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Calcium in PDB 3s6j: The Crystal Structure of A Hydrolase From Pseudomonas Syringae

Protein crystallography data

The structure of The Crystal Structure of A Hydrolase From Pseudomonas Syringae, PDB code: 3s6j was solved by Z.Zhang, B.Syed Ibrahim, S.K.Burley, S.Swaminathan, New York Sgx Researchcenter For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.89 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.535, 74.887, 75.113, 59.77, 67.49, 88.00
R / Rfree (%) 19.5 / 24.3

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of A Hydrolase From Pseudomonas Syringae (pdb code 3s6j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the The Crystal Structure of A Hydrolase From Pseudomonas Syringae, PDB code: 3s6j:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 3s6j

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Calcium binding site 1 out of 9 in the The Crystal Structure of A Hydrolase From Pseudomonas Syringae


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of A Hydrolase From Pseudomonas Syringae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4

b:33.0
occ:1.00
 O A:ASP115 2.4 30.0 1.0
O A:HOH360 2.5 32.0 1.0
O A:HOH356 2.5 27.6 1.0
OD2 A:ASP113 2.5 31.3 1.0
OD1 A:ASP273 2.5 30.4 1.0
O A:HOH355 2.6 30.8 1.0
OD2 A:ASP273 3.0 30.0 1.0
CG A:ASP273 3.1 28.8 1.0
OD1 A:ASP113 3.1 29.2 1.0
CG A:ASP113 3.2 28.6 1.0
C A:ASP115 3.5 30.0 1.0
OD2 A:ASP277 4.1 30.2 1.0
CB A:ASP115 4.3 29.5 1.0
CA A:ASP115 4.4 30.9 1.0
OG1 A:THR117 4.4 30.2 1.0
OD2 A:ASP115 4.4 34.1 1.0
O A:HOH357 4.4 22.4 1.0
N A:GLY116 4.5 29.1 1.0
CG A:ASP115 4.5 33.7 1.0
CB A:ASP113 4.5 28.9 1.0
CG2 A:VAL122 4.6 28.0 1.0
CA A:GLY116 4.6 28.2 1.0
CB A:ASP273 4.6 26.4 1.0
CB A:ALA274 4.6 26.7 1.0
N A:ASP115 4.6 28.6 1.0
CA A:GLY150 4.7 33.9 1.0
N A:ASP273 4.9 25.1 1.0
N A:ALA274 5.0 28.1 1.0
O A:ILE149 5.0 34.8 1.0
C A:GLY116 5.0 28.1 1.0
CG A:ASP277 5.0 28.3 1.0

Calcium binding site 2 out of 9 in 3s6j

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Calcium binding site 2 out of 9 in the The Crystal Structure of A Hydrolase From Pseudomonas Syringae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of A Hydrolase From Pseudomonas Syringae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:33.9
occ:1.00
 O B:HOH12 2.4 26.1 1.0
OD1 B:ASP273 2.4 29.5 1.0
OD2 B:ASP113 2.5 31.5 1.0
O B:ASP115 2.5 30.4 1.0
O B:HOH343 2.5 28.2 1.0
O B:HOH344 2.6 25.0 1.0
CG B:ASP113 3.2 31.4 1.0
CG B:ASP273 3.2 28.5 1.0
OD1 B:ASP113 3.2 30.5 1.0
OD2 B:ASP273 3.2 30.2 1.0
C B:ASP115 3.6 29.9 1.0
OD2 B:ASP277 4.0 29.2 1.0
OD2 B:ASP115 4.4 34.7 1.0
O B:HOH4 4.4 23.1 1.0
OG1 B:THR117 4.4 30.0 1.0
CA B:ASP115 4.4 30.9 1.0
CB B:ASP115 4.4 30.4 1.0
N B:GLY116 4.5 29.6 1.0
CA B:GLY116 4.5 28.1 1.0
CG B:ASP115 4.5 32.1 1.0
CB B:ASP113 4.5 28.6 1.0
CG2 B:VAL122 4.5 28.4 1.0
O B:HOH354 4.6 34.2 1.0
CA B:GLY150 4.6 30.2 1.0
CB B:ALA274 4.6 28.4 1.0
N B:ASP115 4.6 27.1 1.0
CB B:ASP273 4.7 26.4 1.0
O B:ILE149 4.8 27.4 1.0
N B:ASP273 4.9 26.2 1.0
C B:GLY116 4.9 28.8 1.0
N B:ALA274 5.0 27.6 1.0

