7 31.9 1.0
CG2 A:VAL24 4.8 19.9 1.0
CG E:GLU108 4.9 31.7 1.0
C E:LEU107 5.0 31.2 1.0

Zinc binding site 4 out of 14 in 6m4u

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Zinc binding site 4 out of 14 in the Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2201

b:19.2
occ:1.00
 OE1 B:GLU2032 1.9 18.5 1.0
OE1 F:GLU2025 2.0 21.6 1.0
NE2 B:HIS2028 2.1 17.7 1.0
CL B:CL2207 2.2 19.8 1.0
CD F:GLU2025 2.8 21.8 1.0
CD B:GLU2032 2.8 18.9 1.0
CD2 B:HIS2028 3.0 17.6 1.0
OE2 F:GLU2025 3.0 21.8 1.0
CE1 B:HIS2028 3.1 17.4 1.0
OE2 B:GLU2032 3.2 19.1 1.0
CG B:HIS2028 4.1 17.7 1.0
ND1 B:HIS2028 4.1 17.5 1.0
CG B:GLU2032 4.2 18.8 1.0
CG F:GLU2025 4.3 21.5 1.0
NE2 F:HIS2024 4.3 22.2 1.0
CG F:HIS2028 4.3 19.1 1.0
ND1 F:HIS2028 4.4 19.5 1.0
CD2 F:HIS2024 4.5 21.7 1.0
CG F:LYS2113 4.5 35.9 1.0
CB B:GLU2032 4.5 18.9 1.0
CD2 F:HIS2028 4.5 19.2 1.0
CB F:HIS2028 4.6 18.8 1.0
CE1 F:HIS2028 4.7 19.4 1.0
NE2 F:HIS2028 4.8 19.4 1.0
CA F:GLU2025 4.8 21.4 1.0
CB F:GLU2025 4.8 21.4 1.0
CB F:LYS2113 4.9 35.7 1.0
N F:LYS2113 4.9 34.5 1.0
CZ B:PHE2108 5.0 18.6 1.0

Zinc binding site 5 out of 14 in 6m4u

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Zinc binding site 5 out of 14 in the Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2202

b:45.6
occ:1.00
 NE2 B:HIS2106 2.0 21.9 1.0
OD2 B:ASP2077 2.3 32.8 1.0
O B:HOH2301 2.4 33.6 1.0
OD1 B:ASP2077 2.7 31.9 1.0
CG B:ASP2077 2.8 33.0 1.0
NH1 B:ARG2110 2.9 31.8 1.0
CE1 B:HIS2106 3.0 21.9 1.0
CD2 B:HIS2106 3.1 21.4 1.0
NH1 B:ARG2076 3.8 45.7 1.0
CZ B:ARG2110 4.1 31.4 1.0
ND1 B:HIS2106 4.1 21.5 1.0
CG B:HIS2106 4.2 20.8 1.0
CB B:ASP2077 4.3 33.1 1.0
CD B:ARG2110 4.4 29.0 1.0
O B:HOH2326 4.6 34.5 1.0
NE B:ARG2110 4.7 30.1 1.0
CZ B:ARG2076 5.0 45.4 1.0

Zinc binding site 6 out of 14 in 6m4u

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Zinc binding site 6 out of 14 in the Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2203

b:25.0
occ:1.00
 O B:HOH2347 1.9 22.0 1.0
ND1 B:HIS2024 2.1 22.8 1.0
O B:HOH2350 2.2 6.6 1.0
O B:HOH2340 2.2 31.7 1.0
CG B:HIS2024 3.0 22.6 1.0
CE1 B:HIS2024 3.1 22.9 1.0
CB B:HIS2024 3.3 22.9 1.0
NZ B:LYS2113 3.5 38.0 1.0
O B:HOH2322 3.6 35.0 1.0
O B:HOH2357 3.7 35.8 1.0
O B:HOH2323 4.1 35.5 1.0
CD2 B:HIS2024 4.1 22.5 1.0
NE2 B:HIS2024 4.1 22.7 1.0
N B:HIS2024 4.3 23.4 1.0
CB B:LEU2022 4.4 28.4 1.0
CA B:HIS2024 4.5 23.3 1.0
CD1 B:LEU2022 4.6 28.2 1.0
CD2 B:PHE2070 4.8 27.8 1.0
CE B:LYS2113 4.9 36.5 1.0
CG B:LEU2022 4.9 28.7 1.0

