Calcium in PDB 5u95: Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum

Enzymatic activity of Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum

All present enzymatic activity of Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum:
6.2.1.12;

Protein crystallography data

The structure of Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum, PDB code: 5u95 was solved by W.P.Morioka, C.M.Bianchetti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.42 / 2.25
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 108.259, 108.259, 183.220, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 26

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum (pdb code 5u95). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum, PDB code: 5u95:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5u95

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Calcium binding site 1 out of 5 in the Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:42.4
occ:1.00
 O A:ILE178 2.4 28.6 1.0
O B:HOH731 2.5 32.2 1.0
OE1 B:GLU268 2.5 37.9 1.0
OE2 B:GLU268 2.5 44.9 1.0
CD B:GLU268 2.9 42.4 1.0
C A:ILE178 3.6 24.1 1.0
O A:HIS24 4.3 28.6 1.0
CG B:GLU268 4.4 43.3 1.0
N A:ILE178 4.4 28.9 1.0
CA A:ILE178 4.5 24.3 1.0
NE2 B:GLN271 4.6 54.4 1.0
N A:GLN179 4.6 24.5 1.0
CA A:GLN179 4.6 30.0 1.0
CD A:PRO26 4.8 21.7 1.0
OE1 A:GLN179 4.8 68.4 1.0
CG A:PRO26 4.9 21.9 1.0
CE1 B:TYR297 4.9 40.7 1.0
OH B:TYR297 5.0 45.7 1.0
CB A:ILE178 5.0 30.3 1.0
O A:HOH789 5.0 35.3 1.0

Calcium binding site 2 out of 5 in 5u95

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Calcium binding site 2 out of 5 in the Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:0.4
occ:1.00
 OD2 D:ASP434 2.4 68.9 1.0
OD1 D:ASP434 2.6 67.5 1.0
O D:LEU436 2.7 64.7 1.0
OD1 A:ASN169 2.8 56.0 1.0
CG D:ASP434 2.8 61.5 1.0
C D:LEU436 3.8 53.5 1.0
CB D:LEU436 3.8 49.5 1.0
CG A:ASN169 3.8 48.5 1.0
OE2 A:GLU170 4.1 47.5 1.0
OE2 D:GLU438 4.1 97.3 1.0
CB D:ASP434 4.3 49.9 1.0
CA D:LEU436 4.3 47.2 1.0
CB A:ASN169 4.3 37.3 1.0
CG D:LEU436 4.5 51.7 1.0
CA A:ASN169 4.5 36.3 1.0
O D:LYS437 4.5 62.5 1.0
N D:LEU436 4.6 42.9 1.0
CD D:GLU438 4.7 96.5 1.0
C D:LYS437 4.7 66.8 1.0
CD A:GLU170 4.8 48.3 1.0
OE1 D:GLU438 4.8 96.8 1.0
ND2 A:ASN169 4.9 41.7 1.0
N D:LYS437 4.9 54.4 1.0
OE1 A:GLU170 4.9 47.9 1.0

Calcium binding site 3 out of 5 in 5u95

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Calcium binding site 3 out of 5 in the Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:62.3
occ:1.00
 OD1 B:ASP434 2.4 80.8 1.0
O B:LEU436 2.4 66.2 1.0
OD2 B:ASP434 2.7 65.5 1.0
CG B:ASP434 2.9 69.1 1.0
C B:LEU436 3.6 61.7 1.0
CB B:LEU436 3.9 67.2 1.0
CA B:LEU436 4.2 63.9 1.0
CB B:ASP434 4.4 59.3 1.0
N B:LEU436 4.4 68.1 1.0
N B:LYS437 4.7 61.1 1.0
C B:LYS437 4.7 67.1 1.0
CG B:LEU436 4.7 70.7 1.0
N B:GLU438 4.9 73.0 1.0
O B:LYS437 4.9 65.7 1.0
CA B:LYS437 5.0 65.5 1.0

Calcium binding site 4 out of 5 in 5u95

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Calcium binding site 4 out of 5 in the Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:0.6
occ:1.00
 OD2 C:ASP434 2.4 93.7 1.0
O C:LEU436 2.5 80.6 1.0
OD1 C:ASP434 2.6 80.7 1.0
CG C:ASP434 2.9 84.1 1.0
C C:LEU436 3.6 76.2 1.0
CB C:LEU436 3.7 72.5 1.0
CA C:LEU436 4.1 75.7 1.0
O C:LYS437 4.1 79.9 1.0
OD1 B:ASN169 4.4 60.0 1.0
N C:LEU436 4.4 74.7 1.0
CB C:ASP434 4.4 68.5 1.0
OE1 B:GLU170 4.5 68.6 1.0
O B:HOH708 4.5 42.5 1.0
CG C:LEU436 4.5 72.6 1.0
N C:LYS437 4.7 71.7 1.0
CG B:ASN169 4.8 53.6 1.0
NZ B:LYS64 4.8 47.0 1.0
C C:LYS437 4.9 83.6 1.0
CB B:ASN169 4.9 50.0 1.0
OE2 B:GLU170 5.0 66.7 1.0

Calcium binding site 5 out of 5 in 5u95

Go back to Calcium Binding Sites List in 5u95
Calcium binding site 5 out of 5 in the Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:0.7
occ:1.00
 O D:ILE178 2.4 37.7 1.0
O D:HOH815 2.6 34.0 1.0
C D:ILE178 3.7 24.7 1.0
O D:HIS24 4.2 45.6 1.0
N D:ILE178 4.5 31.1 1.0
O D:HOH778 4.5 42.6 1.0
N D:GLN179 4.5 35.6 1.0
CA D:ILE178 4.6 32.2 1.0
O D:HOH801 4.6 34.9 1.0
CA D:GLN179 4.7 35.8 1.0
OE1 D:GLU177 4.9 64.7 1.0
CD D:PRO180 5.0 31.8 1.0
CD D:PRO26 5.0 25.0 1.0
CG D:PRO26 5.0 23.3 1.0

Reference:

W.P.Morioka, C.M.Bianchetti. Structure of the Open Conformation of 4-Coumarate-Coa Ligase From Nicotiana Tabacum To Be Published.
Page generated: Sat Dec 12 05:45:44 2020

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