Calcium binding site 3 out of 9 in 3s6j

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Calcium binding site 3 out of 9 in the The Crystal Structure of A Hydrolase From Pseudomonas Syringae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of A Hydrolase From Pseudomonas Syringae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca7

b:42.7
occ:1.00
 O B:GLY295 2.3 30.8 1.0
O F:GLY295 2.4 32.1 1.0
O B:HOH360 2.7 34.5 1.0
OD2 B:ASP297 2.9 42.2 1.0
O B:HOH358 2.9 38.8 1.0
O B:HOH359 3.0 35.3 1.0
OD1 B:ASP297 3.1 41.8 1.0
CG B:ASP297 3.3 39.3 1.0
C B:GLY295 3.5 31.6 1.0
C F:GLY295 3.6 31.8 1.0
CA B:TYR296 4.1 30.5 1.0
CA F:TYR296 4.2 30.6 1.0
N B:TYR296 4.3 28.6 1.0
N F:TYR296 4.4 31.6 1.0
C B:TYR296 4.4 33.0 1.0
N B:ASP297 4.4 31.6 1.0
C F:TYR296 4.5 32.0 1.0
OE1 B:GLU300 4.5 36.7 1.0
N F:ASP297 4.5 35.3 1.0
CA B:GLY295 4.5 28.8 1.0
CA F:GLY295 4.6 30.5 1.0
CB B:ASP297 4.8 33.7 1.0
OE1 F:GLU300 4.9 41.2 1.0
CE1 F:HIS146 5.0 28.7 1.0
CE1 B:HIS146 5.0 31.5 1.0

Calcium binding site 4 out of 9 in 3s6j

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Calcium binding site 4 out of 9 in the The Crystal Structure of A Hydrolase From Pseudomonas Syringae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Crystal Structure of A Hydrolase From Pseudomonas Syringae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca5

b:38.9
occ:1.00
 O C:HOH356 2.5 34.6 1.0
O C:ASP115 2.5 34.4 1.0
OD2 C:ASP113 2.5 36.9 1.0
OD1 C:ASP273 2.6 33.7 1.0
O C:HOH357 2.6 40.8 1.0
O C:HOH358 2.8 32.6 1.0
OD1 C:ASP113 2.9 36.4 1.0
CG C:ASP113 3.0 34.8 1.0
CG C:ASP273 3.4 31.9 1.0
OD2 C:ASP273 3.5 31.2 1.0
C C:ASP115 3.7 31.7 1.0
OD2 C:ASP115 3.9 42.7 1.0
OD2 C:ASP277 4.1 33.0 1.0
N C:ASP115 4.3 33.6 1.0
CA C:GLY150 4.4 42.1 1.0
CA C:ASP115 4.5 35.7 1.0
CB C:ASP113 4.5 31.5 1.0
OG1 C:THR117 4.6 34.4 1.0
N C:GLY116 4.7 30.5 1.0
CG C:ASP115 4.7 40.6 1.0
CB C:ASP273 4.8 28.2 1.0
CG2 C:VAL122 4.8 29.0 1.0
CA C:GLY116 4.8 30.4 1.0
N C:GLY150 4.9 44.5 1.0
NZ C:LYS248 4.9 40.6 1.0
N C:ASP273 4.9 28.5 1.0
CG C:ASP277 5.0 32.8 1.0
OD1 C:ASP277 5.0 36.1 1.0

