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Calcium in PDB 5cy4: Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii

Protein crystallography data

The structure of Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii, PDB code: 5cy4 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.49 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.710, 102.880, 184.870, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.2

Calcium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii (pdb code 5cy4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii, PDB code: 5cy4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in 5cy4

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Calcium binding site 1 out of 14 in the Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:41.4
occ:1.00
 OE2 A:GLU15 2.4 46.5 1.0
O A:HOH403 2.5 42.8 1.0
O A:HOH385 2.6 54.4 1.0
O A:LEU14 2.6 34.6 1.0
OD2 A:ASP13 2.6 30.3 1.0
O A:HOH328 2.7 42.4 1.0
OD1 A:ASP13 2.7 25.4 1.0
CG A:ASP13 3.0 26.9 1.0
CD A:GLU15 3.4 44.3 1.0
C A:LEU14 3.6 29.4 1.0
OD2 A:ASP164 4.1 72.4 1.0
O A:HOH321 4.1 40.4 1.0
OE1 A:GLU15 4.2 48.4 1.0
CA A:CA202 4.2 34.6 1.0
CG A:ASP164 4.2 54.8 1.0
N A:LEU14 4.3 25.5 1.0
CG A:GLU15 4.3 38.0 1.0
O A:HOH393 4.4 62.6 1.0
N A:GLU15 4.4 26.8 1.0
CA A:GLU15 4.5 26.6 1.0
OD1 A:ASP164 4.5 52.7 1.0
CB A:ASP13 4.5 25.4 1.0
CA A:LEU14 4.6 27.6 1.0
CB A:ASP164 4.7 37.2 1.0
O A:HOH345 4.7 45.9 1.0
O A:HOH368 4.9 38.4 1.0
OD1 A:ASP113 5.0 36.5 1.0
C A:ASP13 5.0 28.1 1.0

Calcium binding site 2 out of 14 in 5cy4

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Calcium binding site 2 out of 14 in the Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:34.6
occ:1.00
 O A:HOH345 2.3 45.9 1.0
O A:HOH321 2.4 40.4 1.0
O A:ASN108 2.4 26.5 1.0
OD1 A:ASP13 2.5 25.4 1.0
O A:HOH316 2.5 23.5 1.0
OD2 A:ASP113 2.5 40.0 1.0
O A:HOH328 2.8 42.4 1.0
O A:HOH385 3.4 54.4 1.0
CG A:ASP113 3.4 34.7 1.0
OD1 A:ASP113 3.6 36.5 1.0
C A:ASN108 3.6 27.7 1.0
CG A:ASP13 3.7 26.9 1.0
O A:HOH306 4.0 38.3 1.0
O A:SER109 4.1 32.3 1.0
OD1 A:ASP164 4.1 52.7 1.0
CA A:CA201 4.2 41.4 1.0
N A:ASN108 4.2 27.9 1.0
CB A:ASP13 4.3 25.4 1.0
CA A:ASN108 4.4 27.8 1.0
C A:SER109 4.4 30.2 1.0
CA A:ASP13 4.4 30.2 1.0
O A:HOH405 4.5 51.2 1.0
N A:SER109 4.6 28.8 1.0
O A:ILE12 4.6 24.0 1.0
CB A:SER109 4.6 42.2 1.0
OD2 A:ASP13 4.6 30.3 1.0
CB A:ASN108 4.7 28.5 1.0
CA A:SER109 4.8 33.8 1.0
CB A:ASP113 4.8 27.9 1.0
N A:LEU14 4.8 25.5 1.0
CG A:ASP164 5.0 54.8 1.0

Calcium binding site 3 out of 14 in 5cy4

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Calcium binding site 3 out of 14 in the Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:35.9
occ:1.00
 NZ A:LYS173 3.2 30.0 1.0
N A:VAL40 3.3 35.1 1.0
CA A:ASN39 3.8 28.8 1.0
O A:LEU38 3.9 29.5 1.0
CB A:VAL40 4.1 28.5 1.0
CG2 A:VAL40 4.1 22.3 1.0
C A:ASN39 4.1 32.1 1.0
CA A:VAL40 4.3 31.6 1.0
CE A:LYS173 4.4 32.7 1.0
OD1 A:ASN39 4.5 36.5 1.0
CB A:ASN39 4.7 30.0 1.0
C A:LEU38 4.7 33.7 1.0
N A:ASN39 4.8 30.6 1.0
O A:VAL40 4.9 32.3 1.0

Calcium binding site 4 out of 14 in 5cy4

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Calcium binding site 4 out of 14 in the Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:66.5
occ:1.00
 O B:HOH314 2.4 55.6 1.0
O B:HOH377 2.5 44.0 1.0
O B:LEU14 2.6 36.0 1.0
O B:HOH318 2.6 40.8 1.0
OD1 B:ASP13 2.6 34.7 1.0
OE2 B:GLU15 2.8 49.6 1.0
OD2 B:ASP13 3.0 38.5 1.0
CG B:ASP13 3.1 33.0 1.0
CD B:GLU15 3.6 43.5 1.0
C B:LEU14 3.7 34.2 1.0
OE1 B:GLU15 4.0 40.7 1.0
CA B:CA202 4.0 52.9 1.0
O B:HOH380 4.2 34.8 1.0
ND1 B:HIS159 4.2 81.7 1.0
N B:LEU14 4.2 27.4 1.0
CE1 B:HIS159 4.4 78.6 1.0
O B:HOH336 4.4 55.1 1.0
OD2 B:ASP164 4.6 73.6 1.0
N B:GLU15 4.6 29.0 1.0
CB B:ASP13 4.6 34.1 1.0
CA B:LEU14 4.6 28.8 1.0
CG B:GLU15 4.7 41.7 1.0
CA B:GLU15 4.7 27.4 1.0
O B:HOH329 4.7 29.8 1.0
OD1 B:ASP113 4.9 42.5 1.0
CG B:ASP164 4.9 66.4 1.0

Calcium binding site 5 out of 14 in 5cy4

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Calcium binding site 5 out of 14 in the Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:52.9
occ:1.00
 O B:HOH321 2.5 28.4 1.0
O B:HOH336 2.5 55.1 1.0
OD2 B:ASP113 2.5 46.8 1.0
O B:ASN108 2.6 39.4 1.0
OD1 B:ASP13 2.6 34.7 1.0
O B:HOH318 2.7 40.8 1.0
O B:HOH380 2.8 34.8 1.0
O B:HOH377 2.8 44.0 1.0
CG B:ASP113 3.4 36.9 1.0
OD1 B:ASP113 3.6 42.5 1.0
C B:ASN108 3.8 36.2 1.0
CG B:ASP13 3.8 33.0 1.0
O B:SER109 4.0 34.0 1.0
CA B:CA201 4.0 66.5 1.0
O B:HOH360 4.1 49.7 1.0
CB B:ASP13 4.3 34.1 1.0
CA B:ASP13 4.3 30.8 1.0
C B:SER109 4.4 34.7 1.0
O B:ILE12 4.4 32.6 1.0
N B:ASN108 4.4 27.5 1.0
O B:HOH314 4.5 55.6 1.0
CA B:ASN108 4.6 32.3 1.0
CD1 B:ILE110 4.7 43.0 1.0
CB B:SER109 4.7 44.7 1.0
N B:SER109 4.7 36.2 1.0
N B:LEU14 4.7 27.4 1.0
OD2 B:ASP13 4.8 38.5 1.0
CB B:ASP113 4.8 28.5 1.0
CA B:SER109 4.9 37.6 1.0
CB B:ASN108 4.9 36.3 1.0

Calcium binding site 6 out of 14 in 5cy4

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Calcium binding site 6 out of 14 in the Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:37.1
occ:1.00
 OD2 C:ASP113 2.4 36.6 1.0
O C:HOH308 2.4 30.9 1.0
O C:HOH371 2.4 42.3 1.0
O C:ASN108 2.5 24.2 1.0
OD1 C:ASP13 2.5 30.2 1.0
O C:HOH320 2.6 24.2 1.0
O C:HOH321 3.0 37.5 1.0
CG C:ASP113 3.4 33.6 1.0
C C:ASN108 3.6 25.8 1.0
OD1 C:ASP113 3.7 39.7 1.0
CG C:ASP13 3.7 27.5 1.0
O C:SER109 4.0 31.9 1.0
O C:HOH313 4.1 40.0 1.0
O C:HOH302 4.1 32.8 1.0
CA C:CA202 4.1 39.4 1.0
OD1 C:ASP164 4.2 38.5 1.0
N C:ASN108 4.3 24.9 1.0
C C:SER109 4.3 28.4 1.0
CB C:ASP13 4.3 25.5 1.0
CA C:ASN108 4.4 28.1 1.0
CA C:ASP13 4.5 23.9 1.0
N C:SER109 4.5 29.5 1.0
CB C:SER109 4.6 44.5 1.0
O C:ILE12 4.6 21.8 1.0
OD2 C:ASP13 4.6 32.1 1.0
CB C:ASP113 4.7 24.9 1.0
CA C:SER109 4.7 35.6 1.0
CB C:ASN108 4.7 29.9 1.0
N C:LEU14 4.9 24.5 1.0
CD1 C:ILE110 4.9 26.9 1.0
N C:ILE110 4.9 26.4 1.0
CG C:ASP164 5.0 39.8 1.0

Calcium binding site 7 out of 14 in 5cy4

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Calcium binding site 7 out of 14 in the Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:39.4
occ:1.00
 O C:HOH313 2.4 40.0 1.0
O C:LEU14 2.4 31.9 1.0
OE2 C:GLU15 2.4 37.5 1.0
OD2 C:ASP13 2.7 32.1 1.0
O C:HOH321 2.7 37.5 1.0
OD1 C:ASP13 2.7 30.2 1.0
CG C:ASP13 3.0 27.5 1.0
C C:LEU14 3.5 27.2 1.0
CD C:GLU15 3.5 38.3 1.0
N C:LEU14 4.1 24.5 1.0
CA C:CA201 4.1 37.1 1.0
OE1 C:GLU15 4.3 40.5 1.0
N C:GLU15 4.4 27.1 1.0
O C:HOH371 4.4 42.3 1.0
CG C:GLU15 4.4 35.3 1.0
OD2 C:ASP164 4.4 47.7 1.0
O C:HOH308 4.4 30.9 1.0
CA C:LEU14 4.5 25.9 1.0
CA C:GLU15 4.5 34.1 1.0
CB C:ASP13 4.5 25.5 1.0
CG C:ASP164 4.5 39.8 1.0
O C:HOH357 4.5 43.5 1.0
OD1 C:ASP113 4.7 39.7 1.0
OD1 C:ASP164 4.8 38.5 1.0
C C:ASP13 4.9 24.7 1.0
CB C:ASP164 5.0 35.1 1.0

Calcium binding site 8 out of 14 in 5cy4

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Calcium binding site 8 out of 14 in the Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:29.6
occ:1.00
 O D:LEU14 2.3 27.3 1.0
OE2 D:GLU15 2.4 36.2 1.0
O A:HOH314 2.4 26.1 1.0
OD2 D:ASP13 2.6 28.5 1.0
OD1 D:ASP13 2.6 29.5 1.0
O A:HOH309 2.7 25.6 1.0
O D:HOH329 2.8 29.9 1.0
CG D:ASP13 2.9 28.7 1.0
CD D:GLU15 3.4 37.9 1.0
C D:LEU14 3.5 26.9 1.0
N D:LEU14 4.0 27.5 1.0
OE1 D:GLU15 4.1 39.2 1.0
CA D:CA202 4.1 26.3 1.0
NH2 A:ARG65 4.2 30.0 1.0
CG D:GLU15 4.3 34.1 1.0
O D:HOH322 4.3 21.2 1.0
CA D:LEU14 4.4 29.1 1.0
N D:GLU15 4.4 27.0 1.0
OE2 A:GLU61 4.4 40.0 1.0
O D:HOH361 4.4 32.1 1.0
CB D:ASP13 4.4 26.5 1.0
CA D:GLU15 4.5 27.1 1.0
OD2 D:ASP164 4.6 29.4 1.0
OD1 D:ASP113 4.6 33.3 1.0
OE1 A:GLU61 4.6 42.0 1.0
CG D:ASP164 4.6 32.0 1.0
OD1 D:ASP164 4.8 27.7 1.0
C D:ASP13 4.8 29.2 1.0
CD A:GLU61 4.9 39.2 1.0

Calcium binding site 9 out of 14 in 5cy4

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Calcium binding site 9 out of 14 in the Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:26.3
occ:1.00
 OD2 D:ASP113 2.4 26.7 1.0
OD1 D:ASP13 2.4 29.5 1.0
O D:HOH322 2.4 21.2 1.0
O D:ASN108 2.5 23.8 1.0
O D:HOH317 2.5 26.8 1.0
O D:HOH361 2.6 32.1 1.0
O D:HOH329 3.1 29.9 1.0
CG D:ASP113 3.4 31.1 1.0
CG D:ASP13 3.5 28.7 1.0
C D:ASN108 3.6 20.4 1.0
OD1 D:ASP113 3.8 33.3 1.0
O D:SER109 4.1 28.3 1.0
OD1 D:ASP164 4.1 27.7 1.0
CA D:CA201 4.1 29.6 1.0
CB D:ASP13 4.2 26.5 1.0
N D:ASN108 4.2 23.0 1.0
O A:HOH314 4.3 26.1 1.0
CA D:ASN108 4.4 23.7 1.0
C D:SER109 4.4 26.9 1.0
CA D:ASP13 4.4 29.9 1.0
O A:HOH386 4.4 28.9 1.0
O D:HOH309 4.4 30.4 1.0
CD1 D:ILE110 4.5 38.5 1.0
OD2 D:ASP13 4.5 28.5 1.0
O D:ILE12 4.6 24.6 1.0
N D:SER109 4.6 26.5 1.0
CB D:ASN108 4.7 18.5 1.0
CB D:ASP113 4.7 23.1 1.0
CB D:SER109 4.8 30.2 1.0
CA D:SER109 4.8 26.4 1.0
N D:LEU14 4.9 27.5 1.0
N D:ILE110 4.9 26.5 1.0
CA D:ILE110 4.9 28.1 1.0
CG D:ASP164 4.9 32.0 1.0

Calcium binding site 10 out of 14 in 5cy4

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Calcium binding site 10 out of 14 in the Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca203

b:41.7
occ:1.00
 O D:HOH383 3.1 35.7 1.0
NZ D:LYS173 3.2 32.5 1.0
N D:VAL40 3.2 30.8 1.0
CA D:ASN39 3.7 31.5 1.0
O D:LEU38 3.8 34.5 1.0
C D:ASN39 4.0 31.6 1.0
CG2 D:VAL40 4.0 25.2 1.0
CB D:VAL40 4.1 30.1 1.0
O D:HOH328 4.1 45.7 1.0
O D:HOH306 4.2 33.7 1.0
CA D:VAL40 4.2 28.1 1.0
OD1 D:ASN39 4.3 38.4 1.0
CE D:LYS173 4.4 34.1 1.0
CB D:ASN39 4.5 29.8 1.0
C D:LEU38 4.7 34.2 1.0
N D:ASN39 4.7 34.1 1.0
O D:VAL40 4.8 36.6 1.0
CG D:ASN39 4.9 36.9 1.0

Reference:

C.M.Lukacs, J.W.Fairman, D.D.Lorimer, T.E.Edwards. Crystal Structure of An Oligoribonuclease From Acinetobacter Baumannii To Be Published.
Page generated: Sat Dec 12 05:20:41 2020

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