Calcium in PDB 5ug4: Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae

Enzymatic activity of Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae

All present enzymatic activity of Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae:
2.3.1.57;

Protein crystallography data

The structure of Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae, PDB code: 5ug4 was solved by E.V.Filippova, G.Minasov, L.Shuvalova, O.Kiryukhina, W.F.Anderson, Centerfor Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.15
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 71.884, 134.635, 137.346, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae (pdb code 5ug4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae, PDB code: 5ug4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 5ug4

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Calcium binding site 1 out of 9 in the Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:69.6
occ:0.90
 OE1 A:GLU33 2.4 58.9 1.0
OE2 A:GLU75 2.5 53.1 1.0
OE1 C:GLU75 2.7 41.6 1.0
OE2 A:GLU33 2.8 52.5 1.0
O A:HOH362 2.9 51.9 1.0
CD A:GLU33 3.0 52.9 1.0
CA C:CA201 3.4 48.8 0.7
CD C:GLU75 3.7 41.8 1.0
CD A:GLU75 3.7 41.3 1.0
OE2 C:GLU75 4.0 49.4 1.0
CG A:GLU33 4.4 48.4 1.0
CG A:GLU75 4.5 38.6 1.0
OE1 A:GLU75 4.6 43.2 1.0
O A:HOH344 4.7 45.5 1.0
O C:HOH306 4.7 42.5 1.0
O C:HOH375 4.8 54.7 1.0
CG C:GLU75 4.8 40.0 1.0
O C:HOH361 4.9 44.7 1.0
CB C:GLU75 5.0 34.4 1.0

Calcium binding site 2 out of 9 in 5ug4

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Calcium binding site 2 out of 9 in the Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:28.9
occ:0.80
 OE2 A:GLU34 2.3 34.4 1.0
OE2 A:GLU41 2.4 33.7 1.0
O B:HOH361 2.4 39.3 1.0
OD1 B:ASN53 2.5 34.6 1.0
OE1 A:GLU41 2.5 29.1 1.0
O A:PRO35 2.5 33.5 1.0
O B:HOH329 2.5 29.9 1.0
CD A:GLU41 2.8 31.1 1.0
CD A:GLU34 3.4 38.1 1.0
CG B:ASN53 3.5 35.3 1.0
C A:PRO35 3.7 34.0 1.0
ND2 B:ASN53 3.8 35.6 1.0
CG A:GLU34 3.9 36.8 1.0
O B:HIS51 4.2 34.1 1.0
CA A:TYR36 4.2 31.4 1.0
CG A:GLU41 4.3 28.7 1.0
N A:TYR36 4.4 34.5 1.0
CG A:PRO35 4.5 36.9 1.0
C B:HIS51 4.5 32.0 1.0
CA B:HIS51 4.5 31.3 1.0
OE1 A:GLU34 4.5 35.3 1.0
O B:ILE50 4.5 27.1 1.0
CA A:PRO35 4.7 34.0 1.0
O A:HOH341 4.7 28.0 1.0
CB A:TYR36 4.7 32.3 1.0
N A:PRO35 4.8 33.8 1.0
NH2 B:ARG56 4.9 44.0 1.0
O A:HOH356 4.9 44.4 1.0
CB B:ASN53 4.9 31.5 1.0
CD A:PRO35 4.9 37.2 1.0
CB A:PRO35 4.9 36.5 1.0
CZ B:ARG56 5.0 44.9 1.0

Calcium binding site 3 out of 9 in 5ug4

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Calcium binding site 3 out of 9 in the Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:52.0
occ:0.50
 OE2 B:GLU33 2.2 58.1 1.0
OE2 B:GLU75 2.3 44.9 1.0
O B:HOH302 2.7 40.5 1.0
OE1 B:GLU75 2.7 38.9 1.0
CD B:GLU75 2.9 36.9 1.0
CD B:GLU33 3.0 53.5 1.0
OE1 B:GLU33 3.3 67.9 1.0
CA B:CA202 3.7 50.6 0.5
CA B:CA203 4.0 56.0 0.5
CG B:GLU33 4.4 48.9 1.0
CG B:GLU75 4.4 33.4 1.0
O B:HOH322 4.5 25.9 1.0
O B:HOH368 4.9 59.3 0.5

Calcium binding site 4 out of 9 in 5ug4

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Calcium binding site 4 out of 9 in the Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:50.6
occ:0.50
 OE2 B:GLU75 2.4 44.9 1.0
OE2 B:GLU33 2.5 58.1 1.0
O B:HOH364 2.7 46.5 1.0
CD B:GLU75 3.4 36.9 1.0
CD B:GLU33 3.4 53.5 1.0
CG B:GLU33 3.6 48.9 1.0
CA B:CA201 3.7 52.0 0.5
CG B:GLU75 3.9 33.4 1.0
OE1 B:GLU75 4.4 38.9 1.0
OE1 B:GLU33 4.5 67.9 1.0
O B:HOH322 4.5 25.9 1.0
O B:HOH368 4.6 59.3 0.5
CD1 B:ILE74 5.0 27.1 1.0

Calcium binding site 5 out of 9 in 5ug4

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Calcium binding site 5 out of 9 in the Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:56.0
occ:0.50
 OE1 B:GLU75 2.5 38.9 1.0
CD B:GLU75 3.6 36.9 1.0
O B:HOH338 3.9 48.9 1.0
CA B:CA201 4.0 52.0 0.5
OE2 B:GLU75 4.3 44.9 1.0
CB B:GLU75 4.3 32.4 1.0
CG B:GLU75 4.5 33.4 1.0
CA B:GLU75 4.5 29.4 1.0
O B:GLU75 4.7 28.5 1.0
O B:HOH368 4.7 59.3 0.5
C B:GLU75 4.9 29.6 1.0