Calcium binding site 5 out of 9 in 3s6j

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Calcium binding site 5 out of 9 in the The Crystal Structure of A Hydrolase From Pseudomonas Syringae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Crystal Structure of A Hydrolase From Pseudomonas Syringae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca9

b:46.9
occ:1.00
 O D:GLY295 2.3 30.7 1.0
O C:GLY295 2.4 33.5 1.0
O C:HOH362 2.5 39.7 1.0
O C:HOH361 2.6 33.3 1.0
OD1 C:ASP297 2.8 39.0 1.0
O C:HOH359 2.8 42.3 1.0
O C:HOH360 3.5 32.4 1.0
C D:GLY295 3.5 30.9 1.0
C C:GLY295 3.6 31.8 1.0
CG C:ASP297 3.9 39.7 1.0
CA D:TYR296 4.2 31.1 1.0
CA C:TYR296 4.2 32.5 1.0
OD2 C:ASP297 4.3 42.4 1.0
N D:TYR296 4.3 29.2 1.0
N C:TYR296 4.4 31.5 1.0
CA D:GLY295 4.5 26.8 1.0
N C:ASP297 4.5 32.2 1.0
C C:TYR296 4.5 32.2 1.0
CA C:GLY295 4.6 27.6 1.0
C D:TYR296 4.6 31.0 1.0
OE1 C:GLU300 4.6 34.3 1.0
N D:ASP297 4.7 31.3 1.0
CE1 C:HIS146 4.7 27.5 1.0
CE1 D:HIS146 4.9 26.3 1.0
ND1 C:HIS146 5.0 26.6 1.0

Calcium binding site 6 out of 9 in 3s6j

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Calcium binding site 6 out of 9 in the The Crystal Structure of A Hydrolase From Pseudomonas Syringae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Crystal Structure of A Hydrolase From Pseudomonas Syringae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca6

b:31.8
occ:1.00
 O D:ASP115 2.4 32.6 1.0
OD1 D:ASP273 2.5 33.2 1.0
O D:HOH354 2.5 28.3 1.0
O D:HOH17 2.5 27.2 1.0
O D:HOH353 2.5 30.8 1.0
OD2 D:ASP113 2.6 33.9 1.0
OD1 D:ASP113 3.1 31.9 1.0
CG D:ASP113 3.2 32.9 1.0
CG D:ASP273 3.2 30.9 1.0
OD2 D:ASP273 3.2 34.5 1.0
C D:ASP115 3.6 30.9 1.0
OD2 D:ASP277 4.1 30.1 1.0
OD2 D:ASP115 4.2 35.7 1.0
CA D:ASP115 4.4 32.8 1.0
CG2 D:VAL122 4.4 27.7 1.0
CG D:ASP115 4.4 34.0 1.0
CB D:ASP115 4.4 31.7 1.0
OG1 D:THR117 4.5 32.0 1.0
O D:HOH355 4.5 25.3 1.0
N D:GLY116 4.5 30.3 1.0
N D:ASP115 4.5 29.0 1.0
CB D:ASP113 4.5 31.4 1.0
CB D:ASP273 4.6 30.2 1.0
CA D:GLY116 4.6 28.3 1.0
CB D:ALA274 4.6 25.7 1.0
CA D:GLY150 4.8 32.3 1.0
N D:THR117 4.8 28.1 1.0
C D:GLY116 4.9 29.4 1.0
O D:ILE149 4.9 26.9 1.0
CG2 D:ILE149 4.9 30.1 1.0
N D:ASP273 5.0 27.9 1.0

Calcium binding site 7 out of 9 in 3s6j

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Calcium binding site 7 out of 9 in the The Crystal Structure of A Hydrolase From Pseudomonas Syringae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Crystal Structure of A Hydrolase From Pseudomonas Syringae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1

b:34.4
occ:1.00
 OD1 E:ASP273 2.4 31.9 1.0
O E:ASP115 2.4 31.1 1.0
O E:HOH45 2.4 28.4 1.0
OD2 E:ASP113 2.5 32.3 1.0
O E:HOH349 2.5 32.7 1.0
O E:HOH346 2.7 30.5 1.0
CG E:ASP113 3.2 32.7 1.0
OD1 E:ASP113 3.3 31.9 1.0
CG E:ASP273 3.3 30.2 1.0
OD2 E:ASP273 3.5 31.4 1.0
C E:ASP115 3.6 33.3 1.0
OD1 E:ASP277 4.1 31.8 1.0
OD1 E:ASP115 4.2 37.1 1.0
O E:HOH335 4.3 27.8 1.0
CA E:ASP115 4.5 33.6 1.0
OG1 E:THR117 4.5 31.2 1.0
CA E:GLY150 4.5 31.7 1.0
CB E:ASP115 4.5 33.2 1.0
CB E:ASP113 4.6 30.8 1.0
N E:GLY116 4.6 32.2 1.0
CG E:ASP115 4.6 34.2 1.0
N E:ASP115 4.6 32.8 1.0
CB E:ALA274 4.6 27.3 1.0
CA E:GLY116 4.7 28.8 1.0
CB E:ASP273 4.7 28.3 1.0
CG2 E:VAL122 4.8 29.3 1.0
N E:ASP273 4.9 27.9 1.0
O E:ILE149 4.9 31.1 1.0
N E:GLY150 5.0 33.1 1.0