Zinc binding site 7 out of 14 in 6m4u

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Zinc binding site 7 out of 14 in the Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2204

b:0.8
occ:1.00
 O B:HOH2328 2.1 50.2 1.0
OE1 B:GLU2083 2.5 44.0 1.0
O B:HOH2319 3.2 47.7 1.0
CD B:GLU2083 3.3 43.2 1.0
CG B:GLU2080 3.7 39.1 1.0
OE2 B:GLU2083 3.8 44.7 1.0
CG B:GLU2083 4.3 41.2 1.0
CD B:GLU2080 4.4 41.2 1.0
OE2 B:GLU2080 4.4 42.8 1.0
O B:HOH2317 4.6 55.2 1.0
CB B:GLU2080 4.8 37.5 1.0
CB B:GLU2083 4.8 39.0 1.0
NZ B:LYS2087 4.8 41.1 1.0

Zinc binding site 8 out of 14 in 6m4u

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Zinc binding site 8 out of 14 in the Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2205

b:77.6
occ:1.00
 ND1 B:HIS2106 2.4 21.5 1.0
O B:HOH2335 3.1 34.3 1.0
O B:HOH2356 3.2 41.4 1.0
CG B:HIS2106 3.2 20.8 1.0
CB B:HIS2106 3.4 19.9 1.0
CE1 B:HIS2106 3.4 21.9 1.0
O B:HOH2358 3.6 41.1 1.0
CA B:HIS2106 3.7 19.3 1.0
O B:HOH2365 4.0 44.9 1.0
CD2 B:HIS2106 4.3 21.4 1.0
NE2 B:HIS2106 4.4 21.9 1.0
C B:HIS2106 4.7 19.0 1.0
O B:HIS2106 4.7 18.3 1.0
N B:HIS2106 4.8 19.0 1.0

Zinc binding site 9 out of 14 in 6m4u

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Zinc binding site 9 out of 14 in the Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn202

b:80.2
occ:1.00
 O E:HOH357 2.0 45.3 1.0
NE2 E:HIS95 3.2 29.9 1.0
CD2 E:HIS95 3.2 28.9 1.0
CE1 E:HIS95 4.5 29.9 1.0
CG E:HIS95 4.6 28.7 1.0
O E:ALA85 4.6 30.2 1.0
CB E:PRO94 4.7 26.5 1.0
CB E:ALA85 5.0 28.2 1.0

Zinc binding site 10 out of 14 in 6m4u

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Zinc binding site 10 out of 14 in the Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Fkbp-Frb T2098L Mutant in Complex with Rapamycin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn2201

b:19.4
occ:1.00
 OE1 B:GLU2025 1.9 26.0 1.0
OE2 F:GLU2032 1.9 19.9 1.0
NE2 F:HIS2028 2.0 19.4 1.0
CL B:CL2206 2.2 21.5 1.0
CD B:GLU2025 2.7 25.9 1.0
CD F:GLU2032 2.9 20.2 1.0
CE1 F:HIS2028 3.0 19.4 1.0
OE2 B:GLU2025 3.0 26.4 1.0
CD2 F:HIS2028 3.1 19.2 1.0
OE1 F:GLU2032 3.2 20.3 1.0
CG B:GLU2025 3.9 25.8 1.0
ND1 F:HIS2028 4.1 19.5 1.0
CG F:HIS2028 4.1 19.1 1.0
CG F:GLU2032 4.2 20.0 1.0
NE2 B:HIS2024 4.3 22.7 1.0
ND1 B:HIS2028 4.4 17.5 1.0
CG B:HIS2028 4.4 17.7 1.0
CD2 B:HIS2024 4.4 22.5 1.0
CB F:GLU2032 4.5 19.7 1.0
CE1 B:HIS2028 4.7 17.4 1.0
CD2 B:HIS2028 4.7 17.6 1.0
CB B:HIS2028 4.7 17.9 1.0
CZ F:PHE2108 4.8 21.1 1.0
NE2 B:HIS2028 4.9 17.7 1.0
CA B:GLU2025 4.9 24.6 1.0
CE1 F:PHE2108 4.9 20.9 1.0
CB B:GLU2025 4.9 25.1 1.0

Reference:

H.D.Wu, M.Kikuchi, O.Dagliyan, A.K.Aragaki, H.Nakamura, N.V.Dokholyan, T.Umehara, T.Inoue. Rational Design and Implementation of A Chemically Inducible Heterotrimerization System. Nat.Methods V. 17 928 2020.
ISSN: ESSN 1548-7105
PubMed: 32747768
DOI: 10.1038/S41592-020-0913-X
Page generated: Tue Oct 29 02:53:27 2024

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