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Zinc in PDB 7b1w: Crystal Structure of Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii

Enzymatic activity of Crystal Structure of Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii

All present enzymatic activity of Crystal Structure of Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii:
5.1.3.1;

Protein crystallography data

The structure of Crystal Structure of Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii, PDB code: 7b1w was solved by J.Henri, M.Zaffagnini, D.Tedesco, P.Crozet, S.D.Lemaire, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.29 / 1.94
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.293, 297.322, 77.747, 90, 116.3, 90
R / Rfree (%) 18.4 / 21.4

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii (pdb code 7b1w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii, PDB code: 7b1w:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 7b1w

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Zinc binding site 1 out of 12 in the Crystal Structure of Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii


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 Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn301

b:46.2
occ:1.00
 NE2 J:HIS72 2.1 26.4 1.0
OD1 J:ASP74 2.2 32.5 1.0
OD2 J:ASP216 2.2 33.8 1.0
ND1 J:HIS105 2.3 24.6 1.0
CD2 J:HIS72 3.1 23.9 1.0
CE1 J:HIS72 3.1 24.6 1.0
CG J:HIS105 3.2 26.5 1.0
CG J:ASP74 3.3 32.6 1.0
CE1 J:HIS105 3.3 26.5 1.0
CG J:ASP216 3.4 33.5 1.0
CB J:HIS105 3.5 21.9 1.0
O J:HOH431 3.7 40.8 1.0
OD2 J:ASP74 3.7 34.5 1.0
ND1 J:HIS72 4.2 20.1 1.0
CE J:MET107 4.2 28.3 1.0
OD1 J:ASP216 4.2 33.1 1.0
CG J:HIS72 4.2 24.3 1.0
CD2 J:LEU176 4.2 17.3 1.0
CB J:ASP216 4.2 25.5 1.0
NE2 J:HIS105 4.4 26.1 1.0
CD2 J:HIS105 4.4 19.6 1.0
CB J:ASP74 4.5 27.5 1.0
CA J:ASP74 4.8 21.9 1.0
SD J:MET178 4.9 32.4 1.0
SD J:MET107 5.0 52.2 1.0

Zinc binding site 2 out of 12 in 7b1w

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Zinc binding site 2 out of 12 in the Crystal Structure of Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii


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 Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:58.1
occ:1.00
 OD1 A:ASP74 2.2 34.6 1.0
NE2 A:HIS72 2.2 26.3 1.0
ND1 A:HIS105 2.3 26.2 1.0
OD2 A:ASP216 2.4 38.2 1.0
CD2 A:HIS72 3.1 28.2 1.0
CE1 A:HIS72 3.2 29.2 1.0
CG A:ASP74 3.3 33.1 1.0
CE1 A:HIS105 3.3 24.3 1.0
CG A:HIS105 3.3 25.3 1.0
CG A:ASP216 3.6 33.0 1.0
CB A:HIS105 3.6 21.6 1.0
OD2 A:ASP74 3.8 36.7 1.0
CE A:MET107 4.2 28.3 1.0
CG A:HIS72 4.3 24.6 1.0
ND1 A:HIS72 4.3 25.5 1.0
CB A:ASP216 4.3 24.2 1.0
CD2 A:LEU176 4.4 21.3 1.0
OD1 A:ASP216 4.4 34.1 1.0
NE2 A:HIS105 4.4 23.1 1.0
CB A:ASP74 4.5 26.1 1.0
CD2 A:HIS105 4.5 20.4 1.0
SD A:MET178 4.8 31.5 1.0
CA A:ASP74 4.8 26.9 1.0
SD A:MET107 5.0 31.4 1.0
CG1 A:VAL236 5.0 24.8 1.0

Zinc binding site 3 out of 12 in 7b1w

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Zinc binding site 3 out of 12 in the Crystal Structure of Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii


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 Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:57.9
occ:1.00
 OD1 B:ASP74 2.2 36.0 1.0
NE2 B:HIS72 2.2 31.3 1.0
ND1 B:HIS105 2.3 25.4 1.0
OD2 B:ASP216 2.5 36.9 1.0
CD2 B:HIS72 3.1 28.8 1.0
CE1 B:HIS72 3.2 31.9 1.0
CG B:HIS105 3.2 26.9 1.0
CE1 B:HIS105 3.3 24.8 1.0
CG B:ASP74 3.3 40.4 1.0
CB B:HIS105 3.4 23.4 1.0
CG B:ASP216 3.6 34.6 1.0
O B:HOH476 3.8 44.9 1.0
OD2 B:ASP74 3.9 40.4 1.0
CG B:HIS72 4.3 29.2 1.0
ND1 B:HIS72 4.3 26.9 1.0
CD2 B:LEU176 4.3 25.1 1.0
CE B:MET107 4.3 34.4 1.0
CD2 B:HIS105 4.4 25.0 1.0
NE2 B:HIS105 4.4 29.2 1.0
CB B:ASP216 4.4 29.7 1.0
CB B:ASP74 4.4 30.9 1.0
OD1 B:ASP216 4.5 35.9 1.0
CA B:ASP74 4.7 27.3 1.0
SD B:MET178 4.8 34.6 1.0
O B:HOH548 4.9 42.9 1.0
CA B:HIS105 5.0 21.5 1.0
SD B:MET107 5.0 35.6 1.0

Zinc binding site 4 out of 12 in 7b1w

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Zinc binding site 4 out of 12 in the Crystal Structure of Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii


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 Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:54.6
occ:1.00
 NE2 C:HIS72 2.2 28.4 1.0
OD1 C:ASP74 2.2 32.9 1.0
OD2 C:ASP216 2.2 39.6 1.0
ND1 C:HIS105 2.3 26.3 1.0
CD2 C:HIS72 3.1 28.5 1.0
CE1 C:HIS72 3.2 27.6 1.0
CE1 C:HIS105 3.3 26.2 1.0
CG C:ASP74 3.3 36.4 1.0
CG C:HIS105 3.3 23.2 1.0
CG C:ASP216 3.4 34.5 1.0
CB C:HIS105 3.6 22.6 1.0
O C:HOH459 3.7 40.8 1.0
OD2 C:ASP74 3.8 38.3 1.0
OD1 C:ASP216 4.2 38.2 1.0
CG C:HIS72 4.3 28.3 1.0
CB C:ASP216 4.3 30.1 1.0
ND1 C:HIS72 4.3 26.6 1.0
CD2 C:LEU176 4.3 23.9 1.0
CE C:MET107 4.4 29.1 1.0
NE2 C:HIS105 4.4 24.3 1.0
CD2 C:HIS105 4.5 23.9 1.0
CB C:ASP74 4.5 27.4 1.0
CA C:ASP74 4.8 27.2 1.0
SD C:MET178 4.9 32.0 1.0
SD C:MET107 4.9 31.1 1.0
CE C:MET178 5.0 32.3 1.0

Zinc binding site 5 out of 12 in 7b1w

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Zinc binding site 5 out of 12 in the Crystal Structure of Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii


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 Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:55.5
occ:1.00
 OD1 D:ASP74 2.2 36.9 1.0
NE2 D:HIS72 2.2 25.5 1.0
ND1 D:HIS105 2.3 25.4 1.0
OD2 D:ASP216 2.5 35.5 1.0
CD2 D:HIS72 3.1 27.3 1.0
CE1 D:HIS105 3.3 28.4 1.0
CE1 D:HIS72 3.3 27.4 1.0
CG D:HIS105 3.3 27.1 1.0
CG D:ASP74 3.3 38.4 1.0
CB D:HIS105 3.6 25.4 1.0
CG D:ASP216 3.7 32.6 1.0
OD2 D:ASP74 3.8 47.5 1.0
CD2 D:LEU176 4.3 26.2 1.0
CG D:HIS72 4.3 25.7 1.0
ND1 D:HIS72 4.4 28.7 1.0
CE D:MET107 4.4 30.0 1.0
NE2 D:HIS105 4.4 23.3 1.0
CB D:ASP216 4.4 25.6 1.0
CD2 D:HIS105 4.5 23.3 1.0
CB D:ASP74 4.6 33.1 1.0
OD1 D:ASP216 4.6 35.5 1.0
SD D:MET178 4.8 30.6 1.0
CA D:ASP74 4.8 29.2 1.0
SD D:MET107 5.0 31.9 1.0
CE D:MET178 5.0 28.7 1.0

