Atomistry » Calcium » PDB 3rxb-3s9n » 3s6j
Atomistry »
  Calcium »
    PDB 3rxb-3s9n »
      3s6j »

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

Go back to Calcium Binding Sites List in 3s6j
Calcium binding site 1 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 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

Go back to Calcium Binding Sites List in 3s6j
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

Go back to Calcium Binding Sites List in 3s6j
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

Go back to Calcium Binding Sites List in 3s6j
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

Go back to Calcium Binding Sites List in 3s6j
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

Go back to Calcium Binding Sites List in 3s6j
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

Go back to Calcium Binding Sites List in 3s6j
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

Go back to Calcium Binding Sites List in 3s6j
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

Go back to Calcium Binding Sites List in 3s6j
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy