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Calcium in PDB 4ygo: Dodecameric Structure of Spermidine N-Acetyltransferase From Vibrio Cholerae in Intermediate State

Protein crystallography data

The structure of Dodecameric Structure of Spermidine N-Acetyltransferase From Vibrio Cholerae in Intermediate State, PDB code: 4ygo was solved by E.V.Filippova, G.Minasov, O.Kiryukhina, W.F.Anderson, Center Forstructural 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 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 155.118, 135.793, 72.848, 90.00, 117.13, 90.00
R / Rfree (%) 18 / 25.3

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 4ygo

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Calcium binding site 1 out of 6 in the Dodecameric Structure of Spermidine N-Acetyltransferase From Vibrio Cholerae in Intermediate State


Mono view


Stereo pair view

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

b:69.5
occ:1.00
 OE2 A:GLU33 2.3 72.9 1.0
OE2 A:GLU75 2.3 67.3 1.0
OE1 A:GLU75 2.5 58.7 1.0
CD A:GLU75 2.7 55.0 1.0
CD A:GLU33 2.9 67.4 1.0
OE1 A:GLU33 2.9 69.9 1.0
O A:HOH303 3.9 50.3 1.0
CG A:GLU75 4.2 50.5 1.0
O A:HOH302 4.3 66.8 1.0
O A:HOH310 4.4 64.0 1.0
CG A:GLU33 4.4 60.5 1.0
O A:HOH307 4.6 51.7 1.0

Calcium binding site 2 out of 6 in 4ygo

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Calcium binding site 2 out of 6 in the Dodecameric Structure of Spermidine N-Acetyltransferase From Vibrio Cholerae in Intermediate State


Mono view


Stereo pair view

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

b:57.9
occ:0.70
 OE1 A:GLU41 2.3 67.0 1.0
O A:PRO35 2.4 56.3 1.0
OD1 D:ASN53 2.5 71.8 1.0
O A:HOH315 2.7 50.1 1.0
CD A:GLU41 3.0 64.4 1.0
OE2 A:GLU41 3.0 63.7 1.0
CG D:ASN53 3.3 66.9 1.0
ND2 D:ASN53 3.4 69.6 1.0
C A:PRO35 3.5 51.8 1.0
CG A:PRO35 4.2 55.1 1.0
CA A:TYR36 4.2 48.2 1.0
O D:HIS51 4.3 49.0 1.0
N A:TYR36 4.3 49.0 1.0
CA A:PRO35 4.4 52.3 1.0
CB A:PRO35 4.4 53.0 1.0
CG A:GLU41 4.4 59.2 1.0
N A:PRO35 4.6 52.1 1.0
NH1 D:ARG56 4.6 88.8 1.0
C D:HIS51 4.7 47.0 1.0
CA D:HIS51 4.7 45.9 1.0
O D:ILE50 4.8 44.6 1.0
CB D:ASN53 4.8 60.4 1.0
CB A:TYR36 4.8 48.1 1.0
CD A:PRO35 4.9 55.4 1.0
NH2 D:ARG56 5.0 87.1 1.0

Calcium binding site 3 out of 6 in 4ygo

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Calcium binding site 3 out of 6 in the Dodecameric Structure of Spermidine N-Acetyltransferase From Vibrio Cholerae in Intermediate State


Mono view


Stereo pair view

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

b:62.9
occ:0.70
 OE1 C:GLU41 2.3 65.6 1.0
O C:PRO35 2.3 66.6 1.0
OD1 B:ASN53 2.5 72.5 1.0
O C:HOH322 2.7 61.0 1.0
OE2 C:GLU41 2.8 68.5 1.0
CD C:GLU41 2.9 65.8 1.0
CG B:ASN53 3.3 65.0 1.0
ND2 B:ASN53 3.4 68.5 1.0
C C:PRO35 3.4 59.2 1.0
CG C:PRO35 4.1 64.8 1.0
CA C:TYR36 4.1 56.3 1.0
N C:TYR36 4.2 56.3 1.0
CA C:PRO35 4.4 61.7 1.0
CG C:GLU41 4.4 61.6 1.0
CB C:PRO35 4.5 62.8 1.0
CD C:PRO35 4.5 61.8 1.0
N C:PRO35 4.5 60.7 1.0
O B:HIS51 4.8 55.6 1.0
CB B:ASN53 4.8 59.9 1.0