Zinc binding site 6 out of 12 in 7b1w

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Zinc binding site 6 out of 12 in the Crystal Structure of Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii


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 Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:69.4
occ:1.00
 OD1 E:ASP74 2.2 41.8 1.0
NE2 E:HIS72 2.3 28.2 1.0
ND1 E:HIS105 2.3 24.6 1.0
OD2 E:ASP216 2.3 43.2 1.0
CD2 E:HIS72 3.2 25.8 1.0
CE1 E:HIS105 3.2 28.3 1.0
CG E:ASP74 3.3 33.4 1.0
CE1 E:HIS72 3.3 29.4 1.0
CG E:HIS105 3.4 26.0 1.0
CG E:ASP216 3.5 36.8 1.0
O E:HOH441 3.6 39.6 1.0
CB E:HIS105 3.7 25.3 1.0
OD2 E:ASP74 3.9 40.4 1.0
CE E:MET107 4.3 34.3 1.0
CB E:ASP216 4.3 25.6 1.0
CD2 E:LEU176 4.3 22.1 1.0
CG E:HIS72 4.4 28.0 1.0
NE2 E:HIS105 4.4 24.5 1.0
OD1 E:ASP216 4.4 35.3 1.0
ND1 E:HIS72 4.4 27.1 1.0
CB E:ASP74 4.5 28.9 1.0
CD2 E:HIS105 4.5 23.5 1.0
O E:HOH539 4.6 47.0 1.0
SD E:MET178 4.7 30.9 1.0
CE E:MET178 4.9 28.8 1.0
CA E:ASP74 4.9 20.8 1.0
SD E:MET107 5.0 32.0 1.0

Zinc binding site 7 out of 12 in 7b1w

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Zinc binding site 7 out of 12 in the Crystal Structure of Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii


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 Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:55.6
occ:1.00
 OD1 F:ASP74 2.2 33.5 1.0
ND1 F:HIS105 2.2 27.7 1.0
NE2 F:HIS72 2.2 25.3 1.0
OD2 F:ASP216 2.4 36.1 1.0
CD2 F:HIS72 3.1 26.0 1.0
CE1 F:HIS105 3.2 27.0 1.0
CG F:HIS105 3.2 27.9 1.0
CG F:ASP74 3.3 34.8 1.0
CE1 F:HIS72 3.3 28.5 1.0
CB F:HIS105 3.5 28.0 1.0
CG F:ASP216 3.5 38.0 1.0
OD2 F:ASP74 3.8 37.4 1.0
O F:HOH441 4.0 41.2 1.0
CD2 F:LEU176 4.3 22.7 1.0
CG F:HIS72 4.3 26.6 1.0
NE2 F:HIS105 4.3 29.0 1.0
CB F:ASP216 4.3 26.9 1.0
CE F:MET107 4.3 27.8 1.0
CD2 F:HIS105 4.3 26.5 1.0
OD1 F:ASP216 4.4 36.1 1.0
ND1 F:HIS72 4.4 27.7 1.0
CB F:ASP74 4.5 26.8 1.0
O F:HOH551 4.6 46.3 1.0
CA F:ASP74 4.8 24.9 1.0
SD F:MET178 4.9 31.0 1.0
SD F:MET107 4.9 32.0 1.0
CA F:HIS105 5.0 26.1 1.0

Zinc binding site 8 out of 12 in 7b1w

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Zinc binding site 8 out of 12 in the Crystal Structure of Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii


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 Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:75.5
occ:1.00
 NE2 G:HIS72 2.2 35.1 1.0
OD1 G:ASP74 2.3 44.5 1.0
ND1 G:HIS105 2.4 31.3 1.0
OD2 G:ASP216 2.4 37.2 1.0
CD2 G:HIS72 3.1 31.7 1.0
CE1 G:HIS72 3.3 34.3 1.0
CE1 G:HIS105 3.3 32.4 1.0
CG G:HIS105 3.3 31.1 1.0
CG G:ASP74 3.4 42.8 1.0
CG G:ASP216 3.6 37.4 1.0
CB G:HIS105 3.6 31.2 1.0
O G:HOH430 3.7 42.8 1.0
OD2 G:ASP74 3.8 45.6 1.0
CD2 G:LEU176 4.2 26.2 1.0
CB G:ASP216 4.2 29.4 1.0
CG G:HIS72 4.3 31.0 1.0
ND1 G:HIS72 4.3 27.9 1.0
CE G:MET107 4.4 32.1 1.0
NE2 G:HIS105 4.4 28.2 1.0
CD2 G:HIS105 4.5 29.1 1.0
OD1 G:ASP216 4.5 37.2 1.0
CB G:ASP74 4.6 34.8 1.0
SD G:MET178 4.7 34.2 1.0
CE G:MET178 4.9 30.9 1.0
CA G:ASP74 4.9 29.6 1.0