Calcium binding site 6 out of 9 in 5ug4

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Calcium binding site 6 out of 9 in the Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:26.4
occ:0.80
 OE1 B:GLU34 2.2 33.0 1.0
OE2 B:GLU41 2.4 32.7 1.0
O B:PRO35 2.5 29.1 1.0
OE1 B:GLU41 2.5 27.4 1.0
CD B:GLU41 2.8 30.0 1.0
CD B:GLU34 3.3 35.5 1.0
C B:PRO35 3.6 28.6 1.0
CG B:GLU34 3.8 34.6 1.0
CA B:TYR36 4.2 28.7 1.0
CG B:GLU41 4.3 28.0 1.0
N B:TYR36 4.4 27.8 1.0
CG B:PRO35 4.4 32.7 1.0
OE2 B:GLU34 4.4 33.1 1.0
O B:HOH320 4.5 30.7 1.0
CA B:PRO35 4.6 30.1 1.0
N B:PRO35 4.7 29.6 1.0
CB B:TYR36 4.7 27.8 1.0
CD B:PRO35 4.8 30.1 1.0
CB B:PRO35 4.8 31.5 1.0

Calcium binding site 7 out of 9 in 5ug4

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Calcium binding site 7 out of 9 in the Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:48.8
occ:0.70
 OE2 C:GLU33 1.9 52.5 1.0
OE2 C:GLU75 2.0 49.4 1.0
OE2 A:GLU33 2.1 52.5 1.0
OE2 A:GLU75 2.2 53.1 1.0
O C:HOH306 2.6 42.5 1.0
OE1 A:GLU75 2.6 43.2 1.0
O A:HOH344 2.7 45.5 1.0
OE1 C:GLU75 2.8 41.6 1.0
CD C:GLU75 2.8 41.8 1.0
CD A:GLU75 2.8 41.3 1.0
CD C:GLU33 3.0 55.8 1.0
CA C:CA202 3.2 76.7 0.9
CD A:GLU33 3.4 52.9 1.0
CA A:CA201 3.4 69.6 0.9
OE1 C:GLU33 3.5 71.8 1.0
O C:HOH346 4.1 59.4 1.0
OE1 A:GLU33 4.1 58.9 1.0
CG C:GLU33 4.2 49.1 1.0
CG C:GLU75 4.3 40.0 1.0
O A:HOH316 4.3 66.0 1.0
CG A:GLU75 4.3 38.6 1.0
O A:HOH362 4.4 51.9 1.0
CG A:GLU33 4.4 48.4 1.0
O A:HOH330 4.6 30.9 1.0
O C:HOH310 4.7 30.0 1.0
O C:HOH375 4.8 54.7 1.0

Calcium binding site 8 out of 9 in 5ug4

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Calcium binding site 8 out of 9 in the Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:76.7
occ:0.90
 O C:HOH346 2.3 59.4 1.0
OE2 C:GLU75 2.4 49.4 1.0
O A:HOH316 2.4 66.0 1.0
OE2 C:GLU33 2.6 52.5 1.0
OE1 A:GLU75 2.9 43.2 1.0
CA C:CA201 3.2 48.8 0.7
CD C:GLU33 3.3 55.8 1.0
CD C:GLU75 3.5 41.8 1.0
CG C:GLU33 3.7 49.1 1.0
CD A:GLU75 3.9 41.3 1.0
O C:HOH375 4.1 54.7 1.0
OE1 C:GLU33 4.1 71.8 1.0
CG C:GLU75 4.2 40.0 1.0
OE2 A:GLU75 4.2 53.1 1.0
OE1 C:GLU75 4.5 41.6 1.0
O A:HOH344 4.8 45.5 1.0
O C:HOH306 4.8 42.5 1.0

Calcium binding site 9 out of 9 in 5ug4

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Calcium binding site 9 out of 9 in the Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca203

b:35.0
occ:1.00
 OE2 C:GLU34 2.2 34.0 1.0
OE2 C:GLU41 2.4 33.5 1.0
O C:PRO35 2.5 30.5 1.0
OE1 C:GLU41 2.5 30.8 1.0
CD C:GLU41 2.8 31.4 1.0
CD C:GLU34 3.4 37.7 1.0
C C:PRO35 3.6 32.1 1.0
CG C:GLU34 3.9 36.6 1.0
CA C:TYR36 4.2 31.3 1.0
CG C:GLU41 4.3 30.1 1.0
N C:TYR36 4.4 32.3 1.0
CG C:PRO35 4.4 33.1 1.0
OE1 C:GLU34 4.5 34.1 1.0
O C:HOH314 4.5 26.4 1.0
CA C:PRO35 4.7 32.4 1.0
CB C:TYR36 4.7 29.9 1.0
N C:PRO35 4.7 33.1 1.0
CB C:PRO35 4.9 33.4 1.0
CD C:PRO35 4.9 33.2 1.0

Reference:

E.V.Filippova, G.Minasov, L.Shuvalova, O.Kiryukhina, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). Structure of Spermidine N-Acetyltransferase Speg From Vibrio Cholerae To Be Published.
Page generated: Sat Dec 12 05:46:06 2020

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