Calcium binding site 8 out of 9 in 3s6j

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Calcium binding site 8 out of 9 in the The Crystal Structure of A Hydrolase From Pseudomonas Syringae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Crystal Structure of A Hydrolase From Pseudomonas Syringae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca8

b:43.2
occ:1.00
 O E:GLY295 2.3 32.4 1.0
O A:GLY295 2.4 32.3 1.0
O A:HOH362 2.5 38.9 1.0
O E:HOH363 2.6 35.9 1.0
O E:HOH364 2.8 39.8 1.0
O A:HOH363 2.9 38.2 1.0
C E:GLY295 3.5 30.6 1.0
C A:GLY295 3.6 29.4 1.0
CA E:TYR296 4.2 33.1 1.0
OE1 E:GLU300 4.2 36.5 1.0
CA A:TYR296 4.3 29.9 1.0
N E:TYR296 4.3 26.8 1.0
OE1 A:GLU300 4.4 38.0 1.0
N A:TYR296 4.4 27.7 1.0
N E:ASP297 4.4 32.9 1.0
CA E:GLY295 4.5 29.2 1.0
C E:TYR296 4.5 31.1 1.0
N A:ASP297 4.5 34.5 1.0
C A:TYR296 4.6 31.9 1.0
CA A:GLY295 4.6 27.7 1.0
CE1 A:HIS146 5.0 29.9 1.0

Calcium binding site 9 out of 9 in 3s6j

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Calcium binding site 9 out of 9 in the The Crystal Structure of A Hydrolase From Pseudomonas Syringae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of The Crystal Structure of A Hydrolase From Pseudomonas Syringae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca3

b:32.5
occ:1.00
 O F:ASP115 2.4 28.4 1.0
O F:HOH356 2.4 29.7 1.0
OD1 F:ASP273 2.5 34.4 1.0
OD2 F:ASP113 2.5 31.5 1.0
O F:HOH355 2.6 32.1 1.0
O F:HOH357 2.6 30.3 1.0
OD1 F:ASP113 3.1 32.4 1.0
CG F:ASP113 3.2 31.9 1.0
CG F:ASP273 3.3 32.2 1.0
OD2 F:ASP273 3.5 31.9 1.0
C F:ASP115 3.5 29.2 1.0
OD2 F:ASP277 4.1 31.1 1.0
OD2 F:ASP115 4.3 33.9 1.0
O F:HOH68 4.4 33.5 1.0
CA F:ASP115 4.4 32.2 1.0
O F:HOH9 4.4 25.8 1.0
CA F:GLY150 4.4 32.4 1.0
N F:GLY116 4.5 28.6 1.0
CB F:ASP115 4.5 31.3 1.0
N F:ASP115 4.5 29.4 1.0
OG1 F:THR117 4.5 31.4 1.0
CB F:ASP113 4.6 29.6 1.0
CA F:GLY116 4.6 28.2 1.0
CG F:ASP115 4.6 32.3 1.0
CG2 F:VAL122 4.6 28.0 1.0
CB F:ASP273 4.7 27.4 1.0
N F:ASP273 4.9 30.0 1.0
N F:GLY150 4.9 32.6 1.0
CB F:ALA274 4.9 28.1 1.0
O F:ILE149 4.9 31.3 1.0
N F:THR117 5.0 30.1 1.0
C F:GLY116 5.0 30.6 1.0

Reference:

Z.Zhang, B.Syed Ibrahim, S.K.Burley, S.Swaminathan. The Crystal Structure of A Hydrolase From Pseudomonas Syringae To Be Published.
Page generated: Sat Jul 13 19:03:58 2024

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