Zinc binding site 9 out of 12 in 7b1w

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Zinc binding site 9 out of 12 in the Crystal Structure of Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii


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 Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:73.8
occ:1.00
 ND1 H:HIS105 2.2 33.6 1.0
OD1 H:ASP74 2.3 40.8 1.0
NE2 H:HIS72 2.3 33.8 1.0
OD2 H:ASP216 2.6 42.9 1.0
CG H:HIS105 3.2 31.8 1.0
CE1 H:HIS105 3.2 30.1 1.0
CD2 H:HIS72 3.2 29.7 1.0
CE1 H:HIS72 3.3 33.1 1.0
CB H:HIS105 3.4 30.2 1.0
CG H:ASP74 3.4 41.2 1.0
CG H:ASP216 3.8 38.8 1.0
OD2 H:ASP74 3.9 44.3 1.0
O H:HOH402 4.1 38.1 1.0
CD2 H:LEU176 4.1 30.2 1.0
CE H:MET107 4.3 33.2 1.0
CD2 H:HIS105 4.3 30.0 1.0
NE2 H:HIS105 4.3 28.6 1.0
ND1 H:HIS72 4.4 31.4 1.0
CB H:ASP216 4.4 29.8 1.0
CG H:HIS72 4.4 29.5 1.0
CB H:ASP74 4.6 36.6 1.0
OD1 H:ASP216 4.7 42.2 1.0
SD H:MET178 4.8 34.5 1.0
CA H:ASP74 4.8 29.5 1.0
CA H:HIS105 4.9 25.4 1.0
SD H:MET107 4.9 34.2 1.0

Zinc binding site 10 out of 12 in 7b1w

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Zinc binding site 10 out of 12 in the Crystal Structure of Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii


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 Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn301

b:74.4
occ:1.00
 ND1 I:HIS105 2.3 31.1 1.0
NE2 I:HIS72 2.3 41.6 1.0
OD1 I:ASP74 2.3 42.0 1.0
OD2 I:ASP216 2.5 49.3 1.0
CE1 I:HIS105 3.2 28.8 1.0
CD2 I:HIS72 3.3 40.0 1.0
CG I:HIS105 3.3 30.0 1.0
CE1 I:HIS72 3.3 36.8 1.0
CG I:ASP74 3.5 42.6 1.0
CB I:HIS105 3.6 28.8 1.0
CG I:ASP216 3.7 48.0 1.0
O I:HOH465 4.0 44.2 1.0
OD2 I:ASP74 4.0 47.9 1.0
CE I:MET107 4.2 38.5 1.0
CD2 I:LEU176 4.3 33.0 1.0
NE2 I:HIS105 4.4 31.7 1.0
CB I:ASP216 4.4 39.1 1.0
CD2 I:HIS105 4.4 26.9 1.0
ND1 I:HIS72 4.4 36.9 1.0
CG I:HIS72 4.4 36.6 1.0
OD1 I:ASP216 4.6 44.0 1.0
CB I:ASP74 4.6 30.7 1.0
SD I:MET178 4.7 43.9 1.0
CE I:MET178 4.9 36.4 1.0
CA I:ASP74 4.9 35.4 1.0
SD I:MET107 4.9 37.0 1.0

Reference:

J.Henri, M.Zaffagnini, D.Tedesco, P.Crozet, S.D.Lemaire. Crystal Structure of Plastidial Ribulose Epimerase RPE1 From the Model Alga Chlamydomonas Reinhardtii To Be Published.
Page generated: Tue Oct 29 17:17:09 2024

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