Calcium binding site 4 out of 6 in 4ygo

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Calcium binding site 4 out of 6 in the Dodecameric Structure of Spermidine N-Acetyltransferase From Vibrio Cholerae in Intermediate State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Dodecameric Structure of Spermidine N-Acetyltransferase From Vibrio Cholerae in Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:87.3
occ:1.00
 OE2 D:GLU75 2.3 66.2 1.0
OE1 D:GLU33 2.3 76.7 1.0
CD D:GLU33 2.9 68.0 1.0
OE2 D:GLU33 3.0 71.1 1.0
CD D:GLU75 3.2 56.2 1.0
OE1 D:GLU75 3.4 62.7 1.0
CG D:GLU33 4.4 64.8 1.0
CG D:GLU75 4.6 49.9 1.0
O D:HOH305 4.9 59.9 1.0

Calcium binding site 5 out of 6 in 4ygo

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Calcium binding site 5 out of 6 in the Dodecameric Structure of Spermidine N-Acetyltransferase From Vibrio Cholerae in Intermediate State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Dodecameric Structure of Spermidine N-Acetyltransferase From Vibrio Cholerae in Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:51.1
occ:0.70
 OE1 D:GLU41 2.3 59.1 1.0
O D:PRO35 2.3 58.5 1.0
O C:HOH316 2.4 49.8 1.0
OD1 C:ASN53 2.5 59.2 1.0
OE2 D:GLU41 2.8 59.4 1.0
OE1 D:GLU34 2.8 69.6 1.0
CD D:GLU41 2.9 56.4 1.0
CG C:ASN53 3.4 57.0 1.0
C D:PRO35 3.5 55.9 1.0
ND2 C:ASN53 3.7 56.4 1.0
CD D:GLU34 4.0 72.1 1.0
CA D:TYR36 4.2 52.7 1.0
O C:HIS51 4.2 44.2 1.0
CG D:GLU41 4.3 54.7 1.0
N D:TYR36 4.4 53.6 1.0
CG D:PRO35 4.4 61.1 1.0
C C:HIS51 4.6 45.1 1.0
CA D:PRO35 4.6 56.0 1.0
CA C:HIS51 4.6 47.6 1.0
O C:ILE50 4.7 52.3 1.0
N D:PRO35 4.7 57.2 1.0
OE2 D:GLU34 4.8 77.0 1.0
CB D:PRO35 4.8 58.8 1.0
CB C:ASN53 4.8 55.5 1.0
CD D:PRO35 4.9 60.9 1.0
CB D:TYR36 4.9 48.5 1.0
NH1 C:ARG56 4.9 76.3 1.0
CG D:GLU34 5.0 71.5 1.0

Calcium binding site 6 out of 6 in 4ygo

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Calcium binding site 6 out of 6 in the Dodecameric Structure of Spermidine N-Acetyltransferase From Vibrio Cholerae in Intermediate State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Dodecameric Structure of Spermidine N-Acetyltransferase From Vibrio Cholerae in Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:70.7
occ:1.00
 OE1 E:GLU33 2.3 80.2 1.0
OE2 E:GLU75 2.3 73.8 1.0
OE1 E:GLU75 2.6 63.5 1.0
CD E:GLU33 2.7 70.8 1.0
OE2 E:GLU33 2.7 77.9 1.0
CD E:GLU75 2.8 61.7 1.0
CG E:GLU33 4.0 65.0 1.0
CG E:GLU75 4.2 58.8 1.0
O E:HOH302 4.2 57.6 1.0

Reference:

E.V.Filippova, S.Weigand, J.Osipiuk, O.Kiryukhina, A.Joachimiak, W.F.Anderson. Substrate-Induced Allosteric Change in the Quaternary Structure of the Spermidine N-Acetyltransferase Speg. J.Mol.Biol. V. 427 3538 2015.
ISSN: ESSN 1089-8638
PubMed: 26410587
DOI: 10.1016/J.JMB.2015.09.013
Page generated: Sun Jul 14 14:55:31 2024

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